Version history
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June 1, 2011:
Jstacs 1.5 released
- new package de.jstacs.algorithms.alignment for sequence alignment algorithms
- new class de.jstacs.models.ModelFactory with static classes to construct many standard models
- de.jstacs.utils.galaxy.GalaxyAdaptor, an adaptor to Galaxy, which allows for creating Galaxy applications using Jstacs ParameterSets, also requires new interface GalaxyConvertible
- new package de.jstacs.models.hmm for a variety of hidden Markov models, which can be learned by different learning principles including generative and discriminative learning principles, maximization and sampling methods
- new package de.jstacs.sampling that contains general infrastructure for parameter sampling
- new class de.jstacs.scoringFunctions.MappingScoringFunction that allows for internal mapping of symbols from the alphabet
- new package de.jstacs.classifier.scoringFunctionBases.sampling containing classifiers that sample their parameters by the Metropolis-Hastings algorithm
- new interface de.jstacs.scoringFunctions.SamplingScoringFunction for NormalizableScoringFunctions that can be used in Metropolis-Hastings sampling of parameters
- bugfix in XMLParser for cases, where the tag of interest also occurrs within other, nested tags
December 31, 2010:
Jstacs 1.4 released
- added DincleotideProperty for computing properties like melting temperature, twist, or G/C content
- support for multidimensional sequence data
- more widespread use of TerminationConditions
- completely rewritten XMLParser
- extension of motif discovery to weighted data
- OneSampleLogGenDisMixFunction for using the same Sample with different weights for the different classes
- Jstacs requires Java 1.6 now
March 2, 2010:
Jstacs 1.3.1 released
- Partitioning of Samples including weights
- Release of Dispom (de-novo discovery of differentially abundant transcription factor binding sites including their positional preference)
- Several bugfixes
December 2, 2009:
Jstacs 1.3 released
- generalized termination of numerical optimization in de.jstacs.algorithms.optimization.termination
- Added a unified generative-discriminative learning principle in de.jstacs.classifier.scoringFunctionBased.gendismix
- Implemented a multi-threaded variant of MCL/MSP and GenDisMix in the LogGenDisMixFunction
- Added a convenience class DNASample for samples of DNA sequences
- Added the class ParameterSetTagger to use parameter sets in command line programs
- Several bugfixes
April 8, 2009:
Jstacs 1.2.2 released
- Bugfix-Release
February 19, 2009:
Jstacs 1.2.1 released
- Bugfix in EnumParameter
February 2, 2009:
Jstacs 1.2 released
- Bugfixes
- Discriminative de-novo motif discovery
- Transformed Dirichlet Prior for numerical optimization
October 29, 2008:
Jstacs 1.1 released
- Bugfixes
- Improved Javadoc
- De-novo motif discovery
September 8, 2008:
The first version of Jstacs has been released.
