{ C O N T E N T S }
Volume 9, Issue 1

President’s Letter

Call for Leadership Nominations

ISCB Membership

URLs in Grant Proposals
Your Feedback Requested

Announcing MentorNet
E-Mentoring Program

ISMB 2006 News & Updates:

- ISMB 2006 Registration
Now Open

- SwissProt 20

- SIGs & Satellite Meetings

- Introducing the PLoS Track of Oral Presentations

- Student Council Symposium

- Help Send a Student to ISMB

- Advertise in the ISMB 2006 Newsletter

Other Conferences News
and Reports:

- RECOMB Celebrates 10 Years

- Affiliate Focus: OKBIOS

- Travel Fellowships Available

- Key Conferences: Key Dates

Student Travel Fellowships Yearbook

Bioinformatics Books New Online Features

Post your Events & News to ISCB Website

Upcoming Conferences & Events

News From the Field



Copyright © 2006 International Society for Computational Biology.
All rights reserved

ISMB SIG & Satellite Meetings in 2006

As is the tradition of ISMB, two days of Satellite and Special Interest Group Meetings will precede the conference (partially filling the gap between Swiss-Prot 20 and ISMB 2006 – see related article in this newsletter).

Registration for all SIG and Satellite Meetings is accomplished through the online ISMB 2006 conference registration form. You may use this form to register for any one of the meetings described below. Registration for the main ISMB 2006 conference is not required to attend a SIG or Satellite Meeting. Therefore, if you will be attending Swiss-Prot 20 meeting and would like to stay over for any of the SIG/Satellite Meetings, you may do so without the commitment of also staying for the additional days of ISMB 2006.

3Dsig: Structural Bioinformatics and Computational Biophysics Satellite Meeting
Friday, August 4 and Saturday, August 5
9:00am - 6:30pm

We are happy to announce the second 3Dsig: Structural Bioinformatics and Computational Biophysics Satellite meeting. Following the success of 3Dsig-2004, we will have two full days (don't plan anything for the evening!) with a balance of invited talks, short presentations, novel laptop-sessions and critical, topic focused discussions.

On Friday, August 4, 3Dsig will host an evening session at the Oasis Hotel Atlantico which includes a panel discussion and keynote speaker, both on a central topic to Structural Bioinformatics and Computational Biophysics, and dinner. Registration to the 3Dsig Satellite meeting includes the 3Dsig Evening Session and Dinner. Delegates from other SIGs and Swiss-Prot 20 may purchase a ticket to this evening session for a small fee. Following the successful format launched in 2004, the panel discussion will include audience participation, informal round-table discussions and interactions, all nurtured by the good food that Brazil has to offer.

Please note, registration for the 3Dsig Satellite meeting allows access to the 3Dsig meeting only.

Relevant topics include:

  • Structure representation, structure prediction, structural genomics
  • Structural databases and 3D data-mining
  • Structure-based function prediction
  • Evolution studied through structure
  • Docking: protein-protein, and protein-ligand, and RNA interaction 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

Call for abstracts: We are looking for fresh, effective voices, and new, high impact ideas and results. The program will be build around the accepted and invited talks. Abstracts will be placed on a discussion web site prior to the meeting, and participant input considered in choosing oral presentations.

Abstract submission deadline: May 1, 2006

The scientific committee of 3Dsig is chaired by John Moult (CARB, UMBI) and includes Phil Bourne (UCSD), Steven E. Brenner (UC Berkeley), Joel Sussman (Weizmann Institute of Science) and Janet Thornton (EBI).

To better appreciate the wealth of leading topics and presenters, explore the 3Dsig 2004 book at: 3dsig.weizmann.ac.il/2004/3dsigbook.pdf

Sponsorship opportunities are available!See 3dsig.weizmann.ac.il/3dsig/2006/sponsors.html for full details.

Alternative Splicing (AS – SIG)
Friday, August 4 and Saturday, August 5
9:00am - 6:30pm

This is an exciting time for the field of transcripomics, combining new discoveries from genomics, bioinformatics, and molecular biology. Alternative splicing has now emerged as a ubiquitous mechanism of regulation, accounting for the complexity of higher eukaryotes, where one gene could give rise to several gene products. Whereas the Human Genome Project has uncovered 20,000 – 25,000 genes, alternative splicing evidently produces over 100,000 distinct transcript forms. Identifying, quantifying, and analyzing the regulation, function and evolution of these forms constitutes a “Human Transcriptome Project”, and will require a tremendous community effort. Above all, it will require close collaboration between bioinformaticists and experimentalists, to build a community of shared tools, databases, nomenclature and standards. This SIG aims to establish a permanent forum for bioinformaticists and experimentalists to meet and discuss transcriptome issues together, especially in the light of diseases implicated by alternative splicing.
The purpose of this SIG is to cover the latest results and questions in this exciting field, and to bring together bioinformaticists and experimentalists, focusing on questions that demand their collaboration. The SIG will include studies of alternative splicing both in human and other organisms, and will consist of two days of talks (approximately 20 minutes each), and a poster session. Talks will be grouped in four major areas:

  • Bioinformatics: algorithms and analysis of alternative splicing, including topics such as analysis of alternative splicing evidence, products, and functional impact; comparative genomics; alternative splicing regulation; and data-mining.
  • Biology: Biological mechanisms of splicing and regulation; biological functions such as the impact of splice variants on protein structure and biological pathways; phenomena such as nonsense-mediated decay and disease associations.
  • Splicing and Diseases: Identification and characterization of splice variants as a consequence of disease; diagnostic tools and therapeutic stratagies based on splicing pattern variations between normal and diseases states; classification of splice forms based on disease progression.
  • Databases, and Standards for the “Human Transcriptome Project”: Transcript repositories; data interchange formats; standards for annotating the transcriptome.

Talks will be selected from submitted long abstracts based on scientific quality and novelty. Selected speakers will be asked to present a 20-30 minute talk, and the talk abstract will be published in the AS-SIG proceedings.

Abstract submission deadline: May 1, 2006
Abstract acceptance notification: May 29, 2006

Bioinformatics Open Source Conference (BOSC)
Friday, August 4 and Saturday, August 5
9:00am - 6:30pm

The Bioinformatics Open Source Conference 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 2006 is shaping up to be an exciting conference. We have two keynote speakers this year. Amos Bairoch, of the Swiss Institute of Bioinformatics, will be speaking about his monumental efforts in the development of some of the most important Bioinformatics databases, software, and services in the world research community. Our second keynote speech features Alberto Davila, of the DBBM, Rio de Janeiro, Brasil, who has been a staunch advocate for researchers in developing countries faced with the challenge of addressing the impending genomics divide between them and the developed world.

Our agenda this year will consist of two sections per day, one for long talks from submitters chosen to present from a larger group of submitted abstracts, and one for smaller lightning talks and demos where presenters are allowed a few minutes to raise awareness of their work, software usage practices, or research needs. 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.

Abstract submission deadline: June 5, 2006
Abstract Acceptance Notification: June 19, 2006

Friday, August 4 and Saturday, August 5
9:00am - 6:30pm

The SIG meeting is organized by the BioPathways Consortium an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological networks.

As in previous years, the meeting will include plenary sessions, presenting invited talks on various aspects of computational pathway biology such as systems scale analysis of molecular networks, reconstruction of pathways from heterogenous types of high throughout data, the evolution of molecular pathways, and the representation and visualization of pathway data. Each plenary session will include several long invited presentations (45'), followed by a panel discussion on the 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 2006, please send a 200 word abstract describing your work to: bpc-cfp _at_ biopathways.org. Authors are encouraged to add URLs of web-based tools, and selected tools will be featured on the biopathways web site.

Abstract submission deadline: May 1, 2006
Abstract acceptance notification: May 30, 2006

Joint BioLINK and Bio-Ontologies Meeting (JBB)
Friday, August 4 and Saturday, August 5
9:00am - 6:30pm

This year, the two long standing ISMB SIGs, Bio-Ontologies and BioLINK will hold a joint two-day workshop. The meeting will consist of sessions that focus on the intersection of bio-ontologies and text mining, as well as individual sessions on the use of ontologies in the life sciences and on biomedical text mining.

The Bio-Ontologies SIG is concerned with research and applications of ontologies in the life sciences. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years there has been a surge of interest in their use within bioinformatics, particularly for providing computationally accessible annotation, or standard data models for complex microarray or pathway knowledge.

BioLINK focuses on the application of techniques from natural language processing, information extraction and information retrieval to automate knowledge discovery from biomedical text, and on linking text from a variety of sources with structured biomedical resources, such as curated biological databases and ontologies.

There is a natural synergy between the two SIGs: both fields are cross disciplinary; both exist against a large backdrop of computer science literature; and, finally, both are relatively new to the life sciences. More recently a more direct technological link is being formed as ontologists are using text-mining to test, check and build ontologies, while the knowledge in ontologies is being used to augment text-mining techniques.

BioLINK and Bio-Ontologies have previously held joint activities; this year we take this further, giving an excellent opportunity to explore work crossing the boundaries, while still supporting the needs of the respective communities.

Short papers (up to 4 pages) submission deadline: May 1, 2006
Poster-abstracts (1 page) submission deadline: May 1, 2006
Notification of paper/poster acceptance: June 10, 2006
Final version due: June 20, 2006