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CiteXplore, BioMart 0.5, BioRS 5.6, LabSynch, Pfam 21.0, CAS Registry, DC-ENM, JChem 3.2

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The European Bioinformatics Institute has released CiteXplore, a freely available resource for integrating biomedical literature and bioinformatics databases. CiteXplore integrates abstracts from Medline, patent applications, and the Shanghai Information Center for Life Sciences at the Chinese Academy of Sciences and links these abstracts to EBI databases. CiteXplore is available here.
 
EBI also released BioMart 0.5. Code is available here and a new web interface is available here. The BioMart web code has been re-implemented in order to make it easier to set up and run queries, and the web service and Perl APIs have been simplified to improve user-friendliness. The release also includes a new tool for creating BioMart-compatible schemas from existing relational data sources.
 

 
Biomax Informatics has released BioRS 5.6. The new version of the company’s biological data integration and retrieval system includes improvements in the display of query results. The company said that queries can be saved as “virtual databanks,” to enable new results to be searched with subsequent queries. BioRS 5.6 also includes the Biomax Database Update Tool for specifying and performing automatic database upload and processing.
 

 
John McNeil & Co. has released LabSynch, a web-based software program that integrates an electronic lab notebook, a web-based collaboration service, a sample-tracking system, and an R-based data capture and analysis tool. The software is available here. It is freely available over the web, and workgroup packages are available for a monthly fee. Source code is available under the GPL.
 

 
The Wellcome Trust Sanger Institute has released Pfam 21.0. The release includes 8,957 protein domain families, matching 74 percent of sequences in UniProt 8.0. It includes 669 new families, while eight families have been deleted since the last release. Pfam 21.0 is available here.
 

 
The American Chemical Society’s Chemical Abstract Service said this week that it will begin implementing “significant changes in chemical substance nomenclature” in CAS databases in mid-December. Among the nomenclature improvements are “more uniformly cited locants, reduction in the number of stereoparent names, and the elimination of nearly 3,000 obscure stereoparents,” CAS said. Chemical names produced through the new system will begin to appear in CAS Registry database records in December. Old CA index names will be converted to the new nomenclature in 2007, but the old names will also be displayed in the Registry records.
 
The AD-ENM (Analysis of Dynamics of Elastic Network Model) project at the National Heart, Lung, and Blood Institute has released DC-ENM, a server that builds a structural model for a protein at an unknown state by using the lowest normal modes that are solved from an elastic network model built from an initial-state structure along with a distance constraints for the unknown state. DC-ENM is available here.
 

 
ChemAxon has launched JChem 3.2. New features include .NET support, new GUIs, and an installer to simplify installation and operation. The libMCS GUI allows users to navigate and filter within an interactive dendogram and hierarchical tree viewer, the Reactor GUI takes users through the steps and options available during virtual library design, and the Standardizer GUI helps users build custom business rules for structure canonicalization, beautification, and structure conversion useful during compound registration and post processing.

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The Scan

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Additional Genes

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Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.