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Downloads and Upgrades: JCB DataViewer, CLC Genomics Workbench 5.5, GeneMarkerMTP, and more


Glencoe Software and the Journal of Cell Biology have updated the JCB DataViewer, a platform for presenting, sharing, and archiving published scientific image data that is based on technology developed by the Open Microscopy Environment.

The latest version of the tool can accept and publish very large images, made up of many individual tiles, and make them viewable online.

This week, CLC Bio released CLC Genomics Workbench 5.5, the latest version of its desktop software; and CLC Genomics Server 4.5, the newest release of its enterprise software.

Both software packages now include tools to build complete resequencing workflows including read mapping, variant detection, and downstream analysis. Additionally, users can create workflows that combine various tools from the toolbox into a single analysis step; have access to tools for advanced variant detection, which are well suited for genomes of higher ploidy; and can easily download genomic sequences and annotation data from public databases among other capabilities.

SoftGenetics has released GeneMarkerMTP, a multi-template processor for use in genotyping applications.

According to its developers, GeneMarkerMTP can process varying chemistries or size standards in a single analysis run. Users also have access to applications in the GeneMarker software suite, such as multiplex ligation-dependent probe amplification, trisomy analysis, and more.

SoftGenetics has also released a new version of its NextGene software, which is used for analyzing next-generation sequence data.

The release includes new tools for HLA analysis and accepts the SOLiD XSQ data format. It also improves the assembly of data from Ion Torrent’s PGM and adds a new coverage normalization capability to NextGene’s Floton assembler; generates reports automatically; and imports and filters data from the Catalogue of Somatic Mutations in Cancer among other updates.

OpenEye Scientific Software has released SZMAP v1.1.0, the latest version of the company’s software for studying water’s role in molecular interactions.

The release includes a new command-line program called GamePlan that runs several SZMAP calculations and analyzes the results to examine how the existing ligand chemistry aligns with the pocket environment. It also produces hypotheses of ligand modifications to improve affinity, based on the energetics of the water environment directly adjacent to the ligand. Also in this version, the water orientation VIDA extension has been completely rewritten to make it easier to use and to find key waters and understand their interactions; and several bugs have been fixed.

Ensembl Genomes 15 is available here.

This release adds two new genomes to Ensembl Fungi — Leptosphaeria maculans and Trichoderma virens — bringing the total genomes supported to 354. It also includes a migration to version 68 of Ensembl; a new variation dataset for Puccinia graminis; a structural variation dataset for Sorghum bicolor imported from the database of genomic variants archive; and improvements to assembly, annotation and variation datasets among other updates.