Diff for "MoyezDharsee" - Bader Lab @ The University of Toronto

Diff for "MoyezDharsee"

Last updated at 2009-07-07 00:48:16

Differences between revisions 23 and 27 (spanning 4 versions)

Moyez Dharsee

Email: <mdharsee AT SPAMFREE infochromics DOT com>

416-889-1624 (mobile)

http://www.infochromics.com

Skype Name: moe_dee

CategoryHomepage

MoyezDharsee (last edited 2009-07-07 00:48:16 by localhost)

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-  ⇤ ← Revision 23 as of 2007-04-12 01:42:01 → 
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-Email: [[MailTo(mdharsee AT SPAMFREE infochromics DOT com)]]
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-=== Code Notes ===

 * '''Apr 11 2007:'''
  * Added new node attributes Motif Start, Motif End, SNPs (Motif Hit) (CytoscapeUtil::addSequenceSearchResultSetToCytoscape, CytoscapeUtil::addGenPeptFeaturesToNode)
  * Added "Unique peptides" checkbox in profile chooser panel (BrainParameterChangeDialog)
   * new boolean parameter ''uniquePeptides'' and getter/setter in BrainParameterSet
 * '''Feb 12 2007:''' Cytoscape API changes:
  * CyNet.set*AttributeValue (where *=[Node,Edge]) and CyNet.get*Attribute (* = [Integer,Double,...]) is deprecated as of v2.2 - replaced with CyAttributes instead (CytoscapeUtil)

=== Code ToDo ===
 * '''Apr 11 2007:'''
  * Clarify whether "unique peptides" checkbox applies to codon bias file option or to profile loading (only load unique peptides?)
 * '''Feb 12 2007:''' BiNGO 2.0
  * Tried using the latest BiNGO v2.0 but method MultipleTestingCorrection (among others) not supported; reverted back to previously used version 
 * '''Feb 21 2007:''' Plugin issues to resolve in Cytoscape 2.4:
  * 'bytecode.jar' for biojava-1.5-beta2.jar was causing java.lang.IllegalAccessError exception when loading ; had to revert back to biojava-1.4.jar and bytecode.jar dated Oct 13 2004
  * NoClassDefFound exception due to missing org.mskcc.dataservices.vocab.CommonVocab referenced in CytoscapeUtil.java. This class is contained in data-aux.jar which was removed as of Cytoscape 2.4 due to CPath package reorganization. Copied data-aux.jar in plugins folder to overcome this for now.
  * "Link Out" feature from node context menu fails to open selected database in web browser. This error only occurs when searching mammalian RefSeq db I downloaded, apparently because of the format of the FASTA file header, e.g. ''gi|119943093|ref|NP_001073324.1| glycogenin 2 isoform a [Homo sapiens]''. The file "smallDB.fasta" in the PDZ testData folder does not present this error. It's format is ''YAL001C TFC3 SGDID:S0000001, Chr I from 151168-151099,151008-147596, reverse complement, Verified ORF''

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