Bio-Rad Integrates ADMET Modeling Tools with Aureus Databases
Bio-Rad said last week that is integrating its KnowItAll ADME/tox software with Aureus Pharma's ADME/Drug-Drug Interaction and hERG Channel AurScope databases.
KnowItAll customers will be able to use data in the Aureus knowledgebases to design in silico models for preclinical research.
Bio-Rad's software partner Equbits is also participating in the collaboration, enabling its Foresight ADME Tox Edition software to analyze the structure-activity relationships of the molecules in the Aureus databases. The Foresight software is based on a support vector machine approach, and can be used to build a prediction model that can act as input in the KnowItAll environment, Bio-Rad said.
The AurScope ADME/DDI database contains information on 7,045 molecules from 4,700 journal articles, while the hERG Channel database includes information about 2,540 molecules from 650 journal articles.
"One of the biggest problems with building good models is the data," said Greg Banik, general manager of Bio-Rad's informatics division, during a press conference at DDT last week. "We're very excited about modeling hERG toxicity using the Aureus database."
Tripos, MDL to Integrate Isentris and Benchware Products
Tripos and Elsevier MDL said last week that they will partner to integrate Tripos' Benchware suite of laboratory informatics software with MDL's Isentris platform.
Under the agreement, Tripos has become a "strategic member" of the MDL Isentris Alliance, and Elsevier MDL has joined the Tripos Alliance Program as a "global strategic partner."
Tripos will develop web services compatible with the Isentris platform, including a service based on Tripos' Concord product for 3D molecular structure generation. Tripos' new Benchware Notebook will also be compatible with MDL's Isentris and ISIS, and will use the MDL Draw chemical-rendering software as its "preferred" sketching program.
The agreement follows on the heels of Tripos' announcement last month that it was partnering with another one of its primary competitors, when it joined Accelrys subsidiary SciTegic's independent software vendor partner program [BioInform 07-04-05].
The shift to embrace one-time rivals as partners is part of a strategy to "make it easier to use Tripos tools," Bryan Koontz, senior vice president and general manager of discovery informatics at Tripos, told BioInform.
John McAlister, Tripos president and CEO, agreed. The company's newly released Benchware Notebook will only be successful "if it can reach the relevant data," he said. Citing MDL's franchise of registry systems, McAlister said that it made sense to ensure that Tripos customers who have already invested in MDL's products could easily access that data.
Novell, HP Tap TurboWorx as Workflow Provider for Validated HPC Stack
TurboWorx said that it has completed the integration and interoperability testing required for inclusion in the Novell Validated Configuration Program, an initiative that Novell and HP kicked off in early August to ensure that certain products run optimally on HP BladeSystem clusters running SUSE Linux Enterprise Server.
According to a statement from TurboWorx, the Novell initiative "represents a significant advance over ordinary industry certification programs that confine themselves to ensuring a particular application or hardware platform performs stand-alone — but not necessarily in conjunction with other components."
Alter said that TurboWorx has also evolved its partnership with IBM to include on-demand services using IBM's BlueGene supercomputers as part of its distributed workflow offering. Customers can use this feature to build informatics workflows that can access BlueGene on a fee-for-service basis when they need extra computational power for certain tasks.
MiraiBio, Redasoft Enter Integration and Co-Development Partnership
MiraiBio, a division of Hitachi Software Engineering America, and Redasoft announced an agreement to integrate MiraiBio's DNASIS MAX sequence-analysis software with Redasoft's Visual Cloning molecular cloning design package.
The companies said that upgraded versions of the products with the integration capability will be provided free of charge to existing customers.
The upgrades — DNASIS MAX 2.6 and Visual Cloning 3.2 — will be released later this month, the companies said.
Semantic Web for Life Sciences Seeks Pharma Involvement
The World Wide Web Consortium's Semantic Web for Life Sciences working group is seeking partners from the pharmaceutical industry to help drive the effort forward, Eric Neumann, a consultant working for the initiative, told BioInform.
Neumann demonstrated an updated version of the BioDash semantic browser — which is able to dynamically integrate clinical, gene expression, toxicity, and chemistry data into a single view — during the informatics track of DDT.
Neumann said that semantic web technologies should be an effective method for merging clinical trial data with toxicogenomics data and other biological information. As proof of principle, the working group has converted a dataset from Gene Logic's GeneExpress database to RDF format, and has also written an RDF translator for NCBI's PubChem small-molecule database. Neumann said that it is relatively easy to write RDF translators for XML and other formats.
Interest in semantic web technologies appears to be growing in the life science community, but Neumann said that formal involvement from the pharma will help the working group ensure that it is developing tools that are of interest to the industry. "We need to make it clear what is demonstrable," he said.
— Bernadette Toner ([email protected])