Search Results for "api"

PolyJen: Polymerization in a digital laboratory

Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.

This project and all source code has moved to GitHub, see https://github.com/virtualcell

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

This will be next version of PHIbase.

NMR Spectroscopy tools. See http://connjur.uchc.edu

ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.

ToxOtis is a Java interface to the predictive toxicology services of OpenTox. ToxOtis is being developed to help both those who need a painless way to consume OpenTox web services and for ambitious service providers...

JTHERGAS (a JAVA implementation of THERGAS) estimates thermodynamic information from two dimensional graphical representations of molecules and radicals based on the Benson additivity method.

primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.

ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

DEPRECATED PROJECT! SolexaTools is becoming the SeqWare project (http://seqware.sourceforge.net) to better reflect its expanded sequencer support. Please go to this project page for code and documentation.

A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.

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

Grid-Enabled Molecular Simulation Repository (GEMS)

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 Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

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.

Bioinformatics tools and applications for the analysis of genomic sequence data.

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

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

Crude Metabolic Pathway Analysis visualization software. For a software engineering class.

PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format