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Downloads and Upgrades: Cytoscape.js 2.0.0, ChemAxon 6.0, Floragenex Analytics Service, and more

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Cytoscape.js 2.0.0 is available here.

This version of the tool, according to the developers, performs better than Cytoscape Web, includes built-in support for touch devices, gesture support, core extensions, UI plugins, and an intuitive API modeled after jQuery among other updates.

Also available from the Cytoscape app store are two GPU-accelerated plugins for Cytoscape 2.6.x, 2.7.x, and 2.8.x.

AllegroMCODE 2.0 helps users find clusters, or highly interconnected groups of nodes in huge complex networks such as a protein interaction networks. It is designed for the fast analysis, low memory consumption, and interactive cluster exploring without creating a network view.

AllegroLayout 1.0 is a graph layout plugin designed for large-scale networks that offers features such as force-based layout algorithms and real-time layout animation.


This week, ChemAxon launched version 6 of its cheminformatics suite.

The release introduces four new products: Marvin for JavaScript, Instant JChem Web Client, REST Web Services, and the Plexus project, a web-based discovery application for bench scientists. The release also includes enhancements that the company says improve user experience, computational performance, and collaboration support to enable more effective chemistry data management.

These include improved integration with Microsoft Office, new search features and indexing support for ISIS and ChemDraw Excel workbooks in JChem for SharePoint, and enhanced compound registration capabilities, including project-related data storage.


Floragenex has launched a new analytics service that will be part of its newly minted genomics service.

According to the company, the analytics arm will develop low cost cloud-based bioinformatics tools for the service. Two other arms of the offering include Floragenex Discovery, which will provide expertise in SNP marker development, and Floragenex Genotyping, which will support clients interested in genotyping solutions using next-gen DNA sequencing.


Simulations Plus has released ADMET Predictor 6.5, the latest version of its program predicting molecular properties from structure.

The release includes 18 new models that predict metabolic rate parameters for each atom in a molecule likely to be metabolized by certain Cytochrome P450 enzymes; a new method that provides confidence levels for predictions from classification models; updated rules for ADMET Risk for metabolism and toxicity; and enhanced multidimensional graphics for easier data interpretation among other updates.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.