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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.
The purpose of this project is to develop ontology-based tools for the study of animal behavior (ethology). The goal is not to produce a general ontology or editor, but comparative methods
and (behavior) data entry tools (ethontos and owlwatcher).
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
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The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.
GAME stays for Generic Architecture based on Multiple Experts.
Its main purpose is to make easy prototyping, test and release of prediction systems.
Released by IASC group, university of Cagliari
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D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.
Este projeto objetiva a criação de um Toolbox para utilização de algoritmos de Computação Bioinspirada. O Toobox oferece uma vasta coleção de algoritmos de ferramentas para o projeto de Algoritmos Genéticos e Redes Neurais.
cy2reposition: Cytoscape 2 plugin for layout reuse
CyReposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects.
This project migrated to github
https://github.com/matthiaskoenig/cy2reposition
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
Multimedia, Medicine Computing and BioInformatics --- This Project is a collection of several subprojects for Solutions in Multimedia, Medicine Computing and BioInformatics focus on video-,EEG- & Multichanels-signals developped in Web 20, J2EE.
J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).
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.
E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.