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Downloads and Upgrades: Feb 18, 2011

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BioJava 3.0.1 is available here.

Features in this release include a bug fix for the recent 3.0 code base, new utility methods for memory-efficient parsing of large Fasta files, and a new algorithm to automatically infer protein domain boundaries.


The National Center for Integrative Biomedical Informatics at the University of Michigan has released the MetScape 2.0 plugin for Cytoscape.

The plugin provides a bioinformatics framework to visualize and interpret metabolomic and expression profiling data in the context of human metabolism. It allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in
metabolite data.

Gene expression and/or compound concentration data can be loaded from files in CSV, TSV, or Excel formats, or the user can directly enter individual compounds or genes using KEGG compound IDs or Entrez Gene IDs to build metabolic networks without loading a file.


Cytoscape 2.8.1 is now available.

This release repairs several bugs including fixes to group handling and tunable presentations, among other changes.


GenBank 182.0 is available via FTP from the National Center for Biotechnology Information.

Uncompressed, version 182.0 flatfiles require roughly 479 gigabytes for sequence files only or 517 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 394 gigabytes.


This week, CLC Bio said that it has updated CLC Main Workbench 6.0 and CLC DNA Workbench 6.0 to improve in silico cloning and Blast tools. The new versions also include an interactive motif search function, improved viewing and navigation of annotation data, as well as options for recording auditing data and for custom configuration of restriction enzyme databases and codon frequency tables.


SoftGenetics has incorporated STR human identity analysis capabilities into its NextGENe software.

The company said that the new capability could be employed to reduce the current backlog of the Combined DNA Index System and other identity-profiling databases.


This week, Simulations Plus launched MedChem Designer, a molecule-drawing tool that complements its MedChem Studio and ADMET Predictor offerings for the design of pharmaceutical and other new molecular structures.

MedChem Designer's features include an intuitive interface with several features for molecular structure drawing and manipulation and several predicted key molecular properties from the ADMET Predictor software, among other capabilities.


Sigma Life Science has released

The Scan

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.

Machine Learning Improves Diagnostic Accuracy of Breast Cancer MRI, Study Shows

Combining machine learning with radiologists' interpretations further increased the diagnostic accuracy of MRIs for breast cancer, a Science Translational Medicine paper finds.

Genome Damage in Neurons Triggers Alzheimer's-Linked Inflammation

Neurons harboring increased DNA double-strand breaks activate microglia to lead to neuroinflammation like that seen in Alzheimer's disease, a new Science Advances study finds.

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.