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Downloads and Upgrades: Aug 6, 2010

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Affymetrix has launched ChAS 1.1, the latest version of its Chromosome Analysis Suite software.

Version 1.1 includes improvements to the allele peaks algorithm, such as the addition of new parameters, and to the loss-of-heterozygosity detection algorithm, as well as changes to the minimum and default values of the median-smooth-marker-count algorithm.


The California Institute of Technology has released CRdata, an open source cloud computing web service for R programming and Bioconductor software users.

According to its developers, CRdata gives users without computational expertise an intuitive graphical interface to Bioconductor while computational biologists can use CRdata to share their models and algorithms with non-expert users and to “manage shared cloud computing resources for multiple user groups.”

The service lets users read and write SBML, run R data analysis and modeling scripts in the cloud, share data and scripts, and provide tailored data and analysis resources to subscribers among other capabilities.

Programmers can also download CRdata and extend it to provide private instances of the service behind firewalls, computation on processor nodes other than Amazon’s cloud, and data aggregation and filtering web services.

SparkTech Software contributed code for CRdata and Bioconductor contributions came from the Fred Hutchinson Cancer Research Center.

The development of CRdata was supported in part by a grant from the National Heart, Lung, and Blood Institute.


NCBI Entrez Utilities and Chemistry service sets are now available for Taverna Workbench 2.2.

The NCBI Entrez utilities service set provides access to the National Center for Biotechnology Information’s EGQuery, ESummary, EInfo, ELink, ESearch, ESpell, EPost, and EFetch utilities.

The chemistry service set contains a set of web services for chemistry provided by ChemSpider, ChEBI, and PubChem.

Further information on how to download the sets is available here.


The Taverna project has released the Taverna DataViewer Tool 2.2.0, Taverna 2 Server 1 and Virtual Machine, and the Taverna 2 Web Demonstrator client interface

Taverna DataViewer Tool 2.2.0 lets users view Baclava files containing data from workflow inputs and outputs from the Workbench command line tool or server.

This version of the tool, which can be downloaded here, uses an updated version of the dataviewer command prompt script that used to be shipped with Taverna Workbench 1.x. The updated script uses some of the Taverna 2.x codebase and is available for download separately.

Taverna 2 Server 1 manages workflows and makes the results of the workflows available to users, tools, web pages, and portals.

Among its features, the tool runs Taverna 2 workflows, has both REST and SOAP interfaces, manages files for workflows, and calls the Taverna Command Line 2.2.0.

Taverna 2 Server 1 currently runs only on Linux and Mac OS. Users who wish to run the system on Windows or on other systems have to install the server as a Virtual Machine.

The virtual machine includes both the server and the demonstrator client interface.

The Taverna 2 Web Demonstrator client interface is a web-based interface that accesses some of Taverna 2 Server 1’s functionalities such as uploading and running workflows and viewing results and uses a Ruby gem to access Taverna 2 server’s REST interface. The source code for the gem is available here.


This week, biotechnology company Evogene launched ATHLETE 3.0, the third version of its plant gene discovery platform.

According to the company, the newest version of the platform incorporates new data types and additional layers of biological data such as protein-protein interactions, transcription networks, SNP data, metabolomic levels, and non-coding RNA data as well as phenotypic data based on large-scale field experiments.

The tool also incorporates data-mining tools, and algorithms and methods to improve prediction capabilities such as tools for genome wide association studies, unique analysis of phenotypic data, and gene-gene interaction maps.


This week, Genedata released Genedata Selector 1.0, the company’s integrated data management and analysis platform specifically for industrial biotechnology research and development.

Among other features, the platform automates, identifies and evaluates mutations, identifies novel metabolic engineering targets, provides integrated pathway analysis for identifying complex genetic effects, and integrates genome, operon, pathway, transcriptomic, and proteomic experimental data.


This week, Simulations Plus released its MedChem Studio data mining software for drug discovery.

Among other features, version 1.0 has a variety of algorithms to generate new molecular structures and when combined with the company’s predictive modeling software ADMET Predictor 5.0 allows chemists to see the effects of modifying drug molecular structures on activity and other key properties related to drug development.


Ensembl 59 is available here.

The release includes five new human cell lines from the Encyclopedia of DNA Elements project, data from the Catalogue of Somatic Mutations in Cancer, and a new masthead design with links to popular content.