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HumanCyc, Agent, GastroPlus, PINTS, caCORE, caBIO, ActivityBase

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Menlo Park, Calif.-based SRI International is launching HumanCyc, a database of predicted human metabolic pathways and the latest offering in SRI’s BioCyc family of pathway and genome databases. Peter Karp, director of SRI’s bioinformatics research group, said that the computational prediction component of HumanCyc is nearly complete, “at which point we will begin a literature-based curation effort to connect the predicted pathways with experimental knowledge about them.” The HumanCyc analysis tools will be available on a subscription basis this spring, and the database will be freely searchable at www.biocyc.org.

Celera Genomics subsidiary Paracel is releasing Agent (Automated Genotyping Tool), a software package for sequence-based genotyping data handling. Agent automates input trace file management, calls sequence bases, creates a multiple sequence alignment, and then compares the consensus sequence to a specified reference sequence. The company is offering a 10 percent discount on Agent through Feb. 28.

Simulations Plus has released version 3.3 of its GastroPlus software for the simulation of drug absorption and pharmacokinetics. The company has adapted a numerical integration software engine originally developed at

Lawrence Livermore National Laboratory

to increase the analysis speed. According to the company, a virtual clinical trial of 2,000 patients that formerly took an entire workday can be completed in about an hour on a 1 GHz machine, or 20 minutes on a 3 GHz computer.

PINTS (Patterns in Non-homologous Tertiary Structure), a software package to detect similar spatial arrangements of amino acids in protein structures, is available from the EMBL structural bioinformatics group at www.russell.embl.de/pints. PINTS can be used to resolve ambiguities that arise during fold comparisons or suggest convergent similarities not apparent when comparing sequences or complete structures, according to its developers.

The National Cancer Institute Center for Bioinformatics has made version 1.1 of its caCORE research information management system available at http://ncicb.nci.nih. gov/core. The new release includes updates to caBIO, the cancer Bioinformatics Infrastructure Objects model and architecture.

IDBS has released version 5.1 of its ActivityBase platform for integrating biological and chemical information. The new release offers improved access to inventory and test information, and provides new 3D data visualization and graphical interface functionality, the company said.

Filed under

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.