{ 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


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
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.