Skip to main content
Premium Trial:

Request an Annual Quote

CLIMS, COBrA, Map Viewer, Sequin, Chmoogle, NAG C Library, FSA-Blast, FirstGlance, Tonya Hongsermeier, Eric Neumann , Chris Brannen, Peter Kraus

Premium

Downloads & Upgrades

The Victorian Bioinformatics Consortium, based at Australia's Monash University has released version 2.1 of CLIMS (Crystallography Laboratory Information Management System) at http://clims.med.monash.edu.au. CLIMS 2.1 includes a template import facility, which enables commercial screens to be imported into the system as comma-separated values. The new release also provides settings for three types of users: Normal, Super User, and Secured User.


The University of Edinburgh has released a new version of its COBrA ontology tool at http://www.xspan.org/cobra/download.html. COBrA, an ontology editor originally designed for Gene Ontology-style bio-ontologies, allows two ontologies to be displayed simultaneously to enable mapping terms. The release is compatible with OBO 1.0.


The National Center for Biotechnology Information has released an annotation of the cow genome assembly (build 2.1) through its Map Viewer at http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913. NCBI has also released Sequin version 6.00, a new version of its software tool for submitting and updating GenBank entries, at ftp://ftp.ncbi.nih.gov/sequin/.


eMolecules has launched Chmoogle, a free chemistry search engine, at http://www.chmoogle.com. Chmoogle's mission "is to discover, curate, and index all of the public chemical information in the world, and make it available to the public," the company said in a statement. The company has also released the code for Chmoogle so that users can embed the search engine into their own web sites.


The Numerical Algorithms Group has released a new version of the NAG C Library. New functionality includes routines for stepwise linear regression and mixed effects regression.


FSA-Blast is available at http://www.fsa-blast.org/. FSA (faster search algorithm)-Blast is twice as fast as NCBI-Blast, according to its developers, with no loss in accuracy. It is available under the BSD license agreement.


FirstGlance, a browser-based tool for molecular visualization based on the Jmol java applet, is available at http://www.bioinformatics.org/firstglance.

People in the News

Tonya Hongsermeier and Eric Neumann have been appointed co-chairs of the World Wide Web Consortium's new Semantic Web Health Care and Life Sciences Interest Group (see briefs, this issue). Hongsermeier is corporate manager for clinical knowledge management and decision support at Partners Healthcare. Prior to that, she was vice president for knowledge management solutions and patient safety at Cerner. Neumann most recently served as global head of knowledge management at Sanofi-Aventis. He was previously VP of bioinformatics and knowledge research at Beyond Genomics (now BG Medicine) and also held positions at 3rd Millennium, NetGenics, and Bolt, Beranek & Newman.


Nonlinear Dynamics has appointed Chris Brannen as Western regional sales manager and Jason Attanucci as Eastern regional sales manager of the company's US subsidiary, Nonlinear USA Inc. Nonlinear has also named Peter Kraus as a field applications scientist. Brannen joins Nonlinear after three years with Bio-Rad Laboratories, where he served as sales account manager. Attanucci was previously national sales manager for ChemImage, an imaging technology firm. Kraus joins the company from postdoctoral research positions with both Yale University and Duke University Medical Center after obtaining a PhD in biomedical sciences from the University of Connecticut in 2001.

Filed under

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.