Blueprint to Redevelop STKE Connections Maps Database
The Blueprint Initiative said last week that it will develop, maintain, and populate the journal Science’s STKE (Signal Transduction Knowledge Environment) Connections Maps database.
The American Association for the Advancement of Science, which publishes the journal, contracted Blueprint for the task. The database — a component of the broader STKE portal that includes information on cellular signaling pathways and components provided by experts — was previously maintained by Stanford University’s HighWire Press.
Under the agreement, Blueprint will take on primary responsibility for the maintenance and curation of the Connections Maps database content and will add 12 to 15 new pathways and authorities, while also updating and editing existing entries for clarity and conformity.
A key component of the project is the Connections Maps Authority Data Entry System (CMADES), software developed by HighWire Press and owned by Stanford University that serves as the portal through which scientists enter data into the STKE Connections Maps system. Blueprint said it will redevelop and redesign the display aspects of the Connections Maps site, and will also integrate new features into CMADES.
HighWire will grant to Blueprint a non-exclusive, royalty-free worldwide license to CMADES in perpetuity, which will include the source code, architecture, user interfaces, and documentation, while retaining the intellectual property rights. Blueprint will operate and maintain CMADES, and any enhancements made by Blueprint will become the intellectual property of Stanford.
Software independently developed by Blueprint that can be integrated with CMADES will remain the intellectual property of Blueprint’s host, Mount Sinai Hospital.
The agreement is Blueprint’s second pact with Science. Earlier this year, the editors of Science and Nature pledged to support the deposition of molecular interaction records into Blueprint’s BIND database [BioInform 08-09-04].
Draft Chicken Sequence May Help Crack Human Code
The draft sequence of the wild chicken, Gallus gallus, which was published last week in the journal Nature, should provide new insights into the human genome, according to the bioinformatics team that led the analysis.
Ewan Birney of the European Bioinformatics Institute, whose Ensembl team performed much of the computational analysis of the genome, said in a statement that the chicken genome “is at the right evolutionary distance from humans” to provide information about the non-coding regions of the human genome.
The genomes sequenced so far, Birney said, have been either too closely related or too distant from humans. For example, he said, “the mouse genome gave us lots of useful information about coding regions but we were surprised at how much of the junk DNA was almost identical in mouse and human. This is because not enough time has passed since humans and mice diverged from their common ancestor. As a result, we gained very little new insight into the non-coding regions of the human genome.”
During the 310 million years since the human and chicken genomes diverged, however, functional regions, such as genes and their regulatory motifs, have been conserved, while “junk” DNA has been under no selective pressure, and is therefore distinct in the two genomes.
Using the chicken genome, researchers discovered strong conservation in regions of humans that were previously thought to be junk DNA, and were also able to pinpoint non-coding RNA genes, as well as the “control switches” within protein-coding genes.
Japan’s Infocom to Globally Market Gene Network Inference Software
Japan’s Infocom said last week that it will collaborate with OmniViz and Ariadne Genomics to globally market Auto Net Finder, a gene network inference software program it has developed jointly with researchers at the University of Tokyo.
Beginning in January, Infocom’s US partners will embed the software into OmniViz, OmniViz’s data visualization software, and PathwayAssist, Ariadne Genomics’ pathway analysis software, the company said.
Infocom said that Auto Net Finder uses a network inference algorithm based on graphical Gaussian modeling to analyze large numbers of inter-gene networks “in a practical time frame” on a PC.
The company said it expects to sell a total of 200 licenses globally in 2005.
Geospiza Partners with Helio on Systems Integration
Geospiza said last week that it has selected Helio Solutions, a Sun Microsystems reseller for life sciences, as a “preferred” hardware, instrument, and software systems integrator for the Geospiza Finch Sequencing Center software suite.
Helio and Geospiza said they will provide the Finch software running on Sun Fire SPARC and AMD-Opteron servers, and will work together to integrate these systems with customers’ existing equipment.
Boston Datacenters to Provide IT Hosting for BioTeam
Boston Datacenters, an Internet hosting facility, said last week that it will partner with informatics consultancy The BioTeam to provide computational hosting and co-location solutions for large-scale life science computing activities.
Currently located in Cambridge, Mass., The BioTeam will relocate its research lab space to Boston Datacenters’ secure facility in Charlestown, Mass.
“This is an opportunity for us to add hosted services to our service menu,” said Stan Gloss, managing director of The BioTeam, in a statement.
Inpharmatica Completes Financing
Inpharmatica said last week that it has completed the £13.8M ($26 million) third-round financing that it announced in November [BioInform 11-15-04].
Reed Elsevier Ventures — the VC arm of publisher Reed Elsevier — was the lead investor in the financing, contributing nearly £3 million.
Other investors included Abingworth, Advent, Gilde, GIMV, and 3i.
Axogenic, U of Sydney Awarded Aus$150K for Microarray Visualization Tools
Axogenic and the University of Sydney have been awarded an Aus$150,000 ($113,000) Australian Research Council Industry Linkage Grant to “examine new technologies for the interactive visualization of DNA microarray data” using artificial intelligence and signal-processing technology, according to a statement from Axogenic.
The three-year project will develop new technologies for human interaction with DNA microarray data — specifically, 2D and 3D interactive visualizations.
The new technologies will be integrated into Axogenic’s product line, the company said.
Uppsala Researchers Computationally Model Malaria Enzyme
A research team at Sweden’s Uppsala University said last week that it has used computational modeling to elucidate the structure and the function of a newly discovered enzyme of Plasmodium falciparum, the parasite that causes malaria.
Using the amino acid sequence of the enzyme, the Uppsala team ran computer simulations of all possible structures for the protein, along with combinations for how a small peptide might dock with the enzyme.
“In the past researchers have managed to predict reaction mechanisms on the basis of known structures, but this time we started from scratch,” said Johan Åqvist, an Uppsala researcher, in a statement.
The research was carried out under the RAPID (Rational Approaches to Pathogen Inhibitor Discovery) project at the Uppsala University Center for Structural Biology, Medical Chemistry, and Computer Chemistry.
The results of the study appear in the current issue of the journal Biochemistry.
Definiens and BioImage to Partner on High-Content Screening Software
Definiens and BioImage last week announced a worldwide, non-exclusive co-development and -marketing agreement to deliver high-content screening applications.
Under the terms of the agreement, BioImage will provide its Redistribution cell-based pathway screening assays in combination with Definiens’ Cellenger image analysis software.
The agreement also includes a co-development effort to create new applications specific to high-content screening.
Hopkins, U of Delaware, LANL Win $2.7M from DOE for Computational Biology Center
Johns Hopkins University, the University of Delaware, and Los Alamos National Laboratory have won a three-year, $2.7 million grant from the US Department of Energy to establish a multidisciplinary computational biology research institute, according to a Johns Hopkins newspaper.
The Institute for Multi-Scale Modeling of Biological Interactions will study biological systems at several levels, ranging from protein interactions to the behavior of complex networks. It will include more than 20 faculty and researchers from all three participating institutions, covering biophysics, chemistry, physiology, chemical and biomolecular engineering, biomedical engineering, mechanical engineering, and electrical and computer engineering.
The new institute builds on a program in computational biology established at Johns Hopkins in 1999. Besides research, the DOE grant will support a PhD program there.
Michael Paulaitis, a Johns Hopkins professor of chemical and biomolecular engineering, will serve as director of the new institute.