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PubChem, CentiScaPe, GastroPlus

The National Center for Biotechnology Information has released abeta version of a SOAP web services interface for its PubChem database. A description of the service, as as well examples of how to use it with the Taverna workflow software, is available here.

The Center for BioMedical Computing at the University of Verona has released CentiScaPe release 1.0, a Cytoscape plug-in that calculates network centralities —  topological parameters that allow node-by-node quantification of the reciprocal relationship between the nodes in a biological network.
In biological networks, nodes have specific topological properties that are important to score. Computing centrality indexes may help accomplish this goal, by classifying nodes according to their capability to influence the function of other nodes in the network, according to the CentiScaPe developers. By combining this analysis with experimental data concerning node attributes, it may be possible to identify critical nodes and regulatory circuits in a context-specific manner, they said.

Simulations Plus has released an upgrade to its GastroPlus software used to simulate absorption, pharmacokinetics, and pharmacodynamics of drugs in oral and intravenous dosage forms.
The company said that the new IVIVCPlus Module provides a better way for formulation scientists to perform in vitro-in vivo correlations. Another module, PKPlus, which is used to fit pharmacokinetic parameters to data from a single intravenous dose, can now be applied to multiple data sets and also a mix of both intravenous and oral doses, the company said.
The company said it has also developed a new kidney model that provides more accurate prediction of how drugs are cleared in the urine.

Filed under

The Scan

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.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.