Open Source Java Bio-Informatics Software - Page 33

This project aims to develop various tools for artificial life and complex systems simulations: from the simulator itself to generic generation tools.

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

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.

eClims (Extended Clinical Information Management System) is an Open Source software to help Proteomics researchers to manage clinical data. This project is strongly related to the ePims™ project.

Easy Homozygosity Profiling of Affymetrix SNP Arrays

eQTLexplorer is a database application for the visualization and integrated mining of genetical genomics experiments.

eagle-i is an ontology-driven, RDF-based distributed platform for creating, storing and searching semantically rich data. eagle-i is built around semantic web technologies and adheres to linked open data principles.

A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for EST submission, Batch BLAST and BLAST result parser, etc. easiEST contains JAVA GUI applications for analysing ESTs or other sequences

A Swing Gantt Chart component, used for rendering tasks and entries. Industry uses: Scheduling / Time Management

EOS stands for Entity Oriented Search. The project is a toolkit to support EOS projects on a Lucene and Hadoop platform.

A next gen sequencing analysis pipeline designed to run on hadoop/hdfs written in java and PIG. For more info, contact Zack Ramjan at USC

Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.

ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.

A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed source code (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste

Frida is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. It is open source and written in 100% Java. Frida makes use of functionality from the NIH's ImageJ application. Note: Frida was integr

molecular simulation program for anisotropic particle shape and potential

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

gfit creates an interface between computational models and experimental data and provides tools for their analysis

h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.

helese is an easy to use HL7 message to database converter. It converts messages from your hospital information system (HIS) into an easily accessible database for further processing. helese is free open-source software written in Java.

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.

a network-based multi-user software framework for collecting ground-truth information regarding absence or presence of nodules in Lung CT images.

Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs.

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please see "iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations" Mathias Kuhring and Bernhard Y. Renard (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050246)

Software environment for manipulation of DNA and protein sequences in a phylogenetic context.