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Documents
Publications and Conference Papers
- Bryan Smith, James Hill, Mark Gjukich, Philip Andrews. Tranche Distributed Repository and ProteomeCommons.org. Chapter from Data Mining in Proteomics: Methods in Molecular Biology. Humana Press, 2010.
- James Hill, Bryan Smith, Panagiotis Papoulias, Philip Andrews. ProteomeCommons.org Collaborative Annotation and Project Management Resource Integrated With the Tranche Repository. Journal of Proteome Research, April 2010.
Posters & Presentations
Tutorials
Downloads
Software
- Ontology representation and reasoning with SMem in Soar: Tools for representing OWL ontologies in Soar's semantic memory module, and an agent with an inference module. Visit project page »
- MALDI 4700/4800 utilities: A simple, object-oriented API for remotely accessing peak lists from the mass spectrometer's database, and a sample application with a GUI using this API searches for peak mass differences of specified size to help find crosslinks. Visit project page »
- Genetic algorithms and Traveling Salesman problem: Simple (but heavily parameterized) tool for testing genetic algorithms on the traveling saleman problem. All parameters are optional, and have default values; the real value of this tool is to learn how various variables in genetic algorithm impact its efficacy.
- MIDI HTTP Server: A silly, RESTFUL server that plays MIDI notes. Run the server and fire up your browser! Three shell scripts that play major, minor and chromatic scales. Requires JRE 5 or greater. ZIP, 41KB
- Sudoku solver: C++ source ZIP, 240KB
- randomf: Unix command-line utility for creating files with random sizes of any specific size. Intended for creating test files on demand. Contains man page, uses Make to install (but easily installed without). Requires JRE 5 or greater. ZIP, 5.6KB
- Tranche project: Distributed archiving software used to provide redundancy, data pedigree and integrity for scientific data sets. Optional AES encryption, compression and SSL. This software is used for the ProteomeCommons.org Tranche Network.
Other
- Unix shell scripts: collection of scripts for a variety of tasks such as counting number of lines of code in a software project to monitoring the size of a directory.
- Unix performance worksheet: worksheet with instructions for consistent measurement of CPU, disk and network performance PDF ODT
- Generic budget for OpenOffice: a useful spreadsheet that is easy to customize. Put your spending categories at the top, and every entry will include a drop down. Allows you to monitor your spending and balance your bank account, and is easy to maintain. ZIP, 13KB
- FI expenses worksheet for OpenOffice: Spreadsheet to track and analyze spending based on the FI program as outlined in Your Money or Your Life (Robin et al.). Contains brief descriptions, but is most useful if following the program. ODS, 21KB
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