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Thermo Fisher Scientific, Matrix Science, OpenHelix, NHGRI, IO Informatics, Entelos, GeneGo, Partek, ABI, Mettler Toledo, Biobase, OpenEye

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Thermo, Matrix Science to Integrate Mascot and Sequest Protein Search Engines
 
Thermo Fisher Scientific said this week that it will integrate Matrix Science's Mascot search engine for protein identification with its BioWorks software, which includes the Sequest protein identification algorithm from the University of Washington.
 
Thermo said in a statement that Mascot and Sequest are “the two most widely accepted search engines in the field for protein identification and PTM characterization.”
 
This integration will allow users to consolidate and cross-validate results from the two products.
 
“Studies have shown that different search engines match different spectra, resulting in a large overlap and some unique protein identifications for each,” Thermo said, adding that including both search engines in the same software platform “provides a new level of confidence in protein identification.”
 

 
OpenEye Launches 'SAMPL' Challenge for Protein and Ligand Modeling
 
OpenEye Scientific Software this week launched the Statistical Assessment of the Modeling of Proteins and Ligands, or SAMPL, challenge — a blind test of protein and ligand modeling that is intended to help developers test their methods.
 
“Third party testers, particularly professional modelers, are encouraged to participate so as to allow comparisons of single methods when used by several, independent, participants,” OpenEye said in a statement.
 
SAMPL will consist of two sets of protein-ligand binding data provided by Abbott Labs and Vertex Pharmaceuticals and 63 vacuum-water transfer energies from Peter Guthrie at the University of Western Ontario and Chemical Computing Group.
 
The assessment will consist of three parts: virtual screening, predicting binding poses, and predicting binding affinities.
 
The results of SAMPL-1 will be presented at the OpenEye-sponsored CUP IX meeting, March 17-19, in Santa Fe, NM.
 
The deadline for submission of results is Feb. 18.
 
Further information is available here.
 

 
NHGRI Awards OpenHelix $1M To Develop Genomics Training Portal
 
OpenHelix said this week that the National Human Genome Research Institute has awarded it a Small Business Innovation Research grant worth $1 million to develop an online training portal for genomics resources.
 
The company said that it expects the tools will “greatly reduce the amount of time necessary to locate and use the vast genomics and bioinformatics resources available to scholars and scientists.”
 
OpenHelix said that many genomics and bioinformatics resources are currently “underutilized” because researchers are not aware of their existence. In addition, the company said, these tools all use different navigation methods and documentation, which can make it difficult for researchers to use them.
 
Warren Lathe, chief scientific officer at OpenHelix and the principal investigator on the grant, said in a statement that the company is exploring “some very innovative ways to search a large number of resources, including semantic search using widely used and accepted ontologies.”
 

 
iCAPTURE Licenses IO’s Sentient for Integrating Heart and Lung Research Data
 
IO Informatics said this week that the James Hogg iCAPTURE Center, a member of the Providence Heart + Lung Institute at St. Paul’s Hospital in Vancouver, Canada, has signed a multi-year site-wide license for the use of its Sentient data-integration platform.
 
The iCAPTURE (Imaging, Cell Analysis, and Phenotyping Toward Understanding Responsive, Reparative, Remodelling, and Recombinant Events) Center will use Sentient to integrate and analyze data from several internal and external sources, IO said. 
 
IO said that its Sentient Suite allows users to manage, search, view, annotate, link, and share research data without any programming expertise.
 
Financial terms of the licensing agreement were not disclosed.
 

 
UCB Pharma to Use Entelos PhysioLab for Rheumatoid Arthritis Research
 
Entelos said this week that UCB Pharma will use its PhysioLab biosimulation platform for rheumatoid arthritis research.
 
The Rheumatoid Arthritis PhysioLab is a predictive computer model that simulates arthritic patients and drug effects.
 
The company said that researchers use the system to select targets and compounds, find the best doses for patients, and support clinical trial design.
 
Financial terms of the agreement were not disclosed.
 

 
Finnish Red Cross to Use GeneGo's Software for Blood, Transplant Studies
 
The Finnish Red Cross has licensed GeneGo’s pathway analysis software for use in clinical and research projects it plans to conduct on blood taken from transfusion patients.
 
The FRC Blood Service will use the MetaCore and MetaDrug bioinformatics and chemoinformatics suites for blood group and cell type analysis from blood transfusions as well as for tissue typing of donors involved in organ, bone marrow, cord blood, and bone marrow stem cell replacement transplants.
 
MetaCore 5.0 is used to help target, validate, and identify biomarkers for disease states and toxicology, and MetaDrug 5.0 is used to predict toxicity, metabolism, and the effects of novel small molecules.
 
Financial terms of the agreement were not released.
 

 
Quimica Valaner to Distribute Partek Software in Mexico
 
Partek said this week that Quimica Valaner will distribute its statistical and interactive data visualization software in Mexico.
 
Under the agreement, Quimica Valamer will provide sales and marketing for the entire Partek software line, including Genomics Suite, Discovery Suite, QSAR Solution, and the Screener’s Solution.
 

 
ABI, Mettler Toledo to Integrate LIMS
 
Mettler Toledo and Applied Biosystems said this week that they have agreed to integrate Mettler Toledo’s LabX Data Management Software with ABI’s SQL*LIMS.
 
The integration will allow customers “to completely control their balance and titration instruments within SQL*LIMS, without the need for specialist LIMS training,” the companies said in a statement.
 

 
Biobase Opens Japanese Subsidiary
 
Biobase of Wolfenbuttel, Germany, said this week that it has opened a new subsidiary in Yokohama, Japan, called Nihon Biobase KK.
 
The company previously marketed its products in Japan via distribution partners.
 
Biobase said in a statement that it expects the subsidiary to coordinate the activities of its distributors and enable “enhancement of customer contact, improved cooperation with partners, and the building of a new market for biomarker discovery.”
 
The company said that it received “professional support” in opening the subsidiary from the City of Yokohama, the Kanagawa Prefecture, and the Japan External Trade Organization.

Filed under

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.