March 26, 2005

binfoPlasma - the bioinformatics encyclopedia is here!!!!

It brings us immense pleasure to announce the release of binfoPlasma the Bioinformatics Encyclopedia (

On binfoPlasma you can find:

1. Definitions to key terms in bioinformatics and related fields
2. Links to related terms in the encyclopedia
3. Suggested Reading : Links to sources of more information on each term (books, journals, research papers, web sites and other online resources, etc)

BinfoPlasma is an online encyclopedia "by the bioinformatics community, for the bioinformatics community".

As a binfoPlasman, you can

1. Search binfoPlasma for a specific term definition using the Search/Go option.
2. Browse through subject categories like Mathematics/Life Sciences/Statistics etc for terms.
3. Browse through alphabetical categories for terms
4. Contribute new term definitions to binfoPlasma's growing repository
5. Add more information (text or images) to existing term definitions
6. Share your views on specific topics with other binfoPlasmans through discussions on the "talk pages/user pages".

Visit binfoPlasma at today!!!!!

Once again extending a warm invitation to join us on our journey to bioinformatics excellence.

~Team binfoPlasma


Posted by Kevin Messner at 2:09 AM

March 24, 2005

NCBI Consensus CoDing Sequence (CCDS) Project

The Consensus CoDing Sequence (CCDS) project aims to identify a core set, or master list, of human protein-coding regions that are consistently annotated and of high quality. CCDS was made public on March 2, 2005 and is available at

The long-term goal is to support convergence toward a standard set of gene annotations on the human genome.

The CCDS set is built by consensus among the collaborating members, which include:
- European Bioinformatics Institute (EBI)
- National Center for Biotechnology Information (NCBI)
- University of California, Santa Cruz (UCSC)
- Wellcome Trust Sanger Institute (WTSI)

The Approach:
- Compare NCBI vs Ensembl and Vega annotation of coding sequence regions.
- Identify those that have identical locations on the genome.
- Quality tests are applied to the initial candidate set
- Candidates that fail tests are rejected
- Those that pass QC are given a CCDS ID and version
- The CCDS will be tracked through annotation and genome sequence updates.
- Rejected candidates may be added to the CCDS set in a future release. This is dependent on:
- additional transcript data becomes available
- continued improvements to automatic annotation methods
- curation

Assessing Quality. CCDS status is conservatively applied:
- Any member of the collaboration may contribute to quality testing.
- Any member of the collaboration may unilaterally 'reject' an annotation from the candidate set.

Quality assessment tests may change over time. For the first release, these measures included:
- Consensus splice sites
- Valid start and stop codons
- No internal stops - translation of genome sequence coordinates does result in the protein expected
- Protein homology
- Supporting transcripts
- Genome conservation
- Pseudogene unlikely

The genome browsers available at each of the project collaborators' web sites contain links to CCDS records. The links are displayed in various ways, depending on the browser. In MapViewer, if a gene has a CCDS, you will see that acronym in the links that are displayed when the Genes_seq map is the master map.

Posted by Kevin Messner at 2:28 AM

March 14, 2005

FEMS journals to be published by Blackwell beginning in 2006

The Federation of European Microbiological Societies (FEMS) and Blackwell Publishing have announced a new publishing partnership. The Federation selected Blackwell Publishing to publish its five journals: FEMS Microbiology Letters, FEMS Microbiology Reviews, FEMS Microbiology Ecology, FEMS Immunology and Medical Microbiology, and FEMS Yeast Research. Blackwell will take over publication of the journals from Elsevier in January 2006.

Posted by Kevin Messner at 2:31 AM


BiosciEdNet (BEN) provides access to resources from BEN Collaborative partner organizations and is managed by the American Association for the Advancement of Science (AAAS). Over 3,500 reviewed resources covering 76 biological sciences topics are now available.


Posted by Kevin Messner at 12:05 AM is a website for students just being introduced to the field. Included on the website are slides that cover introductory molecular biology, introductory algorithmics, and applications of algorithms to molecular biology.

The site also functions as a class website: rather than each instructor maintaining a separate website, can host all classes. Discussion groups, chat rooms, online quizzes, creating assignments, and disseminating grades are some of the features of this free service. It has powerpoints, practical problems, implementation problems, solutions, etc as well as a large list of Bioinformatics Professors worldwide with links to their sites (about 200 links). Finally, we are building a comprehensive directory of the bioinformatics community and presenting this as a portal from


Posted by Kevin Messner at 12:01 AM

March 11, 2005

European Journal of Biochemistry changes name to FEBS Journal

EJB. European Journal of Biochemistry has changed its title to:

FEBS Journal. ISSN: 1742-464X. Full text from 2005 volume 272 issue 1.

Posted by Kevin Messner at 2:17 AM

March 5, 2005

Evolutionary Bioinformatics Online: Call for papers

Evolutionary Bioinformatics Online is an international peer-reviewed Open Access journal focusing on evolutionary bioinformatics. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context - history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. Being an Open Access journal means that the papers published are freely available to everyone via the Internet. Further, our authors retain copyright of their work. We do not charge our readers any form of subscription, but we normally ask our authors to make an article-processing payment when papers are accepted for publication. However for our launch issue we are waiving all article processing payments. Fees will apply for subsequent issues. Institutions can also support Evolutionary Bioinformatics Online and the other Libertas Academica Open Access journals by becoming a member institution. An unlimited number of authors from member institutions can publish papers without paying the article-processing fee. Details are available at our website. For detailed author instructions, go to Author Instructions. Please do not hesitate to contact me if you have any comments or questions. Yours sincerely Tim Hill Publisher Libertas Academica Ltd * This is a new title and is the official journal of THE BIOINFORMATICS INSTITUTE.
Posted by Kevin Messner at 2:01 AM