Software and Web servers

The following is a list of software and web servers which I have developed or contributed to. Unless mentioned otherwise, software below is released under the GNU Public License. Web servers are available for access to anyone.

Other software to be added. Let me know by e-mail if there is something you were looking for.

In addition, as a courtesy to me, I would appreciate it if you let me know if you find any bugs or have any comments or suggestions. Thank you!

Small software tools / scripts

• A small Perl script that takes a set of LaTeX file(s) and a directory of BibTeX files and selects only those entries which are relevant to the LaTeX file(s). This is useful if your set of BibTeX files is getting large and either processing it using bibtex is taking too much time or the publisher wants your .bib file and it is too large to send to them. Archive contains only one file.

  Version 1.0, January 7, 2010
  [Download]

• A small Perl script that recursively compares the files in two directories using external calls to md5sum to calculate MD5 signatures. Files that have different signatures or exist in one directory but not the other are reported. Archive contains only one file.

  Version 1.0, May 3, 2010
  [Download]

• KDE Kate syntax highlighting file for the Graphical Models Toolkit (GMTK) language, a toolkit developed by Prof. Jeff Bilmes and others at the University of Washington for constructing graphical models (typically for speech processing). See the attached README for further details. Distributed under the LGPL license.

  Version 1.1, June 10, 2010
  [Download]

Bioinformatics

• HAMSTER (Helpful Abstraction using Minimum Spanning Trees for Expression Relations)
  A tool for depicting experiments in a microarray data set as a set of minimum spanning trees. Both web-based and a downloadable versions are available.

  Version 1.2.1, February 23, 2010
  [HAMSTER link]

• Parse protein-protein interaction data in MIF v2.5 format from the Database of Interacting Proteins.

  Version 1.0, February 2, 2009
  [Download]
  [Publication]

• Map human transcription factor binding sites to another species using data from UCSC's Genome Browser. Details in the accompanying PDF file.

  Version 1.0, December 28, 2005
  [Download]

Data Compression / Information Retrieval

• Probabilistic latent semantic analysis (PLSA) (Note: There may be a problem with this software and I hope to find the cause soon. This message will be removed when I am done. Sorry for the inconvenience! [2010/03/07])

  Baseline version (v1.0.1), March 7, 2010
  [Download]
  [Publication]

  Multiprocessor version (v1.0.1), March 7, 2010
  [Download]
  [Publication]

• Re-Store phrase browsing system (including the Re-Pair compression algorithm)
  [Subpage]

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