{ 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.
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NEWS FROM THE FIELD
News Title: Between CASPs
Public Meeting 2006 – May 1
Date Posted: Apr 05, 2006
In contrast to the CASP (Critical Assessment of Structure Prediction)
meetings that are restricted to groups that participate in the challenge,
i.e. predictors, this one day meeting (May 1) will present the CASP
findings to the public. Registration for the meeting is free, however,
we have only a limited number of slots (thus, if interested, register
soon).
URL: www.forcasp.org/
News
Title: Training Course on Bioinformatics and
Functional Genomics Applied to Tsetse Fly - Vector of Human African
Trypanosomiasis
Date Posted: Apr 3, 2006
An initiative sponsored by UNICEF/UNDP/World Bank/WHO Special Programme
for Research and Training in Tropical Diseases and The South African
Medical Research Council. To be held 3 – 14 July 2006 at South
African National Bioinformatics Institute (SANBI), University of
the Western Cape, Cape Town, South Africa. This is an initiative
designed as part of the activities of WHO/TDR in collaboration with
the SANBI, to promote capability of scientists from endemic countries
to exploit genome resources that are rapidly being developed for
Glossina, the vector of Human African Trypanosomiasis. The objective
is to introduce the participants to basic information on the application
of genome information and the potential for development of functional
genomics tools that can be applied in vector control. The regional
course will run over 12 days, with a focus on bioinformatics (computational
biology) concepts and implementations relevant to functional genomics
of the Tsetse fly, with lectures as well as hands-on computer sessions.
Emphasis will be placed on the analysis, application and translation
of molecular resources being developed in the run-up to the full
sequencing of the tsetse fly genome. Students will be trained to
use existing Bioinformatics tools to analyze public and in-house
data in the context of genomic data. Trainees will receive continued
assistance and support from SANBI and future access to available
resources. PhD students, postdoctoral fellows and young faculty
members at the beginning of their careers who are active in tsetse
fly research, who can demonstrate clear ability to exploit bioinformatics
and post-genomics tools for their future research, are highly encouraged
to apply for this course. Up to fifteen candidates will be selected
from scientists in African endemic countries. There is no registration
fee for the course. Successful applicants will be provided training
materials, economy round-trip airfare, accommodation and food during
the entire period of the training course.
Application deadline: May 2, 2006. For further information please
see the course website: www.sanbi.ac.za/mrc/tdr2006/index.html
News Title: National Academies of Science
Release “Computing and Biology” Report
Date Posted: Mar 31, 2006
The first ever NAS analysis report on computing and biology is now
available at www.doegenomestolife.org/pubs/NRCComputingandBiology/index.
Computing and
Biology is not simply a captive report of a single agency, but
at 400 pages a tome of great impact across all areas of computational
biology. As one of the sponsors of the report, the U.S. Department
of Energy has made a PDF copy of the report available in full and
for free at the above URL. An Executive Summary and smaller versions
are also being developed for future release.
News Title: AFP 2006: call
for participation
Date Posted: Mar 30, 2006
Call for participation: Automated Function Prediction (AFP) 2006
August 30 - September 1, 2006 University of California San Diego,
CA, USA. AFP 2006 will feature three exciting days of discussions
on computational function prediction in molecular biology. The meeting
program includes plenary talks delivered by leading researchers
in the field, a special discussion panel on gene and protein annotation
and a poster session. Talk abstracts will be published as an article
in a special section of BMC Bioinformatics. Speakers include: Russ
B. Altman, Stanford University; Philip E. Bourne, University of
California, San Diego, USA; Steven E. Brenner, University of California,
Berkeley, USA; Terry Gaasterland, Scripps Institute of Oceanography,
La Jolla, USA; Adam Godzik, Burnham Institute for Medical Research
and University of California, San Diego USA; Christos Ouzounis European
Bioinformatics Institute, Cambridge, UK; Anna Tramontano, University
of Rome, "La Sapienza", Rome, Italy; Shoshana Wodak, Hospital
for Sick Children, and Departments of Biochemistry and Medical Genetics,
University of Toronto, Canada.
URL: biofunctionprediction.org/
News Title: Vital-IT: Integrated
Computational Genomics Resource
Date Posted: Mar 20, 2006
The Vital-IT high performance computing facility of the Swiss Institute
of Bioinformatics, through funding provided by the EU 6th Framework
Programme, is pleased to invite proposals for cost-free use of its
"Integrated Computational Genomics Resource" (ICGR) from
individuals, institutions and SME’s from any of the EU Member
and Associated States (excluding Switzerland). The ICGR facility
comprises several compute clusters and a large storage system which
mirrors all the internationally-important genome, transcriptome
and proteome sequence repositories, as well as providing access
to a range of locally-developed specialized databases. Visiting
Developer Programme: Visiting developers may stay for a period from
one week to two months at Vital-IT in Lausanne, Switzerland. Their
activities may include the development of new software for HPC applications
in life-science, parallelization and optimization of existing software,
and large data analysis projects making use of the rich database
collection offered by this facility. Vital-IT staff will provide
technical support for projects under this programme, and limited
travel support is available. Remote Access Programme: Remote access
to the HPC infrastructure and computational genomics environment
will be provided. Successful applicants will have a user account
on Vital-IT and adequate CPU and disk storage quotas to carry out
the proposed project. Periodic training courses will be offered
to familiarise remote users with the use of Vital-IT’s facilities.
Further information, and an Application Form, are available at www.vital-it.ch/vitalit-ICGR.htm.
All proposals will be reviewed by a panel of academic and industry
experts. The programme begins on April 1, 2006. Applications will
be reviewed regularly and every effort made to give applicants a
timely decision.
News
Title: International Journal of Data Mining
& Bioinformatics
Inaugural Issue
Date Posted: Mar 10, 2006
Mining bioinformatics data is an emerging field at the intersection
of its two composite disciplines, bioinformatics and data mining.
The objective of the International Journal of Data Mining and Bioinformatics
(IJDMB) is to facilitate collaboration between data mining researchers
and bioinformaticians by presenting cutting edge research topics
and methodologies in this emerging area. The journal’s perspective
acknowledges the inter-disciplinary nature of the research in data
mining and bioinformatics and provides a unified forum for researchers,
practitioners, students, and policy makers to share the latest developments
in this fast growing, multidisciplinary research area . IJDMB aims
to publish articles highlighting the latest research and developments
in the areas of bioinformatics, data mining and knowledge discovery,
techniques for integrating and interpreting bioinformatics data
sets, and methods for improving the effectiveness, efficiency, and
quality of bioinformatics data analysis. The major objective of
IJDMB is to stimulate new multidisciplinary research and the development
of cutting-edge data mining methods, techniques and tools to solve
problems in bioinformatics. The journal aspires to help readers
understand the state-of-the-art techniques, algorithms and methods
used in bioinformatics data gathering, data pre-processing, data
mining and data management, and disseminate these ideas to a large
audience. The intended audiences include data mining researchers
and practitioners; bioinformatics specialists in academia and industry;
chemists; systems and molecular biologists who rely on computer
tools for data integration, management and analysis; mathematicians
and statisticians interested in model development and simulation
for life science data; computer scientists; and post-graduate students
with an interest in developing or applying novel algorithms and
methods to biology or biomedical domains. The five papers that comprise
the inaugural issue of IJDMB are excellent examples of the type
of high-quality submissions that the journal seeks to publish .
“Adaptive Fuzzy Association Rule Mining for Effective Decision
Support in Biomedical Applications,” by Yuanchen He, Yuchun
Tang, Yan-Qing Zhang and Rajshekhar Sunderraman “Text Analysis
of MEDLINE for Discovering Functional Relationships among Genes:
Evaluation of Keyword Extraction Weighting Schemes,” by Ying
Liu, Shamkant B. Navathe, Alex Pivoshenko, Venu Dasigi, Ray Dingledine
and Brian J. Ciliax “Bi-Level Clustering of Mixed Categorical
and Numerical Biomedical Data,” by Bill Andreopoulos, Aijun
An and Xiaogang Wang “State-space Approach with the Maximum
Likelihood Principle to Identify the System Generating Time-course
Gene Expression Data of Yeast,” by Rui Yamaguchi and Tomoyuki
Higuchi “Kernel Design for RNA Classification Using Support
Vector Machines,” by Jason T.L. Wang and Xiaoming Wu I hope
that our readers find these articles as informative and stimulating
as I did, and I thank the authors for contributing their research
and writing to ijDMB. I would also like to offer my special thanks
to everyone who has been working hard behind the scenes of ijDMB
: Our editorial board members who have devoted their valuable time
and thought to creating a high-quality resource for our intellectual
community; Inderscience Publishers, whose experience has guided
us from the beginning; the iSchool at Drexel, whose support for
and dedication to the advancement of scholarship has been unparalleled;
and the efforts of all the other support staff, consultants and
organizations without whom this journal would not have been possible.
I thank you all for your continued support. Finally, I would like
to extend my thanks outward, to all the members of our intellectual
community. Without you—the researchers, the scientists, the
teachers, the students, the curious—there would be no need
for ijDMB or publications like it, and the world would be a lesser
place as a result. If you need a complementary copy of the inaugural
issue, please send an email with your mailing address to ijdmb@cis.drexel.edu.
News
Title: 2007 Career Awards at the Scientific
Interface
Date Posted: Jan 16, 2006
2007 Career Awards at the Scientific Interface $500,000 award over
five years for postdoctoral fellows Deadline: May 1, 2006 Burroughs
Wellcome Fund is accepting electronic applications only.
- These portable awards support up to two years
of advanced postdoctoral training and the first three years of
a faculty appointment
- Candidates must hold a Ph.D. in mathematics,
physics, biophysics, chemistry (physical, theoretical, or computational),
computer science, statistics, or engineering and must not have
accepted, either verbally or in writing, a faculty appointment
at the time of application
- Candidates should propose innovative approaches
to answer important biological questions
- BWF encourages proposals that include experimental
validation of theoretical models
- Degree-granting institutions in the U.S. and
Canada may nominate up to two candidates
Complete program information, eligibility guidelines,
and application instructions are available on BWF’s website
at www.bwfund.org or by telephone
at 919/991.5100 or by fax at 919/991.5160 or by mail to Post Office
Box 13901 21 T.W. Alexander Drive Research Triangle Park, NC 27709-3901.
The Burroughs Wellcome Fund is an independent private foundation
dedicated to advancing the biomedical sciences by supporting research
and other scientific and educational activities.
URL: www.bwfund.org
News
Title: HFSP: Funding Opportunities for International,
Interdisciplinary Research Projects in the Basic Life Sciences
Date Posted: Jan 13, 2006
The Human Frontier Science Program is an international funding program,
supported by Australia, Canada, France, Germany, Italy, Japan, Republic
of Korea, Switzerland, U.K., U.S.A. and the European Union. HFSP
promotes international collaboration through a prestigious program
of grants which support interdisciplinary research in the basic
life sciences. The program is intended to bring teams of scientists
from various fields such as physics, mathematics, chemistry, computer
science and engineering together with biologists to open up new
approaches to understanding complex biological systems. Teams applying
for research grants must first submit a letter of intent online.
The next deadline for our long-term and cross-disciplinary fellowship
program is 31 August 2006. Guidelines for award year 2007 will be
available on our website in May 2006 and pre-registration and electronic
application forms in early July 2006. See www.hfsp.org
for further details.
News
Title: Introduction to Ontologies for the
Biosciences
Date Posted: Dec 28, 2005
The University of Manchester, UK, has received funding to develop
a new distance learning course, Introduction to Ontologies for the
Biosciences. This course is being developed by members of the Bio
and Health Informatics group at The University of Manchester. It
will be an additional option on the existing online programme in
Bioinformatics. The current online modules are:
- Introduction to Molecular Biology for Computer Scientists
- Introduction to programming (C or Java)
- Intermediate Java
- Introduction to Bioinformatics
- Introduction to Microarray Data Analysis
- Theory and Applications in Bioinformatics
- The Bioinformatics of Protein Structure
- The Science of Proteomics
- Medicinal Chemistry (provided by the University of California,
San Diego)
- Molecular Modelling and Structure-based Drug Design
- Biocomputing
- Object-oriented analysis and design with UML
URL: www.cs.man.ac.uk/biomed/bioinformatics.html
News
Title: FASEB Directory of Members 2006
is Now Available
Date Posted: Dec 21, 2005
The FASEB Directory of Members 2006 is now available for purchase
through the FASEB website at www.faseb.org. This version of the
directory comprises an alphabetical listing with contact information
for nearly 60,000 FASEB Society Members. Click here to purchase
your copy of the 2006 Directory of Members. Data in the directory
reflects information received by October 25, 2005. For a number
of years several FASEB societies have provided a print version of
the directory to their members. Due to prohibitive costs, the print
directory will no longer be provided to those members. The limited
interest of FASEB Member Societies to purchase print copies of the
directory in bulk has resulted in FASEB’s decision to focus
on enhancing the online directory while making the print available
through individual purchase. The electronic version of the directory
is accessible to all FASEB society members at. For additional information,
please contact the FASEB Office of Publications at directoryinfo@faseb.org.
News
Title: Search Tool for Life Sciences
Researchers
Date Posted: Oct 21, 2005
A community based search tool for life scientists was recently launched
and can be found at www.siphs.com.
Siphs aims to simplify the process of searching for relevant scientific
content by leveraging the combined knowledge of researchers world
wide. Traditional information search tools rely upon cataloguing,
indexing, and ranking a wide variety of scholarly sources found
on the web. Unlike traditional search engines, Siphs search queries
are tagged with “areas of expertise” and then distributed
to scientists who are members of the Siphs community for review.
The tool was designed by taking a clue from the offline world in
that the most relevant search results can be found by asking the
people with the right set of experiences. For more information,
please visit www.siphs.com.
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