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Downloads and Upgrades: Jan 7, 2011


BioJava 3.0 is now available here.

BioJava, an open-source project that enables rapid bioinformatics application development in the Java programming language, contains powerful analysis and statistical routines, tools for parsing common file formats, and packages for manipulating sequences and 3D structures.

According to the developers, the latest version of the package now contains small, re-usable components including biojava3-core, which offers the basic tools required for working with biological sequences of various types; and biojava3-genome, which provides support for reading and writing of gtf, gff2, gff3 file formats.

Other modules include biojava3-alignment, which provides implementations for pairwise and multiple sequence alignments; biojava3-structure, which provides parsers and a data model for working with PDB and mmCif files as well as an implementation of the CE and FATCAT structural alignment algorithms and support for chemical component definition files; and biojava3-protmod, which can detect more than 200 protein modifications and crosslinks in 3D protein structures.

Gene Logic, a subsidiary of Ocimum Biosolutions, has released Ascenta version 4.0.

According to the company, the new version of the tool, designed for use in gene expression studies, integrates two generations of gene expression content on the Affymetrix platform and includes enhancements such as a Gene Ontology view that help users comprehend expression profile patterns.

Ascenta was developed to provide access and enable information retrieval from BioExpress, Gene Logic’s proprietary gene expression database. The software helps researchers identify and prioritize drug targets with respect to specific therapeutic and large-scale human biological considerations.

Velvet 1.0.17 is available here.

This release of the short-read alignment algorithm corrects several bugs that were introduced in the previous release, including problems in the multiple k-mer iteration and an error in the online help message.

MolSoft has released version 3.7 of its ICM-Browser.

New features in this release of the structural biology visualization software include the ability to display ligand pocket surfaces colored by binding property. In addition, users can add and optimize hydrogens to a PDB structure as well as display transparent surfaces among other capabilities.

Tata Consultancy Services, an IT and consulting firm, and Parseon have launched BioAppliance Platform, a suite of products that let users access scientific and technical information from multiple databases and publications.

The system include several components including a service that lets users navigate the content of PubMed abstracts and PubMed Central articles; a database containing semantic relationships that have been extracted from PubMed and PubMed Central; a network analyzer tool that functions as a plug-in to Cytoscape; and a parser that reads full-text content from scientific literature and/or internal documents, and extracts and indexes relevant relationships among other resources.

SoftGenetics has launched version 2.1 of its NextGene software.

This version includes a transcriptome analysis module for use with short sequence reads generated by Illumina GA/HiSeq, Applied Biosystems’ SOLiD System, and Roche Genome GS Titanium and Junior platforms. Also included is a Forensic STR Analysis module for use with the Roche platforms. The software also includes additional analysis tools, filtering options, annotation, and a variant call scoring algorithm among other functionalities.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.