Search Results for "java project with source code" - Page 3

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

This project has moved to http://code.google.com/p/synthetic/

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

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

DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.

QSAR is a project that aims to build a GUI that enables people to build quantitative structure activity (or property) relationship models. It will use parts of CDK (cdk.sf.net), JOELib (joelib.sf.net), R (www.r-project.org) and other projects.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions...

Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.

http://ewi.utwente.nl/~biorange/rshell - The RShell project is a plugin for the Taverna workflow system. It enables one to execute R scripts within the Taverna workflow system. The RShell processor is built on the RServe project. For more info:

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.

The Swiss Protein Identification Toolbox (swissPIT) is a project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims at the development of an automated analysis system to identify proteins using MS and MS/MS based data.

The metabolomics standards initiative (msi) will develop a Core Information for Metabolomics Reporting (CIMR) recommendation and a more formal and semantically defined corresponding ontology (msi-ontology).

NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.

The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.

PRIDE: PRoteomics IDEntifications database. Please note that the PRIDE project has relocated to http://code.google.com/p/ebi-pride

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

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.

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.

PANDA (Protein And Nucleotide Data Archive) unifies the archival of the sequences from Taxonomy,GenBank,RefSeq,UniProt,PDB,and PRF on a regular interval to build and maintain a Protein and Nucleotide data archive. This project is part of BRC project fund