Search Results for "java projects on linux" - Page 11
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Showing 792 open source projects for "java projects on linux"
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SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/ -
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ADOPS
Automatic Detection Of Positively Selected Sites
ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML). -
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Fylogenetica
Constructing level-1-networks consistent with a set of quartets
This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets. -
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CytoCopteR
A Cytoscape plug-in for training logic models, based on CellNOptR.
Homepage: www.cellnopt.org Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R. -
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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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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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WHATCH'EM
WHATCH’EM simulates mosquito container water temperature
WHATCH’EM simulates the highly non-linear manner in which atmospheric conditions and container characteristics determine water temperature and height, leading to results that are not always intuitive and likely not simulated by simpler empirical models. WHATCH’EM has the capacity to be utilized for other mosquitoes and other container-inhabiting arthropods. -
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Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations,... -
Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email... -
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PIVOT
PIVOT is a simple yet flexible visualization data tool
PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image... -
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SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
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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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PathMEN
A Java tool for mining pathway mentions from literature
PathNER is a tool for the identification of specific pathway mentions from biomedical literature. PathNER is built upon the GATE embedded framework.It's based on soft dictionary matching and rules-based detection. The dictionary is generated from ConsensusPathDB and Pathway Ontology and the rules are implemented in JAPE. Using PathNER, you can identify all occurrences of informative pathway names (e.g. 'the Wnt pathway'). PathNER can be used to assist studies that aim at uncovering... -
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Based on HL7 v.2.3.1 Orders & Results Reference Information Model (RIM)s, The project is NOT a CPOE per-se. Instead, the project provides "applications" that allow EHR's to perform Outpatient Orders and Results via HIE, and collect these into their EHRs to feed the EHR "CPOE module / section" (ex. with prescribed drugs, ordered labs and results, ....) The first module in the project was the "ePrescribing application"; certified by RxHub and SureScripts back in 2007. New...
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DeNovoCheck
DeNovoCheck: Inheritance analysis for NGS trio data
DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. -
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This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *
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mobycore
The lightweight java library that implements BioMOBY protocol
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cnvHiTSeq
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.
cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input. -
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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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GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
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A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
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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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AgED
AgED - Analysis given Experimental Data
AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in...
