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BONDplus, IQbase 2.5, database of endogenous small silencing RNA data, Plant Ontology Database #0907, SQL*LIMS Plug and Play Pharma Package, Blast 2.2.17

Thomson Scientific has released BONDplus, an integrated, web-based data platform for biological analysis.
Culled from 15 assembled resources including GenBank, RefSeq, Entrez Gene and UniProtKB/Swiss-Prot, BONDplus allows researchers to tap into publicly available biological sequence data, BINDplus biomolecular interaction data, as well as GENESEQ, a database of patented biological sequences.
The subscription service also includes pre-computed data sets with Blast functionality, visualization tools, and more than 80 million public domain sequences.

Media Cybernetics has released version 2.5 of its IQbase scientific image management software. The software allows organizations to store, query, and share numerous images and related data through a company network or via the web, the company said.
With IQbase, users can perform image searches based on keywords or using more detailed context-sensitive search parameters. Images and data can be shared with others through the use of automatic PDF report templates, one-step export to PowerPoint tools, and web-based image searching and downloading. IQbase allows users to further explore their images with qualitative visualization tools like image overlays and annotations, as well as with quantitative graphs and charts for interactive data analysis.

Researchers at the University of East Anglia and the Sainsbury Laboratory have published an online database of endogenous small silencing RNA data for the unicellular green-alga Chlamydomonas reinhardtii. It is available here.
The database currently contains 46,672 sequence reads — the results of a single 454 high-throughput pyrosequencing run of RNA extracted from vegetative Chlamydomonas strain J3(mt-) cells.

The Plant Ontology Consortium has announced release #0907 of the Plant Ontology Database, which includes a new interface, users’ guide and tutorials, as well as 109 PO terms with 32,104 annotations. Additionally, a Gene Ontology feature links associations to Arabidopsis genes. More details can be found here.

Applied Biosystems has released a new laboratory information management system designed to help pharmaceutical companies maintain regulatory compliance and decrease the cost of managing their manufacturing operations. The SQL*LIMS Plug and Play Pharma Package is a pre-configured and validated LIMS developed specifically for the pharmaceutical industry, the company said.
According to ABI, a typical LIMS implementation takes approximately eight months, with most of that time spent configuring and validating the system, while the SQL*LIMS Plug and Play Pharma Package can be implemented in as little as two months.

The National Center for Biotechnology Information has released Blast 2.2.17 here.
New features include composition-based statistics available by default for blastp and tblastn as well as blastp- and tblastn-compressed alphabets.
Bugs fixed include the D 3 option of fastacmd, which was not behaving properly on Linux, as well as a performance regression in Megablast.

NCBI has also released its annotation of Nasonia vitripennis (jewel wasp), build 1.1. This build includes annotation of the reference assembly Nvit_1.0 from the Baylor College of Medicine Human Genome Sequencing Center.
The annotation is displayed in Map Viewer and other resources such as RefSeq and Gene and is available by FTP here.

Filed under

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.