Integrated Genomics, NCI SBIRs, Entelos, QuantumBio, Nature Methods, Nature Biotech, FuGE, Tripos, Partek, DNAStar

 

John Elling, president of Integrated Genomics, told BioInform this week that the company is seeing a “substantial” negative financial impact from a freely available software product developed at the Department of Energy’s Joint Genome Institute that it considers to be competing with its own ERGO bioinformatics platform.

 

Integrated Genomics has filed suit against two former staffers for allegedly breaking the non-compete clause of their employment contracts when they left the company in 2004 to join the bioinformatics staff at the JGI [BioInform 03-09-07].

   

In the suit, the company claims JGI’s freely available IMG (Integrated Microbial Genomes) system “directly competes with Integrated Genomics’ ERGO software,” and that the employees breached their employment contracts as well as their “duty of loyalty” when they joined the institute.

 

IG did not provide details in the suit of any negative economic impact it has suffered as a result of IMG’s availability, but Elling told BioInform this week that the company has lost some customers to the free product.

 

“We’ve had customers who used to subscribe to ERGO who have now found a replacement technology in the IMG software,” he said, adding that the company estimates that it risks losing “a third to a half” of its customer base.

 

Elling stressed that IG’s suit is against its former employees, not the JGI. “The world is free to develop competitive products,” he said. “We’re just concerned that it be done appropriately. We don’t want to compete with our own ex-employees when they’re obligated not to.”

 

 

 

Integrated Genomics has received a $70,000 Small Business Innovation Research grant from the Environmental Protection Agency to develop techniques to improve butanol production.

 

Butanol is a biofuel that offers some advantages to ethanol, IG said.

 

Integrated Genomics is working to lower the effects of solvent toxicity on important microbes that die in the butanol production process.

 

The company said it will use comparative genomic and molecular genetic approaches to develop microbial strains with higher butanol tolerance.

 

Integrated Genomics called early results “promising” and said that within about six months it hopes to find a partner that will help it scale up the technology.

 

 

 

The National Cancer Institute has launched a new Small Business Innovation Research program that will award $1.4 million in fiscal years 2007 and 2008 to support the development of software tools and other technologies that will enable “integrative cancer biology” research, a term that NCI defines as “understanding cancer as a complex biological system by utilizing both computational and experimental biology to integrate heterogeneous data sources and ultimately to generate predictive computational models of cancer processes.” 

 

According to the program announcement, available here, NCI plans to award between five and 10 grants to small businesses under the program, titled “Technologies and Software to Support Integrative Cancer Biology Research.”

 

The goal of the program “is to support the development of software, computational/mathematical methods, and laboratory technologies that will facilitate, accelerate, and/or enhance integrative cancer biology research,” NCI said in the program announcement. 

 

“Central to the integrative cancer biology approach is the construction and validation of sophisticated predictive computational models of cancer processes,” NCI said. “These models require the input and integration of large quantities of heterogeneous data ranging from molecular/cellular data to clinical information.”  

 

“However,” NCI added, “significant gaps remain in our ability to effectively model and understand complex cancer processes,” which will require new software tools, computational methods, and other technologies “to bridge these gaps and enhance ongoing integrative biology efforts.”

 

 

 

Entelos this week said that two of its customers have “reprioritized their internal clinical programs,” which will lead to a decrease in the company’s expected revenue for 2007.

 

The company said that the contracts have not been cancelled, but will result in a delay in the receipt of revenues from these customers “and in expected follow-on research being delayed into later periods.”

 

Entelos, which trades on the London Stock Exchange’s AIM market, did not provide details on the negative impact of the delayed contracts, but said that 2007 revenues will be “in line” with 2006 levels.

 

The company is scheduled to disclose its 2006 financial report on April 12.

 

James Karis, president and CEO of Entelos, said in a statement that the company plans to review the status of these delays on a quarterly basis. “In the meantime, we will be taking actions to align our costs with the now-expected business level,” he said.

 

 

 

QuantumBio said this week that the National Institute of Health has awarded it a Phase II Small Business Technology Transfer grant worth $950,000 to develop improved molecular modeling software for nuclear magnetic resonance analysis.

 

The project, titled “Enhancement and Deployment of the Quantum Mechanical NMR Pose Scoring Method,” will focus on commercializing quantum mechanically based refinement technologies developed in the lab of Kenneth Merz, a professor of chemistry at the University of Florida and chief scientific officer of QuantumBio.

 

QuantumBio said in a statement that Phase I of the project, which began in late 2006, “expanded on the early, academic development of the methodology and added technologies more applicable to the pharmaceutical and biotechnology industries.”

 

The goal for Phase II is to develop a user-friendly version of the application that will be integrated with the company’s Chemix molecular modeling platform.

 

 

 

 

In its current issue, Nature Methods clarifies its position on releasing software and algorithms upon publication.

 

An editorial in the March issue of the journal reminds authors that they are “required to make materials, data and associated protocols available to readers promptly on request,” and notes that “the definition of ‘materials, data and associated protocols’ includes custom-designed software necessary for the method’s implementation.” 

 

The journal outlines several “levels” of disclosure for software described in published papers. “If a software program is the focus of the report, we expect the programming code to be made available. Without the code, the software — and thus the paper — would become a black box of little use to the scientific community,” the editorial notes.

 

In other cases, where the software is only “an ancillary part of the method,” releasing the code “may not be a requirement for publication,” but the software or algorithms should still be made available to readers “in a usable form,” the editors write.

 

In addition, they note, “any restrictions to a program's accessibility must be specified at the time of submission, and editors will consider the amount of information made available, case by case, in consultation with the reviewers.”

 

 

 

An editorial in the March issue of Nature Biotechnology asks that authors of large-scale proteomics and molecular-interaction studies deposit their raw data in public repositories before submitting their manuscripts to the journal.  

 

“Beginning this month, Nature Biotechnology is recommending that raw data from proteomics and molecular-interaction experiments be deposited in a public database before manuscript submission,” the journal editors wrote.

 

“The lack of raw data sets associated with proteomics and molecular-interaction papers is a long-standing and pernicious problem,” according to the editorial, which notes that this dearth of public information “stymies the exchange, comparison and reanalysis of experimental results,” “inhibits the development of new algorithms and statistics,” and “undermines the ability of referees to fully evaluate the quality of data supporting a manuscript's conclusions.”

 

The Nature Biotech editors note that there are now a number of public databases that could serve as effective community repositories for this data, including the European Bioinformatics Institute's PRIDE and IntAct, the Institute for Systems Biology's PeptideAtlas, the University of Michigan's Tranche, and Rockefeller University’s GPMDB.

 

“For the moment we prefer PRIDE and IMEx databases (IntAct, DIP, MINT) because they not only are true databases with complex interfaces and accession numbers, but also offer a mechanism for referees to anonymously review submitted data sets,” the editors note.

 

“Although our new policy on data deposition is a recommendation rather than a requirement, we strongly urge authors to comply,” they add.

 

 

 

The National Cancer Institute said this week that it will host a caBIG developer “boot camp” in Rockville, Md., April 18-19.

 

The training session “will focus on the processes and tools used to create a caBIG compatible system,” NCI said. Participants will learn how to reuse existing metadata and models to generate UML models; how to map UML models to vocabulary concepts using the Semantic Integration Workbench; how to transform annotated UML models into caDSR metadata; and how to complete the caBIG compatibility review process.

Registration is available here.

 

 

 

The Human Proteome Organization’s Proteomics Standards Initiative has made the FuGE (Functional Genomics Experiment) model specification available for public comment here.

 

The public comment period “enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardization process,” PSI said in a statement, noting that “there is no requirement that people commenting should have had any prior contact with the PSI.”

 

 

 

Tripos shareholders this week approved the company’s plan to sell its Discovery Informatics business to Vector Capital and liquidate the company.

 

Vector Capital is expected to close the acquisition early next week.

 

The company plans to liquidate “following resolution of all corporate debts and obligations, and will commence approximately six months from now.”

 

 

 

A German government agency has purchased Partek Genomics’ software to analyze data from studies of cancer, heart disease, and lung disease, Partek said this week.

 

The National Research Center for Environment and Health, or GSF, will use Partek’s Genomics Suite with Affymetrix GeneChip data at its facility in Neuherberg.

 

GSF studies disease by focusing on genetic dispositions, environmental factors, and biological systems, Partek said.

 

Partek’s software suite analyzes gene expression, exon expression, chromosomal copy number, promoter tiling arrays, and SNP arrays.

 

Financial terms of the agreement were not released.

 

 

 

DNAStar said this week that it has signed a distribution agreement with GATC Biotech under which GATC will serve as the exclusive distributor for DNAStar products in Germany, France, Switzerland, and Austria.

 

The companies have already worked together for more than 10 years. The new agreement also gives GATC a site license for all DNAStar products that it will use as part of its DNA sequencing services business.

 

Additional terms of the agreement were not disclosed.