Join the BioQuery Project

BioQuery is an open-source software development effort which began as a grant-funded bioinformatics project at the Oregon Health & Science University. BioQuery version 1.1 is a production release that is currently being used by researchers worldwide. However, we need contributors of all experience levels to help with the development of the next version of BioQuery.

This pages gives a quick introduction to the project, and tells potential contributors how to get started.

Getting Started

If you are thinking about contributing to the BioQuery project, please follow the steps below (feel free to skip some, but not all of these steps):

1. Read the Brief History of BioQuery.
2. Read the Policy for Contributors.
3. Download and install the program. Try it out by making and saving some basic searches (for those who don't usually search biomedical databases, try making a PubMed search with the words 'bioinformatics software').
4. Look at the Tasks and (volunteer) Jobs at BioQuery's project site (hosted by sourceforge.net) to see if anything looks interesting.
5. Read the article on BioQuery in the journal Bioinformatics (only 2 pages).
6. Read the Design Documents.
7. Peruse the Javadocs and learn some of the classes (particularly in package query). Try to relate the JavaDoc description of a class with it's position in the Design Documents UML diagrams. This may help get the big picture of how the program is structured.
8. Subscribe to the BioQuery-contributors mailing list.
9. Download or browse the source code.
10. Write us at: support@bioquery.org and tell us what you're interested in!

Brief History of BioQuery

BioQuery began as the postdoctoral research project of James Brundege working under Christopher Dubay in the Division of Medical Informatics and Outcomes Research at OHSU. The project was funded by a BISTI grant from the NIH, and started in Winter of 2001 with an evaluation of existing software and the initial requirements gathering. The initial design took place in Spring of 2001, and coding of the first prototype began in August of that year. Development then continued along an evolutionary model characterized by frequent iterations, continuous integration of new code, and periodic refactoring of existing code to refine the design.

Version 1.0 was released early in May 2002, and the user base has slowly expanded every since. Version 1.1 was released in Summer 2002, with several bug fixes and enhancements. In October 2003 the grant that funded this project ended, and James has since moved to a new position in the Center for Information Analysis and Decision Support at OHSU. The BioQuery project, however, is still moving forward. Consistent with the directives of NIH and the Freedom of Information Act, BioQuery was developed under the GNU lesser public license, and is free, open-source software. The project has shifted to an open-source development model, and volunteers are contributing to the code and moving the application toward version 2.0.

In May 2003 the user base of BioQuery suddenly increased with the publication of an article on the program in the journal Bioinformatics. The project is still gaining momentum from these early successes, and the demand for new features is growing. Anyone interested in contributing should feel free to contact us.

Statistics of the code base as of February 2003:

• Technologies used: Java, XML, HTML, JSP/Servlets
• Number of packages: 5
• Number of named classes: 55
• Total number of lines (in *.java files): 17303
• Blank lines: 2429
• Comment-only lines: 5579
• Lines of true code: 7117

Send feedback to: support@bioquery.org