ISMB 2008 ISCB




















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Satellite Meetings and SIGs

ISMB/ECCB 2009 will hold a number of one-day and two-day specialized meetings in computational biology. These meetings will be held on Saturday, June 27 and Sunday, June 28. All meetings will be held at the Stockholmsmässan (Stockholm International Fairs). Program information and registration details are noted below.

To inquire about the possibility of forming a new SIG for ISMB 2010 or beyond, please address your inquiry to steven@iscb.org

SATELLITE MEETINGS

Registrants are not required to register as delegates for the ISMB/ECCB 2009 conference to attend a Satellite Meeting. You may select "Satellite only" to register just for the 3Dsig Satellite Meeting. Please note Satellite Meeting registration does not allow access to the SIG Meetings.

The registration fee for the Satellite Meeting includes daily lunches and the 3Dsig Evening Session and Dinner. Each Satellite Meeting participant will receive a booklet that includes meeting notes.

Two-Day Satellite Meeting - Saturday, June 27 and Sunday, June 28

3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting


SPECIAL INTEREST GROUP MEETINGS (SIGs)

SIG Registrants are not required to register as delegates for the ISMB/ECCB 2009 conference to attend a SIG meeting. You may select "SIG only" to register just for a SIG.

Registering for a SIG allows you to move freely between all SIGs that take place on the same day as the meeting for which you are registered, to the extent that the room capacities can accommodate. SIG registration does not allow access to the Satellite Meeting.

Each SIG participant will receive a booklet that includes handouts from all SIGs and daily lunches are included.

Please register for the SIG in which you are most interested so that we can assign SIGs to larger and smaller rooms as appropriate.

NOTE: One-Day SIG registrants are able to participate in SIG meetings only on the day for which they have registered unless registering for two one-day SIG meetings.

One-Day SIGs (Pre-conference) - Saturday, June 27, 2009
DAM: Data and Analysis Management
M3: Metagenomics, Metadata and Metaanalysis
One-Day SIG (Pre-conference) - Sunday, June 28, 2009
Bio-Ontologies
Short-SIG: Next Generation Sequencing and Algorithms for Short Read Analysis

Two-Day SIG - Saturday, June 27 and Sunday, June 28, 2009
Alternative Splicing AS-SIG
Bioinformatics Open Source Conference (BOSC)
BioPathways
Two-Day SIGs - Sunday, June 28 and Monday, June 29, 2009
BioLINK
*BioLINK – Day 2 of the SIG runs in parallel with the main conference on Monday, June 29. The afternoon program on Monday, June 29 is open to all delegates of ISMB/ECCB


SATELLITE MEETINGS

3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting

URL: http://www.ebi.ac.uk/~rafi/3dsig09

Date: Saturday, June 27 and Sunday, June 28

Start time: 8:30 a.m. - End time: *6:30 p.m.

Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

*Saturday, June 27 - 3Dsig Dinner and Evening Presentation
7:00 p.m. Reception (Cash bar)
7:30 p.m. Dinner

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The 2009 3DSIG: Structural Bioinformatics and Computational Biophysics satellite meeting is in its fifth instalment  in what has become the most important annual meeting serving the computational structural molecular biology community. Over the years 3DSIG has presented a very dynamic program comprising two full days bringing together the established as well as up-and-coming leaders in the field in a series of 6 keynote lectures, 20 oral presentations chosen from within the contributed abstracts, a reception followed by a dinner and a post-dinner presentation and our very own signature poster/laptop session where all accepted contributors are invited to present their work as a traditional poster but also as an interactive laptop presentation and demonstration.

In 2008, the best two student presentations were awarded a prize (sponsored by MGMS). The list of past keynote speakers includes but is not restricted to: Rob Russell, Ron Unger, Gunnar von Heijne, Cyrus Chothia, Phil Bourne, Nick Grishin, Wah Chiu, John Moult, Jeff Saven, Janet Thornton, Steven Brenner, Anna Tramontano, Thomas Lengauer, Kevin Karplus, Sandor Vajda, Burkhard Rost, Ivet Bahar, Barry Honig, Alfonso Valencia, Tamar Schlick, Tanja Kortemme, Brian Shoichet. All aspects of computational molecular biology are welcome. The deadline for submissions is June 4th. For more information, including key dates and the list of confirmed keynote speakers for 2009, please visit: http://www.ebi.ac.uk/~rafi/3dsig09

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3DSig Organizing Committee:

John Moult
Biotechnology Institute
University of Maryland, USA
 
Ilan Samish
Dept of Biochemistry & Biophysics and Dept. of Chemistry
University of Pennsylvania, USA
 
Rafael Najmanovich
Département de Biochimie
Faculté de Médecine
Université de Sherbrooke, Canada

Contact: 3dsig09@googlemail.com

Keydates:

February 16, 2009 - Registration opens for 3Dsig and ISMB/ECCB

March 18, 2009 - Deadline for submitting an abstract to 3Dsig to be considered for oral presentation.

April 2, 2009 - Deadline for travel fellowship application for the main ISMB/ECCB conference. Remember to be eligible to receive an ISMB/ECCB travel fellowship you must have an accepted paper or poster for the 2009 conference.

April 15, 2009 - Tentative date for the announcement of the abstracts selected for oral presentation and laptop/poster session (full program and online abstracts will be posted soon afterwards).

April 29, 2009 - Late 3Dsig abstract submission deadline. Late submissions will not be considered for oral presentation. Late submission deadline for ISMB/ECCB posters.

May 15, 2009 - Early registration deadline to the main ISMB/ECCB conference. Note: you may register only for 3Dsig.

June 27-28, 2009 - 3Dsig 2009

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SPECIAL INTEREST GROUP MEETINGS (SIGs)


Alternative Splicing (AS-SIG)

To register by fax for the AS-SIG informal dinner on Saturday, June 27 click here

URL: http://www.alternative-splicing.org/as-sig-09/
Date: Saturday, June 27 and Sunday, June 28, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

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Deciphering the splicing code: the role of protein-RNA interactions

In order to unravel the complete regulatory expression network, it is necessary to systematically identify protein-RNA interactions. In vitro techniques have been successful in identifying the motifs bound by regulators. However, these motifs are relatively short and bioinformatics searches produce a large number of false positives. Recent advances in sequencing technologies and systematic structural studies have provided new insight in how proteins interact with RNA. These technological advances provide an unprecedented opportunity to explore how RNA is regulated at a global level. These advances also pose new computational challenges. An extensive interaction between computational and experimental researchers is therefore required, aimed at building a community of shared resources and tools.

The AS-SIG meeting provides a forum for the discussion of the latest findings and to establish new collaborations in the field of splicing and RNA biology. AS-SIG 2009 format follows previous successful AS-SIG meetings at Detroit (ISMB2005), Fortaleza (ISMB2006), Vienna (ISMB2007) and Toronto (ISMB2008). AS-SIG 2009 will take place immediately before ISMB/ECCB 2009. This year's location, Stockholm, Sweden, provides an excellent opportunity for attracting scientists from all over Europe and the world, and will facilitate broadening the scope of the AS-SIG meeting, as well as the interactions with the international community.

This year there will be special emphasis on high-throughput technologies in the study of RNA processing and protein-RNA interactions. Planned topics are:

RNA processing and protein-RNA interactions
Protein-RNA and RNA-RNA interactions in gene regulation and the pathogenesis of cancer and other diseases. Coupling of transcription and splicing and regulation of splicing by chromatin modification. Special emphasis will be given on structure-function relationships.

RNA regulatory maps
Splicing factors and their cognate cis-regulatory elements; next-generation sequencing for the analysis of protein-RNA interactions, RNA expression, and the detection of regulatory RNAs.


Keydates
February 2009 AS-SIG call for papers
March 2009 AS-SIG announcement of accepted papers
April 2009 AS-SIG selection (late) of posters
June 27-28 2009 AS-SIG meeting

Contacts:
Eduardo Eyras, Pompeu Fabra University, PRBB, Barcelona, Spain
Email: eduardo.eyras@upf.edu

Dirk Holste, Austria Research Centers – ARC and University of Vienna, Austria
Email: holste@imp.ac.at

Frederic Allain, ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
E-mail: frederic.allain@mol.bio.ethz.ch

Rickard Sandberg, Karolinska Insititute, Stockholm, Sweden
E-mail: rickard.sandberg@ki.se

Graziano Pesole, University of Bari and Istituto Tecnologie Biomediche del CNR (sede di Bari) via Orabona, Italy
E-mail: graziano.pesole@biologia.uniba.it


Bioinformatics Open Source Conference (BOSC)

URL: http://www.open-bio.org/wiki/BOSC_2009
Date: Saturday, June 27 and Sunday, June 28, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

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The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies.  In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.

This year’s conference will mark the 10th anniversary of BOSC.  To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead:  Open Source Solutions to Grand Challenges in Bioinformatics.”  We are inviting abstracts for two different types of talks:

  • Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.
  • Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.

In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session.  This year’s topics include:

  • Design Patterns in Bioinformatics
  • Regulatory Genomics
  • Multicore and GPGPU computing
  • Data & Analysis Management (shared session with DAM SIG)
  • Computational Grids
  • Visualization

There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.

Abstract deadline is April 13, 2009 .

BOSC Coordinator:

Kam D. Dahlquist, Ph.D.
Department of Biology
Loyola Marymount University
Los Angeles, California, USA
Email: kdahlquist@lmu.edu or bosc@open-bio.org

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Bio-Ontologies

URL: http://bio-ontologies.org.uk/
Date: Sunday, June 28, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

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(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

Bio-Ontologies has been a Special Interest Group (SIG) at ISMB for the last 11 years, providing an environment for sharing knowledge and learning about ontologies and their application to biology. Over the years, the Bio-Ontologies SIG has provided a forum for discussion on the latest and most innovative topics in this area. Last year, the scope was increased to include formal and informal approaches to organizing, curating, representing and disseminating knowledge in biology. Papers will be welcomed in traditional areas, such as the biological applications of ontologies, newly developed Bio-Ontologies, and the use of ontologies in data communication standards. In addition, papers will also be welcomed in the following areas:

  • Semantic and/or scientific wikis
  • Folksonomies and tag clouds
  • Collaborative curation platforms
  • Collaborative ontology authoring and peer-review mechanisms
  • Automated ontology learning
  • Mapping between ontologies

Each year, we focus on a specific theme in our keynote and panel sessions. For 2009 the theme will be: “The emergence, use and success of wikis for collaborative knowledge capture for biology”.

Key Dates

Friday, April 10, 2009 Paper Submissions Due
Friday, May 1 2009 Notification of Accepted Papers
Friday, May 8, 2009 Final Version Due

Contacts

General Contact: bioontologies2009@gmail.com

Nigam Shah, Stanford University
Email: nigam@stanford.edu

Phillip Lord, Newcastle University
Email: phillip.lord@newcastle.ac.uk

Susanna-Assunta Sansone, EBI
Email: sansone@ebi.ac.uk

Larisa Soldatova, University of Aberswyth
Email: lss@aber.ac.uk

Susie M Stephens, Eli Lilly
Email: stephens_susie_m@lilly.com

SIG URL
www.bio-ontologies.org.uk

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BioPathways

URL: http://www.biopathways.org
Date: Saturday, June 27 and Sunday, June 28, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

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The 10th BioPathways meeting is organized by the BioPathways Consortium, an open forum aimed at fostering computational approaches to the understanding of biological networks in biotechnology and biomedicine.

Previous BioPathways meetings have focused on a variety of themes, such as computational reconstruction of molecular networks, pathway evolution, integration of models and experiments, models and ontologies for pathways, modeling of interactions and regulation on a systems scale and network approaches for discovering disease associations, among others.

This year’s meeting will remain within the broad spectrum of computational and semantic approaches for molecular network analysis and systems modeling, featuring also presentations on pathway analysis tools, metabolism, signaling or regulation, selected from the most notable recently published work or from yet unpublished work. In addition, one session each will be dedicated to the three specific thrusts, namely,

a) Design Tools for Synthetic Biology, 
b) Network Analysis of Metagenomes,
c) Computational Pathway Methods for Translational Medicine.

Brief descriptions of the scope of each of these themes are available at the BioPathways site (www.biopathways.org). As customary, the meeting will consist of two full days with a balance of invited talks, short oral presentations, and critical, topic-focused panel discussions. We strongly encourage the presentation of work-in-progress in cutting-edge research.

If you wish to present a contributed talk at BioPathways 2009, please send a 250-word abstract describing your work. Authors are encouraged to add URLs of web-based tools, and selected tools will be featured on the BioPathways web site. Abstracts should arrive by April 21, 2009, and presenters will be notified no later than May 21, 2009. Submissions should be sent to: BioPathways@Helmholtz-HZI.de

We look forward to seeing you at BioPathways 2009 - from the organizers: Vítor Martins dos Santos, Helmholtz Centre for Infection Research, Germany (chair), Vincent Schächter, Genoscope, France, Vincent Danos, University Edinburgh, Joanne Luciano, MITRE Corp. and Predictive Medicine Inc, Eric Neumann, Clinical Semantics Group and Aviv Regev, Broad Institute and MIT.

Contact:
Vítor Martins dos Santos
Helmholtz Centre for Infection Research
Germany (chair)
Email: vds@helmholtz-hzi.de

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BioLINK: Linking Literature, Information and Knowledge for Biology

URL: http://www.cs.queensu.ca/biolink09
Date: Sunday, June 28 and Monday, June 29, 2009
Start time: 8:30 a.m. - End time: *6:00 p.m.
Room Location: TBD

(Note: BioLINK – Day 2 of the SIG runs in parallel with the main conference on Monday, June 29. The afternoon program on Monday, June 29 is open to all delegates of ISMB/ECCB)

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The Annual Meeting of the ISMB BioLINK Special Interest Group:  Text Mining, Image Analysis, and the future of Scientific Publishing

The BioLINK SIG meeting has been regularly held in association with the ISMB conference since 2001, focusing on the development and application of resources and tools for biomedical text mining. The SIG is interdisciplinary in nature, and brings together researchers applying natural language processing, text mining, information extraction and retrieval in the biomedical domain, with scientists from bioinformatics and biology.

This year the SIG will go beyond text to take into account the analysis of images and figures in scientific publications because of their critical information content. Furthermore, we will include a session about the future of scientific publishing, and the impact of information extraction methods (be they based on text or on images) on producers and consumers of scientific information. The SIG will feature a special session (on Monday), including presentations and discussions by representatives from scientific journals and community members. This session is jointly organized with PLoS, and is open to all ISMB attendees.

The meeting includes invited talks, presentations of peer-reviewed contributed papers, reports from recent evaluations and workshops, as well as a poster session. The SIG solicits papers that discuss current biological image- and text-related needs, the challenges of meeting them, and the tools that may help address them. Specific topics include: biological image analysis and its relationship to biomedical text mining, application of text-mining tools to biomedical research, automated indexing of the biomedical literature, generation of structured digital abstracts, new evaluation measures to measure utility and usability of text mining tools integrated into the biologists’ workflow, as well as new tools and applications, and future directions in biomedical text mining.

We anticipate a productive workshop that will facilitate discussion and exchange of ideas by bringing together multiple communities:  the users of text mining tools, including curators of biological databases, bench scientists and bioinformaticians; and the researchers applying natural language processing, ontologies, text mining, image analysis, information extraction and retrieval to problems in the biomedical domain.

Information about last year's meeting is available at the BioLINK08 web site

Keydates:

April 5: Short papers due
April 15: Poster Abstracts (up 350 words) due
May 5: Notification to authors
May 15: Final version due

Contacts:

Christian Blaschke
Bioalma, Spain
Email: blaschke@almabioinfo.com

Hagit Shatkay
Queen's University, Canada
Email: shatkay@cs.queensu.ca

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DAM: Data and Analysis Management

URL: http://dam-sig.org
Date: Saturday, June 27, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

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Over the last few years we have seen another explosion in the data generation capacity of experimental biology. New DNA sequencing and high-density array technologies have enabled a variety of novel genome scale experimental techniques. What is perhaps most unique about this recent data explosion is that it is distributed – relatively inexpensive instruments allow any lab or institution to produce enormous amounts of data. Because of this change, the traditional model of centralized data warehouses for biological data is no longer sufficient. This has led to a new generation of systems for data management and analysis which are designed to put make it possible for experimentalists to effectively manage and analyze the wealth of data they can now produce, and integrate that data with existing date warehouses and literature, with little or no expert informatics support.

These new approaches are critical if the promise of next generation experimental techniques is to be realized. This session will serve as an open forum for introduction of cutting edge applications that mold data sources and analysis tools into a singular medium benefitting both extremes on the user spectrum: experimentalists and computational researchers.


Confirmed Speakers:
Carole Goble (University of Manchester)
Christopher Lee (UCLA)
Jill Mesirov (Broad Institute)
Gos Micklem (Cambrigde)

Contacts:
James Taylor
Emory University, Atlanta, UA
Email: james.taylor@emory.edu
http://bx.mathcs.emory.edu

Anton Nekrutenko
Penn State University
University Park, USA
Email: anton@bx.psu.edu
http://nekrut.bx.psu.edu


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M3: Metagenomics, Metadata and Metaanalysis

URL: http://gensc.org/
Date: Saturday, June 27, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

(*Please note that the program ends Sunday, June 28 at 6:00 p.m. to allow movement to Stockholm City Hall for the Opening Reception hosted by the City of Stockholm)

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While genomes represent the full genetic (DNA) complement of a single organism, metagenomes represent the DNA of an entire community of organisms. Metagenomes are partial samples of complex and largely unknown communities that can only be poorly assembled. This SIG will explore the latest concepts, algorithms, tools, informatics pipelines, databases and standards being developed to cope with the analysis of vast quantities of metagenomic data.  Contributed submissions based on talks and posters that describe studies that demonstrate the power of using curated (e.g. habitat or host) and measured (e.g. geographic location, salinity, temperature, or pH) contextual data in comparative metagenomic studies of large numbers of samples are encouraged. Likewise, papers describing new approaches, tools, databases, standards, ontologies or substantial new sets of curated metadata that aid in the integration and inter-operablility of disparate datasets are welcomed.

The M3 meeting will include 3 sessions, presenting talks on Metagenomics, Metadata and MetaAnalysis.  The meeting will also include a Panel discussion and lightening talks (5) minutes from selected poster submissions.

If you wish to present a contributed talk or poster at M3 2009, please prepare an abstract describing your work. Abstracts should arrive by April 1, 2009 and presenters will be notified no later than April 15, 2009. Further details can be found on the M3 homepage at http://gensc.org.

We look forward to welcoming you to the GSC's M3 in 2009.

Contacts:
Dawn Field
Email: dfield@ceh.ac.uk
Iddo Friedberg Email: idoerg@gmail.com

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Short-SIG: Next Generation Sequencing and Algorithms for Short Read Analysis

URL:Date: Sunday, June 28, 2009
Start time: 8:30 a.m. - End time: *6:30 p.m.
Room Location: TBD

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While the promise of next generation sequencing (NGS) technologies has become a reality, and in the past year several computational methods for assembly and alignment with short reads have been developed, realizing the full promise of these technologies requires the development of methods that can analyze the resulting assemblies and mappings of the reads to infer biological meaning – genome variation, novel transcript discovery, microRNA expression analysis, and metagenomic analysis.

In particular, we are interested in presentations describing methodology to infer various polymorphisms (SNPs, large insertions/deletions, copy number variations) with short read data.. As the HapMap project has increased our understanding of SNPs, structural variation (including insertions, deletions, translocation, inversions, and CNVs) have come to the forefront as one of the main sources of variation within a species. NGS technologies offer the potential of high resolution detection of most types of genomic variants that are just beginning to be explored.

Another exciting application of NGS technologies is RNA sequencing. RNA sequencing is currently used for several applications, including RNA expression, de-novo transcriptome sequencing for non-model organisms, and novel transcript discovery, however computational methods for analysis of this data is in its infancy. For RNA and micro-RNA expression profiling, NGS has significant advantages compared to microarray methods in that it is better able to identify quantities of very common and very rare transcripts. Transcriptome profiling is also increasingly used for sequencing the RNA of non-model organisms for phylogenetic and population studies, and methods for transcriptome assembly and co-assembly need to be improved.

NGS Sequencing is also commonly used for discovery of transcription factor binding sites (and nucleosome positioning) using CHiP-SEQ, for methylation profiling, and for analysis of metagenomic samples. We will certainly welcome presentations on these topics, as well as any other important methods related to NGS technologies.

Submission information: TBA, watch website.

Coordinator:
Michael Brudno, brudno@cs.toronto.edu
Francisco M De La Vega, francisco.delavega@appliedbiosystems.com
Jens Stoye, stoye@techfak.uni-bielefeld.de

SIG URL: http://compbio.cs.toronto.edu/ismb09-sig/

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