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Gene Network Sciences, Biogen Idec, Institute for Systems Biology, Swedish Neuroscience Institute, GeneGo, NCI, IO Informatics, Centre of Excellence for the Prevention of Organ Failure, CambridgeSoft, Temis, Merck KGaA, Golden Helix, CDC, GenomeQuest, Inv

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Gene Network Sciences and Biogen Idec Pen Software Partnership
 
Gene Network Sciences said this week that it has entered into an agreement with Biogen Idec under which GNS will use its proprietary REFS, or Reverse Engineering and Forward Simulation, software platform to process genomic and clinical data provided by Biogen in order to identify targets and biomarkers that play a role in inflammation.
 
The platform will help scientists by generating and scoring “billions of hypotheses,” GNS said.
 
A forward simulation model generated from the Biogen Idec data will be licensed to the biotech firm when the project is concluded.
 
Financial terms of the agreement were not disclosed.
 

 
ISB, Swedish Neuroscience Institute Form Brain Disease Alliance
 
The Swedish Neuroscience Institute, a non-profit specialized healthcare provider with multiple hospital centers in the Seattle area, is collaborating with the Seattle-based Institute for Systems Biology on research geared toward diseases of the brain and nervous system.
 
One of the partnership's first research collaborations is the creation of a brain tumor tissue bank and an associated genomic database derived from samples removed during surgery.
 

 
CLC Bio Joins Illumina Connect Partnership Program
 
CLC Bio said this week that it has joined Illumina’s bioinformatics software partnership, Illumina Connect.
 
The firm said that as an Illumina Connect partner it will have access to information in the ongoing development of its software for next-generation sequencing.
 
CLC noted that in addition to Illumina’s Genome Analyzer, its Genomics Workbench platform can analyze and visualize data from all next-generation sequencing platforms including Applied Biosystems’ SOLiD, Roche’s 454 GS FLX, and Helicos BioSciences’ HeliScope.
 

 
GeneGo Receives NCI Grant to Develop Systems Biology Tools for Nutrient Analysis
 
GeneGo has received a $140,537 Phase I Small Business Innovation Research grant from the National Cancer Institute for the development of a platform for understanding the influence of nutrients on cancerogenesis and cancer prevention.
 
GeneGo will collaborate with FDA investigator Jim Kaput on the project. The new platform will include a comprehensive manually curated database on nutrition, an -omics data repository, an advanced search function, and statistical modeling tools.
 
“We will assemble the first specialized database on the topic and develop automated tools for data analysis,” GeneGo CEO Yuri Nikolsky said in a statement.
 

 
NCI Selects CambridgeSoft for Chemical Biology Consortium
 
The National Cancer Institute has selected the ChemBioOffice Enterprise suite as the informatics platform for its collaborative drug discovery partnership, the Chemical Biology Consortium.
 
Cambridgesoft said that the platform will allow members of the consortium to manage and share vital scientific information.
 
Financial terms of the agreement were not provided.
 

 
Organ Failure Center to Use IO Informatics’s Sentient for Data Integration
 
The Centre of Excellence for the Prevention of Organ Failure, or PROOF, in Vancouver, Canada has selected IO Informatics’ Sentient software suite as its data integration environment, the company said this week.
 
IO will supply $4.1 million worth of Sentient components along with consulting services to the PROOF Centre, the company said.
 
The PROOF team is developing biomarker discovery platforms for the assessment of genes, proteins, and metabolites in blood, urine, and tissue.
 
“Sentient will play an integral role in helping us deal with the data complexity and volume that PROOF’s work will generate,” Bruce McManus, director of PROOF, said in a statement. “It is essential that we are able to pull all data types from the various sources into one place and make it available to the spectrum of disciplinary specialists involved in the PROOF endeavor,”
 

 
Temis Provides Merck KGaA Text Analytics Solution
 
Temis announced a licensing agreement for its text analytics solution to support researchers at Merck KGaA’s knowledge management department.
 
Merck researchers will use the software for a number of tasks, such as scanning the scientific literature, patents, adverse event reports, company reports, news, and patient-generated content.
 
Temis has also entered into a software and services agreement with drug developer LIFE Biosystems, for its Luxid for Life Sciences solution to be applied in the analysis of clinical and molecular data from diverse textual information sources, the company said.
 
Life Biosystems, which uses patient information and molecular data to develop predictive medicine products, will use Temis’ Luxid software to analyze molecular information under a new software and services agreement, Temis said.
 
Mathias Goeschl, Life Biosystems’ head of text mining, said in a statement the software offers “enhanced text mining capabilities to our existing in silico discovery infrastructure and further supports us in generating novel clinical insights and hyphotheses.”
 
Financial terms of the agreements were not disclosed.
 

 
CDC to Use Golden Helix Software for Blood Disorder GWAS Research
 
Golden Helix has expanded an existing license agreement with the US Centers for Disease Control and Prevention for the use of its software in whole-genome association studies, the company said.
 
The CDC will use the software, including the HelixTree software for population-based studies, the PBAT software for family-based studies, and the CNAM copy number association tool, in its Division of Blood Disorders.
 
This is the third division within the CDC to use Golden Helix platforms, the company said, but did not release financial details of this agreement.
 

 
GenomeQuest Integrates Sequence Analysis Software with Invitrogen; Inks Distribution Deal with 454
 
GenomeQuest said this week that its sequencing data handling platform will now operate with Invitrogen’s sequence analysis software.
 
The Westborough, Mass.-based company said that it has worked with Invitrogen to interconnect its GenomeQuest 5.0 platform with the Invitrogen Vector NTI Advance software.
 
“The result of our collaboration expands the capabilities of both applications in the increasingly important realm of sequence search, analysis, and data management,” GenomeQuest CEO Ronald Ranauro said in a statement.
 
The GenomeQuest platform now interoperates with the Vector NTI Advance Versions 9 and 10, and it also will operate with the upcoming Version 11, the company said.
 
“The two platforms are highly complementary, and the combination of our desktop solution with GenomeQuest’s web-based application and worldwide sequence databases access will provide ... users with new, compelling sequence search options,” said James Caffey, business area manager for bioinformatics software at Invitrogen, in a statement.
 
GenomeQuest 5.0 users will be able to select sequences of interest and send them to the Vector NTI Advance software for analysis including DNA assembly, multiple sequence alignment, protein analysis, and recombinant molecule construction.
 
Vector users also will be able to choose sequences and send them to the GenomeQuest platform for advanced searching, which includes a collection of over 225 million sequences, and the information could then be exported back to the Vector software for analysis.
 
Separately, GenomeQuest and 454 Life Sciences, a Roche company, announced a co-marketing agreement through which GenomeQuest’s on-demand informatics services are now available to users of the 454 Genome Sequencer.
 
The agreement is the result of a pilot collaboration to see if GenomeQuest’s algorithms and informatics platform were scalable, according to a statement.
 

 
ABRF Invites Submissions for Proteomics Lab Survey
 
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group is inviting the scientific community to participate in a collaborative study focusing on the evaluation of proteomics laboratories in determining the significantly different proteins between two complex samples.
 
In this study, datasets representing five technical replicates of each sample will be provided, enabling participants to evaluate reproducibility of differences. This study will allow participants to evaluate their capabilities and approaches relative to others in analyzing a common data set.
 
Requests to participate must be submitted by e-mail to [email protected] prior to Monday, Oct. 20.

Filed under

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.