Bioinformatics Resource Manager Software

Linking scientific applications and heterogeneous data sources

The BRM version BRM 2.0 was released June 23rd, 2008

+ New Feature
- Bug fixed
* General comment

June 23rd, 2008 - Version 2.0:: + Microarray quality control workflow introduced. For details refer to user manual.; + Microarray normalization workflow introduced. For details refer to user manual.; + Files that are not tab-delimited, csv or .xls can also be imported. Current functionality will launch these files with their associated applications.; + Enhanced connectivity with Experimental Database Management System (EDMS) for all users.; + Advanced Search and query functionalities added for the EDMS database.; + Ability to save data files to the EDMS database.; + Capability to launch the ArrayNavigator goose from Battelle Memorial Institute.; + Compatible with GAGGLE latest API version; + Functional enrichment workflow available using both KEGG and GO databases.; * Dataset metadata screen has been updated; * KEGG, GO and NCBI databases updated to latest available version.; * User Manual upated; * Numerous bug fixes and user interface enhancements have been made.; - When creating a union of two datasets with no common entries, an error was previously returned. We fixed this to return the correct union.; - When editing a dataset, an extra row was appended to the end of the dataset. This bug is now fixed.

December 21st, 2007 - Version 1.6:: + Connection to NCBI data source has been revised to include species information. This leads to faster retrieval times.; + New cross reference information can be obtained starting from Protein GI numbers as well as Refseq Protein Identifiers. Previously only Entrez Gene Ids could be used.; + Connection to the Prolinks protein interaction database has been established.; + KEGG data retrieval now open to non-collaborators. Licensing agreements have been sorted out.; + Import functionality has been extended to allow for importing of EXCEL™ spreadsheets; + Connection to the Experimental Data Management System has been established. The database requires additional authentication.; + Get Started Interface was redesigned and updated.; * Updated user manual reflects new functionality.; * Species information is incorporated while importing datasets and across BRM. This facilitates further interaction with GAGGLE tools; * Users can modify and update species information for datasets.

June 15th, 2007:: + Update mechanism to simply have a one-click client update solution. Users no longer have to uninstall and re-install BRM; + Connection to NCBI data source has been revised and is available for use. Users can start with Entrez Gene Ids for retrieving NCBI Data.; + Connection to GO (Gene Ontology) database has been established to pull out GO terms; + Connection to TIGR CMR database has been established to obtain TIGR roles; + Latest version of PQUAD software that works for large datasets is provided; * User Manual has been updated to reflect GAGGLE changes and connection information; - Bug related to Extract Feature for large datasets has been fixed. This process is memory efficient and returns results in less time.

March 19th, 2007:: + Connectivity to Institute of Systems Biology GAGGLE Framework; + Faster loading of datasets using advanced import facilities; + PQuad version updated; + CABIN version updated; * Replaced algorithms for merging of datasets; * Replaced algorithms for adding of data to existing datasets; * Old clients will not work with new version of server; * Users will have to download and install the new client

December 1st, 2006:: * BRM version 1.0 released; * Faster and more robust merge procedure; * Faster loading times for large datasets; * Bug Fixed:
Creating new dataset using XREF values works as expected; + Fully functional data set editing features using SharpTools; + Additional web search applications like IPI, InterPro, Pfam; + Version checking mechanism to inform users of version mismatches; + Direct launching of Proteomics Peptide Data Exploration (PQuad); + Dataset column names can be renamed; + Upgraded to Cytoscape version 2.3; + Distributing CABIN: Collective Analysis of Biological Interaction Networks
* Coming Soon: * Connectivity to GAGGLE framework from Institute of Systems Biology; * Connectivity and remote job launching of BioConductor R routines; * Connectivity and remote job launching of BioConductor R routines; * Offline retrieval of NCBI/KEGG Data

September 1st, 2006:: * BRM Alpha version released; * User manual
Functionality includes: -> Data Import; + Supports tab-separated and comma separated text files; -> Data Retrieval; + National Center for Biotechnology Information (NCBI) ( 100 rows limit); + Kyoto Encyclopedia of Genes and Genomes (KEGG) - Available only to collaborators; + Biomolecular Interaction Network Database (BIND); -> Regular Expression based Parser tools; + Parsers to extract identifiers from Affymetrix and Nimblegen experiments; + Users can add custom regular expressions; -> Merging functionality and cross reference identifiers tables from International Protein Index, UniProt/SWISSPROT
-> Generic Data Merging capabilities: + Merge Microarray experiment files (e.g. Nimblegen and Affymetrix formats); + Merge Microarray and Proteomics files
-> Application tools: + Cytoscape Version 2.2 - Plugins need to download by users separately; + TIGR Annotations, KEGG Pathways, Entrez Gene and Protein Search and Pubmed Search Features
-> Column splitting - Column values can be split on delimiters to create additional columns
-> New datasets can be created from delimiter separated lists
-> Data can be exported as comma separated and tab-delimited files

*Report bugs, functionality requests, suggestions, and comments to brm@pnl.gov

Systems Biology at PNNL