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In the PennBioTokenizer_Util.java file, you call a nonexistent constructor:
bt = new BioTokenizer(tokenizerModelFile);
This cannot compile. The only BioTokenizer constructor available in the latest Penn BioTagger release takes no arguments. This may be a problem with the BioTagger release because it seems as though a model should be specified and not hard-coded, as it is in the Penn...
2008-10-20 06:11:56 UTC in BioNLP UIMA Component Repository
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The StanfordParser_Util.java file has an include statement pointing to a package that does not (or no longer) exists in the latest Stanford BioTagger release.
import edu.stanford.nlp.trees.TypedDependencyList;
The code compiles at least if you just use a Collection of TypedDependency objects.
2008-10-05 04:45:01 UTC in BioNLP UIMA Component Repository
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rndlph committed patchset 47 of module MutationFinder to the MutationFinder CVS repository, changing 16 files.
2008-02-16 17:42:23 UTC in MutationFinder
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Okay, the new binary seems to work just fine. This bug can be closed.
2008-01-18 04:25:36 UTC in MutationFinder
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rndlph registered the DARx: Dimensional Analysis for Rx project.
2007-09-04 20:05:11 UTC in DARx: Dimensional Analysis for Rx
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Actually, py2exe is free and seems to work great. It is also good because Python is the default (initial) language for the project.
2007-07-27 17:00:57 UTC in MutationFinder
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One thing we have been silent about in the papers is the actual running time of the program. Our approach is considerably more expensive than the Horn approach.
I note that, at a high level at least, it should be trivial to parallelize the processing of the individual documents to improve the running time of the application.
On the perl side (on UNIX at least), I could use fork() to pull...
2007-07-27 14:47:41 UTC in MutationFinder
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The MIT license agreement should be appear in all source files:
# Copyright (c) 2007 Regents of the University of Colorado
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use,
# copy, modify...
2007-07-27 02:29:04 UTC in MutationFinder
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If we are going to have a binary distribution, it would be nice to have a mechanism for changing the mutation_finder_home setting. An environment variable seems like a more flexible mechanism.
2007-07-27 02:11:00 UTC in MutationFinder
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The perl version prints these in the order in which they occur in the text, not by sequence position. The sequence position order might be complicated if more than one protein sequence is being discussed. I think ordering by position should be a separate option.
2007-07-24 20:53:30 UTC in MutationFinder
