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Knowledge Discovery and Data Analysis in Biology

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Project description

BioWeka is an extension library to the data mining framework Weka for knowledge discovery and data analysis tasks in biology, biochemistry and bioinformatics. It is distributed under the GNU General Public License and maintained as an open source project by the Ludwig Maximilians-Universität München.

Read the tutorial to find out more about BioWeka.

Features

BioWeka 0.7.0 offers the following functionality:

Data converters for

FASTA, GenBank, EMBL and Swiss-Prot sequence files
XML files, e.g. MAGE-ML, ProML and InterProScan result sets
tab-delimited microarray data, e.g. TIGR, Stanford and Spot

Classification methods based on

BLAST and other aligners
Eclat: reimplementation of Eclat method
LibSVM: integration of the Weka LibSVM project

Filter tools to

translate sequences (DNA to RNA to Protein, DNA/RNA to its reverse complement)
generate the open reading frames of DNA/RNA sequences
analyze amino acid properties based on the Amino Acid Index database
calculate the codon frequencies or amino acid composition
normalize numeric feature vectors
Multifactor Dimensionality Reduction (MDR): integration of the Weka-CG project

Other components to

merge ARFF files
save ARFF files in a sequence format
create filter pipelines

A change log is also available: [TXT] [HTML] [XML] [RSS]

Team

Jan Gewehr (LMU): project initiation and coordination
Martin Szugat (LMU): main developer

Acknowledgements

Ludwig Maximilians-Universität München for supporting the BioWeka project
University of Waikato for Weka
Ahmed Moustafa for JAligner
Participants of the BioJava project

Publications

Jan E. Gewehr¹, Martin Szugat¹ and Ralf Zimmer. BioWeka - extending the Weka framework for bioinformatics. Bioinformatics. 2007 Mar 1;23(5):651-3. HTML

¹authors contributed equally

News:

Click here to update the news

BioWeka 0.7.0 released - please update: This release contains some important changes and bug fixes:

* We changed the architecture of the alignment packages. The new aligner classes are found in packages which refer to the source of the underlying algorithm code (e.g. bioweka.aligners.jaligner.SmithWatermanGotohAligner).

* The new release solves a problem when using the "supplied test set" option with BlastClassifier or SimpleAlignmentClassifier, which lead to incorrect results in previous releases (other options like cross-validation or percentage split were not affected).

* The interface of the BlastParser and the converter classes for sequence-based data formats have been updated. (0 comments)
Paper about BioWeka published: Bioinformatics published the paper "BioWeka - extending the Weka framework for bioinformatics" (doi:10.1093/bioinformatics/btl671) written by Jan E. Gewehr, Martin Szugat and Ralf Zimmer. (0 comments)
BioWeka 0.6.1 released: The previous release didn't contain the documentation of Weka-CG. This was fixed. No functional changes were made in this release. (0 comments)
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. (0 comments)
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 forbids 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. (0 comments)