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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.

Recent and Upcoming Developments in the Tranche Distributed Data Repository: Human Proteome Organization (HUPO) Toronto conference 2009 poster presentation. PDF, 1.4MB (2009)
ProteomeCommons.org Annotations and Project Management Resource: Human Proteome Organization (HUPO) Toronto conference 2009 poster presentation. PDF, 3.0MB (2009)
Babel Fish: Conversion of MS File Formats and Standards : American Society for Mass Spectrometry (ASMS) Philadelphia conference 2009 poster presentation. PDF, 795KB (2009)
Annotation and Project Management Resource Integrated with the ProteomeCommons.org Tranche Repository : American Society for Mass Spectrometry (ASMS) Philadelphia conference 2009 poster presentation. PDF, 2.0MB (2009)
Tranche and ProteomeCommons.org Group Meeting Presentation: Introduce both Tranche and ProteomeCommons.org, focusing on uploading, downloading and managing data. 42 slides. PDF, 1.5MB (2009)

Dragging and dropping panels in Java 5: Tutorial with sample application. Screenshots included. HTML (2008)
Implementing a JButton with Rounded Corners: Create buttons in Swing with rounded corners, including screenshot and code. Java 5. HTML (2008)
Reading in Base64-encoded binary data from mzML 1.0: Includes functional Java example. HTML (2009)

Cannot commit to SVN, simple solution: Probably a permissions problem, but easier to dump and recreate the repository.
Crontab script stops permaturely: If crontab stops unexpectedly during a task, likely due to limit on output.
Data recovered from partition, "attempt to access beyond end of device": Used TestDrive to recover data from partition with disk errors, "unable to read inode block".
DriveStatusError: Finding the offsending disk on multi-disk computer: Disk controller problems result in disk errors. Shows how I identified the correct disk/disk controller. With shell script.
Setting memory for JUnit tests in NetBeans 6: Set the heap space allocation for JUnit tests running in NetBeans 6. Note there is no way to set this from the development environment as of January 5 2009.
USB disk woes: Volume unmounts during copy, so stagger copy. With shell script.

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.
- Executable: Cross-platform. Jar with README. ZIP, 12KB
- Java Source: ZIP, 42KB
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
mzSquash: mzSquash is a compression tool for mzML files, an XML-based standard developed by HUPO PSI for spectrometer output. The resulting .mzsquash file can be decompressed back into a mzML file, or read using an included SAX reader. View project site for more information. sourceforge.net
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.

check-for-files-with-same-path.sh.txt: looks in multiple directories for any files with identical relative paths.
count-files-in-directories.sh.txt: total count of all files in multiple directories.
count-lines-java-code.sh.txt: count total lines of all the java code in a directory. Easily adaptable to any file type, e.g., C, C++, etc.
info-directory.sh.txt: total number of files and size of a directory.
monitor-directory.sh.txt: prints out the size of a directory every minute. Also prints the size change, along with an average of rate of change. Useful when monitor downloads or activities generating data.
stagger-copy-for-failing-drives.sh.txt: copies directories with pause so, if a failing drive unmounts, has time to remount. Also generates a script of directories that failed so can try to copy again. Useful when copying many directories off failing drive.
try-find-disk-error.sh.txt: find disk or disk controller that is throwing disk errors.
verify-copy-many-to-one.sh.txt: after copying files from many different directories (think partitions) to one, verify that everything from all the directories was copied.

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

CC Zero: A New Tool to Push Your Work Immediately Into the Public Domain: While reporting release of CC0, briefly mentions Tranche project as well as Personal Genome Project (PGP). March 11, 2009. nytimes.com
Expanding the Public Domain: Part Zero: Tranche and Personal Genome Project (PGP) mentioned as early adopters during official Creative Commons CC0 release. March 11, 2009. creativecommons.org

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