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Downloads and Upgrades Dec 3, 2010

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This week, Biomatters announced that a beta version of its Geneious Biocode laboratory information management system is now available as a free plugin for its customers.

The LIMS software was developed in partnership with the University of California, Berkeley, the Smithsonian Institution, and other partners to help researchers involved in the Moorea Biocode Project to handle the volume and diversity of samples collected. The project aims to create a comprehensive inventory of all non-microbial species in a complex tropical ecosystem.

The tool lets users connect to field databases in Excel or TAPIR format and search and retrieve data, bin sequences based on quality, verify taxonomy and loci, and submit sequences to Genbank, among other features.


Premier Biosoft has released SimGlycan 2.92, the latest version of the company’s mass spectrometry analysis tool.
According to the developers, this release supports both multi-stage and sequential MS data analysis.


Glencoe Software and PerkinElmer have released Columbus Scope, a cellular imaging software solution for microscopy that’s built on Glencoe Software's Open Microscopy Environment's open source OMERO platform.

According to the developers, Columbus Scope allows researchers to read, visualize, and re-analyze different vendor-specific research imaging file formats as well as to save and use their experimental metadata parameters, and to share images.

Columbus Scope is third in a family of tools built by PerkinElmer on the OME platform. Other products include the Columbus Conductor and Columbus Gallery data management systems.


Biopython 1.56 is now available.

In this release, the Bio.SeqIO module has been updated to support protein EMBL files, IMGT files, and UniProt XML files. The developers also note that the SeqFeature object gained some new methods, and the Bio.Seq translation function can now be used with an arbitrary genetic code.


This week, the European Bioinformatics Institute announced its plans to launch a new, user-friendly search service next February. To that end, the group has made a beta version available for users to test.

According to the developers, the main feature of the new search is a gene and protein summary that lets researchers explore gene or protein sequences in Ensembl, Uniprot, or the Gene Expression Atlas.

Other features include a species selector, which lets users switch between organisms. The tool shows orthologs across species, and in cases of gene duplication lists paralogs so that users can decide which ones are most relevant. A literature tab organizes published resources and offers a list of articles that have been selected by database curators and a reporting view allows users to share summary searches.


This week, the Chemical Computing Group released MOE 2010.10, the latest version of the company’s drug discovery software package.

The release includes streamlined interactive modeling interfaces and integrates NAMD Engine, which lets users farm out molecular dynamic simulations to NAMD and import trajectories back into MOE for subsequent analysis. It also includes a kinase structural database and explorer/browser, which allows users to extract complex data sets by searching and visualizing ligand topologies and ligand-receptor structural domain information, among other features.


The National Database for Autism Research, a database created by the National Institutes of Health, recently released data from 10,000 participants enrolled in autism spectrum disorder studies.

Researchers can now use the NDAR portal to perform queries that yield results from multiple datasets.
The portal was designed to provide tools to define and standardize data collected by different laboratories under different protocols and to ensure a collaborative approach and open data access to the whole ASD research community.


Integromics has launched SeqSolve, the company’s first product for the next-generation sequence analysis market.

According to the company, the first version of SeqSolve includes a broad RNA-seq analysis portfolio, which includes differential gene expression measurement and interactive scientific visualizations for transcriptome data, among other features.

The company disclosed its plans to release the sequence-analysis software in October (BI 10/8/2010).


Decodon has released Delta2D 4.2

According to the developers, the latest release includes an extension of the company's scout technology, which now enables users to retrieve protein information from UniProt, such as function, sequence, keywords, Gene Ontology information, amino acids, and references for identified proteins, among other features.


This week, Integrated DNA Technologies and Rensselaer Polytechnic Institute have added RPI’s UNAFold to IDT’s SciTools website.

IDT's customers can use the software to more accurately detect secondary structures within sequences they submit for nucleic acid synthesis. Users do not need to place an order with the company in order to use the software.

UNAFold is a nucleic acid folding and hybridization prediction tool that can be used to predict melting profiles for nucleic acids.

The software is freely available to academics and non-commercial users through a web-based interface on IDT’s SciTools website, but commercial users must obtain a license.


Release 7 of Ensembl Genomes is available here.

The new version includes software migration to Ensembl 60, 66 new bacterial genomes and updated functional genomics databases for Escherichia, Shigella, and Staphylococcus.

Also included are new fungal genomes and updates to the databases for the O. sativa indica, O. sativa japonica, A. thaliana, and A. pisum genomes.


Cytoscape 2.8.0 is now available.

This release includes custom graphics applied to nodes for rich visualizations, spreadsheet-like equations in the attribute browser for manipulating attribute data, and improved groups. In addition, the network analyzer plugin is now delivered as a core plugin.

Separately, researchers at the University of Toronto released version 2.0 of the GeneMania Cytoscape plugin for gene function prediction.

The latest release of the plugin is compatible with Cytoscape 2.8 and features command-line tools for data set creation, manipulation, prediction, and analysis, functional analysis based on GO annotations, support for using an arbitrary Cytoscape network in GeneMania predictions, Quickfind compatibility, and proxy server support, among other features.


The University Of California, Santa Cruz's Bioinformatics Group has updated the UCSC Genome Browser to include a new track search feature that will help users find and display specific annotation data sets.

The search feature is available via the "track search" button on the browser gateway and tracks display pages. The default search takes one or more terms as input, and returns a list of all the browser tracks in which the name, description, group, or associated metadata contains the terms. The advanced search option lets the user fine-tune the search based on the track name, description, and group.

The Scan

Steps for Quick Review

The US Food and Drug Administration is preparing for the quick review of drugs and vaccines for the Omicron variant, according to the Wall Street Journal.

Moving Away From Using Term 'Race'

A new analysis finds that geneticists are using the term "race" in their papers less than in years past, as Science reports.

Point of the Program

The Guardian writes that some scientists have called the design of a UK newborn sequencing program into question.

Science Papers Present Multi-Omic Analysis of Lung Cells, Regulation of Cardiomyocyte Proliferation

In Science this week: a multi-omic analysis of lung cells focuses on RIT1-regulated pathways, and more.