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Downloads and Upgrades: CLC Genomics Workbench, Reactome, ROCS 3.2, and Pathway Studio Web Plant


CLC Bio and BioBam Bioinformatics have released an integrated workflow for researchers working with non-model organisms without reference sequences that combines the Blast2GO PRO plugin and CLC Genomics Workbench.

The solution covers NGS data quality control and assembly all the way through to genome-wide functional annotations and interpretations of genomes and transcriptomes.

Reactome 46 is available here.

Topics with new or revised events include disease, signal transduction, extracellular matrix organization, transmembrane transport of small molecules, cell cycle, and cellular response to stress. Also, the plant reactome has a new batch of rice pathways associated with cofactor biosynthesis, hormone biosynthesis, fatty acids, and lipids biosynthesis; and the Reactome FI plugin, which was designed to find network patterns related to cancer and other types of diseases within a gene list, has been upgraded to support Cytoscape 3, and is now available at the Cytoscape app store.

Reactome also has a new web interface. The redesigned site provides faster and more flexible tools to query, analyze, and visualize pathway and network data.

Its features include access to visualization and data analysis tools via a simpler home page; new data model and visualization strategies to annotate and display disease counterparts of normal human processes; a revised event hierarchy panel to provide interactivity and access to the entire listing of all the Reactome pathways; and a merged pathway identifier mapping, over-representation, and expression analysis tools into a tabbed data analysis portal with integrated visualization for improved pathway diagram colorization with user-supplied experimental data.

OpenEye Scientific Software has released ROCS 3.2.

This release includes several bug fixes, an option for improving substructure alignments; and a rocs-report application that uses 2D depiction technology to make PDF reports of hit lists displayed with 2D similarity, shape and color overlaps, as well as property histograms.

Elsevier has released Pathway Studio Web Plant, a new research solution that will help plant scientists explore breeding through trait analysis, and enable them to make more informed decisions at critical stages of crop production and protection research.

The new solution offers access to a knowledgebase of more than 130,000 molecular relationships and curated pathways from three model plant organisms: Arabidopsis thaliana, maize, and rice. It also provides analytical and visualization tools that will help plant biologists contextualize complex biology involved in conditions that affect crop yield, such as drought sensitivity and disease resistance. It also includes filtering and inferred relationship capabilities that can be used to annotate proteins and reconstruct pathways.