{ 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
ACCESS
THE STUDENTCOUNCIL NEWSLETTER
ACCESS
NEWSLETTER ARCHIVES
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
3dsig.weizmann.ac.il/
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)
www.biolinfo.org/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)
www.open-bio.org/wiki/BOSC_2006
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
BioPathways
www.biopathways.org
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)
www.jbb06.org
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 |
 |