ISMB/ECCB 2007

ISMB/ECCB 2007 will hold a number of smaller, specialized meetings in computational biology on Thursday, July 19 and Friday, July 20. These meetings include one-day and two-day meetings. Program information and registration details are noted below.

To inquire about the possibility of forming a new SIG for 2008 or beyond, please address your inquiry to steven@iscb.org

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SATELLITE MEETING

Registrants are not required to register as delegates for the ISMB/ECCB 2007 conference to attend a Satellite Meeting. You may select “Satellite only” to register just for the 3Dsig Satellite Meeting. 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. The Satellite Meeting will take place at the Austria Center Vienna.

Two-Day Satellite Meeting — Thursday, July 19 and Friday, July 20, 2007
3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting

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SPECIAL INTEREST GROUP MEETINGS (SIGs)

SIG Registrants are not required to register as delegates for the ISMB/ECCB 2007 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 at the same time 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. All SIG meetings will be held at the Austria Center Vienna.

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 SIG — Thursday, July 19, 2007
BioLINK

One-Day SIGs — Friday, July 20, 2007
Bio-Ontologies
Micro-SIG: Comparative genomics, evolution, and regulation in microbes

Two-Day SIGs — Thursday, July 19 and Friday, July 20, 2007
Alternative Splicing AS-SIG
Bioinformatics Open Source Conference (BOSC)
BioPathways
Joint AFP-Biosapiens SIG

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3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting

URL: http://structure.bu.edu/3DSig/
Date: Thursday, July 19 and Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

The third 3Dsig meeting will consist of two full days with a balance of invited talks, short oral presentations, two laptop/poster-sessions, and critical, topic-focused discussions. A truly unique event bringing together in one place the structural computational biology community.

Relevant topics include:

• Structure representation, structure prediction, structural genomics
• Structural databases and 3D data mining
• Structure-based function prediction
• Evolution studied through structure
• Protein-protein, protein-ligand, and protein-RNA/DNA interactions (docking, analysis & prediction)
• Prediction and analysis of domains
• Membrane protein structure prediction and analysis
• The role of geometry and energetics in protein and RNA structure and function
• Protein and RNA dynamics and simulation: folding, stability, interactions, conformational gating
• Computer-aided protein and RNA design
• Structure-based drug design and pharmacophore analysis

3Dsig 2007 is continuing the tradition established through the successful 3Dsig 2006 and 3Dsig 2004. To better appreciate the wealth of leading topics and presenters, please explore the programs and proceedings from past 3Dsig 2004 and 2006 meetings. The program will be built around talks from accepted abstracts and invited speakers.

The scientific committee is looking for fresh, effective voices with new, high impact ideas. Accepted abstracts will fall into two categories: oral presentation and laptop/poster presentation. Participants with accepted abstracts for the latter type will have the choice of presenting their work as either a regular poster, a laptop presentation, or a combination thereof. Those choosing to use a laptop to substitute or augment their poster presentation will have a stand or table and electric socket for a personal laptop (presenters must bring their own laptops). The aim of the poster/laptop session is to facilitate interactions between the presenter and the viewers.

Key Dates:

• June 1, 2007 – Deadline for submitting an abstract to 3Dsig laptop session AND/OR oral presentation.
• June 15, 2007 – Announcement of the abstracts selected for oral presentation and laptop/poster session (full program and online abstracts will be posted soon afterwards).
• June 1, 2007 – Early registration deadline to the main ISMB2007 conference. Note: you may register only for 3Dsig and not to the main ISMB/ECCB 2007 conference.
• July 19-20, 2007 – 3Dsig

3Dsig Sponsor Opportunities:
Please contact the organizers at 3dsig07@googlemail.com for sponsorship possibilities.

Contact:
Rafael Najmanovich, European Bioinformatics Institute, UK, rafael.najmanovich@ebi.ac.uk

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Alternative Splicing (AS-SIG)

URL: http://www.alternative-splicing.org
Date: Thursday, July 19 and Friday, July 20, 2007
Start time: 9:00 a.m – End time: 6:30 p.m.
Room Location: TBD

Jointly organized by the Alternative Splicing Organizing Committee (ASORG) and the European Alternative Splicing Network (EURASNET)

Alternative splicing (AS) is positioned at the interplay of genomes, regulatory networks and evolution, and has emerged as a ubiquitous and dynamic mechanism of gene regulation. This picture is further emphasized by the central role played by AS in multiple diseases mechanisms, by a stream of new insights and discoveries derived from the fields of genomics, bioinformatics and molecular biology, as well as from new approaches in the measurements of expressed isoforms across cell types and tissues. Analyzing the regulation, function and evolution of AS constitutes a decisive part in the understanding of the transcriptome. This will require close collaboration between computational and experimental researchers, enabling us to build a community of shared tools, databases, nomenclature and standards. The AS-SIG meeting aims to establish a forum for researchs to discuss about AS, focusing on questions that demand collaborative inputs. The AS-SIG will address latest results and questions in this exciting field, and bring (“splice”) together bioinformatics and biology. In addition to oral presentations and a poster session, the meeting will feature a panel discussion. The content of the meeting will be divided into four areas:

• Experimental and bioinformatics methodologies for alternative splicing

  RT-PCR-based screens; minigene systems; RNA interference-mediated screens; cross-linking and immunoprecipitation (CLIP-) based screens; small molecule approaches; transcript repositories; standards for annotating primary transcript structures; algorithms (spliced-alignments, new tools for data-mining) and computational analysis of AS events, types and rates, AS gene products and functional impact; data exchange formats; comparative genomics and evolution of introns and AS; structure of AS information (databases, ontologies, abstract representations of AS events).

• Biology of regulatory mechanisms of alternative splicing

  Regulatory mechanisms of splicing; biological functions (impact of splice variants on protein structure and biological pathways); differentiation of AS types between model organisms; functional nucleotide sequences as cis-regulatory elements; splicing-regulatory SR proteins and hnRNPs; NMD as a surveillance (quality control) pathways linked to AS.

• Aberrant splicing, human disease, and concepts for medical treatment

  Identification and characterization of splice variants linked to human disease; classification of AS forms based on disease progression; diagnostic tools and therapeutic strategies related to AS pattern variations between normal and diseases states.

• Forum discussion

  EURASNET: aims, workgroups and outcomes; milestones achieved due to the formation of the network; possibilities for collaboration.

Contacts:
Shoba Ranganathan, Macquarie University, Australia, shoba@cbms.mq.edu.au
Dirk Holste, Institute of Molecular Pathology, Austria, holste@imp.ac.at
Eduardo Eyras, Pompeu Fabra University, Spain, eduardo.eyras@upf.edu,
Andrea Barta, University of Vienna, Austria, andrea.barta@meduniwien.ac.at

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Bioinformatics Open Source Conference (BOSC)

URL: http://www.open-bio.org/wiki/BOSC_2007
Date: Thursday, July 19 and Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

The Bioinformatics Open Source Conference (BOSC) is held annually as a special interest group in conjunction with the International Systems in Molecular Biology conference. It is sponsored by the Open Bioinformatics Foundation, a non-profit group dedicated to promoting the development of Open Source Bioinformatics Software, and Open Standards of data communication and representation.

BOSC 2007 is shaping up to be an exciting conference. Carol Goble, of Manchester University, will be presenting our Keynote session this year. She will be speaking about hard problems in Bioinformatics. Our agenda this year will consist of a few different sessions this year. Our main series of sessions will be devoted to allowing presentations of specific use-cases of areas of Informatics or Bioinformatics which are not currently served by existing toolkits. We will then have a session devoted to talks on new software design patterns such as webservices, folksonomies, and others which have been collectively referred to as web 2.0. We will then have a series of update talks about the main Open Source Bioinformatics Software suites. A special session will be devoted to setting the stage for the creation of a distribution CD of Bioinformatics software to be distributed at BOSC 2008. There will be talks from submitted abstracts over various aspects of Open Source Bioinformatics development. Finally, the last session will allow presenters to present ideas for addressing a hard problem presented in the first session. In addition to these presentations, BOSC always facilitates the meeting of like minds over a range of subjects in small Birds of a Feather meetings. We are very much looking forward to this exciting event.

Contact:
Darin London, Duke University, darin.london@duke.edu

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BioLINK SIG

URL: http://www.cs.queensu.ca/biolink07
Date: Thursday, July 19
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

The BioLINK SIG workshop focuses on text mining for the linkage of information from the biomedical literature to support biomedical applications. It brings together researchers from a wide variety of research areas including molecular biology, bioinformatics, biochemistry, natural language processing, knowledge representation and ontologies, information extraction and information retrieval, all working toward the goal of identifying and accessing pertinent information from biomedical text.

BioLINK 2007 will focus on recent assessments, on standards for annotation both in biological databases and in biomedical text corpora, and on new tools for biomedical text mining. The SIG will solicit papers and talks that discuss text mining tools and their application to biomedical research and to biological database curation; the interrelations between database curation and text mining; and the utility of existing resources – as well as the development of future ones – to expedite progress in the interdisciplinary research field of biomedical text-mining.

The workshop will include plenary sessions with contributed papers, 1-2 keynote talks, a discussion session, and a poster session. We solicit papers on these topics, including:

New validated and/or tools in current use for biomedical text mining;
Lessons learned from the BioCreAtIvE and TREC Genomics track assessments;
Methods, measures and corpora for testing and evaluating text mining in the biomedical domain; Use of text mining to assist database curation; Improvement in task-specific biomedical text mining by utilizing biomedical resources; New directions in biomedical text mining, including new applications, new resources, and the incorporation of new types of data.

Contact:
Christian Blaschke, Bioalma, Spain, blaschke@almabioinfo.com
Hagit Shatkay, Queen’s University, Canada, shatkay@cs.queensu.ca

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Bio-Ontologies SIG

URL: http://bio-ontologies.org.uk
Date: Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

Bio-Ontologies provides an environment for discussion of the latest developments in ontologies and their application within the Life Sciences. Now in its tenth year, the use of Ontologies has moved from niche to mainstream usage within bioinformatics. We provide a forum for the latest and most cutting edge research, often enabling presentation of work a year before formal publication.

This meeting will be the tenth consecutive meeting of the Bio-Ontologies SIG, and we take this occassion to celebrate with the theme of “Bio-Ontologies: ten years past and looking to the future”. We will have four presenters from the first bio-ontologies tutorial (Mark Musen, Peter Karp, Russ Altman and Steffen Schulze-Kremer) who will be discussing the changes that have occurred and the challenges that await us.

In addition to the invited section, we are accepting submissions (deadline, 1st May) of papers and posters from any aspect of bio-ontologies research or the use of ontologies within bioinformatics. Topics include:

• Biological Applications of Ontologies
• Reports on Newly Developed or Existing Bio-Ontologies
• Tools for Developing Ontologies
• Use of Semantic Web technologies in Bioinformatics.
• The implications of Bio-Ontologies or the Semantic Web for the drug discovery process
• Current Research In Ontology Languages and its implication for Bio-Ontologies

Previous history has shown the SIG to be of direct relevance and interest to many at ISMB/ECCB. Past meetings have been interesting, discoursive and informative.

Contacts:
Phillip Lord, Newcastle University, phillip.lord@newcastle.ac.uk
Robert Stevens, University of Manchester, robert.stevens@cs.man.ac.uk
Robin MacEntire, GlaxoSmithKline, robin.a.mcentire@gsk.com
Susanna-Assunta Sansone, European Bioinformatics Institute, sansone@ebi.ac.uk

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BioPathways

URL: http://www.biopathways.org

Date: Thursday, July 19 and Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

The 8th BioPathways meeting will be held on the 19th and 20th of July, in Vienna, Austria as a satellite of ISMB/ECCB’07 (http://www.iscb.org/cms_addon/conferences/ismbeccb2007/ ). The meeting is organized by the BioPathways Consortium (www.biopathways.org ), an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological networks.

The meeting will include 3-4 plenary sessions, presenting invited talks on various aspects of computational systems biology, including:

• computational methods for synthetic biology
• modelling of interactions within bacterial communities
• evolution of metabolic networks
• evolution of regulatory networks
• computational methods for metabolomics
• computational network approaches for discovering disease associations
• reconstructing network dynamics from experimental data

Each plenary session will include several long invited presentations (45′), followed by a panel discussion on the session theme. To encourage presentation of cutting-edge research and work-in-progress in computational approaches to molecular pathways, we will also include contributed talks as part of the meeting’s session. A contributed talk consists of a short presentation of relevant method, tools and analyses. Particular emphasis will be made on works along the themes of the plenary sessions, as well as research in pathway visualization and reconstruction, all of which are subjects followed by the consortium’s workgroups.

If you wish to present a contributed talk at BioPathways 2007, please send a 200 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 31st, and presenters will be notified no later than May 20th.

bpc-cfp@biopathways.org

Looking forward to seeing you at BioPathways ‘07,
For the organizing committee,
Vincent Schachter, Vincent Danos, Joanne Luciano, Aviv Regev

Contact:
Vincent Danos, danos@pps.jussieu.fr
Vincent Schachter, vs@genoscope.cns.fr

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Joint AFP-Biosapiens SIG

URL: http://2007.biofunctionprediction.org/
Date: Thursday, July 19 and Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

AFP and the Biosapiens European network of excellence are teaming up to hold a two-day Special Interest Group (SIG) meeting in ISMB/ECCB 2007.

The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through predicting the function form protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations.

Talks are sought in, but not limited to:

• All aspects of gene and protein function prediction
• Function prediction using sequence based methods. This would include “classic” methods such as detection of functional motifs and inferring function from sequence similarity.
• Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss.
• Phylogeny based methods
• Function from molecular interactions
• Function from structure
• Function prediction using combined methods
• “Meta-talks” discussing the limitations and horizons of computational function prediction.
• Assessing function prediction programs
• Genomic annotation
• Gene finding
• Genome visualization
• Collaborative annotation
• Cooperation between experimental and computational biologists

Confirmed speakers include:

Janet Thornton, European Bioinformatics Institute, Cambridge, UK
David Jones University College, London, UK
Rob Russell EMBL, Heidelberg, Germany
Christine Orengo, University College London, UK
Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain
Ewan Birney, European Bioinformatics Institute, Cambridge, UK
Shoshana Wodak, University of Toronto, Canada
Russ Altman, Stanford University, USA

Important Dates
(as of April 30, 2007; subject to change)

May 6 2007: Talk and Poster abstracts due (11:59 pm, time zone of choice)
May 21 2007: Notification of acceptance
May 28, 2007: Final abstracts due

The AFP / BioSapiens SIG is organized by Adam Godzik and Iddo Friedberg, Burnham Institute for Medical Research, USA and by Christine Orengo of University College London, UK.

Primary contact:
Iddo Friedberg, idoerg@ucsd.edu

Alternate contacts:
Christine Orengo, orengo@biochem.ucl.ac.uk
Adam Godzik, adam@burnham.org

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Micro-SIG: Comparative genomics, evolution, and regulation in microbes

URL: http://micro-sig.lbl.gov
Date: Friday, July 20, 2007
Start time: 9:00 a.m. — End time: 6:30 p.m.
Room Location: TBD

With more than 400 microbial genomes sequenced and more than 900 in the sequencing pipelines comparative genomics is turning into a major tool for the annotation and analysis of sequences and genomes. To solve many problems related to ever-growing number of bacterial sequences, new algorithms and software programs for post-sequencing functional analysis are being developed by the scientific community. Among them are whole genome comparison and visualization, discovery of coding regions and regulatory signals, and deducing the mechanisms and history of genome evolution has been a very active area of research in the last years. Metagenomics, an emerging subdiscipline of microbiology, allows for study of genomic sequences found in ecosystems, including genomes of species that are difficult to culture. They provide exciting opportunities to discover the extent of co-existing genetic diversity within natural ecosystems, and even microdiversity within populations of the same species.
This one-day SIG will be devoted to discussing the latest advances in computational techniques and biological insights in the area of comparative microbial genomics and regulation in bacteria. This session will bring together bioinformaticians and experimentalists, and will consist of invited talks and discussions chaired by leaders in the field.

Talks will be grouped in four major areas:
I. Comparative, population, and environmental genomics
II. Elucidation of gene regulation in microbes
III. Inference of genome phylogenies and dynamics
IV. Building and optimization of publicly available computational tools and databases for microbial analysis.

Contact:
Adam Arkin, aparkin@lbl.gov
Eric Alm, ejalm@mit.edu;
Inna Dubchak, ildubchak@lbl.gov