Informatics Groups Pit Software, Data, and IT Against SARS Crisis
Last week, a number of bioinformatics companies and research groups announced a range of contributions to research projects worldwide seeking diagnostics and treatments for severe acute respiratory syndrome:
InforSense of London said it had donated its discovery informatics platform, and a range of life science applications, to the Shanghai government for use in their research initiative to discover a vaccine against SARS.
The software donation includes the company’s Kensington Discovery Edition enterprise discovery platform and the KDE GeneSense ontology-based genomics data interpretation solution, jointly developed by InforSense and Affibody AB.
The donated software will be installed at the Shanghai Center for Bioinformation Technology, which will provide technical support to SARS researchers.
Meanwhile, Belgium-based vaccine development company AlgoNomics last week posted SARS data on its website “in order to contribute to a rapid development of a vaccine against SARS.”
The data, available at www.algonomics.com, is a list of CTL (cytotoxic lymphocyte) epitopes for SARS — fragments of the SARS virus that can contribute to a strong SARS vaccine, according to the company.
The company identified the SARS epitopes using its computational platform Epibase, which uses three-dimensional models of receptors of the human immune system to predict possible epitopes.
In addition, the Hindustan Times reported that scientists at India’s Institute of Genomics and Integrative Biology (IGIB) have assigned functions to six proteins of the SARS virus using a software tool called PLHost (Peptide Library-based Homology Search Tool), which compares the protein sequences of several organisms and reports unique peptide sequences.
According to the report, Samir Brahamachari, director of the IGIB, said that three of the proteins have a role in viral replication and the other three have “some biochemical functions.” The team has submitted a paper on its work to a scientific journal.
Finally, Artificial Life, an intelligent software robot firm that recently moved its offices to Hong Kong, said it plans to shift more of its resources to life science com- puting applications, partly in response to the SARS crisis. “We will release a new web service based on distributed computing dedicated to fighting the virus very soon,” said Eberhard Schoeneburg, CEO of Artificial Life. The company added that the SARS outbreak, which has spread through its target markets of Hong Kong, the People’s Republic of China, Taiwan, and other parts of Asia, “may have a lasting negative effect on the economy of these target markets and therefore may also have a negative impact on the company’s overall business prospects and revenues for the upcoming quarters and the current fiscal year 2003.”
IBM, RIKEN Collaborate on T. thermophilus Bioinformatics, Grid Technology
Japan’s Institute of Physical and Chemical Research (RIKEN) and IBM Japan have agreed to collaborate on a bioinformatics research project that involves the RIKEN Genomic Sciences Center, RIKEN’s Structurome Research Group, and IBM’s Tokyo Research Laboratory.
RIKEN and IBM Japan will jointly develop computational methods to analyze gene expression data for RIKEN’s Thermus thermophilus project, which aims to study the functions of an entire cell at the molecular level by analyzing higher-order structures and functions of most of the proteins of the thermophilic bacterium.
IBM’s Tokyo Research Laboratory will provide computational technology for gene expression analysis, gene prediction, and gene sequence analysis, as well as genetic structure and gene network analysis technology to support the T. thermophilus project.
Results of the joint research will be made available through OBIGrid (Open Bioinformatics Grid), a grid-computing network for bioinformatics researchers in Japan launched in 2002 (www.obigrid.org).
RIKEN and IBM plan to develop additional computational tools to enable the analysis of data from the T. thermophilus project within the grid infrastructure, as well as an authentication mechanism to improve security for researchers using the grid framework.
Electric Genetics Secures VC Funding
Capetown, South Africa-based Electric Genetics said last week that it had secured 10 million rand (US$1.3 million) from Bioventures, South Africa’s first biotechnology venture capital fund.
CEO Tania Broveak Hide said the funding would help Electric Genetics hire more sales and R&D staff.
“The company is now afforded the stability we need to meet the narrow window of opportunity we are so often faced with, particularly when it comes to intro- ducing new products into the rapidly changing biotechnology marketplace,” said Hide in a statement.