ISCB Community News

CFP: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM12)

2012-01-30T13:59:00.001-08:00

2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM12)

http://www.ischool.drexel.edu/ieeebibm/bibm12/
October 4-7, 2012, Philadelphia, PA, USA,

The IEEE International Conference on Bioinformatics and Biomedicine
(BIBM) has established itself as the premier research conference in
bioinformatics and biomedicine. IEEE BIBM 2012 provides a leading
forum for disseminating the latest research in bioinformatics and
health informatics. It brings together academic and industrial
scientists from computer science, biology, chemistry, medicine,
mathematics and statistics.

We solicit high-quality original research papers (including
significant work-in-progress) in any aspect of bioinformatics and
biomedicine. New computational techniques and methods in machine
learning; data mining; text analysis; pattern recognition; knowledge
representation; databases; data modeling; combinatorics; stochastic
modeling; string and graph algorithms; linguistic methods; robotics;
constraint satisfaction; data visualization; parallel computation;
data integration; modeling and simulation and heir application in life
science domain are especially encouraged Relevant topics include but
are not limited to:

1. Genomics and Molecular Structure, Function and Evolution
a. Next-Gen Sequencing and Metagenomics
b. Evolution, Phylogeny, Comparative Genomics
c. SNPs and haplotype analysis, GWAS
d. Protein/RNA Structure, Function and Interactions

2. Computational Systems Biology
a. Transcriptomics - Microarray Data Analysis
b. Gene Regulation, Alternative Splicing, Network/Pathway Analysis
c. Proteomics, PTMs, Metabolomics
d. Epigenomics, non-coding RNA analysis, DNA methylation analysis

3. Medical Informatics and Translational Bioinformatics
a. Biomedical Intelligence, Clinical Data Analysis, and Electronic
Health Record
b. Biomedical Signal/Image Analysis
c. Genome-Phenome Analysis
d. Biomarker Discovery

4. Cross-Cutting Computational Methods and Bioinformatics Infrastructure
a. Biomedical Text Mining and Ontologies
b. Biological Data Mining and Visualization
c. Computational Modeling and Data Integration
d. High Performance Computing

5. Healthcare Informatics
a. Healthcare knowledge representation & reasoning
b. Health data acquisition, analysis and mining
c. Healthcare information systems
d. Clinical Decision Support and Informatics

INDUSTRIAL Track

The Industrial Track solicits papers describing implementations of
Bioinformatics and Biomedicine solutions relevant to industrial
settings. The focus of industry track is on papers that address the
practical, applied, or pragmatic or new research challenge issues
related to the use of bioinformatics and biomedicine technologies in
industry.

* Journal special issues: IEEE BIBM has a tradition to publish
selected papers as special issues in highly respected journals. So
far we have confirmed the special issues publications with 7
journals: IEEE Transactions on Information Technology in
Biomedicine, IEEE Transactions on System, Men and Cybernetics,
International Journal of Data Mining and Bioinformatics, BMC
Bioinformatics, BMC Proteomics, BMC Genomics, BMC Proteomics
Science, Proteomics, Journal of Network Modeling and Analysis in
Health Informatics and Bioinformatics (In the past BIBM conference,
the number of special issues is: BIBM 2011-8 special issues, BIBM
2010-7 special issues, BIBM 2009-4 special issues; BIBM 2008-4
special issues)

* Student Travel Award: BIBM 2012 will offer as many as possible
student travel awards to student authors (including post-doc) (BIBM
2011-28 student travel awards, BIBM 2010-22 student travel awards,
BIBM 2009-16 student travel awards )

* Panel on Bioinformatics and Biomedicine Research Challenges and
Opportunities led by top researchers and program managers from NSF
and NIH

Conference Co-Chairs:

Prof. Lyle Ungar, University of Pennsylvania, USA, ungar@cis.upenn.edu
Prof. Cathy Wu, University of Delaware, USA, wuc@dbi.udel.edu

Program Co-Chairs:

Prof. Reda Alhaij, University of Calgary, Canada, rsalhajj@gmail.com
Prof. Jean Gao, University of Texas at Arlington, USA, gao@uta.edu
Prof. Dubitzky Werner, University of Ulster, UK, W.Dubitzky@ulster.ac.uk

Industry Program Committee Chair:

Dr. Anastasia Christianson, AstraZeneca, USA,
anastasia.christianson@astrazeneca.com

BIBM Steering Committee Chair:

Prof. Xiaohua Tony Hu, Drexel University, USA, thu@cis.drexel.edu

Paper Submission:

Please submit a full-length paper, up to 8 pages in IEEE double-column
format, through the online submission system. Formatting instructions
for Latex and Word are available at the online submission
site. Electronic submissions (in PDF or Postscript format) are
required. Selected participants will be asked to submit their revised
papers in a format to be specified at the time of acceptance.

Online Submission:

http://wi-lab.com/cyberchair/2012/bibm12/cbc_index.html

Important Dates:

Electronic submission of full papers: May 10, 2012
Notification of paper acceptance: July 20, 2012
Camera-ready of accepted papers: August 15, 2012
Conference: October 4-7, 2012

URL: http://www.ischool.drexel.edu/ieeebibm/bibm12/

Contact Person: Umit V. Catalyurek (catalyurek.1@osu.edu)

Announcement of HSB 2012

2012-01-24T14:00:00.000-08:00

*********************************************************************
Call for Papers --- HSB 2012
First International Workshop on Hybrid Systems and Biology
Newcasle upon Tyne, UK, September 3, 2012
Colocated with CONCUR 2012

http://hsb2012.units.it/
*********************************************************************

The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical rea ctions, signaling pathways and cardiac tissues electrophysiology.
This workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments.

Topics of interest include, but are not limited to:
* Hybrid models of biological systems (case studies of genetic, cellular
networks,
models of tissues, etc.)
* Computational and mathematical analysis techniques for hybrid systems
(i.e. reachability, model checking, abstract interpretation, bifurcation
theory
for hybrid dynamical systems, etc.), with applications in Systems Biology.
* Hybrid system identification techniques (learning the model from the
experimental
data)
* Efficient simulation techniques for hybrid systems.
* Hybrid modeling languages for biological systems.
* Hybrid systems coping with incomplete and uncertain information.
* Sensitivity analysis for hybrid systems.
* Behaviour-driven parameters identification for hybrid systems.
* Analysis and simulation tools.

We solicit the submission of unpublished results that address on both
theoretical and
applied aspects of hybrid modeling techniques in systems biology.
The proceedings will be published in the Electronic Proceedings in
Theoretical Computer
Science (EPTCS) series. A special issue in a journal will be considered at
the end of the workshop.

Paper submission
Full papers should be no more than 15 pages long, typesetted in the
EPTCS-style.
Electronic submissions of abstracts and of full-length papers (in PDF
format), can be done through
the online submission system:
https://www.easychair.org/conferences/?conf=hsb2012

Important dates
June 15, 2012 - Abstract submission deadline
June 22, 2012 - Full paper submission deadline
July 30, 2012 - Notification of paper acceptance
August 7, 2012 - Camera-ready of accepted papers

Program co-chairs
Ezio Bartocci, University of Stony Brook, USA
Luca Bortolussi, Univerity of Trieste, Italy

Program committee
Marco Antoniotti, University of Milano Bicocca
Gregory Batt, INRIA Paris-Rocquencourt, France
Alberto Casagrande, University of Trieste, Italy
Edmund Clarke, Carnegie Mellon, USA
Thao Dang, VERIMAG Lab, Grenoble, France
Alexandre Donzé, VERIMAG Lab, Grenoble, France
James R. Faeder, University of Pittsburgh, USA
Jasmin Fisher, Microsoft Research, Cambridge, UK
Vashti Galpin, University of Edinburgh, UK
Colas Le Guernic, NYU, USA
Oded Maler, VERIMAG Lab, Grenoble, France
Emanuela Merelli, University of Camerino, Italy
Bud Mishra, NYU, USA
Carla Piazza, University of Udine, Italy
Alberto Policriti, University of Udine, Italy
Scott A. Smolka, University of Stony Brook, USA
Gouhei Tanaka, University of Tokyo, Japan
Verena Wolf, Saarland University, Germany
Paolo Zuliani, Carnegie Mellon, USA
URL: http://hsb2012.units.it/

Contact Person: Luca Bortolussi (luca@dmi.units.it)

Integrative Network Biology 2012: Network Medicine

2012-01-23T07:16:00.000-08:00

The Technical University of Denmark (DTU) is organizing a meeting of world-leaders in systems and network biology.

This symposium will take place in Helsingør, Denmark, on the 11th and 13th of May 2012.

The theme of this conference will be the use of novel experimental and computational approaches to study signalling networks, and how network models can be applied to the study and targeting of complex diseases such as cancer, diabetes and neurological disorders.
URL: http://www.networkbio.org

Contact Person: Rune Linding (networkbio@cbs.dtu.dk)

AREADNE 2012 Call for Abstracts

2012-01-21T06:39:00.001-08:00

AREADNE 2012
Research in Encoding and Decoding of Neural Ensembles
Nomikos Conference Centre, Santorini, Greece
21-24 June 2012
http://areadne.org
info@areadne.org

The AREADNE conferences bring scientific leaders from around the world to present their newest findings on the functioning of neuronal ensembles in an informal yet spectacular setting on Santorini. The conference emphasizes interaction with a size and pace that encourages in-depth discussion. Interested researchers are strongly encouraged to submit an abstract for poster presentation as attendance is strictly limited, and even with spots preferentially going to presenters, the conference typically sells out.
URL: http://areadne.org

Contact Person: John Pezaris (info@areadne.org)

Call for Nominations 2012 National Medal of Science

2012-01-19T13:15:00.000-08:00

The National Medal of Science and the National Medal of Technology and Innovation are the highest honors the Presidentbestows in science, technology, and innovation – help recognize the contributions of your colleagues by submitting a nomination for these prestigious awards before March 31.

National Medal of Science
The National Medal of Science, established in 1959, is the Nation's highest honor for American scientists and engineers. The Medal is given to individuals deserving of special recognition by reason of their outstandingcumulative contributions to knowledge in the chemical, physical, biological, mathematical, engineering, or behavioral or social sciences, in combinationwith exemplary service to the Nation. It is administered by the National Science Foundation and, to date, has been awarded to over 450 individuals.

Nominations must be submitted by March 31, 2012. A complete submission consists of a nomination form and three letters of support. These items must be received via the National Science Foundation's FastLane system at https://www.fastlane.nsf.gov/honawards. If you have any questions, please contact the program manager at nms@nsf.gov or 703-292-8040. For more information, please visit http://www.nsf.gov/od/nms/medal.jsp.

National Medal of Technology and Innovation
The National Medal of Technology and Innovation, first awarded in 1985, is the Nation's highest honor for technological achievement and innovation. The Medal is given to individuals, teams, companies, or divisions for their outstanding contributions to the Nation's economic, environmental, and social well-being through the development and commercialization of technology products, processes, and concepts; technological innovation; and development of the Nation's technological manpower.

Nominations must be submitted by March 31, 2012. A complete submission consists of a nomination form and six letters of support. These items should be submitted to the U.S. Patent and Trademark Office at nmti@uspto.gov. If you have any questions, please contact the program manager at nmti@uspto.gov or 571-272-8333. For more information, please visit http://www.uspto.gov/about/nmti/guidelines.jsp.
URL: http://www.nsf.gov/od/nms/medal.jsp

Contact Person: Program Manager (nms@nsf.gov)

Oxford Summer School in Computational Biology 2012

2012-01-15T06:52:00.001-08:00

From July 9th until August 17th 2012, a project-based summer school in computational biology will take place at the University of Oxford. Applications are invited from students with a strong background in mathematics, statistics, computer science, physics or chemistry, who will have completed at least two years of undergraduate study by summer 2012.

Students will work in teams of three for the six-week period on a cutting-edge research project in bioinformatics/computational biology, working with researchers from Oxford, as well as a number of collaborators visiting from overseas.

The programme will also include a series of lectures and tutorials covering key topics in bioinformatics and genome analysis, and presentations from researchers in the field.

Accepted students will be offered university accommodation for the duration of the programme, and will receive a stipend towards living expenses.

Applications will be assessed in two rounds, and students whose applications are received by the first deadline (27th January) may be eligible for additional funding.

Final application deadline: 5th March, 2012

For more information, and to apply, visit www.stats.ox.ac.uk/genome/summer_school

URL: http://www.stats.ox.ac.uk/genome/summer_school

Contact Person: Ms Madeline Mitchell (mitchell@stats.ox.ac.uk)

VIZBI 2012 early registration closes soon!

2012-01-12T02:37:00.001-08:00

VIZBI 2012 early registration closes soon!

A quick reminder that early registration for VIZBI 2012 closes in just under three weeks: the deadline is midnight on January 29 in any time zone. After this date, registration costs €50 more. The deadline for poster submission is 26 February 2012.

URL: http://vizbi.org/2012

Contact Person: VIZBI Organisers (contact@vizbi.org)

Inference in complex systems - currently FREE to access

2012-01-07T04:19:00.001-08:00

Royal Society Publishing has just published an issue of Interface Focus: Inference in complex systems, organized by David Balding which is free to access online until 29th February 2012. See – http://bit.ly/sNRY1k for further details or you can go straight to the issue contents at http://rsfs.royalsocietypublishing.org/content/1/6 which are free to access online until 29th February 2012.

The print issue is available at the special price of £49.00. You can order online via the above web page (enter special code Focus/1/6 when prompted) or, alternatively, you can contact debbie.vaughan@royalsociety.org
URL: http://bit.ly/sNRY1k

Contact Person: Felicity Davie (felicity@tou-can.co.uk)

2012 PASI short course A Systems Biology Approach to Understanding Mechanisms of Organismal Evolution

2011-12-22T05:55:00.000-08:00

Satellite short course to the Sixth International Meeting of the Latin American Society for Developmental Biology, April 16-25, 2012, Montevideo, Uruguay. This Pan-American Advanced Studies Institute will be held at the Universidad de la Republica and Institut Pasteur de Montevideo and is funded by a PASI program grant from NSF and DoE. It is aimed for advanced graduate students, postdoctoral fellows and junior faculty interested in enhancing their understanding for evolutionary processes by integrating genomics, systems biology, gene regulatory network with traditional experimental approaches. Latin American citizens, US nationals and permanent residents are invited to apply. Deadline for submission is January 6, 2012, 6 PM Eastern time.
URL: http://www.sdbonline.org/2012Course/course.htm

Contact Person: Ida Chow (ichow@sdbonline.org)

Protein 3D Structure from High-Throughput Sequencing Â

2011-12-15T21:06:00.000-08:00

Fifty years after the pioneering discovery hat a protein's three-dimensional structure is determined solely by the sequence of its amino acids, an international team of researchers has taken a major step toward fulfilling the tantalizing promise: predicting the structure of a protein from its DNA alone.

The team at Harvard Medical School (HMS), Politecnico di Torino / Human Genetics Foundation Torino (HuGeF) and Memorial Sloan-Kettering Cancer Center in New York (MSKCC) has reported substantial progress toward solving a classical problem of molecular biology: the computational protein folding problem.

In molecular biology and biomedical engineering, knowing the shape of protein molecules is key to understanding how they perform the work of life, the mechanisms of disease and drug design. Normally the shape of protein molecules is determined by expensive and complicated experiments, and for most proteins these experiments have not yet been done. Computing the shape from genetic information alone is possible in principle. But despite limited success for some smaller proteins, this challenge has remained essentially unsolved. The difficulty lies in the enormous complexity of the search space, an astronomically large number of possible shapes. Without any shortcuts, it would take a supercomputer many years to explore all possible shapes of even a small protein.

The team tested this hypothesis: That evolution can provide a roadmap to how the protein folds. Their approach combined three key elements: evolutionary information accumulated for many millions of years; data from high-throughput genetic sequencing; and a key method from statistical physics.

Using the accumulated evolutionary information in the form of the sequences of thousands of proteins, grouped in protein families that are likely to have similar shapes, the team found a way to solve the problem: an algorithm to infer which parts of a protein interact to determine its shape. They used a principle from statistical physics called "maximum entropy" in a method that extracts information about microscopic interactions from measurement of system properties.

With these internal protein interactions inhand, widely used molecular simulation software generated the atomic details of the protein shape. The team was for the first time able to compute remarkably accurate shapes from sequence information alone for a test set of 15 diverse proteins, with no protein size limit in sight, with unprecedented accuracy.

To test their method, the researchers initially focused on the Ras family of signaling proteins, which has been extensivelystudied because of its known link to cancer. The structure of several Ras-type proteins has already been solved experimentally, but the proteins in the family are larger–with about 160 amino acid residues–than any proteinsmodeled computationally from sequence alone. And there is no reason that the method couldn't work with even larger proteins.

The researchers caution that there are other limits, however: experimental structures, when available, generally are more accurate in atomic detail. And, the method works only when researchers havegenetic data for large protein families. But advances in DNA sequencing have yielded a torrent of such data that is forecast to continue growing exponentially in the foreseeable future.

The next step, the researchers say, is to predict the structures of unsolved proteins currently being investigated bystructural biologists, before exploring the large uncharted territory of currently unknown protein structures; and, collaborating with computational and experimental structural biologists to further refine the "evfolded" proteins and to make structure determination more efficient.

Adapted from text by R Alan Leo, Harvard Medical School.

A full news report: http://www.sciencedaily.com/releases/2011/12/111207175635.htm

_________________________ details:

Supplement, images, 3D structures, restraint lists and more: http://evfold.org
URL: http://bit.ly/tob48p

Contact Person: EVfold team (foldingproteins@cbio.mskcc.org)

New Preventing Preterm Birth Initiative

2011-11-08T11:40:00.000-08:00

The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an initiative of Seattle Childrens, is now accepting letters of inquiry for a new grant program, the Preventing Preterm Birth initiative (PPB).

GAPPS seeks projects that explore gestational origins, biological mechanisms and the immunological response to infection and nutritional deficiency which lead to preterm birth, especially in the developing world.

GAPPS will fund several projects for $1-2 million each to discover the biological mechanisms that lead to preterm birth. The Preventing Preterm Birth initiative was funded by the Bill & Melinda Gates Foundation as part of the Grand Challenges in Global Health.

Details and application instructions are available at http://www.gapps.org/healthybirth. Letters of inquiry are being accepted online until 31 January, 2012.

The PPB review committee will review all letters of inquiry submitted, and selected applicants will be invited to submit a full grant proposal.

We look forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you do not submit a letter of inquiry yourself, we hope you will forward this message to someone else who might be interested.

URL: http://www.gapps.org/healthybirth

Contact Person: GAPPS (gappsgrants@seattlechildrens.org)

EMBO practical course on Bioinformatics and Comparative Genome Analyses 2012 (Stazione Zoologica Anton Dohrn, Naples - Italy. 7 - 19 May, 2012)

2011-11-08T03:41:00.000-08:00

Announcement and Call for Application to the EMBO practical Course on "Bioinformatics and Comparative Genome Analyses"
(http://events.embo.org/12-comparative-genomics/index.html) that will take place in the Stazione Zoologica Anton Dohrn, Naples - Italy, 7 – 19 May, 2012.

The main objective of this intensive course is to strengthen capacities of Phd students and young scientists, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies.
The course topics will include among others, theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, Methods for reapeats detection in genomes sequences, orthologs prediction and classification, Genome data visualization, Methods and tools used in Next Generation Sequencing Data analyses.
Practical sessions in a Linux environment will involve Unix and Perl scripting.
Participants are expected to be familiar with this environment.

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Ph.D students and Post-Doctoral Researchers in Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running research projects and on expressed motivations.
Selected students will have free accommodation and meals and are expected to contribute with 400 euros and to pay for their travel expenses.
All participants (students and invited speakers) will stay in the same hotel.

Detailed indications are available on the course web site: http://events.embo.org/12-comparative-genomics/index.html

Candidates are advised to complete carefully the application form, together with a "one-page CV" and a personal Identity Picture (Photo).

The application deadline is March 30, 2012.

The organizers:
Giuseppe D'Onofrio (Stazione Zoologica Anton Dohrn, Naples - Italy)
Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html
http://events.embo.org/12-comparative-genomics/index.html
URL: http://www.pasteur.fr/~tekaia/BCGA2012.html

Contact Person: Fredj Tekaia (tekaia@pasteur.fr)

Benelux Bioinformatics Conference

2011-10-17T07:12:00.001-07:00

Putting the Lux on BeNeLux

The BeNeLux Bioinformatics Conference (BBC) will be hosted in Luxembourg for the first time, and CRP-Santé will lead its organization in partnership with other local institutions. BBC will be held on 12 and 13 December 2011, and will showcase research advances from the region and beyond.

A key theme of BBC2011 will be "Bioinformatics: Enabling Translational Biomedical Research".

The conference is an official ISCB affiliated conference.

Go to Conference web-site

Invited speakers

Thomas Lengauer, Max-Planck-Institut für Informatik, Saarbrücken, Germany

Burkhard Rost, Technical University Munich, Germany

Peter van der Spek, Erasmus Medical Center, Rotterdam, The Netherlands

Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT, Lausanne, Switzerland

Genetic Engineering & Biotechnology News (GEN) Celebrates 30 years with Collector's Edition

2011-10-03T13:20:00.001-07:00

For Immediate Release
Contact: Linda Muskat-Rim, 914-740-2251, lmuskat@liebertpub.com, Mary Ann Liebert, Inc., publishers

Genetic Engineering & Biotechnology News(GEN)
Celebrates 30 Years with 130-Page Collector's Edition

New Rochelle, NY, October 3, 2011— Genetic Engineering & Biotechnology News (GEN) celebrates 30 years as the world's
first and most widely read magazine for the biotechnology industry. Universally heralded as the definitive information
source in this field, GEN covers the technology, trends, products, services, and advances that shape and drive the industry
forward. GEN's 130-page commemorative issue features articles written by luminaries, and an original poster that
tracks the milestones that have altered the course of biotechnology, leading to today's most groundbreaking scientific and
therapeutic discoveries.

"Genetic Engineering & Biotechnology News was there at the inception of this field and remains the single most useful
resource I use for keeping abreast of new developments," said James Wilson, M.D., Ph.D., Professor of Pathology and
Laboratory Medicine, Gene Therapy Program, University of Pennsylvania School of Medicine.

GEN was founded in 1981 by Mary Ann Liebert, who identified the untapped need for a publication dedicated to the
rapidly evolving biotech industry from applied research through commercialization. David Weiner, Ph.D., Professor of
Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, said, "Mary Ann practically willed
the biotech revolution."

"GEN is biotechnology. It always has been and always will be," said Mary Ann Liebert, president and CEO of the
company that bears her name. John Sterling, GEN's Editor-in-Chief for the past 27 years, confirms that "Genetic
Engineering & Biotechnology News impacts the industry. It fosters critical international collaborations among academia,
industry, and government."

Publishing October 1, the Collector's Edition includes contributions from Leroy Hood, M.D., Ph.D., on Biological
Complexity Under Attack; James M. Wilson, M.D., Ph.D., on The History and Promise of Gene Therapy; Elaine R.
Mardis, Ph.D., on Future of DNA Sequencing Technology; Rita Colwell, Ph.D., on Combating Infectious Disease Agents;
N. Leigh Anderson, Ph.D., on Proteomics: Pathways and Biomarkers; G. Steven Burrill on Tracking Operational
Financing Trends; and articles on bioprocessing and synthetic biology.

Over the years, GEN's guest editorials have been penned by notables including: Presidents Bill Clinton and Jimmy Carter;
Vice Presidents Al Gore and Dan Quayle; Speaker of the House Newt Gingrich; Nobel Prize Winner and co-discoverer of
the structure of DNA, James D. Watson, Ph.D.; former Head of 20th Century Fox and Co-Founder of Stand Up To Cancer,
Sherry Lansing; and J. Craig Venter, Ph.D., leader of a team that decoded the human genome. GEN enjoyed its own
celebrity and a film credit as a scientific consultant for the hit film Jurassic Park.

Genetic Engineering & Biotechnology News is published in print 21 times a year. Its 24/7 website, www.genengnews.
com, provides exclusive editorial online, including news and analysis, podcasts, webinars, polls, videos, and application
notes. The publication's focus, both in print and online, includes the entire bioproduct life cycle from bench to bedside.
Biobusiness, drug discovery, OMICS, bioprocessing, and translational medicine form the core of GEN's global
biotechnology coverage.

GEN's Collector's Edition is available free to subscribers. For individual and bulk purchase contact: Nancy Piscitello
(1-800-M-LIEBERT).
URL:

Contact Person: Linda Muskat-Rim (lmuskat@liebertpub.com)

Announcing Critical Assessment of Genome Interpretation & Prediction season open

2011-09-19T10:51:00.001-07:00

The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to assess computational methods for predicting the phenotypic impacts of genomic variation. The CAGI 2011 experiment is now well underway with 11 datasets available at the CAGI website: http://genomeinterpretation.org/. Remaining deadlines to submit predictions start September 30, 2011 and continue until 31 October.

In the CAGI experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and make predictions of resulting molecular, cellular, or organismal phenotype. These predictions are evaluated against experimental characterizations, and independent assessors perform evaluations. The CAGI Conference 2011 will be held 9 - 10 December at UCSF Mission Bay campus to disseminate results, assess our collective ability to make accurate and meaningful phenotypic predictions, and better understand progress in the field. From this experiment, we expect to identify bottlenecks in genome interpretation, inform critical areas of future research, and connect researchers from diverse disciplines whose expertise is essential to methods for genome interpretation.

The CAGI 2011 challenges include:
• Disease-associated variants of a human metabolic enzyme.
• Variants from the resequencing of breast cancer patients and control subjects.
• Disease-associated variants of a human sodium channel.
• Genome and RNA-seq data from identical twins with discordant disease.
• Multiple genomics data for cancer cell lines, with differential response to drugs.
• Exomes of Crohn's disease patients and healthy individuals.
• Double mutants of p53 to identify mutations that restore the activity of inactive p53.
• Predicting the medical phenotypes of individuals with genome data.
• Microbial dataset measuring the effect of gene disruptions under stress conditions.
• The riskSNPs dataset to identify potential causative SNPs from lists of candidates in the disease-associated loci for seven complex trait diseases.
The CAGI submission deadline for the mouse exomes challenge already passed, but we are accepting submissions for archival purposes.

The first CAGI experiment, called pre-pro-CAGI, was organized in 2010. Assessors are preparing a manuscript to discuss these results. While the identities of the prediction methods have been embargoed for this "training" CAGI, we will de-anonymize methods from predictors who give us the permission to do so and future CAGI experiments will be more open. The next CAGI experiment is anticipated for 2013.

In order to access the challenges, download datasets, and submit predictions to CAGI 2011, please go to the website http://genomeinterpretation.org and register. For more information, contact the organizers at cagi@genomeinterpretation.org.

We are grateful to the following:

Data providers:
Adam Arkin, George Church, Andre Franke, Joe W. Gray, Rick Lathrop, Jasper Rine, Jeremy Sanford, Nicole Schmitt, Jay Shendure, Michael Snyder, and Sean Tavtigian.

Confirmed Assessors:
Rui Chen, Iddo Friedberg, Gad Getz, Sean Mooney, Pauline Ng, and Sean Tavtigian.

Confirmed CAGI Advisory Board:
Russ Altman, George Church, Tim Hubbard, Scott Kahn, and Sean Mooney.

Confirmed CAGI Scientific Council:
Patricia Babbitt, Atul Butte, Garry Cutting, Rachel Karchin, Robert Nussbaum, Michael Snyder, and Liping Wei.

URL: http://genomeinterpretation.org

Contact Person: Susanna Repo (srepo@compbio.berkeley.edu)

BeNeLux Bioinformatics Conference (BBC) - Enabling Translational Biomedical Research - ISCB affiliated conference

2011-09-11T03:03:00.000-07:00

BeNeLux Bioinformatics Conference (BBC)
Luxembourg - Luxembourg
Hosted by:	CRP-Santé
Venue:	Alvisse Parc Hotel
Dates:	Dec 12, 2011 through Dec 13, 2011
Call for Papers or Oral Presentations:	2011-09-01 through 2011-10-28
Event Registration:	2011-08-15 through 2011-11-27

Description

Putting the Lux on BeNeLux The BeNeLux Bioinformatics Conference (BBC) will be hosted in Luxembourg for the first time, and CRP-Santé will lead its organization in partnership with other local institutions. BBC will be held on 12 and 13 December 2011, and will showcase research advances from the region and beyond. A key theme of BBC2011 will be "Bioinformatics: Enabling Translational Biomedical Research". Invited speakers Thomas Lengauer, Max-Planck-Institut für Informatik, Germany Burkhard Rost, Technical University Munich, Germany Peter van der Spek, Erasmus Medical Center, The Netherlands Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT

Additional Information

Event URL:	http://www.bbc11.lu
ISCB Member Discount:	15 percent
Contact Person:	Francisco Azuaje ( francisco.azuaje@crp-sante.lu)

BioVis 2011 registration open

2011-09-07T09:06:00.000-07:00

Registration for the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011) is now open. BioVis is an affiliated conference of the ISCB and will take place in Providence, RI (USA), co-located with IEEE VisWeek, the premier forum for visualization advances for academia, government, and industry.

Early registration (reduced rate) for this meeting ends on Friday, 16 September. Single day and two day registrations are available in addition to full week registration. Discounts are available for ISCB, IEEE and ACM members, details are can be found on the registration page.

The goal of BioVis is to create the premier international and interdisciplinary event for all aspects of visualization in biology. This symposium will bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. As the first annual BioVis Symposium, this event seeks to emphasize inclusion and interaction between these communities as its primary impact.

The program of the meeting includes:

a keynote by Lynda Chin (MD Anderson Cancer Center / Broad Institute of MIT and Harvard)
a primer by Lawrence Hunter (UC Denver) and Kun Huang (Ohio State)
a special session on BioVis challenges with invited speakers Arthur Olson (The Scripps Research Institute), Cydney Nielsen (BC Cancer Agency Genome Sciences Centre) and Willy Supatto (California Institute of Technology)
four paper sessions with 24 presentations from all areas of biology
27 posters and demos
presentation of the results from the BioVis Contest

The full list of accepted papers, posters, demos, and videos is available on the BioVis website.

Alan T. Waterman Award-Call For Nominations

2011-08-18T11:45:00.000-07:00

The National Science Foundation's Highest Honor

The Alan T. Waterman Award is the highest honor awarded by the National Science Foundation. Since 1975, when Congress established the award to honor the agency's ﬁrst director, the annual award has been bestowed upon individuals who have demonstrated exceptional individual achievement in scientiﬁc or engineering research of sufficient quality to place them at the forefront of their peers.

The annual award recognizes an outstanding young researcher in any ﬁeld of science or engineering supported by the National Science Foundation. In addition to a medal, the awardee receives a grant of $500,000 over a three year period for scientiﬁc research or advanced study in the mathematical, physical, biological, engineering, social or other sciences at the institution of the recipient's choice.

Eligibility and Selection Criteria

• Candidates must be U.S. citizens or permanent
residents, 35 years of age or younger, or not more than
seven years beyond receipt of their Ph.D. degree by
December 31 of the year in which they are nominated.

• Candidates should have demonstrated exceptional
individual achievements in scientific or engineering
research of sufficient quality to place them at the
forefront of their peers. Criteria include originality,
innovation, and significant impact on their field.

To nominate a candidate, please go to:
www.fastlane.nsf.gov/honawards/

Information on the award and past recipients is also available at: www.nsf.gov/od/waterman/waterman.jsp
URL: http://www.nsf.gov/od/waterman/waterman.jsp

Contact Person: Mayra N. Montrose, Program Manager (waterman@nsf.gov)

Registration open for Therapeutic Applications of Computational Biology and Chemistry (TACBAC) 2012

2011-07-13T07:52:00.000-07:00

12-14 March 2012
Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Abstract deadline: 30 January 2012 Registration deadline: 6 February 2012

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments. You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Scientific Programme Committee:
Lee Harland, Pfizer, UK
John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK
Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK

Speakers include:
Chas Bountra, Structural Genomics Consortium, UK
Paul Flicek, EMBL-European Bioinformatics Institute, Hinxton, UK
Ronald Frank, Helmholtz Centre for Infection Research, Germany
Bobby Glen, University of Cambridge, UK
Roy Goodacre, University of Manchester, UK
Jules Griffin, University of Cambridge, UK
Lee Harland, Pfizer, UK
Aroon Hingorani, University College London, UK
John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK
Julio Saez-Rodriguez, EMBL-European Bioinformatics Institute, Hinxton, UK
Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK
Olivier Tabourieau, Center for Biological Sequence Analysis, Denmark

URL: http://registration.hinxton.wellcome.ac.uk/display_info.asp?id=263

Contact Person: Jemma Beard (j.beard@hinxton.wellcome.ac.uk)

Computational Structural Bioinformatics Workshop

2011-07-03T01:09:00.001-07:00

Computational Structural Bioinformatics Workshop (CSBW) will be held in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011). This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques, and open research problems in computational
structural bioinformatics. Registration of the CSBW will enjoy the benefit of the main conference BIBM2011.
URL: http://www.cs.odu.edu/~lchen/CSBW.htm

Contact Person: Jing He (jhe@cs.odu.edu)

A new concept in online sequence analysis

2011-06-16T11:14:00.001-07:00

I thought I might bring to your attention a revolutionary concept in online research for life sciences.

A website called "Sequilab" has created a virtual research lab for life scientists doing sequence analysis. Sequilab is a sequence-profiling portal with web 2.0 interactivity features built into it. It allows the user to directly link NCBI-BLAST results instantly to an inventory of sequence analysis tools like translate, ORF, CpG islands, View structure (Cn3D), mfold (for RNA) without cutting and pasting.

In addition to the seamless integration of BLAST results with sequence analysis tools, Sequilab also allows users to save the results of their research for later use and they can also create custom toolbars of particular tools that are used most frequently. If assistance is needed, researchers can discuss projects and with peers in the community forums if needed and share research interests via a personal profile.

The portal can be accessed by visiting http://www.sequilab.org. Registration is a free, one-step process.

I think this portal may be of interest to you and your readers. More details on how this concept works can be found at - http://sequilab.org/pages/howItWorks.jsf;jsessionid=6D303B1F5CB0EDACA5AE5F3D6F06E1D4

Thank you

Dr. Natarajan Ganesan,
Sequilab.org
URL: http://www.sequilab.org

Contact Person: Natarajan Ganesan (natarajanganesan@sequilab.org)

Introducing Predict @proteommetal: A tool for prediction of Metal binding domains in Proteins

2011-06-05T20:47:00.000-07:00

"Predict @proteommetal" tool is an informative tool designed to find metal binding sites in proteins structures as well as sequences. It can predict metal binding sites for 16 metals (Cu, Ca, Al, Mo, Ni, Fe Na, K, La, Zn, Mg, Mn, Hg, Cd, Co and Pb) on the basis of coordinating residues specific to the metal.

The information of coordinating residues was gathered in a database. The database was formed on the basis of the binding affinity of metal towards the coordinating residues. At the heart of the tool, effective perl programs had been combined with rich php interface.

This may be used as a platform for the identification and characterization of metal binding site(s) which will further contribute towards a better understanding and evaluation of various facets of contemporary life science areas like protein engineering, epidemiology, evolutionary studies etc. Importantly, In a very less time.

URL: http://www.bitmesra.ac.in/proteommetal/home.php

Contact Person: Shankaracharya, medhavi mallick and A. S. Vidyarthi (shankaracharya@bitmesra.ac.in)

Agilent grants for systems biology software development

2011-06-01T15:07:00.000-07:00

To: International Society for Computational Biology
This announcement is on behalf of Leo Bonilla, Director of Marketing for Integrated Biology, Agilent Technologies, Inc. Agilent is fostering integrated, whole-systems approaches to biological research through two $75,000 US grants (application deadline August 12, 2011). Funds will support academic or nonprofit research projects covering the development of open source software tools for integrating data from different omics platforms—genomics, transcriptomics, proteomics, and metabolomics.
For full details on eligibility, submission, and review process, please visit www.Agilent.com/lifesciences/emerginginsights.
If you have any questions or would like to interview Leo about the grant program, I'd be happy to set up a phone call. Just reply to my email and I'll connect you with Leo.

Sincerely,
Pia Abola, Ph.D.
Scientific Content Manager
The Linus Group
5900 Hollis St., Suite H
Emeryville, CA 94608
(510) 547-7100

URL: http://www.Agilent.com/lifesciences/emerginginsights

Contact Person: Pia Abola (pabola@thelinusgroup.com)

Call for Site Proposals - 2012 ACM Conference on Bioinformatics and Computational Biology

2011-04-24T12:01:00.000-07:00

Call for Site Proposals: ACM-BCB 2012
Site proposals for the Third ACM Conference on Bioinformatics and Computational Biology (ACM-BCB 2012) are invited from interested groups. ACM-BCB is the official conference of the ACM SIG Bioinformatics (http://www.sigbioinformatics.org/ ) . Site proposals should be no longer than 2 page ASCII text (66 lines, 80 columns). Proposals must be submitted by email to the current ACM SIG Bioinformatics Director of Conferences (Vasant Honavar, honavar@cs.iastate.edu) with the subject: "ACM-BCB site proposal - YEAR" (e.g., "ACM-BCB site proposal - 2012") no later than May 31, 2011. The venue for ACM-BCB 2012 will be announced during ACM-BCB 2011 which is being held in Chicago (http://acmbcb.org/ )
Site proposals should cover the following topics:
• Geographic Region: For 2012, the preferred location is North America. In the future, we will consider rotating the location to other regions (Europe, Asia, etc.)
• Potential dates: Potential dates should be chosen so as to avoid conflicts with major conferences in related areas (ISMB, BIBM, CSB, BIBE, RECOMB, etc.)
• Site city:
➢ The city should be located near a major airport, within 1-2 hours of regular train service and/or 45 minutes of cab/shuttle service. The airport should be served at least two airlines with regular service through a major international airport to the 4 major continents of SIG Bioinformatics attendees: Asia, Europe, North and South America.
➢ The city should have one or more conference venues that can accommodate conferences with 300-600 attendees, including suitable facilities for 4-6 concurrent tutorials or workshops with up to 100 attendees each. The venues should include facilities with one to 3 large center screens, with unobstructed views, and projectors and audiovisual equipment appropriate for plenary sessions. The venue should include suitable reception and banquet facilities. Please do NOT contact possible venues regarding availability or cost. ACM negotiates the cost, availability, and contracts directly with candidate venues. However, you may include estimates based on your knowledge of recent conferences, especially ACM conferences (if any), held at the venues under consideration. A sample list of possible venues with a 1-line description addressing logistics (time to get there, need for transportation) would be useful. The availability of low-cost or subsidized venues e.g., the conference facilit ies at a major university would be a plus.
➢ The city should have hotels that can house 500-700 people (attendees and their guests) within easy access to the possible venue. The availability of inexpensive accommodations for student participants is a plus.
• Conference Organizers:
➢ The proposal must include the name and affiliation of an active member of the SIG Bioinformatics community based in or very close to the proposed site city who is willing to serve as general chair; this may eventually require a statement of support from the chair's institution, and possibly administrative and organizational support.
➢ The proposal may include: 2 co-chairs, one of whom must be local; The names and affiliations of a few other candidates that the chair can enlist to serve on the committee, notably a local person as local arrangements chair, a publicity chair, treasurer, etc.
➢ The proposal must not include the names of program committee chairs (The ACM SIG Bioinformatics Board of Directors will select the program chairs).
• Dates and conflicts: Please indicate which dates have conflicts with major local events, etc. that could interfere with the availability of either the proposed site or the proposed conference organizers. The proposed dates should consider conflicts with major conferences on related topics (ISMB, AAAI, IEEE BIBE, IEEE BIBM, RECOMB, PSB, etc.) The dates of ACM-BCB will ultimately be selected by the SIG Bioinformatics Executive Committee, based on the proposals received and feedback from surveys conducted by SIG Bioinformatics.
URL: http://www.sigbioinformatics.org/

Contact Person: Vasant Honavar (honavar@cs.iastate.edu)

Bioinformatics writing contest on en.bioinformatyk.eu

2011-04-21T04:08:00.001-07:00

We are happy to announce a writing contest for beginner-friendly articles on bioinformatics. The web magazine http://en.bioinformatyk.eu collects articles for bioinformatics students that are easy to understand. You are welcome to participate by contributing a short article about a topic of your choice, e.g.:

* Fancy algorithms & bioinformatics tools you have used.
* Amazing discoveries you read about.
* Present your lab and what it has achieved.
* How you survived your BSc, MSc, or PhD thesis.
* Books, events, science news.

You don't need to describe original research (we'd even suggest you save this up for your first paper). What matters more important is to explain bioinformatics in a clear or entertaining way.

To submit an article, prepare a MS Word, OpenOffice or PDF document with your text in English (200-1000 words). Prepare eventual figures as separate files (.jpg or .png). Finally send everything by email to contest[at]bioinformatyk.eu - We will take care of the rest.

The submission deadline for the contest is September 18th, 2011.

Remember that you need to have copyright of everything you are submitting. Also, if your article contains results from your research, please make sure that your supervisor agrees with that.

The best articles will be awarded by an international board of referees:

* 1st prize: 150,- USD
* 2nd prize: 50,- USD
* Reader's prize: 50,- USD
* Book prize sponsored by the Dean of the Biological Faculty, UAM Poznan: ~300 USD

You can find the detailed regulations of the contest on:
http://en.bioinformatyk.eu/the-contest/

The Organizers,
Justyna Wojtczak (Chief Editor)
Teresa Szczepińska (ISCB-SC Vice Chair)
Kristian Rother (Faculty Advisor)

URL: http://en.bioinformatyk.eu

Contact Person: Kristian Rother (krother@genesilico.pl)

Announcing grant writing sessions @ISMB

2011-04-20T17:16:00.000-07:00

Dear colleagues,

We would like to invite you to join us for
information sessions about grant writing during
ISMB/ECCB, July 15-19, 2011 in Vienna, Austria.

Tutorial
Grant-writing 101: how to write a winning grant proposal
Saturday July 16, 1:30 pm - 5:30 pm

Workshop
Navigating the Granting Jungle
Sunday July 17, 2:30 pm – 4:25 pm

Funding availability
Reviewer’s recommendations
Speaking from experience
Finding/selecting funding schemes

Looking forward to seeing you in Vienna!

Yana Bromberg, Rutgers University
Magali Michaut, University of Toronto
Venkata P. Satagopam, EMBL
Andrea Schafferhans, Technical University of Munich

Publication on Virtual workshops for Africa and future prospects

2011-04-11T01:25:00.001-07:00

A paper concerning the Basic Molecular evolution training that virtually took place in July 2010 across Africa has just been published. This can be accessed at the following url

http://onlinelibrary.wiley.com/doi/10.1002/bies.201000139/abstract

A lot of experience was garnered that brought forth the publication which is an aftermath on the "ten simple rules to organize a virtual conference-anywhere".

There are plans to have an on site workshop on molecular evolution early 2012 with a wide range of participants from other regions connected virtually.

Further information will be communicated in due course and it is hoped that more regions will participate this time round.

It is hoped that this will lead to a series of such workshops in different subjects within the field of bioinformatics and computational biology.

Let us endeavor to support and make virtual workshops a success and reality in order to benefit more students/scientists within the developing countries.

URL: http://onlinelibrary.wiley.com/doi/10.1002/bies.201000139/abstract

Contact Person: Sheila Ommeh (scecily@yahoo.com)

Career Advice from a Rock Star of Science

2011-04-10T12:35:00.000-07:00

Elizabeth Blackburn spoke about careers to young scientists during AACR (American Association for Cancer Research) meeting. Jade attended the session and shares useful advice with us on her blog.

How Deep into a Topic should you go?
Choosing a Postdoc
On a Failure
On Collaborations and Letters of Recommendations
Publishing in High Profile Journals
"Alternative" Careers in Science
Mommy Guilt
Chasing Ideas

Read the details...

Call for Tutorials and Demos: IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB'011)

2011-04-01T03:46:00.001-07:00

First IEEE International Conference on
Healthcare Informatics, Imaging, and Systems Biology (HISB)
July 27-29, San Jose, California
http://www.ieee-hisb.org/

*** Call for Tutorials and Demos ....
URL: http://www.ieee-hisb.org/
Contact Person: HISB Tutorial and Demo Chairs (hisbdemo@eecs.umich.edu)

First IEEE International Conference on
Healthcare Informatics, Imaging, and Systems Biology (HISB)
July 27-29, San Jose, California
http://www.ieee-hisb.org/

*** Call for Tutorials and Demos ***

The First IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology now invites proposals for tutorials and demonstrations at the conference to be held in San Jose, July 26-29, 2011.

The purpose of tutorials is to provide a comprehensive overview by subject matter experts on topics relevant to HISB, keeping in mind the inter-disciplinary audience. The purpose of demos is to give researchers the opportunity to showcase the state of the art in areas relevant to HISB. Industrial exhibitors may also demonstrate their products through demos as long as they are relevant to the topic areas of the main conference.

We encourage submissions of tutorial and demonstration proposals on all topics relevant to the conference in the general areas of healthcare informatics, biomedical imaging, bioinformatics, and systems biology. A full list of topics is available in the call for papers for HISB at (http://www.ieee-hisb.org). Specialized subtopics that address computational or clinical aspects of the main topics will also be considered.
Please refer to the main conference site (http://www.ieee-hisb.org) for further details.

Key Dates:

Submission deadline (for both tutorials and demos): April 20, 2011
Notification of Acceptance: May 20, 2011
Conference Dates: July 27-29, 2011
URL: http://www.ieee-hisb.org/

Contact Person: HISB Tutorial and Demo Chairs (hisbdemo@eecs.umich.edu)

Intech Launches Open Access Journal "Nanomaterials and Nanotechnology"

2011-03-28T10:56:00.001-07:00

InTech, the Open Access publisher, has announced the launch of a new Open Access journal, "Nanomaterials and Nanotechnology". The quarterly journal will be available online for free full-text download on the reading platform www.InTechOpen.com.

Open Access publications which are not subsidized by institutional funding are usually financed by payments met by the institutions researchers work for. However, "Nanomaterials and Nanotechnology" will be a "Free for All" publication, with no costs incurred by contributors or readers.

Thanks to the "one at a time" publishing model, accepted papers will be published online immediately following peer review. The complete process from submission to publication will take approximately one month.

The journal's Editor in Chief is Dr. Paola Prete of the Institute for Microelectronics and Microsystems at the Italian National Research Council, Lecce, Italy. Dr. Prete expects that the journal will be a useful source of information for researchers in all areas of nanoscience since it will cover a wide range of topics, such as the synthesis of nanosized materials, nano-characterization techniques, nanobiotechnology and nanomedicine.

The Editorial Board is comprised of international experts, including C. N. R. Rao - Linus Pauling Research Professor at the Jawaharlal Nehru Centre for Advanced Scientific Research and Honorary Professor at the Indian Institute of Science, Bangalore, India. Professor Rao is a member of the Royal Society and the US National Academy of Sciences, and is renowned for his contribution to solid state chemistry and nanomaterials over the last two decades.

The first issue of the Journal is expected to go live in June 2011. The call for papers for inclusion in the first issue is open until 10 May, 2011.

Researchers interested in submitting their papers for consideration for the first issue are invited to find out more at http://www.intechweb.org/nn-first-issue.html.

ABOUT INTECH

InTech (www.intechweb.org) is an Open Access publisher of journals and books covering the fields of Science, Technology and Medicine. InTechOpen is an Open Access reading platform for InTech publications, a space where all users can read, share and download more than 300 books and 8,000 book chapters. All content at InTechOpen (www.intechopen.com) is distributed under the Open Access label and under the Creative Commons license - freely accessible to anyone, anywhere in the world.

URL: http://www.intechweb.org

Contact Person: Nataly Anderson (anderson@intechweb.org)

Announcing RECOMB-BE 2011 in Vienna, Austria, July 20-21, 2011

2011-03-27T10:56:00.001-07:00

Third RECOMB Satellite Conference on Bioinformatics Education
Vienna, Austria
July 20-21, 2011
in Conjunction with ISMB 2011

OVERVIEW

The Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE) will be held in Vienna, Austria, July 20-21, 2011 as an ISMB/ECCB 2011 Satellite Meeting (http://www.iscb.org/ismbeccb2011). The conference follows the first two RECOMB-BE meetings: http://casb.ucsd.edu/bioed/ and http://casb.calit2.net/bioed10/ . RECOMB-BE 2011 will consist of invited presentations, oral presentations selected from submitted abstracts and papers, a poster session, and discussion panels, all of which focus on improving bioinformatics education.

INVITED SPEAKERS

Partial List: Laurie Heyer (Davidson College), Larry Hunter (University of Colorado), Fran Lewitter (Whitehead Institute for Biomedical Research) Ran Libeskind-Hadas (Harvey Mudd College), Florian Markovetz (CRUK Cambridge Research Institute), Bernard Moret (École Polytechnique Fédérale de Lausanne), Tal Pupko (Tel Aviv University), Pavel Pevzner (University of California at San Diego), Ben Raphael (Brown University), Ron Shamir (Tel Aviv University), Beth Simon (University of California at San Diego), Terry Speed (University of California at Berkeley), and Jens Stoye (Bielefeld University).

THEME AND SCOPE

The goal of RECOMB-BE is threefold: to showcase best practices of teaching bioinformatics ideas to biology undergraduates, to discuss existing challenges in bioinformatics education (with an emphasis on undergraduate education), and to promote collaboration among educators with the aim to develop a mature bioinformatics curriculum. In keeping with the focus on undergraduates, the conference will also showcase selected bioinformatics research projects conducted by undergraduate students.

While biology has been transformed into a computational science in the last decade, the biological curriculum remains largely unchanged with respect to computational issues. The question: "How should we teach bioinformatics to biology students?" has become of the utmost importance, since many universities have not only founded undergraduate bioinformatics programs but are considering the addition of new computational courses to the standard biology curriculum—a change which would represent a dramatic paradigm shift in biology education. However, as the first two RECOMB-BE meetings demonstrated, there is a great divide in how even the world's top bioinformaticians thought the subject should be taught, and therefore the above pedagogical question has not been answered satisfactorily to date.

RECOMB-BE therefore aims to demonstrate the intricacy, practicality, and beauty of modern bioinformatics at the undergraduate level, and advance the discussion about its curriculum in the biology classroom. For a summary of RECOMB-BE discussions and the educational challenges that lie ahead for bioinformatics, see Computing has changed biology--biology education must catch up (Science 2009, v.325: 541-542).

FORMAT

RECOMB-BE will have a somewhat unusual format, inspired by the biennial mathematical conference called Gathering for Gardner (G4G) At G4G, leading mathematicians give high-school and undergraduate level lectures; the goal of G4G is therefore to present complex mathematical ideas in a simple form. This objective is one for which the bioinformatics community must also strive in order to establish meaningful future collaborations with biologists and to bridge the cultural gap between computational and experimental scientists.

Unlike previous meetings on bioinformatics education, which have focused on how bioinformatics should be taught, RECOMB-BE showcases how leading bioinformaticians actually teach. Speakers will give short, introductory-level lectures, aimed at undergraduates. These lectures will be complemented by discussion panels focusing on existing challenges in bioinformatics education as well as poster presentations given by undergraduate students on their research projects.

BIOINFORMATICS FOR BIOLOGISTS TEXTBOOK PROJECT

The participants of RECOMB-BE in 2009 and 2010 formed the Bioinformatics Education Alliance, a group of sixteen leading bioinformaticians who have recently collaborated to produce a textbook, called Bioinformatics for Biologists (B4B). The first edition of B4B will be published by Cambridge University Press in the summer of 2011, and test copies will be available at ISMB 2011. Please see the official B4B website for more details: http://cseweb.ucsd.edu/~ppevzner/B4B/

B4B is an open project that will be continuously expanded by new chapters. Therefore, RECOMB-BE invites submissions of proposals for new chapters; accepted chapters will be included in the second edition of B4B which is scheduled for publication in 2012 (see "Important Dates" below).

CALL FOR PARTICIPATION

We invite submissions in four categories:

1. Bioinformatics Education Papers
2. Bioinformatics for Biologists Textbook Chapter Proposals
3. Bioinformatics Education Abstracts (submitted by educators)
4. Undergraduate Bioinformatics Research Abstracts (submitted by undergraduate or first-year graduate students)

Selected papers and abstracts in the first three categories will be invited for either oral or poster presentations. Undergraduate bioinformatics research abstracts will be invited for a poster presentation.

Bioinformatics Education Papers should be submitted via the RECOMB-BE website and must be received by May 5, 2010. Each paper should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Papers should be self-contained and aimed at advanced undergraduate biology students. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. RECOMB-BE imposes no explicit restrictions on format, length, or notation, as we encourage contributors to choose the style they feel is the most appropriate; however, we anticipate that each contributed paper will be at least 10 pages long.

Authors of selected papers will be invited to submit their paper in the journal PLOS Computational Biology (in the Education Article category) as well as a chapter in the second edition of the Bioinformatics for Biologists textbook, which is described above.

Bioinformatics for Biologists (B4B) Chapter Proposals should be submitted via the RECOMB-BE website and must be received by May 15, 2011. Each submission in this category should constitute a brief description of the proposed chapter. Authors of selected proposals will be invited either for oral or poster presentations at RECOMB-BE 2011. In addition, these authors will be asked to submit a full-length chapter for the second edition of B4B shortly after RECOMB-BE. Proposals should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. We anticipate that each chapter proposal will be 1-2 pages long.

Bioinformatics Education Abstracts (submitted by educators) should be submitted via the RECOMB-BE web site and must be received by May 20, 2011. Submissions in this category can discuss practice, challenges, or perspectives in bioinformatics education (e.g., curricula, integration of bioinformatics programs, online courses, etc.) or represent a proposal for a short 20-30 minute introductory lecture aimed at undergraduates. We are specifically looking for lectures that begin with a description of an interesting biological problem, such as "Did we evolve from Neanderthals?" and then show how computational techniques can be used to solve this biological problem. Each abstract should be at most 1 page long.

Undergraduate Bioinformatics Research Abstracts (submitted by undergraduates or first-year graduate students reporting their undergraduate work) should be submitted via the RECOMB-BE website and must be received by May 20, 2011. Each abstract should be at most 1 page long.

TRAVEL SUPPORT

RECOMB-BE and the Howard Hughes Medical Institute offer travel support to undergraduate students interested in bioinformatics. All undergraduate students are invited to apply for travel support. RECOMB-BE will have a poster session showcasing undergraduate bioinformatics research, and we encourage undergraduate students interested in participation to submit an undergraduate bioinformatics research abstract. Students who submit abstracts will be given a priority with regards to travel support. First-year graduate students who wish to present their undergraduate work are also welcome to apply for travel support. All applications for travel support should be made via RECOMB-BE website.

In addition to supporting undergraduate students, RECOMB-BE also has limited funds to support authors of accepted RECOMB-BE papers and B4B chapter proposals.

IMPORTANT DATES

Paper submission deadline: May 5, 2011
Notification of paper acceptance: May 15, 2011
Bioinformatics for Biologists textbook chapter proposals deadline: May 15, 2011
Notification of proposal acceptance: May 25, 2011
Abstract submission deadline: May 20, 2011
Notification of abstract acceptance: May 25, 2011
Application for travel support deadline: June 5, 2011
Notification of travel support: June 15, 2011

RECOMB-BE ORGANIZERS

RECOMB-BE was founded by Pavel Pevzner (UCSD) and Ron Shamir (Tel Aviv University) in 2009.

RECOMB-BE 2011 Program Committee: Fran Lewitter (Whitehead Institute for Biomedical Research), Ran Libeskind-Hadas (Harvey Mudd College), Pavel Pevzner, (UCSD) and Ron Shamir (Tel Aviv University).

RECOMB-BE Organizing Committee: Phillip Compeau (Chair), Sangtae Kim, and Son Pham.

Email contact: pcompeau@math.ucsd.edu

RECOMB-BE SUPPORT

RECOMB-BE is supported by the Howard Hughes Medical Institute (HHMI), the International Society for Computational Biology (ISCB), and the California Institute for Telecommunications and Information Technologies (CalIT2).

ABOUT RECOMB

The RECOMB International Conference on Research in Computational Molecular Biology was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference arose from the need to advance research on the mathematical and computational side of molecular biology, and today the conference maintains its focus on state-of-the-art computational advances in this field. The 15th Annual RECOMB conference (RECOMB 2011) will be held March 28-31, 2011 in Vancouver, Canada. The conference website can be found at http://compbio.cs.sfu.ca/recomb2011/.

The RECOMB Satellites Series was founded by Pavel Pevzner in 2001. It contains today nine focused meetings covering various specialized aspects of bioinformatics: RECOMB Comparative Genomics, RECOMB Regulatory Genomics, RECOMB Computational Cancer Biology, RECOMB Computational Proteomics, RECOMB SNPs and Haplotypes RECOMB Systems Biology, RECOMB Massively Parallel Sequencing and of course RECOMB Bioinformatics Education.
URL: http://casb.ucsd.edu/bioed11/index.php

Contact Person: Phillip Compeau, University of California-San Diego Dept. of Mathematics (pcompeau@math.ucsd.edu)

NEW NSF Solicitation: AVAToL

2011-03-17T10:34:00.000-07:00

AVAToL, Assembling, Visualizing and Analyzing the Tree of Life

The Assembling, Visualizing and Analyzing the Tree of Life (AVAToL) activity supports novel and transformative approaches to the development of an integrated and robust tree of life, as well as visualization and analysis on a dynamic tree of life. This will take place through the Ideas Lab project development and review process. The goal of this activity is to identify opportunities for investment to significantly advance the state-of-the-art in tree construction, visualization, and analysis across the tree of life. Participants selected through an open application process will engage in an intensive five-day residential workshop to generate project ideas through an innovative, real-time review process. New multidisciplinary teams will form during this workshop to engage in creative problem solving directed at outstanding problems concerning the tree of life. Multidisciplinary integrative approaches calling for communication and interaction among diverse scientists are key to the success of the approach. For example, in addition to those working in systematics and phylogenetics, AVAToL might benefit from mathematicians and computer scientists to contribute algorithms and models, bioinformaticians or genomicists to contribute data pipelines and novel molecular characters, or statisticians and artists with an interest in novel methods of visualization and interactive use of the tree of life. Therefore, members of the systematics research community, bioinformaticians, genomicists, morphologists, paleontologists, computer scientists, statisticians, mathematicians, educators involved in training the next generation of researchers, and representatives of any other disciplines that might contribute important ideas are all strongly encouraged to apply.
URL: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629&org=BIO&from=home

Contact Person: Tim Collins (bio-AVAToL@NSF.gov)

SIB Swiss Institute of Bioinformatics Awards 2011-Call for Applications

2011-03-10T00:45:00.001-08:00

The SIB Swiss Institute of Bioinformatics is happy to announce the SIB 2011 Awards, two prizes assigned to young scientists in bioinformatics.
Two categories: SIB Young Bioinformatician Award and SIB Best Graduate Paper Award.

SIB 2011 Young Bioinformatician Award

Prize of CHF 10,000 and award certificate.

Open to any graduate student or young researcher in Europe who has carried out a research project centered on the in silico analysis of biological sequences, structures and processes.
Candidate must not be more than 32 years old at the time of submission and must have worked on a project with a partner in Switzerland for at least 6 months in 2010.

Submitted project must be completed or subject to publication within the period from 1 June 2010 to 1 June 2011.

Applications for the award may be submitted by the candidate, any faculty member or SIB group leader.

SIB 2011 Best Graduate Paper Award

Prize of CHF 5,000 and award certificate.

Open to any graduate student who has not yet completed his/her PhD, at the time the paper was published.

Applicant must have studied in Switzerland for at least 6 months in 2010.
Submitted paper must have been published or be subject to publication within the period from June 1, 2010 to June 1, 2011.

Applications for the award may be submitted by the candidate, by any SIB group leader or by a Swiss university or federal institute of technology.

Both winners will receive their prizes during the [BC]2
Basel Computational Biology Conference on 23-24 June 2011.
Winners will also be invited to present their projects during the conference.

Closing date for entries: 30 March 2011

More information and submission form at:
http://www.isb-sib.ch/research/sib-awards.html

Contact:
Irene Perovsek
00 41 (0)21 692 40 54
Irene.perovsek@isb-sib.ch
URL: http://www.isb-sib.ch/research/sib-awards.html)

Web Publishing of Scientific Data and Services Training Courses

2011-02-25T08:31:00.001-08:00

This series of training courses is mandated to train service providers in the use of modern semantic approaches to publishing informatics resources on the Web using the semantic web services paradigm. The first Web Publishing of Scientific Data and Services Training Course will be held in Fredericton, NB, CANADA on May 19-20th, 2011.

Semantic Web Services have rich descriptions of functional requirements that facilitate service interoperability and make it easier for users to discover and access relevant services in real time. The course provides both theory and practical training in the semantic technologies that underpin the development of semantic web services.The training course is divided into the following modules:

* Semantic Web
* Knowledge Representation and Reasoning
* Web Services
* SADI Semantic Web Services

At the end of the training, attendees will know how to:

* publish their data and algorithms on the Web in a manner that is easy for others to find and access using state of the art toolkits.

* ensure their data and tools integrate well with other resources on the Web.

* enhance query access and service discoverability for target end-user communities.

Target Audience
===============

This training course is primarily of interest to providers of bioinformatic resources seeking to extend the utility and usability of thier data and services. Researchers interested in learning state of the art semantic technologies and their deployment to facilitate web scale interoperability are strongly encouraged to attend. Priority will be given to students and professionals with working knowledge of Perl and/or Java.

Profile of Target Audience:

* Grid Computing Architects and Developers interested in building globally interoperable systems;

* Web Developers and Bioinformatics researchers seeking to ensure the adoption of their technologies in the knowledge discovery;

* Workflow system developers coordinating computational and data resources across the web using semantics;

* Industry pioneers in Workflow, Grid and Semantic technologies;

* Researchers involved in Web-based Knowledge Discovery in Bioinformatics.

URL: http://sadiframework.org/training/

Contact Person: Silvane Paixao (silvane.cbrass@gmail.com)

12th MRC SGDP Centre Summer School: Bioinformatics for Geneticists

2011-02-17T00:45:00.000-08:00

Bioinformatics for Geneticists: This course will teach how to handle data and conduct basic analysis, QC and annotation. It will cover the most common analysis packages and methods and how to do systems biology with each of these datasets singly or in combination. It will teach the essentials of GWAS and web data resources, pathway and network analysis, but a primary focus this year will be on next generation sequencing analysis. It will consider methods for analysis of transcriptome sequencing and exome/whole genome sequencing.

Scientific Directors: Gerome Breen & Richard Dobson
URL: http://www.kcl.ac.uk/schools/summerschool/si/sgdp/index.html

Contact Person: Gerome Breen, Richard Dobson (gerome.breen@kcl.ac.uk)

Announcing New Master of Biostatistics at Duke

2011-02-03T07:50:00.001-08:00

The Duke University Department of Biostatistics and Bioinformatics is excited to launch the new Master of Biostatistics Program in Fall 2011. This two-year degree program seeks to provide students with the analytical, biological, and communication skills that will ensure successful contribution to the rapidly-expanding field of biomedical research.

The program offers both degree and non-degree options. The two-year master degree option leads to a Master of Biostatistics, a professional degree awarded by the School of Medicine at Duke University.

Fall 2011 applications now available.

Application review begins January 31, 2011. Priority is given to Applications received by March 1, 2011. After March 1, 2011, Applications are considered on a space-available basis.

For more details about the Master of Biostatistics Program, please visit the program website: http://biostat.duke.edu/master-biostatistics-program/program-overview

URL: http://biostat.duke.edu/master-biostatistics-program/program-overview

Contact Person: Jonathan Hecht (jonathan.hecht@duke.edu)

Book Release: ADVANCES IN GENOMIC SEQUENCE ANALYSIS AND PATTERN DISCOVERY

2011-02-03T03:53:00.001-08:00

ADVANCES IN GENOMIC SEQUENCE ANALYSIS AND PATTERN DISCOVERY
edited by Laura Elnitski (National Human Genome Research Institute, USA), Helen Piontkivska (Kent State University, USA), & Lonnie R Welch (Ohio University, USA)

Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.

Contents:

1 Pattern Discovery Methods:
1.1 Large-Scale Gene Regulatory Motif Discovery with NestedMICA (M Piipari et al.)
1.2 R'MES: A Tool to Find Motifs with a Significantly Unexpected Frequency in Biological Sequences (S Schbath & M Hoebeke)
1.3 An Intricate Mosaic of Genomic Patterns at Mid-range Scale (A Fedorov & L Fedorova)
1.4 Motif Finding from Chips to ChIPs (G Pavesi)
1.5 A New Approach to the Discovery of RNA Structural Elements in the Human Genome (L Hua et al.)

2 Performance and Paradigms:
2.1 Benchmarking of Methods for Motif Discovery in DNA (K Klepper et al.)
2.2 Encyclopedias of DNA Elements for Plant Genomes (J Lichtenberg et al.)
2.3 Manycore High-Performance Computing in Bioinformatics (J-S Varré et al.)
2.4 Natural Selection and the Genome (A L Hughes)

Readership: Those who perform biological, medical and bioinformatics research.

236pp Pub. date: Jan 2011
ISBN: 978-981-4327-72-5
981-4327-72-7 US$90 / £56
URL: http://www.worldscibooks.com/lifesci/7972.html

Contact Person: Lonnie Welch (welch@ohio.edu)

2nd Bioinformatics for Regulatory Genomics Special Interest Group (BioRegSIG)

2011-01-31T09:05:00.000-08:00

CALL FOR PAPERS and POSTERS for the 2nd Bioinformatics for Regulatory Genomics Special Interest Group (BioRegSIG).

The meeting will be on July 16, 2011 in Vienna, in conjunction with The Nineteenth International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 10th European Conference on Computational Biology.

BioRegSIG is a one-day workshop that focuses on bioinformatics for regulatory genomics. It provides a broad, deep perspective on developments in research, and addresses the topic more extensively than can be done in the main conference.

Extended abstracts (in English) should not exceed 4 pages (2 pages for posters). Submit abstracts (in pdf format) to Sophie.Schbath@jouy.inra.fr. Submission deadline is February 21, 2011. Details about BioRegSIG are available at http://light.ece.ohio.edu/bioreg/2011/.
URL: http://light.ece.ohio.edu/bioreg/2011/

Contact Person: Lonnie Welch (welch@ohio.edu)

VIZBI 2011 workshop on visualizing biological data - early registration closes Jan 31

2011-01-27T19:40:00.000-08:00

Early registration for VIZBI 2011 closes next Monday (Jan 31) – after this date, registration costs $100 more.
URL: http://vizbi.org

Contact Person: Seán O'Donoghue (sean.odonoghue@embl.de)

EMBO practical course on Bioinformatics and Comparative Genome Analysis (Institut Pasteur Paris, France, June 27 - July 9, 2011.

2011-01-11T07:34:00.001-08:00

Announcement and Call for Application to the EMBO practical Course on "Bioinformatics and Comparative Genome Analysis" (http://cwp.embo.org/pc11-09/index.html) that will take place in the Institut Pasteur Paris, France, June 27 – July 9, 2011.
The main objective of this intensive course is to strengthen capacities of Phd students and young scientists, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies. The course topics will include theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, orthologs prediction and classification, Genome data visualization and statistical methods needed in Genome Wide Association Studies.
Practical sessions in a Linux environment will involve Unix and Perl scripting.
Participants are expected to be familiar with this environment.

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Ph.D students and Post-Doctoral Researchers in Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running research projects and on their expressed motivations.
Selected students will have free accommodation and meals and are expected to contribute with 300 euros and to pay for their travel expenses.
All participants (students and invited speakers) will stay in the same hotel.
Details are available on the course web site: http://cwp.embo.org/pc11-09/index.html

Candidates are advised to complete carefully the application form, together with a one-page CV and a personal Identity Picture (Photo).

The deadline application is April 30, 2011.

Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html
URL: http://cwp.embo.org/pc11-09/index.html

Contact Person: Fredj Tekaia (tekaia@pasteur.fr)

FASEB Excellence in Science Award Call for Nominations

2010-12-27T14:52:00.000-08:00

FASEB is seeking nominations for its 2012 Excellence in Science Award, that recognizes the significant accomplishments of women scientists. We look forward to another list of nominees that reads like a 'Who's Who' of international science, containing the names of outstanding women in science who have accomplished scientific work of lasting impact and have contributed substantially to training the next generation of scientists. The 2012 season for the FASEB Excellence in Science Award will begin January 1, 2011.

Nominations must be submitted on the FASEB award website by March 1, 2011.
URL: http://www.faseb.org/What-We-Do/Awards/Excellence-in-Science-Award.aspx

Contact Person: Linda Stricker (lstricker@faseb.org)

Introducing SWIFT MODELLER: A Java Based GUI for Molecular Modelling

2010-12-17T20:37:00.001-08:00

Dear Colleagues,
We are very happy to inform you that we have developed a new GUI for molecular modelling.Now this is online on Modeller\'s website http://salilab.org/modeller/wiki/Links with the link swift modeller. This is freely available to all.

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. The visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and presents it in an interactive way making MODELLER much easier to use than before.

The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. It lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with

It would be great for me if you evaluate this tool and send the feedback, so that we can further improve this GUI.
I am waiting for the suggestions, as these are very important for us.

Thanks and Regards,
Shankaracharya
URL: http://www.bitmesra.ac.in/swift-modeller/swift.htm

Contact Person: Shankaracharya, Abhinav Mathur and Dr. A. S. Vidyarthi (shankaracharya@bitmesra.ac.in)

Recent Science Policy News for ISCB

2010-12-16T08:33:00.000-08:00

This page was initially set up to allow our ISCB representatives to FASEB share information with interested ISCB members on matters of science policy.
URL: http://docs.google.com/Doc?docid=0AQZYSgQ_82j7ZDNmeHhwcV8yMDRnejRic3dkYw&hl=en&authkey=CJP2t_MD

Contact Person: Barbara Bryant (barb.bryant@gmail.com)

Joanne Luciano joins Web Science Research group at Rensselaer

2010-12-15T11:11:00.001-08:00

Luciano brings expertise in health care and life science research to the Tetherless World Research Constellation

Joanne Sylvia Luciano has joined Rensselaer Polytechnic Institute as research associate professor in the Tetherless World Research Constellation. Luciano's research uses computational modeling and the World Wide Web to improve health care and advance medical discovery.

Luciano is an experienced technology consultant to major hospitals, biotechnology, and pharmaceutical companies. In addition to her nearly 30 years as a consultant, she held a joint appointment with Harvard Medical School and Massachusetts General Hospital for nine years, where she served as a lecturer and research scientist using computational modeling to study human disease.

She joins an interdisciplinary research team within the Tetherless World Research Constellation at Rensselaer, dedicated to advancing science and society through understanding and utilization of the World Wide Web.

"There's a vast amount of medically relevant data sitting in databases or websites and not being utilized," Luciano said. "The focus of my research is to create technologies that make it easy to do medical research whether you are a doctor, patient, pharmaceutical company, or searching for alternative therapies or lifestyle changes."

To accomplish these aims, Luciano utilizes ontologies and advanced mathematical modeling and computer simulation to understand illness, share medical data, and advance medical discovery and patient care. She builds computer-based technologies that improve healthcare by translating discoveries made at the laboratory or computer bench to the care received at an individual patient's bedside – known as bench to bedside care.

"There is an urgent need to shorten the time it takes to bring basic life science research results to clinical practice, and to get the clinical observations back to the research lab for further analysis," she said. "To do this, technologies need to be in place that allow scientists to better represent, reuse, and communicate medical data."

Luciano has helped develop several important ontologies including BioPAX, which is an international standard used for data related to cellular processes. BioPAX enables data to be combined in ways that were not possible before, making it possible to ask and answer complex biological questions. The language enables data to be combined automatically by computers, and because the representations are true to the current understanding of biology, other technology can be used to make inferences and reason over the data.

At the MITRE Corporation, she developed InfluenzO, an ontology to support influenza research, surveillance, and outbreak monitoring. She continues to lead this collaboration with the University of Maryland, the University of Texas Southwestern Medical Center, and the Canadian government.

She helped create the World Wide Web Consortium (W3C) Health Care and Life Sciences (HCLSIG) special interest group. The HCLSIG integrates the efforts of pharmaceutical and clinical researchers, doctors, and technologists to build the next generation of medical Web-based technology standards.

She is also a co-organizer of the BioPathways Consortium (BPC), a group of scientists working to support scientific advancement in the area of biological pathways. Such research, which has been a foundation of Luciano's career, uses computation to understand cell development, genetics, drug development, and disease.

In addition to ontologies, Luciano also utilizes mathematical modeling to study the dynamics of medical treatment response, looking for patterns that will help clinicians make more informed treatment choices. Patterns of treatment response often exist in groups of individuals. This study of treatment response patterns leads to so-called "personalized medicine" in which individual response to treatment can be modeled effectively and is important because individuals may respond differently to a treatment. She began this research at McLean Hospital while at Boston University, where she earned her doctorate. The work began as a study of different treatments (drug and therapy) for major depressive disorder (MDD).

That research led to the development of patented methods to select the best treatment for individual patients and predict the expected recovery patterns of treatments.

Luciano holds bachelor's and master's degrees in computer science and a doctorate incognitive and neural systems from Boston University.

About the Tetherless World Research Constellation

The Tetherless World Research Constellation at Rensselaer Polytechnic Institute (RPI) explores the research and engineering principles that underlie the Web, to enhance the Web's reach beyond the desktop and laptop computer, and develop new technologies and languages that expand the capabilities of the Web under three themes: Future Web, Informatics, and Semantic Foundations.

The goals of the constellation include making the next-generation Web natural to use while being responsive to the growing variety of policy, educational, societal, and scientific needs. Research areas include: Web science, privacy, intellectual property, general compliance, Web-based medical and health systems, semantic eScience, data-science, semantic data frameworks, next-generation virtual observatories, semantic data and knowledge integration, ontologies, semantic rules and queries, semantic applications, data and information visualization, and knowledge provenance, trust, and explanation for science.

The faculty, staff, and students (graduate and undergraduate) use powerful scientific and mathematical techniques from many disciplines to explore the modeling of the next-generation Web from network-, data-, and information-centric views.

Published November 23, 2010 Contact: Gabrielle DeMarco
Phone: (518) 276-6542
E-mail: demarg@rpi.edu
URL: http://news.rpi.edu/update.do?artcenterkey=2796

Contact Person: Gabrielle May DeMarco (demarg@rpi.edu)

Bioinformatics Books Collection

2010-12-08T01:09:00.001-08:00

Bioinformatics students, researchers and professionals may be interested in an online collection of scientific books that includes a growing number of titles related to the bioinformatics field.

The books are published by InTech, Open Access publisher of books and journals in science, technology and medicine, and are available on the reading platform www.intechopen.com. The full texts are absolutely free to read online, download in PDF format and share. No registration is required on the site.

The whole collection includes more than 270 books, and 30 new titles are due to come online by Christmas 2010. Books which may be of interest to the bioinformatics community include:

- Data Mining in Medical and Biological Research;
- Bioinspiration;
- Intelligent and Biosensors;
- Finite Element Analysis;
- Stochastic Control, and new on 8 Debember 2010:
- Data Acquisition.

You are most welcome to visit, bookmark and spread the word to your friends and colleagues who you feel may also enjoy the publications.

InTech – Open Access Publishers in Science, Technology and Medicine
Reading platform: www.intechopen.com
Corporate site: www.intechweb.org
URL: http://www.intechweb.org

Contact Person: Nataly Anderson (anderson@intechweb.org)

ISCB congratulates past president Phil Bourne on being awarded Microsoft Research's Jim Gray eScience Award

2010-10-12T11:52:00.000-07:00

Microsoft Research has awarded the 3rd annual Jim Gray eScience Award to ISCB past president Philip E. Bourne. See full announcement at http://research.microsoft.com/en-us/events/escience2010/jim_gray_award.aspx

Sao Paulo School of Advanced Science Advanced Topics in Human Molecular Genetics-with associated practical course in Structural Computational Biology

2010-10-06T07:44:00.001-07:00

São Paulo School of Advanced Science

Advanced Topics in Human Molecular Genetics (with associated practical course in Structural Computational Biology)

Universidade Estadual de Campinas
UNICAMP
Campinas – São Paulo - Brazil

From February 28th to March 4th , 2011

The main purpose of the course is to provide an update on recent research in genetic diseases involving a number of different areas of knowledge, such as genomics, cancer research, hemoglobinopathies, neurosciences, amongst others. In addition, the course will report on the development and application of new tools applied in molecular biology, encouraging the expansion of collaborative research projects among Brazilian and foreign scientists.
Professors invited to participate in offering the courses are scientists with excellent qualifications and prominence in their fields of research, including foreign scientists. Among the teachers are important names in the field of Medical Genetics that focus their research on clinical and laboratory areas, covering key issues for students in the biological and medical sciences.
Selection of students participating:
60 positions will be offered for medical doctors and graduate students in Genetic or Biomedical Sciences. Half of these positions (30) are reserved for applicants from abroad. The other half will be distributed among applicants from the São Paulo metropolitan area (15 positions) and students from other Brazilian States (15 positions).

Note: For approved participants, the organization will cover all costs with return
fares from the candidate's place of residence to São Paulo, in addition to accommodation in double apartments plus meals during the event.
URL: http://www.spschool.com.br

Contact Person: Professor Edi Lúcia Sartorato (spschool@cbmeg.unicamp.br)

New Healthcare Associated Infection Community

2010-09-29T20:32:00.001-07:00

Join the community of healthcare professionals concerned with preventing Healthcare-Associated Infections (HAIs), which at any given moment seriously affect 1.4 million hospitalized patients worldwide. The HAI WATCHDOG forums are intended to provide a place for health care providers to discuss issues and best practices related to Hospital-Associated Infections (HAIs).

Kimberly-Clark is committed to helping win the battle to prevent HAIs. As part of that effort, we are pleased to sponsor this new community site for healthcare providers to discuss HAI without discussion of product-specific information.

Additionally, Kimberly-Clark has created the HAI WATCHDOG Awards in recognition of Healthcare-Associated Infection champions who are making a difference for the reduction and prevention of these infections.
URL: http://haiwatchdog.com

Contact Person: Barbara Dunn (barbara@haiwatchnews.com)

EMBO Global Exchange Lecture Course: Bioinformatics and Comparative Genome Analysis (Institut Pasteur Tunis, Tunisia)

2010-08-31T03:03:00.000-07:00

Announcement and Call for Application to the EMBO Global Exchange Lecture Course on Bioinformatics and Comparative Genome Analysis ( http://cwp.embo.org/glc10-14/) that will take place in the Institut Pasteur Tunis, Tunisia, December 13-18, 2010. The course is co-sponsored by the Institut Pasteur International Network.

The main objective of this intensive course is to strengthen capacities of Phd students and young scientists from African countries, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies (no practical sessions will be included in this course).

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Post-Graduate and Ph.D students in African Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies.

Participants selection will be based on an evaluation process involving an accepted Poster presentation (see Application form).

Detailed information are available on the course web site: http://cwp.embo.org/glc10-14/

Candidates are advised to read the indicated informations, then to complete carefully the application form, together with a one-page CV, a Poster abstract and a personal Identity Picture (Photo).

The deadline application is October 30, 2010.

The organizers:
Balkiss Bouhaouala-Zahar (Institut Pasteur Tunis, Tunisia)
Ahmed Rebai (CBS, Tunisia)
Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://cwp.embo.org/glc10-14/

Contact Person: Fredj Tekaia (tekaia@pasteur.fr)

Evolution may have pushed humans toward greater risk for type-1 diabetes, study shows

2010-08-17T17:00:00.000-07:00

Gene variants associated with an increased risk for type-1 diabetes and rheumatoid arthritis may confer previously unknown benefits to their human carriers, say researchers at the Stanford University School of Medicine. As a result, the human race may have been evolving in the recent past to be more susceptible, rather than less, to some complex diseases, they conclude.
URL: http://med.stanford.edu/ism/2010/august/selection.html

Contact Person: Krista Conger (kristac@stanford.edu)

Critical Assessment of Function Annotations

2010-08-17T14:33:00.001-07:00

When: 15-SEP-2010 through 15-JAN-2011
What: Critical Assessment of Function Annotations
Why: Because we need to assess computational gene and protein function prediction programs
More: http://biofunctionprediction.org

Sequence and structure genomics have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function".
The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
About the CAFA experiment
The problem: There are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are preforming?
The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function and Biological Process. A set of protein sequences is provided by the organizers. Participants are expected to submit their predictions by the submission deadline. The predictions will be evaluated during the Automated Function Prediction (AFP) meeting, which has been approved as a Special Interest Group (SIG) meeting, at ISMB 2011 conference (Vienna, Austria).
How to participate in CAFA?
1.Register for the experiment at http://biofunctionprediction.org
2.(Recommended) Subscribe to the low-traffic announcement list http://groups.google.com/group/afp2011-announce
3.Download target proteins, available September 15, 2010
4.Submit predictions before January 15, 2011
5.Join us at the AFP-SIG at Vienna July 15-16 for the fifth protein function prediction meeting, and to hear the CAFA results, and about the latest research in computational protein function prediction
More details at: http://biofunctionprediction.org
URL: http://biofunctionprediction.org

Contact Person: Iddo Friedberg (idoerg@gmail.com)

NIH Demystifying Medicine

2010-08-17T14:26:00.001-07:00

A DVD has been prepared by NIH/FAES of the 2009-2010 Series of presentations for the Course on "Demystifying Medicine for PhD Students, Fellows and Investigators". This successful Course bridges basic science and medicine by combining patient presentations and state of the art talks by leading clinical and basic science investigators. The topics include a wide range of diseases and research disciplines. The DVD is available on request (email) to basap@faes.od.nih.gov as long as the supply lasts. http://videocast.nih.gov/pastevents.asp?c=45
URL: http://videocast.nih.gov/pastevents.asp?c=45

Contact Person: Support (basap@faes.od.nig.gov)

Burroughs Wellcome Fund Career Awards at the Scientific Interface

2010-08-02T07:33:00.000-07:00

Career Awards at the Scientific Interface Advancing the careers of physical, chemical or computational science researchers and engineers whose work addresses biological questions.

Preproposal Deadline: September 1, 2010

BWF's Career Awards at the Scientific Interface provide $500,000 to bridge advanced postdoctoral training and the first three years of faculty service. These awards are intended to foster the early career development of researchers with backgrounds in the physical/mathematical/computational sciences and engineers whose work addresses biological questions.

These awards are open to U.S. and Canadian citizens or permanent residents as well as to U.S. temporary residents.

In previous years, candidates for this award had to be nominated by a North American degree-granting institution. This year, eligible candidates for this award may self-nominate by submitting a preproposal by September 1, 2010.

Preproposals will be reviewed by the Interfaces in Science Advisory Committee and selected candidates will be invited to submit a full application. Full invited applications must be submitted by January 12, 2011.

For full grant details, see www.bwfund.org
URL: http://www.bwfund.org/

Contact Person: Russ Campbell (rcampbell@bwfund.org)

Free Online Access to special issue of Journal of Biomedical Informatics on Translational Bioinformatics

2010-07-09T06:44:00.001-07:00

Since July 2009, the Journal of Biomedical Informatics (JBI) has changed its editorial policy to focus its publication of bioinformatics articles on the growing area of translational bioinformatics (see JBI editorial 2009;42(2):199-200). JBI publishes articles that introduce new methodologies and techniques that form the basis for the evolving science of biomedical informatics. While such methods often have broad generalizability, their development is typically motivated by specific applications in one of the four principal subfields of biomedical informatics (clinical informatics, public health informatics, imaging informatics, or bioinformatics). It is in the latter category that JBI has now chosen to focus specifically on articles that deal with bioinformatics innovations that are related to solving problems in human disease – its diagnosis, prognosis, prevention, and treatment. We return without review bioinformatics articles that are not translational and ask their authors to consider submitting their paper to another, more appropriate journal.

The move to translational bioinformatics (TBI) arose in part from the success and appeal of the Summit on Translational Bioinformatics that has been held each March since 2008 in San Francisco, California. The meeting, organized by the American Medical Informatics Association (AMIA) with affiliated sponsorship by the International Society for Computational Biology (ISCB), has published a well received Proceedings with top papers referred for journal publication. In honor of JBI's new emphasis on TBI, the 2009 Program Chair, Dr. Yves Lussier (University of Chicago) has served as guest editor of a special issue of JBI, composed in part of expanded papers from that year's meeting. He has been assisted by Dr. Atul Butte (Stanford University) and Dr. Lawrence Hunter (University of Colorado).

The TBI special issue has just appeared as the May-June issue in 2010 (see JBI 2010;43(3):355-357). In honor of ISMB this year, some sample copies have been made available at the Elsevier booth. In addition, JBI has arranged to provide open access to this special issue for a period of two months following the meeting (until September 15th). We invite ISMB attendees to visit the JBI site on Science Direct at:

www.tinyurl.com/JBIonScienceDirect

or go directly to the special issue at:

www.tinyurl.com/JBI-TBI-special-issue

Please familiarize yourself with JBI and consider submitting your best methodological work for possible publication in its pages.

Ted Shortliffe, Editor-in-Chief, JBI

URL: http://www.tinyurl.com/JBI-TBI-special-issue

Contact Person: Vijala Kiruvanayagam (v.kiruvanayagam@elsevier.com)

Rare genetic variants linked to autism

2010-06-10T05:29:00.000-07:00

The search for the genetic underpinnings of autism spectrum disorder has just yielded a new set of clues. In the largest study to date, the Autism Genome Project consortium reports that people with autism have more copy number variants – segments of DNA that have been either duplicated or deleted – in their genes.

The results, published today in Nature, could eventually be used to develop quick diagnostic tests. The consortium was also able to group some of the affected genes into biochemical pathways. These pathways – some of which are clearly linked to brain function -- may then become attractive targets for those who hope to develop drugs to treat the condition

And man made life

2010-06-08T18:41:00.000-07:00

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

We report the design, synthesis, and assembly of the 1.08-MbpMycoplasma mycoides JCVI-syn1.0 genome starting from digitizedgenome sequence information and its transplantation into a Mycoplasmacapricolum recipient cell to create new Mycoplasma mycoidescells that are controlled only by the synthetic chromosome.The only DNA in the cells is the designed synthetic DNA sequence,including "watermark" sequences and other designed gene deletionsand polymorphisms, and mutations acquired during the buildingprocess. The new cells have expected phenotypic properties andare capable of continuous self-replication.

Published in ScienceXpress, May 20th

Some more:

U of T researchers crack the splicing code

2010-05-30T15:48:00.000-07:00

The coding capacity of the vertebrate genome is greatly expanded by alternative splicing, which enables a single gene to produce more than one distinct protein. Alternative splicing shapes how genetic information controls cellular processes, and many human disease mutations affect splicing. The ability to predict expression of different alternatively spliced messenger RNAs from genomic sequence data is a long-sought goal in the field of gene expression. The Frey and Blencowe labs at the University of Toronto have combined forces to develop a 'splicing code' that accurately predicts how hundreds of RNA features work together to regulate tissue-dependent alternative splicing for thousands of exons. It has been used to predict how alternative splicing may play important roles in development and neurological processes, and has provided insights into mechanisms of splicing regulation. The code has also been incorporated into a web tool that allows researchers to scan uncharacterized exon and intron sequences to predict tissue-dependent splicing patterns.

Source: Nature Editor's Summary

Read more:

Nature News and Views
Article: Deciphering the splicing code, Barash et al., Nature
ScienceDaily

LifeDB Autonomous Data Integration System Trial Release

2010-05-19T17:02:00.000-07:00

Announcement
LifeDB Autonomous Data Integration System Trial Release

It is with great excitement and anticipation that we
announce the release of LifeDB Autonomous Data Integration
system [1] for Life Sciences data management and workflow
querying. LifeDB has its own SQL-like query language
called BioFlow [2, 3] using which, most arbitrary
online deep web resources and tools can be used to develop
applications completely dynamically and on an ad hoc basis.
The goal in LifeDB is to allow application development by
end users using SQL-like declarative query language without
having to worry about schema heterogeneity and geographical
distribution of resources. LifeDB relies on two basic fully
autonomous sub-systems: FastWrap [4, 5] for wrapper
generation and table annotation, and OntoMatch [6] for
schema mapping. BioFlow supports horizontal and vertical
integration and autonomous record linkage through entity
identification and resolution. It is based on an extended
parameterized relational algebra called Integra [7] that is
capable of blurring the distinctions between web documents
and traditional SQL tables by uniformly treating both as
relations.

To support end user application development, we have also
developed a visual application development system called
VizBuilder [8] that allows writing BioFlow applications
visually without any knowledge of BioFlow. In our current
LifeDB release, VizBuilder is included as an alternate
interface.

Currently, LifeDB is in a trial phase while it undergoes
internal validation. We believe LifeDB is performing within
its design parameters. We invite interested researchers in
Databases and Life Sciences to register for LifeDB as end
users. Registered users will be able to either download
LifeDB binary for local use, or use LifeDB in our server
with limited user data space. Currently, our goal is to
compile bug reports, if any, and fix the currently unknown
bugs before its final release. Full information on LifeDB
can be found at http://integra.cs.wayne.edu:8080/lifedb.

Our laboratory is fully committed to supporting registered
users and their applications on a long term basis on our
Wayne State Server. Registered users will have their own
data space in our server to store their data, applications
and other resources. For high-end users, we will also
consider offering dedicated processors to support computation
intensive applications, resource permitting. We are
considering a novel resource sharing model and it will be
announced when we finalize our plan and acquire the needed
resource. LifeDB will be an open source system for the
community, following the release of its final version. We
are now compiling user requests for data space over the
next 3-6 months based on which we plan to acquire the needed
hardware to support our users. A request for needed space
(and dedicated processor, subject to agreement) may be made
through an e-mail to the PI at jamil@cs.wayne.edu. Please use
subject heading "LifeDB Resource Request."

Publications related to LifeDB and other projects can be found
at our Integration Informatics Lab home page at
http://integra.cs.wayne.edu. A comprehensive LifeDB user manual
is also available for end users. The user manual will include
test examples and design parameters under which LifeDB is
designed and expected to function well.

LifeDB has been funded in part by National Science Foundation
grants SEIII IIS 0612203 and MRI CNS 0521454.

References:

[1] Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin,
Shahriyar Hossain, Shazzad Hosain, Hasan Jamil and Leonard Lipovich,
"On-the-fly Integration and ad hoc Querying of Life Sciences
Databases using LifeDB", 20th Database and Expert Systems
Applications, Linz, Austria, August 2009.

[2] Hasan Jamil, Bilal El-Hajj-Diab, "BioFlow: A Web-based
Declarative Workflow Language for Life Sciences", IEEE International
Workshop on Scientific Workflows, Hawaii, United States, July 2008.

[3] Hasan Jamil, Aminul Islam, "The Power of Declarative
Languages: A Comparative Exposition of Scientific Workflow Design
using BioFlow and Taverna", IEEE SCC International Workshop on
Scientific Workflows, Los Angeles, California, July 2009.

[4] Mohammad Shafkat Amin, Hasan Jamil, "FastWrap: An Efficient
Wrapper for Tabular Data Extraction from the Web", IEEE
International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[5] Mohammad Shafkat Amin, Anupam Bhattacharjee, Hasan Jamil,
"Wikipedia Driven Autonomous Label Assignment in Wrapper Induced
Tables with Missing Column Names", ACM International Symposium on
Applied Computing, Sierre, Switzerland, March 2010.

[6] Anupam Bhattacharjee, Hasan Jamil, "OntoMatch: A Monotonically
Improving Schema Matching System for Autonomous Data Integration",
IEEE International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[7] Shazzad Hosain, Hasan Jamil, "An Algebraic Language for Semantic
Data Integration on the Hidden Web", IEEE International Conference
on Semantic Computing, Berkeley, California, United States,
September 2009.

[8] Shahriyar Hosain, Hasan Jamil, "A Visual Interface for
on-the-fly Biological Database Integration and Workflow Design
using VizBuilder", International Workshop on Data Integration in
Life Sciences (DILS), Manchester, United Kingdom, July 2009.
URL: http://integra.cs.wayne.edu

Contact Person: Hasan Jamil (jamil@cs.wayne.edu)

ISCB Member Feedback Sought on (Draft) Literature Open Public Access Policy Statement

2010-05-10T17:39:00.000-07:00

International Society for Computational Biology
ISCB (Draft) Literature Open Public Access Policy Statement
Draft approved by the ISCB board of Directors on April 8, 2010

Open for comment from the ISCB membership
and bioinformatics community

Comment period closes June 11, 2010

Preamble.
The International Society for Computational Biology (ISCB) is dedicated to advancing human knowledge at the intersection of computation and life sciences. This (draft) ISCB policy statement is intended to express strong support for open public access to the archival scientific and technical literature and to elucidate in more nuanced detail the position of ISCB on this important issue in scientific publication.

An official ISCB policy statement on the closely related topic of sharing software provides very clear support for Open Source/Open Access (http://www.iscb.org/iscb-policy-statements-/187). ISCB supports many of the principles of the “Budapest Open Access Initiative,” the “Bethesda Declaration on Open Access Publishing,” the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences," and the European “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”

Introduction.
Knowledge is the fruit of the scientific research endeavor, and the archival scientific literature is its practical expression and means of communication. Shared knowledge multiplies its utility because every new scientific discovery is built upon previous scientific knowledge. Access to knowledge is the power to solve new problems and make informed decisions. More open public access to archival scientific and technical knowledge will empower more citizens and more scientists to solve more problems and make more informed decisions.

Recommendations.

There should be free, open, online, public access to research results in the archival scientific and technical literature, with all their existing content including supplementary material and data. This access may be at an interval following publication, which interval should not exceed one year.

Existing models show high impact, scientific benefit, feasibility, and acceptability:

a. The public benefit from open access to the world’s online information via the publicly-funded Internet provides a good model of expected impact.

b. The scientific fertilization from open access to genomic information via the publicly-funded Human Genome Project provides a good model of expected scientific benefit.

c. Open access policies by the U.S. National Institutes of Health, the Howard Hughes Medical Institute, and the Wellcome Trust provide good models of feasibility, acceptability, and implementation.

Open literature access will enable a whole new generation of innovative tools and mechanisms that will endow the literature with enriched commentary and usability and connect the literature and databases via the proper pointers. These tools are already being built by publishers, researchers, and others. The creation of the web of knowledge around publications is an important consequence of semantic enrichment of the literature.

Whether publications are immediately available or delayed, the underlying data and methods must be publicly available in sufficient detail to allow replication of the results and application of other computational methods to the data.

Policy details — which version, where stored, how annotated and organized, what incentives — must be considered carefully. However, it has become essential to put forward a broad policy mandate for eventual public access to research knowledge.

Publishing high-quality peer-reviewed scientific literature incurs costs. We recognize that cost recovery is a serious issue that must be addressed carefully if open access is to be a mandated policy.

The funding policy must:

a. Fund activities of peer review, copy editing, and publishing.

b. Provide fair compensation, if and where needed, to facilitate transitions and adaptations to new models for publishing and sustaining essential revenue.

c. Be consistent with government laws, other existing regulations, and research dissemination through viable commercial mechanisms.

It is undesirable to take funding from current research and thereby risk underfunding basic science, so new funding should be made available for policy implementation. However, the expected total cost for complete open literature access is only a very small percentage of the total cost for the entire international research endeavor.

Conclusion.
Scientific literature represents a substantial investment by governments, foundations, and others. One of our primary missions is the assembly of individual pieces of knowledge from this literature in ways that provide powerful new insights and ideas for next-stage research by the entire scientific community and society in general. We in the ISCB are committed to the continuous enhancement and leveraging of mankind’s knowledge resources. To achieve this goal, investment in open public access to the research literature must be made.

ISCB (Draft) Literature Open Public Access --- Appendix

A. Documents mentioned in the statement text.
1. Text of the “Budapest Open Access Initiative.”
http://www.soros.org/openaccess/read.shtml
http://en.wikipedia.org/wiki/Budapest_Open_Access_Initiative

2. Text of the “Bethesda Declaration on Open Access Publishing.”
http://www.earlham.edu/~peters/fos/bethesda.htm

3. Text of the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences."
http://www.nap.edu/openbook.php?isbn=0309088593
http://www.nap.edu/catalog.php?record_id=10613

4. Text of the “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”
http://oa.mpg.de/openaccess-berlin/berlindeclaration.html
http://en.wikipedia.org/wiki/Berlin_Declaration_on_Open_Access_to_Knowledge_in_the_Sciences_and_Humanities

5. Text of Open Access Policy from the U.S. National Institutes of Health.
http://publicaccess.nih.gov/policy.htm
http://publicaccess.nih.gov/

6. Text of Open Access Policy from the Howard Hughes Medical Institute.
http://www.hhmi.org/about/research/sc320.pdf
http://www.hhmi.org/about/research/QA_papp.pdf

7. Text of the Wellcome Trust's "Position Statement in Support of Open and Unrestricted Access to Published Research."
http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Open-access/Policy/index.htm

B. General Background Material.
1. Academic publishing - Wikipedia, the free encyclopedia.
http://en.wikipedia.org/wiki/Academic_publishing

2. Open access (publishing) - Wikipedia, the free encyclopedia.
http://en.wikipedia.org/wiki/Open_access_(publishing)
http://en.wikipedia.org/wiki/Open_access_%28publishing%29

3. ROARMAP (Registry of Open Access Repository Material Archiving Policies) as recommended by the Berlin Declaration.
http://www.eprints.org/openaccess/policysignup/

C. Other Statements and Materials.
1. Text of Public Library of Science "Open Letter to Scientific Publishers" (signed by ~34,000 scholars worldwide).
http://www.plos.org/about/letter.php

2. Text of Research Councils of the UK "Access to Research Outputs."
http://www.rcuk.ac.uk/cmsweb/downloads/rcuk/documents/2006statement.pdf
http://www.rcuk.ac.uk/cmsweb/downloads/rcuk/news/oareport.pdf
http://www.rcuk.ac.uk/research/outputs/access/default.htm

3. Text of European Research Advisory Board Final Report "Scientific Publication: Policy On Open Access."
http://ec.europa.eu/research/eurab/pdf/eurab_scipub_report_recomm_dec06_en.pdf

4. Text of Bulletin of the World Health Organization "Equitable access to scientific and technical information for health."
http://www.scielosp.org/scielo.php?script=sci_arttext&pid=S0042-96862003001000003

5. UNESCO EBSCO Open Science Directory.
http://www.opensciencedirectory.net/

6. Peter Suber's "Open Access Overview."
http://www.earlham.edu/~peters/fos/overview.htm
http://www.earlham.edu/~peters/fos/brief.htm

Clinical assessment incorporating a personal genome

2010-05-02T03:38:00.001-07:00

Clinical assessment incorporating a personal genome

In a Lancet paper Ashley et.al. undertook "an integrated analysis of a complete human genome in a clinical context." The interpretation of the results: "Although challenges remain, our results suggest that whole-genome sequencing can yield useful and clinically relevant information for individual patients."

Of guerillas and cafés

2010-03-30T14:52:00.000-07:00

Here are a few citations from an EMBO report discussing how scientists are experimenting with new initiatives to talk to the people.

"We want people to engage with other real people who just happen to be scientists"

"The café idea is spreading from its grassroots origins to science festivals and even scientific meetings"

"We're trying to make science part of culture"

Read more...

Call for Chapters: Depth Map and 3 D Imaging Applications:Algorithms and Technologies

2010-03-18T20:18:00.001-07:00

CALL FOR CHAPTER PROPOSALS

Proposal Submission Deadline: April 15, 2010

Depth Map and 3 D Imaging Applications: Algorithms and Technologies

A book edited by Aamir Saeed Malik, Tae‐Sun Choi and Humaira Nisar

Universiti Teknologi Petronas (Malaysia), and Gwangju Institute of Science & Technology (Korea)
To be published by IGI Global: http://www.igi-global.com/requests/details.asp?ID=846

Introduction

With the advent of few 3D consumer electronics products in 2009, the importance of three dimensional(3D) imaging technology has increased significantly. 3D imaging systems offer a richer experience for the consumers and they are expected to replace the traditional systems. In 2010, the leading consumer electronics manufacturers are introducing 3D TVs, 3D cameras, 3D printers and 3D computers. Some of them are Panasonic, Samsung, LG, Sony, Olympus, Canon, JVC, Sharp, Hitachi,HP and Acer. Their technology is currently based on stereoscopic vision and displays. However, as the 3D technology matures over time, autoseteroscopic vision and displays will replace the
stereoscopic technology. It can rightly be said that the next decade is the decade for 3D imaging technology.

Objectives of the Book

This book will aim to provide the relevant theoretical frameworks and the latest esearch findings in 3D imaging. It will cover algorithms and technologies for 3D Imaging as well as discuss their various applications. It will provide the current status of the technologies and will discuss the future trends too.

Target Audience

This book will be an important resource and reference for professionals, scientists, researchers,academics and software engineers in image/video processing and computer vision. It is a multidisciplinary field, so in addition to electrical and electronics engineering, it will also be of interest to those involved in material science, robotics, astronomy, terrain mapping, mechanical engineering and medical sciences. It will be a potential resource for post graduate and senior undergraduate students too.

Recommended topics include, but are not limited to, the following:

• 3D Capture: 3D ‐visual scene capture, multi‐view and multi‐sensor image capture, calibration and synchronization of multiple cameras, stereoscopic capture, and holographic capture.
• 3D Processing: 3D ‐visual scene reconstruction techniques for static and dynamic scenes, 3D data processing, 3D tracking, depth estimation and view synthesis from multi‐view images/videos, and compact representation and compression of multi‐view images/ videos.
• 3D Visualization & Displays: Stereoscopic, auto‐stereoscopic, and holographic display & projectors, 3D projectors, volumetric displays & projectors, head‐mounted 3D displays, 2D‐3D conversion of Images, and 3D representation tools: meshes, points, and voxels.
• 3D Transmission: Source coding, channel coding, transmission, decoding and broadcasting of 3D/ multi‐view images/videos/data, 3D teleimmersion and remote collaboration.
• 3D Applications: 3D television, free viewpoint TV systems, 3D cinema, 3D printing,
educational 3D systems, guidance and advertizing systems, 3D imaging in virtual heritage and virtual archaeology, 3D games, 3D entertainment, 3D virtual studios, augmented reality and virtual environments, medical and biomedical applications, 3D content‐based retrieval and recognition, 3D watermarking, 3D computers and other applications.

Submission Procedure

Researchers and practitioners are invited to submit on or before April 15, 2010, a 2‐3 page chapter proposal clearly explaining the mission and concerns of his or her proposed chapter. Authors of accepted proposals will be notified before May 15, 2010 about the status of their proposals and sent chapter guidelines. Full chapters are expected to be submitted by September 1, 2010. All submitted chapters will be reviewed on a double‐blind review basis.

Publisher

This book is scheduled to be published by IGI Global (formerly Idea Group Inc.), publisher of the "Information Science Reference" (formerly Idea Group Reference), "Medical Information Science
Reference," "Business Science Reference," and "Engineering Science Reference" imprints. For additional information regarding the publisher, please visit www.igi‐global.com. This publication is anticipated to be released in 2011.

Important Dates

April 15, 2010: Proposal Submission Deadline
May 15, 2010: Notification of Acceptance
September 1, 2010: Full Chapter Submission
October 31, 2010: Review Results Returned
November 30, 2010 Revised Chapter Submission
December 15, 2010 Final Acceptance Notification
January 15, 2011 Final Chapter Submission

Editorial Advisory Board Members:

Fabrice Meriaudeau, University of Bourgogne, France
Naeem Azeemi, COMSATS Institute Information Technology, Pakistan
Kishore Pochiraju, Stevens Institute of Technology, USA
Martin Reczko, Biomedical Sciences Research Center \"Alexander Fleming\", Varkiza, Greece
Iftikhar Ahmad, Nokia, Finland
Nidal kamel, Universiti Teknologi Petronas, Malaysia
Umer Zeeshan Ijaz, University of Cambridge, UK
Asifullah Khan, Pakistan Institute of Engineering and Applied Sciences, Pakistan

Inquiries and submissions can be forwarded electronically or by mail to:

Aamir Saeed Malik, Ph.D.
Department of Electrical and Electronics Engineering
Universiti Teknologi Petronas
Tel.: +605‐368‐7853 • Fax: +605‐365‐7443 • GSM: +60‐16‐553‐7853
E‐mail: aamir_saeed@petronas.com.my
URL: http://www.igi-global.com/requests/details.asp?ID=846

Contact Person: Aamir Saeed Malik (aamir_saeed@petronas.com.my)

ALFRED P. SLOAN FOUNDATION AWARDS MORE THAN $6 MILLION;118 EARLY CAREER RESEARCHERS TO RECEIVE PRESTIGIOUS SLOAN RESEARCH FELLOWSHIPS

2010-03-16T11:13:00.001-07:00

The Alfred P. Sloan Foundation is pleased to announce the selection of 118 outstanding early career scientists, mathematicians, and economists as Alfred P. Sloan Research Fellows. The winners are faculty members at 56 colleges and universities in the United States and Canada who are conducting research at the frontiers of physics, chemistry, computational and evolutionary molecular biology, computer science, economics, mathematics and neuroscience.

"The Sloan Research Fellowships support the work of exceptional young researchers early in their academic careers, and often at pivotal stages in their work," says Paul L. Joskow, President of the Alfred P. Sloan Foundation. "I am proud of the Foundation's rich history in providing the resources and flexibility necessary for young researchers to enhance their scholarship, and I look forward to the future achievements of the 2010 Sloan Research Fellows."

The Sloan Research Fellowships have been awarded since 1955, initially in only three scientific fields: physics, chemistry, and mathematics. Since then, 38 Sloan Research Fellows have gone on to win the Nobel Prize in their fields; 57 have received the National Medal of Science; and 14 have been awarded the Fields Medal, the top honor in mathematics. Although Sloan Research Fellowships in economics began only in 1983, Sloan Fellows have subsequently accounted for 9 of the 14 winners of the John Bates Clark Medal, generally considered the most prestigious honor for young economists.

Grants of $50,000 for a two-year period are administered by each Fellow's institution. Once chosen, Sloan Research Fellows are free to pursue whatever lines of inquiry are of most interest to them, and they are permitted to employ Fellowship funds in a wide variety of ways to further their research aims. For a complete list of winners, visit:

http://www.sloan.org/pressroom/item/458/2010-sloan-research-fellowships.

The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution that supports original research and broad-based education in science, technology, engineering, mathematics and economic performance. For more information visit www.sloan.org.

URL: http://www.sloan.org

Contact Person: Erica Stella (Stella@sloan.org)

The John von Neumann Days and The Genome and the Computational Sciences: The Next Paradigms Symposium at Brown University May 3-7, 2010

2010-03-15T13:36:00.001-07:00

Brown University, the Center for Computational Molecular Biology (CCMB), and the Department of Computer Science present the first in the John von Neumann Distinguished Lecture Series and the second in the symposium series "The Genome and the Computational Sciences: The Next Paradigms". This event will bring together influential entrepreneurs, leaders, and visionaries from academia and industry who will build the next paradigms in genomics and biotechnology. Each lecturer will present provocative, critical, and visionary talks on the state of the art in their academic and technological domains, and discuss the emerging paradigm changes made possible by their research and development work. All sessions will feature lively scientific dialogue and rigorous questioning by participants and audience members, including a post-lecture 'sweatbox' question-and-answer session. NSF and RECOMB travel awards are available for graduate students and postdoctoral fellows. Details about the events, which will be held from May 3-7, 2010, can be found at the Symposium webpage or email Lisa Manekofsky at ljm@cs.brown.edu

We look forward to your participation in our Symposium.

Sorin Istrail, Chair of the Symposium

Brown University CCMB Symposium, May 3-7, 2010
Co-organized with the Office of the President
Co-organized with the Department of Computer Science
Supported in part by the National Science Foundation

http://www.brown.edu/Research/CCMB/Conferences/SYMPOSIUMMAY2010/info.htm

John von Neumann Distinguished Lecture Series
organized by Leon Cooper (Physics), Stuart Geman (Applied Mathematics), Sorin Istrail (Computer Science), Roberto Serrano (Economics)

Marina von Neumann Whitman, Professor of Business Administration and Public Policy, University of Michigan

Freeman Dyson, Professor Emeritus of Physics, Institute for Advanced Study, Princeton, NJ

John Conway, John von Neumann Professor of Mathematics, Princeton University

Kenneth Arrow, Nobel Laureate, Joan Kenney Professor of Economics and Professor of Operations Research Emeritus, Stanford University

Richard Karp, University Professor, University of California, Berkeley

David Mumford, University Professor, Department of Applied Mathematics, Brown University

Leon Cooper, Nobel Laureate, Thomas J. Watson Professor of Science and Director, Institute for Brain and Neural Systems, Brown University

George Dyson, historian of science, University of Washington, Seattle

Symposium: The Genome and the Computational Sciences: The Next Paradigms

Eric H. Davidson, Norman Chandler Professor of Cell Biology, California Institute of Technology

Andrew G. Clark, Jacob Gould Schurmn Professor of Population Genetics, Department of Molecular Biology and Genetics, Cornell University

J. Craig Venter, Founder, Chairman and President, J. Craig Venter Institute (not confirmed)

Ellen V. Rothenberg, Albert Billings Ruddock Professor of Biology, California Institute of Technology

Richard Lewontin, Alexander Agassiz Research Professor, Museum of Comparative Zoology, Harvard University

David Botstein, Anthony B. Evnin Professor of Genomics and Director, Lewis-Sigler Institute, Princeton University

Martin Meier-Schellersheim, Team Leader, Computational Biology Group, National Institute of Allergy and Infectious Diseases, NIH

Sean Eddy, Group Leader, Janelia Farm, Howard Hughes Medical Institute

Martha Bulyk, Associate Professor of Medicine and Pathology (and Health Sciences and Technology), Harvard Medical School

Jonathan W. Yewdell, Chief, Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH

David Shaw, Ph.D., Chief Scientist and Founder, D.E. Shaw Research

Marcus Feldman, Ph.D., Professor of Biology, Stanford University

Sam Broder, Chief Medical Officer, Celera, Former Director of the National Cancer Institute
URL: http://www.brown.edu/Research/CCMB/Conferences/SYMPOSIUMMAY2010/info.htm

Contact Person: Lisa Manekofsky (ljm@cs.brown.edu)

InCoB2010 - EasyChair Submission site now open

2010-03-14T21:37:00.001-07:00

International Conference in Bioinformatics (InCoB) 2010,
Tokyo 26-28 September 2010

The Ninth International Conference on Bioinformatics, InCoB2010
(incob.apbionet.org or incob10.hgc.jp) will be held at International Conference
Center, Waseda Campus, Waseda University, Tokyo on 26-28 September 2010.

This year, InCoB is organized in collaboration with the International Immunomics
Society (IIMMS) and Chem-Bio Informatics Society (CBI). Day 3 is held in
conjunction with special CBI sessions and the 3rd Conference of Basic and
Clinical Immunogenomics and Immunomics (BCII).

InCoB, the annual conference of the Asia-Pacific Bioinformatics Network
(http://www.apbionet.org) brings together scientists working in bioinformatics
and computational biology, spanning a wide range of underpinning disciplines
including computer science, biology, biotechnology, genomics, proteomics,
transcriptomics, immunomics, mathematics and statistics.

Clyde Hutchison (J. Craig Venter Institute), Hiroaki Kitano (SONY CSL), and
Japan Academy Prize 2008 winner Yoshiyuki Nagai (RIKEN CNRID), have accepted to
present Keynotes at InCoB2010. Please see the website for the latest list of
other distinguished speakers.

We invite you to participate in the following sessions:
1. Full papers for oral presentation and publication in BMC Genomics or BMC
Bioinformatics, Immunome Research, ISPJ Transactions on Bioinformatics or
Bioinformation.
2. Abstracts for (A) Poster Sessions and (B) Technology, Tools, Methodology,
Resource, Database, Software Demonstrations or Posters.
3. Late-breaking abstracts for short oral presentations
4. Tutorial videos for virtual e-learning sessions
5. APBioNet Annual General Meeting
Submissions to InCoB2010 may cover any aspect of bioinformatics, computational
biology, chem-bioinformatics, bioinformatic-related cloud computing,
biocomputing, personalized medicine, environmental genomics (white bio),
synthetic genomes and organisms, metagenomics, pharmacogenomics, and immunomics
conveying a scientific result.

1. FULL PAPERS: SUBMISSION DEADLINE: 15 APRIL 2010 ACCEPTANCE: 31 MAY 2010
InCoB2009 will feature oral presentations shortlisted from full paper
submissions, for selection in: - BMC Genomics (IF 3.93)
http://www.biomedcentral.com/bmcgenomics/ - BMC Bioinformatics (IF 3.78)
http://www.biomedcentral.com/bioinformatics/ - Immunome Research (unofficial IF
5.33) http://www.immunome-research.com/ - ISPJ Transactions on Bioinformatics
http://www.jstage.jst.go.jp/browse/ipsjtbio or - Bioinformation
http://www.bioinformation.net/

ABBioNet was the first Asia-Pacific bioinformatics society to publish full
papers in BMC Bioinformatics and in 2009, also in BMC Genomics. Supplements from
previous conferences are below:
2009: http://www.biomedcentral.com/1471-2164/10?issue=S3 2009:
http://www.biomedcentral.com/1471-2105/10?issue=S15 2008:
http://www.biomedcentral.com/1471-2105/9?issue=S12 2007:
http://www.biomedcentral.com/1471-2105/9?issue=S1 2006:
http://www.biomedcentral.com/1471-2105/7?issue=S5

After rigorous review by the Program Committee, authors will be asked to revise
their manuscripts, prior to acceptance for publication and oral presentation at
InCoB2010, for which at least one author must register.

2. ABSTRACTS SUBMISSION DEADLINE: 07 JUNE 2010 ACCEPTANCE: 30 JUNE 2010
We solicit high-quality research abstracts for (A) Poster Sessions and (B)
Technology, Tool, Methodology, Resource, Database, Software Demonstrations or
Posters.

At least one author of each selected poster/demonstration must register for
InCoB2010. Furthermore, a single registration can cover only oral presentation
and one poster presentation or two poster presentations. Posters are intended to
convey a scientific result and are not meant to be used as advertisements for
commercial software.

3. LATE-BREAKING ABSTRACTS: SUBMISSION DEADLINE: 01 AUGUST 2010 ACCEPTANCE: 10
AUGUST 2010

We invite abstracts on peer-reviewed journal papers that have accepted for
publication or have been will be published on or after July 20, 2010 (please
provide us email acceptance or online version). A small number of short oral or
poster presentations is available and will be allocated at the discretion of
scientific Program Committee. Decision criteria are the impact of the work on
the field, the likelihood that the study would be of interest to the InCoB
audience and the relevance of the research to bioinformatics and application to
molecular and medical sciences.

4. TUTORIAL VIDEOS SUBMISSION DEADLINE: 01 JULY 2010 ACCEPTANCE: 30 JULY 2010

InCoB2010 will feature shortly before and after the conference virtual
e-learning sessions on new and emerging, cutting-edge topics. Authors for
accepted tutorials agree to be available for feedback and potential questions
fielded by e-mail in the period from Sep 20-Oct 19, 2010. For details see
Submissions/Guidelines at conference website. Tutorial providers who wish to
attend InCoB2010 are required to register.

SUBMISSION DETAILS:
All submissions will be via EasyChair at:
http://www.easychair.org/conferences/?conf=incob2010
Please contact Kenta Nakai (knakai -at- ims.u-tokyo.ac.jp) or Christian
Schoenbach (schoen -at- bio.kyutech.ac.jp) for any queries (replace -at- with @).

5. APBioNet Annual General Meeting The AGM of APBioNet will traditionally be
held in InCoB2010 during the lunch break on Sep 27, 2010.

We look forward to your active participation! Please feel free to pass on this
email to colleagues who might be interested in this meeting.

With best wishes,
Shoba Ranganathan President, APBioNet
Kenta Nakai University of Tokyo, PC Co-Chair
Christian Schoenbach, PC Co-Chair Kyushu Institute of Technology

URL: http://incob.apbiobionet.org

Contact Person: Shoba Ranganathan (shoba.ranganathan1@gmail.com)

Bioinformatics Summer School in Erice (Italy)

2010-03-06T07:44:00.001-08:00

SCIENTIFIC BACKGROUND AND COURSE AIMS AND DESCRIPTION
High-throughput technologies in the life-sciences, from sequencing to microarrays, continue to produce exponentially increasing amounts of data and drive the needs and inspiration for new methods in the computational sciences to efficiently manage and mine these data and provide a better understanding of life from the molecular to the population level.

Bioinformatics, computational and systems biology, and the new -omics sciences, from genomics to metabolomics, all attempt to address these needs and better understand carbon-based computing systems, using silicon-based computing systems, with slightly different perspectives and emphases. Their success is intimately related to progress in mathematics and computer science, in particular in the areas of artificial intelligence, statistical machine learning, and optimization, in order to deal with very complex, high-dimensional, and noisy data.

The aim of the School is to introduce and expose the students to some of the contemporary problems and state-of-the-art solutions at the intersection of the life- and computational- sciences. For this purpose, the School is organized into four themes, at approximately four increasing spatial scales: Chemoinformatics, Proteomics, Genomics, and Systems Biology. Each theme will comprise lectures and invited talks, as well ample time for discussion, over a period of one and a half day. Additional minicourses to cover computational methods in machine learning and optimization will be given in the afternoons.

IMPORTANT DATES
• Registrations Opens: September 15, 2009
• Registrations Closes: April 30, 2010
• Notification of acceptance: May 31, 2010

VENUE
Erice is among the oldest cities of Sicily. The town sits on top of the homonymous mount Eryx, 750 m above sea level. It was the religious center of the ancient Elimi tribes, and is famous for its temple where the Phoenicians worshipped Astarte, the equivalent of Aphrodite or Venus for the ancient Greeks or Romans. Throughout its long contentious history, Erice has fallen to the hands of different tribes and empires, each leaving its own palpable mark on the city. Today, Erice is an enchanting wonderfully-preserved medieval town with the most breathtaking views of Sicily.

DIRECTORS
Pierre Baldi (USA)
Søren Brunak (Denmark)
Raffaele Cerulli (Italy)
Roberto Tagliaferri (Italy)

Lecturers
Pierre Baldi (USA)
Søren Brunak (Denmark)
Paolo Frasconi (Italy)
Panos Pardalos (USA)
Gianluca Pollastri (Ireland)
Gunnar Raetsch (Germany)
Burkhard Rost (Germany)
Michal Rozen Zvi (Israel)
Jean-Philippe Vert (France)

Additional Invited Speakers
Elia Biganzoli (Italy)
Piero Fariselli (Italy)
Alfredo Ferro (Italy)
Salvatore Gaglio (Italy)
Irene Kouskoumvekaki (Denmark)

Local Organizing Committee
Monica Gentili (Italy)

URL: http://www.graphalgorithms.it/Erice2010

Contact Person: Pierre Baldi (pfbaldi@ics.uci.edu)

Call for DREAM5 Computational Systems Biology Modeling Challenges and Datasets

2010-03-01T10:01:00.000-08:00

The Dialogue for Reverse Engineering Assessments and Methods (DREAM) Project is soliciting proposals for the DREAM5 Challenges. We invite your input on the design of new challenges and the contribution pre-publication data sets to assess the efficacy of the systems biology modeling community. Contact the DREAM organizers through the DREAM Project website (http://wiki.c2b2.columbia.edu/dream/).
URL: http://wiki.c2b2.columbia.edu/dream/

Contact Person: Robert Prill (rjprill@us.ibm.com)

International Team Develops Yeast Genetic Interaction Map

2010-01-23T16:40:00.000-08:00

A University of Toronto-led research team reported today that they have come up with a genome-wide genetic interaction map for the model organism Saccharomyces cerevisiae.

Read more...

Nvidia launches Tesla Bio Workbench

2010-01-20T05:36:00.001-08:00

The NVIDIA® Tesla™ Bio Workbench enables biophysicists and computational chemists to push the boundaries of biochemical research. It turns a standard PC into a ‘computational laboratory’ capable of running complex bioscience codes, in fields such as drug discovery and DNA sequencing, more than 10-20 times faster through the use of NVIDIA Tesla GPUs. It consists of:

Bioscience applications
This community site for downloading, discussing, and viewing the results of these applications
GPU-based platforms that enable these applications to run at 1/10th the cost of CPU-only computers"

(Via http://www.nvidia.com/object/tesla_bio_workbench.html.)

EMBL-EBI Launches Open Access Drug Discovery Database

2010-01-20T05:28:00.001-08:00

Open access drug discovery database launches with half a million compounds

Hinxton and London, 18 January 2010 – ChEMBLdb, a vast online database of information on the properties and activities of drugs and drug-like small molecules and their targets, launches today with information on over half a million compounds. The data lie at the heart of translating information from the human genome into successful new drugs in the clinic.

more.....

(Via EBI Press release.)

ISCB Exemplifies Organisations Supporting Scientific Social Networking

2010-01-08T01:22:00.000-08:00

In Bonetta's 2009 Cell article entitled "Should You Be Tweeting?", she explains the benefits---and limitations---of using Twitter as part of a scientist's online persona. Though many of those limitations are solved with the use of FriendFeed, there was no mention of this resource in the Bonetta article. Therefore, following an interesting discussion in some of the FriendFeed Science Groups, a number of people wrote a response, where the usefulness of FriendFeed for scientists was described.

Many FriendFeed scientists contributed, and the three main authors jointly posted the response to the Bonetta article on their blogs. To view this response, please see the jointly-published posts of Björn Brembs (FriendFeed; blog post), Allyson Lister (FriendFeed; blog post) and Daniel Mietchen (FriendFeed; blog post) from 7 January 2009.

What ISCB members and attendees of ISCB conferences and workshops might find most interesting about this response is use of ISMB 2008 and 2009 as examples of how scientific organisations can actively aid scientists in dissemination of conference knowledge through social networking. Through its ISMB conferences (and the co-located conferences such as the ECCB), the ISCB has provided infrastructure, support, and encouragement to scientists wishing to make use of social networking software such as FriendFeed and Twitter during its conferences. For example, the conference organisers integrated the FriendFeed threads from each talk within the ISMB 2009 website, e.g. Keynotes pages from ISMB 2009.

And it's not just the attending scientists who make use of this resource: as can be seen with articles such as the one posted yesterday by Brembs, Lister, Mietchen and other associated FriendFeeders, scientists worldwide have taken note of the good work done by the ISCB and others like it.

Please note that the author of this blog post (Allyson Lister) was both one of the bloggers at ISMB 2009 and one of the co-authors of the January 7 post written in reply to Bonetta. You can find Allyson Lister's main blog at http://themindwobbles.wordpress.com.

Funding biological data resources revisited

2009-12-15T03:05:00.001-08:00

interesting article by Deepak Singh and an editorial in Nature discussing the need to change the way data resources are funded.

Over-optimism in bioinformatics research

2009-12-14T19:48:00.000-08:00

Interesting paper about the research process.

http://www.ncbi.nlm.nih.gov/pubmed/19942585

The Semantic Biochemical Journal experiment

2009-12-11T05:26:00.001-08:00

Have a look at this interesting blog-article at

http://duncan.hull.name/2009/12/11/utopia/

and the review article by T. Attwood et.al.

Calling International Rescue: knowledge lost in literature and data landslide!

Press coverage: ISCB Africa ASBCB Conference

2009-12-10T06:49:00.001-08:00

Here a few links (in french) to articles about the ISCB Africa ASBCB Conference

Mali: Une conférence internationale sur la bioinformatique

Conférence internationale sur la bioinformatique : Une première en Afrique

Discours d’ouverture de Mr Ousmane TOURE, Secrétaire général du Ministère de la Santé

U.S. AMBASSADOR Speech
Conférence Internationale sur la Bioinformatique des Maladies Infectieuses

ISCB Student Council elections

2009-12-09T06:51:00.001-08:00

Next SC leadership : 2010-2011

Jeroen de Ridder : SC Chair

Venkatakrishnan A.J : SC Vice Chair

Jayne Hehir-Kwa : SC Secretary

Avinash K Shanmugam : RSG Committee Chair

Nils Gehlenborg : SC Representative to ISCB Board of Directors

More here: Student Council

Call for Chapters - Computational & Data Grids: Principles, Designs, and Applications

2009-12-07T20:20:00.001-08:00

CALL FOR CHAPTERS
Proposal Submission Deadline: -Extended- December 30, 2009
Computational and Data Grids: Principles, Designs, and Applications
A book edited by Dr.Nikolaos Preve
National Technical University of Athens, Greece

To be published by IGI Global: http://www.igi-global.com/requests/details.asp?ID=748

Introduction
Grid computing is the next generation information technology infrastructure that promises to transform the way organizations and individuals compute, communicate and collaborate. Grid computing is an evolution of distributed computing and it refers to a large-scale high-performance computing which combines distributed heterogeneous computing resources and the result is a unique large virtual supercomputer with a vast amount of shared processing power and data storage. Considering the enormous amount of these underutilized computing resources, the necessity of a grid infrastructure is compulsory. A computational grid provides access to users who want to utilize the shared processing resources in order to efficiently apply high throughput applications on distributed machines. The second most common shared resource used in a grid is data storage and it is known as data grid. This type of grid provides distributed storage capacity such as attached memory to the processor, hard di sk drives or other types of permanent storage. Grid computing can assist grid users in order to utilize to the maximum computing resources by applying tasks and solving a scientific or technical problem that requires a great number of computer processing cycles or the need to process large amounts of data.

Objective of the Book
This book aims to provide relevant theoretical frameworks and will cover the latest empirical research findings in the area of grid computing. The goal of this book is to represent theoretical frameworks, methodologies, implementations, and cutting edge research findings with a critical perspective bridging the gap between academia and the latest achievements of the computer industry. It will be written for professionals, as well as students, who are involved or interested in the study, use, design, and development of grid computing and want to improve and empower their understanding of it. Also, this book aims to help researchers and developers understand the basics of the field, to highlight the various developments over the years in the field by giving an in depth analysis of grid networks.

Target Audience
The target audience of this book will be composed of professionals, engineers, researchers and students who are interested and working in the field of grid computing. Moreover, the book will provide insights and can serve as both literature at an undergraduate level and as an overview of the area.

Recommended topics include, but are not limited to, the following:
1.Theories, definitions, methodologies, models, applications, simulations, and architectures relevant to grid computing
2.Implementations of computational grids, data grids, sensor and mobile grids
3.Grid data storage, grid databases, data management, and data mining
4.Indexing and query optimization over grid databases
5.Grid middleware
6.Web services
7.Security, cryptography, and cryptanalysis
8.Artificial intelligence
9.Algorithms
10.Scheduling, resource management, and optimization
11.Workflow and fault tolerance
12.Programming in grid computing
13.Cloud computing and grids
14.Grid computing in scientific problems (i.e. astrophysics, bioinformatics, chemistry, economy and finance, electromagnetics, geophysics, meteorology, numerical analysis, statistics)

Submission Procedure
Researchers and practitioners are invited to submit on or before December 30, 2009, a 1-2 page chapter clearly explaining the mission and concerns of the proposed chapter. We also highly encourage early full chapter submissions. Please include the title of the book in the subject line of your e-mail. Authors will be notified by January 15, 2010 about the status of their proposals and will be sent chapter guidelines. Full chapters are expected to be submitted by March 31, 2010 or earlier.
All submitted chapters must not have been published elsewhere and will undergo a double-blind peer review by at least two referees. Contributors may also be requested to serve as reviewers for this project.

Publisher
This book is scheduled to be published by IGI Global (formerly Idea Group Inc.), publisher of the "Information Science Reference" (formerly Idea Group Reference), "Medical Information Science Reference," "Business Science Reference," and "Engineering Science Reference" imprints. For additional information regarding the publisher, please visit www.igi-global.com. This publication is anticipated to be released in 2010.

Important Dates
December 30, 2009: Proposal Submission Deadline
January 15, 2010: Notification of Acceptance
March 31, 2010: Full Chapter Submission
June 15, 2010: Review Results Returned
August 15, 2010: Final Chapter Submission
September 15, 2010: Final Deadline

Inquiries and submissions can be forwarded electronically (Word document) or by mail to:
Dr.Nikolaos Preve
School of Electrical and Computer Engineering
National Technical University of Athens, 15773 Zographou, Greece
Tel.: +30 211 770 8053 - GSM: +30 697 750 4197
E-mail: nikpreb@mail.ntua.gr

with cc to:

Editorial Board
E-mail: editorialt@gmail.com
URL: http://www.igi-global.com/requests/details.asp?ID=748

Contact Person: Nikolaos Preve (nikpreb@mail.ntua.gr)

Forensic Bioinformatics Analyses Lead to Suspension of Clinical Trials

2009-12-02T13:11:00.001-08:00

In its December issue the Annals of Applied Statistics feature an article on reproducible research in high-throughput biology by Keith A. Baggerly and Kevin R. Coombes of the M.D. Anderson Cancer Center. In their article they describe how they used "Forensic Bioinformatics" to identify an array of problems - in many cases simple errors - in published studies that are the basis of several ongoing clinical trials. These trials have now been suspended, as the findings by Baggerly and Coombes suggest that patients could be harmed.

Stories published on October 2nd, October 9th and October 23rd in The Cancer Letter contain details about the developments.

IBM Unveils a New Brain Simulator

2009-11-19T05:36:00.001-08:00

IEEE Spectrum: IBM Unveils a New Brain Simulator:

"A big step forward in a project that aims for thinking chips

BY SALLY ADEE // NOVEMBER 2009

18 November 2009—Scientists and engineers at IBM’s Almaden Research Center, in San Jose, Calif., announced today at the Supercomputing Conference (SC09) in Portland, Ore., that they have created the largest brain simulation to date on a supercomputer. The number of neurons and synapses in the simulation exceed those in a cat’s brain; previous simulations have reached only the level of mouse and rat brains. Experts predict that the simulation will have profound effects in two arenas: It will lead to a better understanding of how the brain’s architecture leads to cognition, and it should inspire the design of electronics that mimic the brain’s as-yet-unmatched ability to do complex computation and learn using a small volume of hardware that consumes little power......"

(Via http://spectrum.ieee.org/computing/hardware/ibm-unveils-a-new-brain-simulator.)

Petascale Computing Tools Could Provide Deeper Insight into Genomic Evolution

2009-11-18T04:06:00.001-08:00

Scicasts™: Petascale Computing Tools Could Provide Deeper Insight into Genomic Evolution

"Technological advances in high-throughput DNA sequencing have opened up the possibility of determining how living things are related by analyzing the ways in which their genes have been rearranged on chromosomes. However, inferring such evolutionary relationships from rearrangement events is computationally intensive on even the most advanced computing systems available today....."

Nature Article: Predicting new molecular targets for known drugs

2009-11-18T03:14:00.001-08:00

see the News and Views from A.L. Hopkins:

Drug discovery: Predicting promiscuity

"Computational methods that reliably predict the biological activities of compounds have long been sought. The validation of one such method suggests that in silico predictions for drug discovery have come of age....."

and the full article by Michael J. Keiser et.al.: Predicting new molecular targets for known drugs

(re)Funding Databases II

2009-11-17T02:35:00.001-08:00

There is an interesting update on the discussion about funding/re-funding of databases on The OpenHelix Blog

(re)Funding Databases II | The OpenHelix Blog: ""

Education and Employment of Biological and Medical Scientists: Data from National Surveys

2009-11-08T10:46:00.001-08:00

FASEB published a slideshow presenting data on the education and employment of biologists and medical scientists.

Details can be found here

Do you know that Nature is 140 years old?

2009-11-06T17:03:00.000-08:00

Nature's birthday offers an occasion to reflect on the past and look to the future.

More...

First draft of the pig genome

2009-11-03T02:10:00.001-08:00

Press Release of the Wellcome Trust Sanger Institute
(Via http://www.sanger.ac.uk/Info/Press/2009/091102.shtml.)

Funding Databases

2009-11-02T03:46:00.001-08:00

There is an interesting blog and an article regarding the problems of (continuos) funding of databases.
(de)Funding Databases | The OpenHelix Blog
and
Models for financial sustainability of biological databases and resources, Database (2009) Vol. 2009:bap017

RECOMB-BE 2010 Call for Papers&Abstracts

2009-10-20T11:02:00.001-07:00

The Second RECOMB satellite conference on Bioinformatics Education (RECOMB-BE) will be held at the Center for Algorithmic and Systems Biology at the University of California, San Diego, May 22-23, 2010.

We invite submissions in three categories:
Bioinformatics Education Papers
Bioinformatics Education Abstracts (submitted by educators)
Undergraduate Bioinformatics Research abstracts (submitted by undergraduate or first-year graduate students)

The selected papers and abstracts in each category will be invited either for oral or for poster presentations. Note that the acceptance of poster abstract is conditional on at least one of its authors pre-registering for the RECOMB-BE workshop electronically.

Bioinformatics Education papers should be submitted via the RECOMB BE web site and must be received by January 5, 2010. The papers should focus on a biological problem and on didactic ways to convey computational ideas that can be used to address it. The papers should be self-contained and should be written in the way that it can be understood by advanced undergraduate biology students. Papers focusing solely on computational problems and papers focusing solely on biological problems will not be considered. RECOMB BE imposes no restrictions on format, length, notation, etc. but rather let the contributors choose the style they feel is the most appropriate. However, we anticipate that each contributed paper will be at least 10 pages long.

The papers will be reviewed and the accepted papers will be published in the special Education issue of the Journal of Computational Biology (http://www.liebertpub.com/products/product.aspx?pid=31).
The authors of the accepted papers will be invited to join the Bioinformatics Education Alliance that will meet in San Diego shortly before RECOMB BE with the goal to discuss the planned book "Bioinformatics for Biologists" based on the accepted papers.

Bioinformatics Education abstracts (submitted by educators) should be submitted via the RECOMB BE web site and must be received by January 20, 2010. The abstracts are at most 1 page long. The abstracts in this category can either discuss practice, challenges, and perspectives in bioinformatics education (e.g., curricula, integration of bioinformatics programs, online courses, etc.) or represent a proposal for a short 20-30 min introductory lecture aimed at undergraduates. We are specifically looking for lectures that start with a description of an interesting biological problem, e.g., "Did we evolve from Neanderthals?" and show how computational techniques solve this biological problem.

The selected papers and abstracts will be invited either for oral or for poster presentations. The acceptance of paper/abstract is conditional on at least one of its authors pre-registering for the RECOMB workshop.

Undergraduate Bioinformatics Research abstracts (submitted by undergraduates or 1st year graduate students reporting their undergraduate work) should be submitted via the RECOMB BE web site and must be received by January 20, 2010. The abstracts are at most 1 page long. The selected papers and abstracts will be invited either for oral or for poster presentations. The acceptance of paper/abstract is conditional on at least one of its authors pre-registering for the RECOMB workshop.
URL: http://casb.calit2.net/bioed10/

Contact Person: Sangtae Kim (recomb-be@ucsd.edu)

Nobel Prize In Chemistry: What Ribosomes Look Like And How They Functions At Atomic Level

2009-10-07T17:31:00.000-07:00

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2009 jointly to Venkatraman Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; Thomas A. Steitz, Yale University, New Haven, CT, USA; and Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel, "for studies of the structure and function of the ribosome". Read more...

Work on Telomeres Wins Nobel Prize in Physiology or Medicine

2009-10-07T17:24:00.000-07:00

The Nobel Assembly at Karolinska Institutet has today decided to award The Nobel Prize in Physiology or Medicine 2009 jointly to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak for the discovery of "how chromosomes are protected by telomeres and the enzyme telomerase". Read more...

The 2009 Nobel Prize in Physiology or Medicine will go to three Americans who discovered telomeres, the genetic code that protects the ends of chromosomes, and telomerase, the enzyme that assists in this process, findings that are important in the study of cancer, aging and stem cells. Read more...

Bioinformatics stimulus funding for cancer genomics

2009-10-01T11:13:00.001-07:00

Researchers in the Jack Baskin School of Engineering at the University of California, Santa Cruz, will establish a Cancer Genome Data Analysis Center as part of The Cancer Genome Atlas (TCGA), a $275 million collaborative project led by the National Cancer Institute and the National Human Genome Research Institute.

The TCGA project was highlighted in a White House announcement this week of $5 billion in grants to fund cutting-edge medical research across the country as part of the economic stimulus package. ...
URL: http://www.soe.ucsc.edu/news/article?ID=1793

Contact Person: Tim Stephens (stephens@ucsc.edu)

Older but not wiser

2009-09-30T19:00:00.001-07:00

Almost all peer reviewers get worse, not better, over time, suggests a study presented on 10 September at the Sixth International Congress on Peer Review and Biomedical Publication in Vancouver, Canada.
URL: http://www.nature.com/naturejobs/2009/091001/full/nj7264-681a.html

Contact Person: Magali Michaut (michaut.bioinfo@gmail.com)

A New Biology to Mend Society's Woes

2009-09-29T20:42:00.001-07:00

When a National Academies panel was created last year to examine where to go next in life sciences, some thought it would focus on biomedicine—or merely ask for more money. So many science advocates were pleased last week when the panel called for a multidisciplinary initiative to address four major societal problems involving food, energy, the environment, and health. The report likens these goals to sending a man to the moon and the Human Genome Project.

The advice comes from a panel funded by the National Science Foundation, the National Institutes of Health, and the Department of Energy to examine how to build on the explosion of biological data from DNA sequencing and other efforts...
URL: http://www.sciencemag.org/cgi/content/summary/325/5948/1609-a

Contact Person: Magali Michaut (michaut.bioinfo@gmail.com)

Haussler and Kent honored by American Society of Human Genetics

2009-09-28T11:56:00.001-07:00

The American Society of Human Genetics (ASHG) has honored two researchers in the Jack Baskin School of Engineering at UC Santa Cruz with the 2009 Curt Stern Award. David Haussler, professor of biomolecular engineering, and James Kent, a research scientist in the Center for Biomolecular Science and Engineering, will accept the award on October 24 during the annual meeting of the ASHG in Honolulu.

Haussler's previous awards include the International Society for Computational Biology (ISCB) Senior Scientist Accomplishment Award ...

Kent was awarded the Overton Prize for outstanding achievements in computational biology by the ISCB in 2003 ...
URL: http://www.soe.ucsc.edu/news/article?ID=1789

Contact Person: Daniel Strain (dstrain@ucsc.edu)

Computational Biologist Wins Prestigious Award

2009-09-28T09:10:00.000-07:00

Microsoft Research announced recently that Peer Bork, group leader in the Structural and Computational Biology Unit at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, will receive an award for his contributions to the advancement of science through the use of computational methods.

Bork was named Sept. 22 as the recipient of the fourth annual Royal Society and Académie des sciences Microsoft Award, presented for his work to discover important relationships between the nature of the human microbiome—the union of all microorganisms that live in and around the human body—and various human parameters, such as age, ethnicity, diseases, nutrition, and genetics.

Bork's research is frequently being published in journals such as Nature, Science and Cell.

Leading Universities Launch Initiative to Support Open Access Publishing

2009-09-23T12:28:00.000-07:00

"We think the system is going to fall apart of its own weight," says Thomas Leonard, a university librarian at UC Berkeley, about the traditional publishing system. Inside Higher Ed reports on a new development towards better support for Open Access journals:

On Monday, five leading universities announced a new "Compact for Open Access Publishing Equity" in which they have pledged to develop systems to pay open access journals for the articles they publish by the institutions' scholars. In doing so, the institutions are attempting to put to rest the idea that only older publication models (paid and/or print) can support rigorous peer review and quality assurance.

The five universities that have joined the agreement so far are MIT, Harvard, Cornell, UC Berkeley and Dartmouth College.

Real Lives and White Lies in the Funding of Scientific Research

2009-09-22T06:03:00.000-07:00

In "Real Lives and White Lies in the Funding of Scientific Research" (published on September 15th in PLoS Biology) Peter A Lawrence offers his perspective on the challenges that many (early career) scientists are facing when trying to secure funding for their (first) lab or research group. He discusses the impact of the current system on careers and science itself and argues for a simplified system.

Stem Cells and Bioinformatics

2009-09-15T03:16:00.001-07:00

This is an International Consortium of Stem Cell Networks (ICSCN) event hosted by Scottish Stem Cell Network. This international two day event has attracted some of the field's most prominent figures and will cover disease modelling in stem cells, cellular reprogramming and application of bioinformatics.
URL: http://www.sscn.co.uk/Item.aspx?dept_id=138&item_id=225

Contact Person: Jenna Chambers (jenna@sscn.co.uk)

First EMBO Workshop on Visualizing Biological Data at the EMBL's new Advanced Training Centre in Heidelberg, Germany

2009-09-14T07:18:00.001-07:00

An EMBO Workshop on Visualizing Biological Data (VizBi)

The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). We have assembled an authoritative list of 29 invited speakers who will present an exciting program, reviewing the state-of-the-art and perspectives in each of these areas. The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a 'fastforward' presentation about their work (limited to 30 seconds and 1 slide).

To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. Submissions close on 16 November 2009. Since places are limited, participants will be selected based on the relevance of their work to the goals of the workshop.

Notifications of acceptance will be sent within three weeks after the close of submissions.

We plan to award a prize for the submitted image that best conveys a strong scientific message in a visually compelling manner.

Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring!

Seán O'Donoghue, EMBL

Jim Procter, University of Dundee

Nils Gehlenborg, European Bioinformatics Institute

Reinhard Schneider, EMBL

If you have any questions about the registration process please contact:

Adela Valceanu

Conference Officer

European Molecular Biology Laboratory

Meyerhofstr. 1

D-69117 Heidelberg

Tel: +49-6221-387 8625

Fax: +49-6221-387 8158

Email: valceanu@embl.de

2010 Summit on Translational Bioinformatics- Call for Participation

2009-09-01T08:36:00.001-07:00

AMIA is now accepting abstract submissions to present at the 2010 Summit on Translational Bioinformatics, which will take place March 10-12 in San Francisco, CA. Submissions will be accepted on the AMIA website through September 24, 2009. For more information on this event or to download the Call for Participation please visit http://summit2010.amia.org.
URL: http://summit2010.amia.org

Contact Person: AMIA Office (mail@amia.org)

News and Important Information from Keystone Symposia on Molecular and Cellular Biology!

2009-08-21T10:43:00.001-07:00

Keystone Symposia offers scholarship and travel awards to student and postdoc conference attendees. Historically, Keystone Symposia has awarded an average of one-third of all scholarship applicants. Scholarship and abstract submission deadlines are typically four months prior to the start date of a meeting. With many deadlines fast approaching, take a look at our 2009-2010 conference schedule and obtain information on specific meeting deadlines: www.keystonesymposia.org/2010meetings . In addition to scholarships, student registration rates are also discounted by up to 35% (verification of student status must be provided at the time of registration). Please visit www.keystonesymposia.org/Minority for more information on scholarships and how to apply.

Keystone Symposia on Molecular and Cellular Biology is an educational nonprofit organization that convenes open, international meetings in the biomedical and life sciences. Based on a rigorous peer review process and held in stimulating venues, the conferences provide valuable opportunities for scientists to share their ideas and results with their peers across different disciplines, forge new research collaborations, receive mentoring and support, and ultimately accelerate the pace of their research efforts.

Keystone Symposia has a vision for enhancing the participation of traditional U.S. visible ethnic minority scientists attending its conferences, as well as in the broader life sciences field. It is our belief that a more diverse research community will contribute to a broader, more dynamic perspective at the level of laboratory research where critical judgments are made. Often bringing together converging fields, resulting in stimulating interactions, the conferences are offered in multiple disciplines including:

• Biochemistry
• Cancer
• Cell Biology
• Genetics/Genomics
• Immunology
• Infectious Diseases

There are also many career-enhancing opportunities for attendees including the chance to:

• network with world-class scientists
• participate in scientific inquiry
• obtain mentoring regarding career decision-making and career path progression
• learn effective networking techniques
• learn how to utilize networks in the planning, development and attainment of your career goals

Since speakers for short talks are selected on the basis of abstract submission, you have an excellent opportunity to gain exposure for your work via our abstract book, at a poster session and possibly through a short talk.

Achieving success and accomplishing your career goals in the life sciences requires action to see the results. Take action; visit our website to find deadline information and apply for scholarships.
URL: http://www.keystonesymposia.org

Contact Person: Dana Wood (danaw@keystonesymposia.org)