The new version includes six new publicly available metagenomic datasets, including the Mediterranean gutless worm metagenome, the acid mine drainage metagenome, and the Waseca county farm soil metagenome. The database also includes a new annotation pipeline, improved navigation, improved Blast services, and an enhanced fragment recruitment viewer.
NextEngine, caBIG Life Sciences Distribution, caBIG Clinical Trials Suite, ProteoWizard, ADMET Predictor, Ensembl 49, CAMERA 1.2.6
Active Motif has released the NextEngine accelerator for its TimeLogic DeCypher biocomputing platform. NextEngine is based on larger Xilinx field-programmable gate array chips and a faster PCIe interface in order to improve the processing of Blast, Smith-Waterman, GeneDetective, and hidden Markov model searches, the company said.
Active Motif said the new system offers three-fold to 20-fold greater throughput than its previous generation accelerator. The company said that HMM tests on a 2U DeCypher node with one NextEngine demonstrated a 20-fold speedup with performance equivalent to 550 Xeon CPU cores. Up to three NextEngine cards can be installed in the same 2U server for up to 43 billion cell updates/second, the company said.
The National Cancer Institute Center for Biomedical Informatics and Information Technology has released two software bundles developed as part of the Cancer Biomedical Informatics Grid, or caBIG, initiative.
The first bundle, called the Life Sciences Distribution, includes five caGrid-enabled software tools: caArray, a microarray data management system; caGWAS, a system to manage data from genome-wide association studies; caTissue, a grid-enabled version of the caTissue biobanking management tool; the National Cancer Imaging Archive, a searchable repository for DICOM-based images that are integrated with clinical and genomic data; and the Clinical Trials Object Database System, a repository for clinical trial information.
The second bundle, the Clinical Trials Suite, includes the Cancer Adverse Event Reporting System, the Cancer Central Clinical Participant Registry, the Cancer Data Exchange System, the Patient Study Calendar, and the Clinical Trials Object Database System Lab Viewer.
Information about the software is available here.
Cedars-Sinai Medical Center has released ProteoWizard, a modular set of open-source, cross-platform tools and software libraries for proteomics data analysis, here.
Modules include msconvert, a general data format conversion tool; msdiff, a tool for comparing two data files; and msaccess, which provides command-line access to mass spec data files, including spectrum binary data and metadata, selected ion chromatograms, and pseudo-2D gel image creation.
Simulations Plus has released an upgrade for its ADMET Predictor software for predicting properties of molecules from their structures. The upgrade includes a new module for estimating the rate of hydroxylation and other metabolism parameters.
“While there are some software programs that purport to predict whether or not a particular molecule will be metabolized by a certain enzyme, we believe this is the first prediction tool that provides the ability to predict how fast different compounds will be metabolized by five key CYP P450 enzymes that govern a large fraction of all human metabolism,” the company said in a statement.
Ensembl 49 is available here.
The release includes two new species: Equus caballus (horse) and Pongo pygmaeus (orangutan). In addition, around 1,200 viral genes have been removed from several species, Mus musculus (mouse) transcripts have been updated, and new variation databases are available for mouse, chicken, cow, rat, zebrafish, and human.
Version 1.2.6 of CAMERA (Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) is available here.