News/BioCyc 16.5 Released

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BioCyc version 16.5 has been released! 16.5 is a major new version that includes updates to the Pathway Tools software/database bundle, as well as significant data updates and website changes.

Selected highlights of the Pathway Tools update:

Mac OS 10.8
Pathway Tools 16.5 works under MacOS 10.8; previous versions of Pathway Tools do not.
Phenotype Microarrays and Other Growth Data
The displays of growth media, growth observations, and phenotype microarray data has been substantially revised. Tables for growth observation data on gene and growth medium pages now include aerobicity and osmolarity information. The page describing all growth media has been revamped with improved colors and clearer indications (both in the tables and in the tooltips) of precisely what growth observation data is available. This page includes a new option to generate a heatmap to, for example, show how gene knockouts affect growth on different nutrient sources.
Atom Mappings
Atom mappings define the correspondence between atoms in the reactants of a chemical reaction, and the atoms in the products of that reaction. MetaCyc now contains atom mapping data for thousands of reactions. Pathway Tools uses that atom mapping data to color conserved moieties within chemical reactions, both within MetaCyc and for mapped MetaCyc reactions present in other PGDBs.

Also of interest is the next Pathway Tools workshop, which will be held jointly with the recurring Biology Phenotype Microarray workshop. The workshop will be held from March 4-6, 2013 at SRI International in Menlo Park, CA. From the press release:

Many research groups are interested in cell modeling, and models have begun to gain acceptance and proliferate. But are these models accurate and capable of making useful predictions of cell function? The last several years have seen significant improvements in computational methods for performing phenotypic predictions from metabolic network models. The speed with which such models can be assembled has also advanced. Similarly, experimental methods for high-throughput phenotypic characterization of cells have advanced during this time, and in particular, the use of Phenotype MicroArrays in challenging and improving models has become more widespread. This three-day workshop will bring together researchers in these and related areas to define current gaps and explore potential synergies between these computational and experimental approaches. Presentations describing other aspects of Pathway Tools and Phenotype Microarrays are also encouraged.

See the Pathway Tools workshop website for more information.