BioWeka 0.6.0 released

In this release we added a filter under bioweka.filters.universal called AddLastAttributeByName that adds the last attribute (often the class assignments) from a second data set to the current data set by joining the instances by their first attribute (i.e. name attribute).

Further, the release contains these bug fixes:

• Calling the toString method on an AvgScoreEvaluator object whose initialize method had not been called leads to a NullPointerException. This bug was fixed.
• The default value for the buildCommand property of the BlastClassifier object specified the option "-o T" which tells the formatdb command of the BLAST suite to build an index file for the sequence database. This leads to a better performance. However, as it seems, BLAST behaves differently in different versions with respect to this option, so we decided not to include the option in the default settings.
• Under certain circumstances the PsiBlastParser class fails to grep the output of blastpgp. The new releases solves this problem.
  

BioWeka 0.5.0 released

The BioWeka 0.5.0 release provides a new filter called AddLastAttributeFrom. This filter can be used to add an attribute, e.g. the class annotation, from an external dataset to the current dataset.

In addition, the new BioWeka version includes two minor bug fixes:

• the relation name of a filtered data set does not contain anymore any white spaces or the pipe operator. This change has become necessary because the BlastClassifier uses the relation name as the name for the BLAST database and BLAST uses the database name as the file name for the database. However, Windows permitsforbids the pipe operator within file names.
• the iprscan.xsl stylesheet declares the sequence.name attribute as of type nominal instead of string. This is a workaround for a well-known problem of Weka with sparse instances and string attributes.

BioSchemas at BMC Bioinformatics

This is the first paper mentioning the open community project BioSchemas: BioMed Central | Abstract | 1471-2105-7-490 | XML schemas for common bioinformatic data types and their application in workflow systems