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Bio Browser
Bio Browser is a desktop application which facilitates the searching and browsing of the Cancer Bioinformatics Infrastructure Objects (caBIO) domain model made available via a web service from the National Cancer Institute Centre for Bioinformatics (NCICB). The project code is released as open source under the Apache 2.0 license.
Starting Bio Browser (two methods)
Bio browser requires Java, version 5 or above. Once Java is installed the program can be started using one of these methods:
- Launch from a direct download using Java web start. Launching via web start is the preferred mechanism since it automatically downloads application updates. If the launch link doesn't work Java may not be installed, or the version is too old. Try updating the Java version by downloading and installing the current version from the Java site.
- Download the source code, build the application and run it locally. Instructions on how to download and build the program can be found on the software development page.
Features
- Ability to search for caBIO domain model objects.
- View search results as an interactive tree and static XML document.
- Navigate to related objects by following xlinks embedded in the search result document.
- Open pathway diagrams rendered from the underlying SVG document.
Instructions, with included screenshots, illustrate how to use the program.
History
The Bio Browser project began as a teaching tool designed to illustrate the use of web services, domain models and XML-based data transfer within bioinformatics. However, it proved useful as a general tool for searching and examining the data provided by the caBIO web services, and was released via a web start application and source code download in 2003. This current project is a complete rewrite of the original with the following changes:
- Update to the current caBIO domain model and remote services. This was essential since the original services were no longer available.
- As a example application for both Spring Rich Client and the JIDE-Spring RCP integration project.
Motivation
The caBIO domain model objects represent entities found in biomedical research such as Gene, Chromosome, Sequence, SNP, Library, Clone, and Pathways. The instances of these entities, and their relationships, are constructed from an extensive collection of primarily molecular biology data-sources such as:
- NCBI UniGene
- Cancer Gene Anatomy Project (CGAP)
- UCSC Genome Project
- BioCarta Proteomics Pathway Project
- NCI Cancer Molecular Analysis Project (CMAP)
- Affymetrix, Illumina and Agilent human microarray annotation
- dnSNP
- NCI Cancer Therapeutics Evaluation Program (CTEP)
The following quote, from the caBIO technical guide, best describes both the motivation underlying the caBIO project and its border interest: "examining the relationship between these objects can reveal biomedical knowledge that was previously buried in the various primary data sources."
Author
The author is Jonny Wray and can be contacted at jonny at jonnywray dot com, or by using the project's messaging system.