Search Results for "java framework" - Page 2

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.

LocusVu is a novel Java based software tool that accepts a list of genomic loci (positions on the chromosome) as input and automates fetching of related information (cytogenetic band, gene name, OMIM data etc.) from public databases such as the UCSC genome browser database. It then enables multiple workflows on the retrieved results, like comparing multiple datasets (comparative genomics), viewing neighboring genes for a loci from within the tool itself, or graphically representing...

A software framework to build maps for Neurospora crassa genome based on probabilistic models of meiotic recombination. A netbeans platform application is built to incorporate the computations. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/GENOMEMAP

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein...

Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.

Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

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.

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.

ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

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.

CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.

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.

Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

The Disease Simulation Framework (DiSiF) represents a spatial simulation environment for infectious viral disease spread. The framework currently embodies a very simple framework for simulation in 2D space with focus on SARS and the Common Flu.

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.

The JefNET (Java Evolutionary Framework Network) Proj. consists of three subprojects: JEF, Dna, JXTAJef. Our intent is to provide a distributed genetic programming framework for the Java language, and a network in which classes can spontaneously evolve.

TaxonDNA is a simple but extensible system for performing simple DNA (and other) sequence manipulations in Java. We hope to create a simple framework which can be quickly extended to create bioinformatics applications.

Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet.

OpenEMS™ is the multi platform Grid framework to seamlessly aggregate all your multi platform resources into a virtual super computer.

Dogwood is an ontology-aware Distributed Annotation System (DAS) server framework for the integration of biological, biomedical and clinical data.

CompuCell3D is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the Study of Biocomplexity at the university of Notre Dame.