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Scientific Software, Biomax, Softberry, Supercomputer for Phylogenetics, Blueprint Signs, HSARPA Bioinformatics Grant, SRI International

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Agilent to Acquire Scientific Software for Undisclosed Amount

Agilent Technologies said last week that it plans to acquire chromatographic informatics company Scientific Software for an undisclosed sum.

Through the acquisition, Agilent said it aims to marry its analytical instrumentation, data systems, and services with SSI's chromatographic data systems and informatics. The deal would give Agilent one of the largest installed bases of chromatographic data systems — SSI has more than 120,000 installations — and a broad portfolio of laboratory informatics software in the life science and chemical industries, Agilent said.

SSI had annual sales of more than $18 million in 2004. Based in Pleasanton, Calif., the company employs about 80 people, most of whom are expected to join Agilent, the company said.

SSI's products include OpenLab, a web-based software framework that links chromatography data systems with enterprise content management and business process management; and EZChrom Elite, a chromatography data system with more than 60,000 licenses installed and the ability to control more than 290 instruments from 26 vendors.

Agilent has been the exclusive distributor of SSI's Enterprise Content Manager software since July 2004, and is currently using the technology in-house. An Agilent spokesperson said the unit expects to "expand the application" of this technology within the business group.

More broadly, Agilent said that following the acquisition it plans to "continue development and support of each of these product lines with a commitment to open systems, industry standards, and interoperability with other instrument hardware and software providers." Agilent also plans to support and enhance SSI Instrument's OEM partnerships, the company said.

Agilent did not say when it expects the acquisition to close, but the spokesperson said it will likely take one month.


Biomax, Softberry Partner on Sequence Analysis Package

Biomax and Softberry said last week that they will work together to integrate "a wide array" of Softberry's genome analysis programs into Biomax' Pedant-Pro sequence analysis suite and BioRS integration platform.

Further details of the collaboration were not provided.


SDSC Installs Supercomputer for Phylogenetics

The San Diego Supercomputer Center has installed a new cluster designed for phylogenetic research.

The 16-node, 8-way Fusion A8 by Western Scientific includes 128 Opteron processors each with 4 GB memory, for a total of 0.5 TB memory.

The cluster was purchased with a grant from the National Science Foundation in support of the CyberInfrastructure for Phylogenetic Research (CIPRes) project, a collaboration of biologists, computer scientists, statisticians and mathematicians at 19 institutions.

"The goal of the CIPRes project is to push the size limits of phylogenetic reconstruction from evolutionary trees of 100 to 1,000 species to 100,000 species and more," said SDSC project leader Mark Miller in a statement.

Researchers will be able to access the cluster through an allocation process. Details on obtaining access will be posted on the CIPRes website (http://www.phylo.org/) on Sept. 1.


Blueprint Signs Curation Agreement with Blackwell, Adds E. coli Data to BIND

The Blueprint Initiative said last week that it has entered into a data-curation agreement with Blackwell Publishing under which Blackwell will submit pre-publication manuscripts containing biomolecular interaction from the journal Immunology to Blueprint for curation into BIND (Biomolecular Interaction Network Database).

Separately, Blueprint said that it has added a protein interaction map for Escherichia coli generated by scientists at the University of Toronto, the Hospital for Sick Children, and Affinium Pharmaceuticals to BIND.

Blueprint began curating Immunology for BIND this month, and pre-publication relationships with 17 additional Blackwell titles "will be formalized by Blueprint in the coming weeks," the initiative said.

The agreement with Blackwell brings the number of journals committed to working with BIND on a pre-publication basis to 16.

The new data from the E. coli project, published in Nature in February ("Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 2005, 433:531-537), includes 435 molecular complexes, first identified by tandem affinity purification or sequential peptide affinity, involving 2,262 protein interactions.


U of Houston Gets HSARPA Bioinformatics Grant for Pathogen Detection

The University of Houston has been awarded a grant from Homeland Security Advanced Research Projects Agency to develop a method for identifying bacteria and viruses that could be used in bioterrorism.

HSARPA recently awarded the grant, which could be worth as much as $800,000, to a group of bioinformatics researchers at UH to study DNA probes for detecting emerging or engineered pathogens. The project, titled "Tools for Ultraspecific Probe/Primer Design," started in April as part of HSARPA's Bioinformatics and Assays Development Program.

HSARPA awarded around $300,000 for Phase I of the project, which is expected to last 10 months. Around $500,000 will be awarded for Phase II, "depending upon results and how the agency's program and budget evolves over the next year," the university said in a statement.

The project aims to deliver DNA probes that bind to organisms of interest and carry a highly detectable label to signal the presence of the organism. It will focus on choosing primers that detect — but don't mistakenly amplify — human or background-bacterial DNA.


NIGMS Extends SRI International's Biological Modeling Grant

SRI International said last week that the National Institute of General Medical Sciences had extended its grant to model complex mammalian signaling networks based on signaling of the epidermal growth factor receptor (EGFR).

SRI didn't disclose the amount of funding under the extension, but the NIH funding database lists an SRI project entitled, "Formal Methods Applied to Biological Signaling Networks," which aims to "automatically generate and display the network states of interactions possible when the EGFR is activated," as winning $387,858 in FY 2005.

In the project's first phase, SRI used its Pathway Logic pathway analysis software, based on the Maude computer language, to model biological entities and processes. In the second phase of the project, SRI will "increase the utility and predictive capabilities of Pathway Logic by enhancing the ability of researchers to interact with the models."

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