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Downloads and Upgrades: Feb 27, 2009

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BioRuby 1.3.0 has just been released and is available here. BioRuby is in the open-source programming language Ruby language, a project supported by the University of Tokyo and the Kyoto University.

Some of the changes include support for GenBank/EMBL formatted sequence output with improvements of Bio::Sequence. BioSQL support is completely rewritten by using ActiveRecord and there are Bio::Blast bug fixes and improvements.


BASE 2.10 has been released and it adds several new features, such as a new Biomaterial LIMS system. Base is a free web-based database solution for the microarray analysis data developed at Lund University.

The software can be downloaded here.


Stone Bond Technologies has released MicroLIMS, an on-line software as a service platform for microarray core laboratories, to complement its award-winning EE-LIMS product for life sciences.

MicroLIMS is a subscription-based solution that automates laboratory workflow, invoicing, data and sample tracking, collections, and other laboratory processes.

MicroLIMS allows multiple users to input data and guides the user through the process of building an automated workflow system that fits laboratory needs, the company said in a release.


The National Cancer Institute 's cancer Biomedical Informatics Grid has released an updated version of its caTissue Suite software, caTissue Suite 1.1, available here.

This open-source, web and programmatically accessible tool for managing biospecimens supports multiple biospecimen repositories across an institution using a single installation of caTissue.

It also lets users query key annotations including time between events and patient age.

Scientists can access data locally, or remotely across the caBIG network.

The Scan

Nucleotide Base Detected on Near-Earth Asteroid

Among other intriguing compounds, researchers find the nucleotide uracil, a component of RNA sequences, in samples collected from the near-Earth asteroid Ryugu, as they report in Nature Communications.

Clinical Trial Participants, Investigators Point to Importance of Clinical Trial Results Reporting in Canadian Study

Public reporting on clinical trial results is crucial, according to qualitative interviews with clinical trial participants, investigators, and organizers from three provinces appearing in BMJ Open.

Old Order Amish Analysis Highlights Autozygosity, Potential Ties to Blood Measures

Researchers in BMC Genomics see larger and more frequent runs-of-homozygosity in Old Order Amish participants, though only regional autozygosity coincided with two blood-based measures.

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.