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Downloads and Upgrades: Clarity LIMS 3.1, Garuda 1.0, UniVec, and more


GenoLogics has released Clarity LIMS 3.1. It’s the latest version of the company's laboratory information management system for clinical laboratories. Besides support for HIPAA-covered entities, Clarity 3.1 includes capabilities such as electronic signatures, configurable permissions, and detailed audit trail reporting.

The Garuda Alliance has released a beta version of Garuda 1.0, a software, data, and knowledge platform for systems biology and biomedical research.

Features in this release include access to new gateway, a new local gadget installer, and bug fixes.

The National Center for Biotechnology Information has updated UniVec, its non-redundant database of vector sequences, to build 8.0.

This build adds vector, adapter, and primer sequences, bringing the total number of sequences represented in the UniVec database to 2,282. In addition, users can run searches using the VecScreen tool to detect more of the foreign sequences introduced during the cloning or sequencing process.

The Pistoia Alliance has launched its new online Interactive Project Portfolio Platform (IP3).

Developed in conjunction with Qmarkets, IP3 lets users browse, comment upon, vote for, champion or pledge contributions to existing proposals as well as submit new proposals. Users can check on the current status of their favorite proposals and interact with other users interested in making their ideas a reality.

The system, which is open to anyone, is intended to encourage the life sciences research community to generate and share new, innovative ideas; and support the development of novel, collaborative solutions for research and development.

Scientists at the University of Maryland have developed and released Epiviz, a free web-based tool that enables researchers to visualize and compare large amounts of genomic information from high-throughput sequencing experiments.

According to its developers, Epiviz is based on the Bioconductor infrastructure and can handle data from ChIP-seq, RNA-seq, and DNA methylation analyses. It implements multiple visualization methods for location-based data and feature-based data; and uses interactive data visualization techniques not available in existing web-based genome browsers. Researchers can also easily incorporate their own visualizations into the tool.

Epiviz is described in a recent Nature Methods paper.

Ensembl release 76 is available here.

The release includes an updated human assembly, updated mouse gene set, new regulation displays, and two new species among other changes.

Rancho BioSciences has integrated Omicsoft’s Array Suite with the TranSMART platform.

Array Suite provides statistics, visualization, and storage tools for analyzing quantification data, including expression, CNV/CGH data, genotyping data, and more. Scientists that have access to both platforms will be able to send data in TranSMART to Array Suite for further analysis.

Researchers from the Whitehead Institute for Biomedical Research have released a free application for biological experiments called iPipet that lets users track and transfer samples and reagents using tablets. The tool lets researchers share pipetting experiments, and it includes three-dimensional printing instructions for generating adaptors that can be used to attach plates to iPad. Full details of are available in a recently published Nature Methods paper.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.