Search Results for "linux software development" - Page 4
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Showing 225 open source projects for "linux software development"
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
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The objective of this project is to make available an open-source version of our Multifactor Dimensionality Reduction (MDR) software. MDR is a nonparametric alternative to logistic regression for detecting and characterizing nonlinear interactions.
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bioluminescence
A java library for polymorphic genome assembly.
Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial... -
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AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.
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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms. The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. ... -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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locusvu
Tool for genomics;automates data retrieval from db;enables workflows
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 these... -
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TFAST
Software for analysis of afSELEX-seq data
Transcription Factor Analysis using SELEX with High-Throughput Sequencing (TFAST) is software developed by the Mobley lab at the University of Michigan designed to assist with transcription factor binding site discovery using data generated from aptamer-free SELEX-seq (afSELEX-seq). -
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is-sfe
Information System "Supercritical Fluid Extraction"
Information System "Supercritical Fluid Extraction" has developed as tool for collecting and analyzing the experimental data from various supercritical fluids experiments. The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk). -
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iBRAIN2 Workflow Manager
A system for automated analysis and data handling for RNAi screens
The iBRAIN2 software system for RNAi high-content screening integrates automated analysis and customizable data management. It enables robust and complex parallel processing on computer cluster infrastructure and allows for reliable storage of primary and resulting data sets. -
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PARSEC - PAtteRn SEarch / Context
PARSEC - PAtteRn SEarch and Contextualization
The characterization of genomic sites is a major challenge in the understanding and exploitation of next generation sequencing data. Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites... -
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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
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Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired. Please use the Git-Hub...
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El proyecto central es la conformación de un Sistema de Información Hospitalaria, se pretende ir por subproyectos los cuales formaran las piezas fundamentales que se integraran mediante perfiles IHE que vayan estableciéndose para la norma HL7v3
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
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... -
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TreeGrOSS Forest Growth Simulation
Software for modelling tree growth
Tree Growth Open Source Software is a Java based version of the forest growth simulator for north west Germany BWINPro. -
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Java Proteomic Library
A java proteomic development toolkit.
The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org. -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during the optimization process. ... -
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror... -
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CallSim
low-volume read processing base corrector
CallSim is a software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. CallSim provides a final classification or rescue of a base/indel in reads, where putative variants have been identified via typical SNP/indel workflows. plots rendered by: JFreeChart library http://sourceforge.net/projects/jfreechart/ -
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Linking BPA with RDA
This software system enables publication of ISA-Tab files to RDA.
BioPlatforms Australia (BPA) has funded a number of datasets generation initiatives around important research themes and scientific challenges faced by Australian researchers to provide a unique public resource for the benefit of Australian life sciences research. These large scale genomic, proteomic and metabolomic datasets are being generated and centrally managed by Bioplatforms Australia in collaboration with leading scientists, research institutes and government agencies. With the...
