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Sophic Systems Alliance, Avian Flu Sequence, BioImagene, Entelos, Pharsight, InforSense, SciDAC, Massively Parallel Technologies, Sage-N-Research, BioSolveIT, Aureus Pharma, SoftGenetics

Sophic Achieves Bronze caBIG Certification, Adds Four Biomax Products to Offering
Sophic Systems Alliance said last week that it has achieved bronze caBIG certification for the Biomax BioXM Knowledge Management System. The company has also added four Biomax software products to its GSA Schedule contract, which allows it to sell its software directly to federal government agencies.
Bronze caBIG certification indicates that the company’s software is compatible with tools and services developed under the National Cancer Institute’s Cancer Biomedical Informatics Grid initiative. There are three levels of compatibility — bronze, silver, and gold — with bronze compatibility being the least restricted and targeted toward commercial bioinformatics vendors [BioInform 04-28-06]. 
Sophic and Biomax are the first commercial companies to achieve bronze compatibility, Sophic said in a statement.
The companies are now eying silver compatibility “Based on our review of the NCI Silver standards, it should be very straightforward to install, configure, and implement a Silver compliant installation of BioXM,” Klaus Heumann, president and CEO of Biomax Informatics, said in a statement. “We are actively discussing with NCI making a BioXM web-services API open source to support the caBIG initiative.”
Sophic also said it plans to add four Biomax software products to its GSA contract: BioXM, the BioRS Data Integration and Retrieval System, the BioLT Linguistics System, and the Oncology Knowledge Base.

International Consortium Formed to Share Avian Flu Data …
An international team of researchers has formed a consortium designed to improve the sharing of influenza data, analyze data findings jointly, and publish the results collaboratively.
The consortium, called the Global Initiative on Sharing Avian Influenza Data, has pledged to submit sequence, clinical, and epidemiological data related to influenza to GenBank, EMBL, and DDBJ. GISAID has established policies for rapid and complete data release modeled upon those already established for other initiatives, such as the HapMap project.
The Initiative intends to “work around restrictions which have previously prevented influenza information sharing,” according to a GISAID statement.
The consortium is open to all scientists, “provided they agree to share their own data, credit the use of others’ data, analyze findings jointly, and publish results collaboratively.” The consortium plans to publish data as soon as possible after analysis and validation.
Additional information about GISAID is available here.

… As CDC and APHL Release Data on 650 Influenza Genes
The Centers for Disease Control and Prevention said recently that it is collaborating with the Association of Public Health Laboratories to submit sequence data for 650 influenza virus genes in GenBank.
The initiative aims to provide “greater access to data on a variety of influenza virus samples obtained from patients in the United States, including avian influenza H5N1 if it should arrive here,” according to a CDC statement.
CDC said it plans to provide genetic information for several hundred influenza viruses per year under the collaboration. The sequence data will be available via Genbank as well as through the Influenza Sequence Database hosted by Los Alamos National Laboratories.
The information will include viruses from the annual flu season in the United States, any animal influenza viruses that infect humans, and any novel strains that may emerge such as avian influenza H5N1.
Previously, the influenza sequences were only available to a small number of influenza researchers working with the World Health Organization to recommend which influenza viruses should be included in influenza vaccines around the world.
APHL, a national association representing public health laboratories, gained approval from all 50 state laboratories to make sequence data from influenza viruses tested in these labs publicly available.

BioImagene to Integrate Digital Pathology Software with Stone Bond LIMS
BioImagene and Stone Bond Technologies recently announced a collaboration to integrate Stone Bond’s EE-LIMS system with BioImagene’s digital pathology software platform, which includes SIMS, TissueMine, and CellMine.
The integration is expected to enable pathology labs to automate processes and reduce time spent on administrative tasks. Users will be able to use the integrated platforms to automatically associate patient data stored in EE-LIMS to images generated by tests on patient tissue, the companies said. 

Entelos Signs Research Collaboration with Novartis
Entelos said recently that it has entered into a research collaboration with Novartis Pharma in which it will use its PhysioLab biosimulation platform to study several undisclosed disease areas.
Novartis will use the biosimulation results to support target evaluation, compound optimization, and phase III clinical trial design, Entelos said.
Financial terms were not disclosed. 
The agreement is an example of how the pharmaceutical industry “is realizing the benefits of testing targets and drugs in silico before conducting expensive clinical trials,” James Karis, president and CEO of Entelos, said in a statement.
Pharsight Signs $900K Contract with Undisclosed Partner

Pharsight said recently that it has signed “the largest single project workplan in its history” with an undisclosed client.
Pharsight said it will use its drug-disease modeling, meta-data analysis, and model visualization services under the multi-quarter agreement, which is worth $900,000.
The goal of the project is to “understand the likelihood of client drug candidates outperforming competitive drugs,” Pharsight said.
“We are seeing a number of large contracts integrating multiple Pharsight software tools and methodologies and this new opportunity is the largest such engagement we have achieved to date,” said Shawn O'Connor, president, CEO, and chairman of Pharsight, in a statement.

InforSense and Linguamatics Integrate Text Analysis Tools
InforSense said this week that it is partnering with Linguamatics to integrate Linguamatics’ I2E (Interactive Information Extraction) software tools with its TextSense text analytics platform.
Linguamatics has also joined the InforSense Open Workflow Partner Network as its 25th member.
Linguamatics I2E enables natural language processing and ontology-based querying over large collections of documents, including journal articles, patents, news feeds, and regulatory documents.
InforSense’s TextSense, an extension of the company’s KDE platform, provides a workflow for importing, processing, analyzing, and visualizing the contents of large document collections.
"This is a welcome development that will improve our current post-processing of Linguamatics I2E results using InforSense KDE," said William Hayes, associate director of library and information services at Biogen Idec, in a statement.

DOE Funds Two Life Science Computing Projects Under $60M SciDAC Program
The US Department of Energy’s Office of Science will support two bioinformatics projects as part of a broad computational science program announced this week.
The Scientific Discovery through Advanced Computing (SciDAC) program will award approximately $60 million annually to 30 computational science projects over the next three to five years.
The projects, selected from a total of 240 proposals, include two related to life science research.
One, “Robust and Precise Gene Function Predictions on a Genomic Scale,” and led by Steven Brenner of Lawrence Berkeley National Laboratory, will receive around $300,000 per year for three years. The project will refine a previously developed prototype for automated phylogenomic protein function prediction called SIFTER (Statistical Inference of Function Through Evolutionary Relationships). The researchers will modify the SIFTER algorithms “to make phylogenomics scalable to genomic and metagenomic volumes of sequence; enhance the prediction reliability of our method and rigorously assess it using well-studied families; broaden SIFTER’s applicability to a wider range of proteins, and incorporate a wide variety of functional evidence; and collaborate with the Department of Energy’s Joint Genome Institute to integrate SIFTER into their automated microbial protein annotation system,” according to the project website.
The second project, led by Michael Seibert of the National Renewable Energy Laboratory and titled “Filling Knowledge Gaps in Biological Networks: Integrated Global Approaches to Understand H2 Metabolism in Chlamydomonas Reinhardtii,” aims to construct an in silico simulation of the green alga C. reinhardtii, an organism that is of interest for researchers studying hydrogen production. The project will receive around $700,000 per year for three years.

U of Colorado, Massively Parallel Technologies Partner to Speed Protein ID Software
Massively Parallel Technologies said this week that it is partnering with the University of Colorado to develop and commercialize a software package for proteomics data analysis.
Massively Parallel, a provider of accelerated computational technology, said that it will work with Mark Duncan, director of proteomics shared resources at the University of Colorado at Denver and Health Sciences Center.
The research teams will apply Massively’s parallel processing software technology to a protein identification software application developed by UCDHSC to identify proteins from tandem mass spectrometry.
UCDHSC’s software is expected to enable faster and more accurate results than what is currently possible, “but requires tremendous compute power to process the massive amounts of data in a practical timeframe,” Massively said in a statement.
“Without the high-performance computing resources, expertise, and innovation that Massively brings to the table, this application would not be of practical use due to its computational demands,” Duncan said in a statement.

Sage-N-Research to Distribute Scaffold Proteomic Software with Sorcerer IDA System
Sage-N-Research will distribute the Scaffold data-mining software from Proteome Software, Sage-N-Research said this week.
Under the agreement, Sage-N-Research will sell stand-alone versions of Scaffold as well as a version integrated into its Sorcerer Integrated Data Appliance. The company will distribute the software within North America, Europe, Japan, and Asia-Pacific, except for Taiwan.
Sorcerer IDA with Scaffold will be the first integrated proteomics solution that can handle up to one million spectra or more, Sage-N-Research said. The integrated system also has built-in automated false positive estimation using reverse sequences.
Financial details were not disclosed.

BioSolveIT Integrates FlexX with CCG’s MOE Suite
Chemical Computing Group and BioSolveIT have integrated BioSolveIT's FlexX docking program with CCG's MOE modeling software.
The companies said in a statement that multiple computational techniques are needed to address the challenges of scoring — the prediction of binding affinity from docked structures — and that the integration of the two packages creates a “unique environment” for solving this problem.
The companies will launch the interface between the software packages at the fall meeting of the American Chemical Society in San Francisco, Sept. 10-14.

Origenis Subscribes to Aureus’ AurWeb Portal
Aureus Pharma said this week that Origenis, a Swiss-German drug design firm, has subscribed to its AurWeb portal.
Origenis is the first customer for AurWeb, which provides access to all of Aureus' knowledge databases, including AurScope GPCR, Ion Channel, Kinase, ADME/Drug-Drug interactions, and hERG.
Origenis uses proprietary methods to generate predictive QSAR and QSPR models for its drug-design research.

LSGPA Invests $250K in SoftGenetics To Support SNP Software Development
The Life Sciences Greenhouse of Central Pennsylvania will invest $250,000 in SoftGenetics to develop software for SNP analysis, LSGPA said this week.
SoftGenetics will use the funding to accelerate development of its microarray copy number and SNP chip software.
The investment comes from LSGPA's Technology Development Fund, which funds early-stage life sciences companies. The organization has invested nearly $8 million in the form of pre-seed stage capital and technology development funding in central Pennsylvania.

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The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.