Semantic Motif Hunting » Uncategorized http://bio.adking.co.uk Research Blog Wed, 06 Oct 2010 22:04:10 +0000 en hourly 1 http://wordpress.org/?v=3.0.1 Other Tools http://bio.adking.co.uk/2010/07/07/other-tools/ http://bio.adking.co.uk/2010/07/07/other-tools/#comments Wed, 07 Jul 2010 12:29:55 +0000 Andrew http://bio.adking.co.uk/?p=212 Created txt files of the network, removing the semantics:

  • 1 File seperated by spaces
  • 1 File separataed by tabs

In the format:

node# relation_type node#

]]> http://bio.adking.co.uk/2010/07/07/other-tools/feed/ 0 Round the Twist http://bio.adking.co.uk/2010/06/02/round-the-twist/ http://bio.adking.co.uk/2010/06/02/round-the-twist/#comments Wed, 02 Jun 2010 14:20:11 +0000 Andrew http://bio.adking.co.uk/?p=64 Going around in circles today trying to get Concept ‘proper’ names for compounds (i.e. Cholic Acid), blast scores etc…

]]> http://bio.adking.co.uk/2010/06/02/round-the-twist/feed/ 0 Iterator Solved http://bio.adking.co.uk/2010/05/26/iterator-solved/ http://bio.adking.co.uk/2010/05/26/iterator-solved/#comments Wed, 26 May 2010 13:14:55 +0000 Andrew http://bio.adking.co.uk/?p=52 The iterator problem has been solved by updating the version of ondex-mini to the latest version on the nexus repository.

]]> http://bio.adking.co.uk/2010/05/26/iterator-solved/feed/ 0 Output http://bio.adking.co.uk/2010/05/25/output/ http://bio.adking.co.uk/2010/05/25/output/#comments Tue, 25 May 2010 12:51:52 +0000 Andrew http://bio.adking.co.uk/?p=49 Ondex output

Some Output

]]> http://bio.adking.co.uk/2010/05/25/output/feed/ 0 Iterating ONDEXView http://bio.adking.co.uk/2010/05/20/34/ http://bio.adking.co.uk/2010/05/20/34/#comments Thu, 20 May 2010 10:58:23 +0000 Andrew http://bio.adking.co.uk/?p=34
  • Extracted debugger version of Ondex-mini
  • Put emanticmotif-0.1.1-SNAPSHOT-jar-with-dependencies.jar in plugin folder
  • Created test.xml workflow
  • oxl parser worked but semanticmotif.Filter failed – Unable to iterate through items : ONDEXIterator/Iterator is broken/missing.


    • relationview.Iterator().get(i);
    realationview.getEntity(i);

    NoSuchMethodError.

    ]]>     http://bio.adking.co.uk/2010/05/20/34/feed/ 0