About: Accurate splice site predictor for a variety of genomes.

Asp now supports three formats:

-g fname for gff format

-s fname for spf format

-b dir for a binary format compatible with mGene.

And a new switch

-t which switches on a sigmoid-based transformation of the svm scores to get scores between 0 and 1.

About: Python module to ease pattern classification analyses of large datasets. It provides high-level abstraction of typical processing steps (e.g. data preparation, classification, feature selection, [...]

0.4.4 (Mon, Feb 2 2010) (Total: 144 commits)

Primarily a bugfix release, probably the last in 0.4 series since development for 0.5 release is leaping forward.

• New functionality (19 NF commits):

o GNB implements Gaussian Naïve Bayes Classifier.

o read_fsl_design() to read FSL FEAT design.fsf files (Contributed by Russell A. Poldrack).

o SequenceStats to provide basic statistics on labels sequence (counter-balancing, autocorrelation).

o New exceptions DegenerateInputError and FailedToTrainError to be thrown by classifiers primarily during training/testing.

o Debug target STATMC to report on progress of Monte-Carlo sampling (during permutation testing).

• Refactored (15 RF commits):

o To get users prepared to 0.5 release, internally and in some examples/documentation, access to states and parameters is done via corresponding collections, not from the top level object (e.g. clf.states.predictions instead of soon-to-be-deprecated clf.predictions). That should lead also to improved performance.

o Adopted copy.py from python2.6 (support Ellipsis as well). ed (38 BF commits):

o GLM output does not depend on the enabled states any more.

o Variety of docstrings fixed and/or improved.

o Do not derive NaN scaling for SVM’s C whenever data is degenerate (lead to never finishing SVM training).

o sg : + KRR is optional now – avoids crashing if KRR is not available.

• tolerance to absent set_precompute_matrix in svmlight in recent shogun versions.

• support for recent (present in 0.9.1) API change in exposing debug levels.

o Python 2.4 compatibility issues: kNN and IFS

About: ARTS is an accurate predictor for Transcription Start Sites (TSS).

Initial Announcement on mloss.org.

About: For modern biology, precise genome annotations are of prime importance as they allow the accurate definition of genic regions. We employ state of the art machine learning methods to assay and [...]

Initial Announcement on mloss.org.

About: PALMA computes the optimal spliced alignment of a mRNA sequence to a genomic sequence. The main python script takes two FASTA files containing the target (e.g. a DNA sequence, part of the genome) [...]

Initial Announcement on mloss.org.