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Bioinformatics Resource Manager Software

Linking scientific applications and heterogeneous data sources

The BRM version BRM 2.3 was released January 2012.

New Features/Enhancements/Fixes

  • New microRNA data sources have been updated, allowing users to retrieve targets, mirna_ids or microRNA metadata for human, mouse, rat, macaca mulatta and zebrafish. Data is currently supported from three databases: , , and
  • Added ability to retrieve miRNA sequence 
  • Added the ability to copy data from the clipboard to the Getting Started Window
  • Updated identifiers example page – Additional identifier types are available on the identifiers example help page.
  • Added ability to use all data retrieval options in the Getting Started Window
  • Changes to several web search labels (including pubmed)
  • Changed several retrieval window labels 
  • Added instructions to each retrieval window to clarify the purpose
  • Added button to remove duplicate rows from dataset
  • Added ability to use and retrieve Ensembl ID from the Gene(NCBI) database
  • Updated most databases 
  • Removed links to datasets that are old and no longer available (pquad, functional enrichment)
  • Change error info when data retrieval will be larger than 500,000

The BRM version BRM 2.2 was released March 2011.

New Features/Enhancements/Fixes

  • Java web start installation – The client installation has been updated to use java webstart, so that it will automatically check for updates and download changes that are added to the server. This means that you will no longer need to uninstall and re-install the BRM client when updates are made.
  • MicroRNA datasource – New microRNA data sources have been added, allowing users to retrieve targets, mirna_ids or microRNA metadata for human, mouse, rat, and zebrafish. Data is currently supported from three databases: http://www.microrna.org, http://www.targetscan.org/, and http://mirbase.org/.
  • Cross-Reference Identifiers from Uniprot – The cross-reference identifier database has been updated to use data from uniprot rather than the IPI database which will no longer be supported. This also provides a number of new identifiers that can be used, including three types of ensembl identifiers. Now there are 10 different identifiers that a lookup can be performed on, and 15 identifiers which can be retrieved.
  • Cross species datasource (from Ensembl) – A cross species lookup table has been added based on ensembl ortholog data. This allows users to go between the ensembl_gene id of human, mouse, macaca mulatta, rat, and zebrafish. More species can be added by request.
  • Improved species lookup on many datasource interfaces. Previously if a species was not in the list on the page (such as macaca or zebrafish) it took several steps to find them. Now all species are in the lookup list and there is a filter field, which allows you to start typing a species name and it will automatically find it in the list.
  • Updated identifiers example page – Additional identifier types are available on the identifiers example help page.
  • Workflows (such as normalization workflow) will send link for download instead of file in email if it is too large. Previously it would not send the files if they exceeded 5MB, now users have the option to download the large files.
  • Allow address to be pasted in for delimited and excel data sources. This allows a faster lookup of certain data directories if you already have the path available.

Bug Fixes

  • Fixes to website, require login before download, updates to registration page, help/instructions for new client installation. Test and fix username/password retrieval.
  • Changes to several web search labels (including pubmed)
  • Removed links to datasets that are old and no longer available (pquad, functional enrichment)
  • Allow the data type to be None/Miscellaneous
  • Change error to info when no data is found
  • Fixed gaggle connection
  • Fixed NCBI lookup
  • After adding a new project, the "add data" window was not using the newly added project
  • Fixed file import error when a \ proceeded the delimiter or in the header row
  • Improved calc load speed

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

Legend:

+ New Feature
- Bug fixed
* General comment

Functionality includes:

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

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