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This ohnlp project has released "pipelines" that were contributed by members of the OHNLP Consortium. The pipelines are based on the Apache UIMA framework.
medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0.
MedTime is licensed under GNU General Public License version 3.0 (GPLv3).
cTAKES development has moved to apache.org.
See http://ctakes.apache.org/
Java implementation for the Mascot Generic File Format (MGF).
JMGF is a lightweight framework for handling MGF files. It supports reading, writing and parsing of MGF files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.
JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.
Lightweight framework for handling biological and bioinformatical data
The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later.
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Framework for using the Genetic Algorithms optimization heuristic.
GeneticAlgorithms is a simple and lightweight framework to implement an optimization heuristic following the Genetic Algorithms model. A genetic algorithm mimics the natural processes of evolution, selection and "survival of the fittest". This framework is intuitive and good integrated with Java 1.5 SDK and later.
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.
AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.
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