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


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

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 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

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.