Search Results for "python to java"

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.

openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is...

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

A set of bioinformatics tools for the open source bio-informatics platform "birch"

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

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

A library and associated applications for searching for patterns in protein structures and measuring geometric parameters.

MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

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

PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.

DrPangloss is a python implementation of a three operator genetic algorithm, complete with a java swing GUI for running the GA and visualising performance, generation by generation

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database

A dialect of XUL implementing most of Mozilla XUL's Fourth Draft. XML User Interface Language (XUL) is a method for easily creating GUI applications. Lux XUL supports Python scripting via Jython 2.1.

A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.

The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.

Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.