Search Results for "open source workflow software" - Page 6

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.

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.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

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 of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. ...

XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.

Testing tools source code of the Integrating the Healthcare Enterprise (IHE) PIX and PDQ v3 Integration Profiles

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:

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

CIP-FOSS will serve as a common entry page for Free and Open Source Software developed at the International Potato Center (CIP), Lima, Peru (http://www.cipotato.org).

Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.

The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers

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.

SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison. For this purpose it creates a unique workflow integrating third party tools like NCBI Blast or Primer3.

Data and animal management software for large-scale phenotype screening Used by GNF for mouse ENU mutagenesis project. Data visualization & analysis, animal husbandry management, & automated QTL mapping. Usable as stand alone animal husbandry system.

Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f

The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.

GTdb - Modular genotype database for all markers. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences

The ExactFDR software package is an improvement of permutation-based False Discovery Rate (FDR) estimation methods that takes advantage from exact p-value computations for analyzing Genome-wide association studies data

This is a computer model to study Evo-devo. It is the software of a project described in PLoS Computational Biology.

Tool for knowledge acquisition / ontology building from narrative texts.

The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.

WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.

Adamant is a java application for annotation of microarray array designs. The software enables MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repos

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.