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Downloads and Upgrades: Jul 16, 2010


GeneGo has released ToxHunter, a set of tools and content developed through the company’s industry-FDA MetaTox partnership program, which is aimed at developing a comprehensive systems toxicology suite to assess the safety of compounds used in chemical and pharmaceutical R&D.

According to the company, ToxHunter provides experimental analysis and visualization tools such as an enrichment module for identifying specific gene-pathology associations, a suite of toxicity-focused pathway maps and QSAR models, and the ability to overlay toxicity biomarker information on maps and interaction networks.

GeneGo also said that ToxHunter uses a “detailed ontology" of compound-induced pathological observations covering eight target organs. The ontology includes a manually curated knowledgebase of toxicant associations to pathology terms, along with gene, protein, and metabolite biomarkers of chemical toxicity.

The company also said that ToxHunter can be added on to existing licenses of GeneGo’s MetaCore and MetaDrug systems biology and systems pharmacology platforms.

Emboss 6.3.0 is now available here.

The latest version of the software suite implements the Rabin-Karp multi-pattern search algorithm and includes EDAM ontology identifiers. Other features include network access to BioMart, Ensembl and general SQL databases, and support for BAM/SAM files as well as scalable graphics options. Users can also parse and validate NCBI taxonomy and OBO files.

The native Microsoft port, mEMBOSS, can be downloaded here.

Molport has integrated its compound procurement module with ChemSpider, a free chemistry search engine based on chemical structures from the Royal Society of Chemistry, to provide a single resource for researchers searching for rare chemicals.

ChemSpider is an aggregation and search service linked to more than 300 we-based resources, including patent databases, the scientific literature, and public databases.

The link between ChemSpider and MolPort will allow users order rare chemicals for their research identified through ChemSpider’s website.

Amazon Web Services has released Cluster Compute Instances for the Amazon Elastic Compute Cloud. The new instances are "specifically designed for high-performance computing applications and other demanding network-bound applications," Amazon said.

Cluster Compute Instances provide similar functionality to other Amazon EC2 instances but have been engineered to provide more computational power. In addition, customers can group Cluster Compute Instances into clusters in order to provide the low-latency network performance required for parallel applications.

"Depending on usage patterns, applications can see up to 10 times the network throughput of the largest current Amazon EC2 instance types," Amazon said.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.