Plans are underway to celebrate the 10th birthday of the EMBOSS software package this summer, now that its developers have received word that their funding is secure for at least three additional years — a decision that ends two years of uncertainty around the popular open source bioinformatics suite.
In April, the European Bioinformatics Institute announced that the UK’s Biotechnology and Biological Sciences Research Council had agreed to support the project. While the amount of the funding was not disclosed, project leader Peter Rice says that it is enough to support two developers at the EBI, in addition to himself, for three years as of May 1.
But the funding means more than just three jobs. Rice says the support guarantees that the core software will remain stable, which should encourage developers from academia and industry to begin contributing to the open source project and eventually expand its capabilities.
“We hope in coming years that we’ll have a lot more outside collaborators,” Rice says. “Obviously, nobody wanted to collaborate too much if we could disappear in a few months. It wasn’t a great time to set up collaborations. … Now we’ll be really looking to see who’d like to use EMBOSS as the basis for development.”
Since the UK’s Medical Research Council in 2004 closed the bioinformatics division of the Rosalind Franklin Center for Genomics Research, which housed the bulk of the EMBOSS development team, the three core developers have managed to keep the project alive through “interim” funding from the EBI, but the effort has largely been “on hold,” according to Rice.
The impact of this holding pattern on users and collaborators is unclear, but it appears that many remained loyal to the effort despite the funding uncertainty. Rice notes that letters of support from dedicated EMBOSS users across the world helped convince BBSRC to fund the project.
— Bernadette Toner
The European Bioinformatics Institute is planning a format change for the EMBL Nucleotide Database scheduled to take place this month. In a notice to users, EBI said that the “ID” line will have a different structure and the “SV” line will be removed beginning with release 87 of the database.
Ariadne Genomics joined the Affymetrix GeneChip-compatible Applications Program and says that its PathwayStudio 4.0 pathway analysis software has earned GeneChip-compatible status.
Organizers of the BioCreative (Critical Assessment of Information Extraction Systems in Biology) text-mining challenge have issued the first call for participation in BioCreative II, which will be held in October, with the workshop to be held next spring. Training data will be released this month. The evaluation’s three tracks will focus on finding the mentions of genes and proteins in sentences drawn from Medline abstracts; producing a list of Entrez Gene identifiers for all the human genes and proteins mentioned in a collection of Medline abstracts; and identifying protein-protein interactions from full text papers for curation into the IntAct and MINT databases.
GeneGo and XB TransMed Solutions integrated their platforms — MetaCore pathway software and XB-BioIntegration Suite translational medicine software — to allow shared customers to capture, manage, and mine integrated clinical, preclinical, and molecular data.
US Patent 7,031,847. Method and apparatus for displaying gene expression patterns. Inventors: Yasuyuki Nozaki, Ryo Nakashige, Tsunehiko Watanabe, and Takuro Tamura. Assignee: Hitachi Software Engineering. Issued: April 18, 2006.
This patent “discloses a method for displaying gene expression patterns of multiple genes that change according to the experiment cases, where a first axis represents the genes and a second axis represents the experiment cases,” according to the abstract.
US Patent 7,031,846. Method, system, and computer software for the presentation and storage of analysis results. Inventors: Shantanu Kaushikkar, Teresa Webster, Rui Mei, and Linda McAllister. Assignee: Affymetrix. Issued: April 18, 2006.
This patent describes a computer program “that processes emission intensity data corresponding to probes of a biological probe array. [It] includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. … The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls.”
Decline in Compugen’s first quarter revenue compared to the same quarter a year ago, down to $200,000 from $481,000. Meanwhile, R&D spending decreased 22 percent and net losses declined 19 percent.