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Credits
This project has had support from many different resources, and we wish to credit them all. Thank you to everyone who has supported the ProteomeCommons.org and the Tranche project.
Individuals
Current Team
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Dr. Phil Andrews, Principle Investigator A faculty member of the University of Michigan, Dept of Biological Chemistry, director of the Michigan Proteome Consortium, director of the National Resource for Proteomics and Pathways, and a tireless advocate of this project. Phil is the boss. He both helped plan development of the Tranche project and provided support for development and continued support for maintaining the project. |
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Dr. Jayson Falkner, Lead Developer Lead developer for the Tranche project. Jayson is responsible for designing the Tranche project and for implementing most of the code during his PhD studies at the University of Michigan. Jayson has helped author several Java books and is an expert group member for one of the Java specifications. He is an open-source proponent and a Java-nut who recently finished his Bioinformatics PhD at the University of Michigan. Jayson's current plans are to finish up several projects at the University of Michigan and then move to Portland, OR, as a co-founder of Single Organism Software Inc (SOS). Jayson will remain affiliated with the Tranche project and continue work with Phil Andrew's group through SOS, including providing commercial services for Tranche and related scientific data storage and dissemination. |
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Mark Gjukich, Web Content Administrator Web Content Administrator and official Tranche power user. Mark is responsible for continued development of the Tranche project website and user testing of the Java-based Tranche related programs. Mark provides valuable user insight to the this project. Mark also maintains the news feeds, tools links, e-mail groups, and news letter for both ProteomeCommons.org and Tranche. If you are interested in learning more about Tranche or discussing possible collaborations, Mark is the one to get in touch with. |
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Bryan Smith, Application Developer Bryan has been developing with the team since February of 2007, and really loves to design and build things. He is currently working on an ambitious side project, HundredApps, with the hopeless goal of creating 100 tiny open source web applications. Bryan loves to read and write, and he keeps a blog on technology, his creations and society. Bryan eventually intends to attend graduate school for Computer Science, and wishes to be a professor and writer. He posts links to all of his work — regardless of how shameful, dated and irrelevant it becomes — in his portfolio. |
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James "Augie" Hill, Application Developer Augie has been developing for the Tranche Project since February, 2007. He is primarily responsible for making the graphical user interface for Tranche through both Java Web-Start and some portions of the website. Augie is a Southern Methodist University graduate of Computer Engineering, and hopes to soon enter graduate studies at the University of Michigan. With any spare time, he coaches figure skating and does side website development projects, mainly in PHP+MySQL. A link to his portfolio is available at 828Productions.com. |
Previous team members
- Todd Yocum: (Oct '07 - Feb '08) - Usability tester and web development consultant.
- Patrick Kincaid: (Jan - Aug '07) - Administrative Researcher for ProteomeCommons.org and the Tranche project.
- Rakin Ahmed: (Feb - July '07) - Part of the ProteomeCommons.org data entry team.
- Matthew Osher: (Feb - July '07) - Part of the ProteomeCommons.org data entry team.
- Ben Philip: (Feb - July '07) - Part of the ProteomeCommons.org data entry team.
- Brian Maso: (Nov '06 - Feb '07) - Expert Java programmer who help code and design the initial version of Tranche.
Collaborators
- Bioinformatics Solutions Inc.: Thanks to Iain Rogers and Weiming Zhang for helping set up support for Peaks On-line. Bioinformatics Solutions Inc. has been fantastic in working with us to enable ProteomeCommons.org Tranche users to seamlessly be able to use Peaks On-line to search MSMS data.
- TheGPM: The Global Proteome Machine group is actively working with us to use this resource as a storage facility for data submitted to www.thegpm.org. This is a large amount of MSMS peaklists that have been curated by the various tools offered by TheGPM.
- Pacific Northwest National Labs (PNNL): We would like to acknowledge the "Proteomics Research Resource for Integrative Biology", a national Biomedical Technology Resource Center for collaborative research established and funded by the National Center for Research Resources component of the National Institutes of Health (RR18522). The Resource is managed by Richard D. Smith (Resource Director) and David G. Camp (Associate Resource Director).
- Michigan State University, Wilkerson Lab: The Wilkerson lab was a beta site for this project and they continue to host a dedicated off site server, enabling better reliability and faster downloads for users of this project.
- Peptide Atlas: The peptide atlas group was a beta site for this project and they continue to host an off site server, enabling better reliability and faster downloads for users of this project.
- University of Michigan, Dept. of Biochemistry: The Univeristy of Michigan's Dept. of Biochemistry was a beta site for this project and they continue to host a dedicated off site server, enabling better reliability and faster downloads for users of this project.
Other Projects
- Clover Code Coverage for Java: An excellent tool for determining how much of your code is executed, e.g. how much of your code is covered by JUnit tests. Clover is a commercial product, but they give free licenses to open-source projects including this one. Thanks Cenqua! Awesome tool.
- garGANTuan: A GPL'd icon theme that was used extensively to style this project.
- Jakarta Ant: A powerful cross-platform build tool that powers the code compilation, project distributions, and almost every tedious task associated with maintaining this projet.
- Jakarta Commons: The Commons Upload API and HTTP client are used to power several of the advanced features of this website such as data submission and integration with on-line search tools.
- Jakarta Tomcat: The free, open-source, Java-based reference implementation for JavaServer Pages and Servlets, and the code that powers this website.
- JUnit: The JUnit framework is used to test this codebase and ensure that code doesn't break as features are added.
- Netbeans: An amazing, free developer's environment. Almost all the code used by this project was coded via Netbeans.
- Tango Desktop Project: A GPL'd icon, utility and guideline collection that exists to "help create a consistent graphical user interface experience for free and Open Source software".
Funding Sources
- Project supported in part by the National Resource for Proteomics and Pathways; NCRR award P41-RR018627