Open Source Java Molecular Science Software - Page 2

APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

Agent-based multiscale model of cancer proliferation dynamics

A bi-directional BLAST tool for orthologue listing with extended facilities (global alignment; paralogue list; GO onthology; dN/dS; etc) working on Win32 compiled versions of NCBI BLAST,FASTA,EMBOSS, and PAML. FILES AVAILABLE AT THE HOMEPAGE.(JAVA coded)

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

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!

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.

The Octet-CDK interoperability package.

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).

Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

The Diffraction Image Experiment Repository (DIMER) is an online archive for diffraction experiments, providing secure storage during analysis and publishing of experiments so they can be linked to, searched, and integrated into other databases.

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

FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

Client tools for the FuncNet protein function analysis platform: http://funcnet.eu/

Grid-Enabled Molecular Simulation Repository (GEMS)

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

The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.

A simple tool for molecular biologists (or similar) to estimate the size of electrophoresis gel bands. This can be applied to SDS-Page-,Native-Protein-, DNA, RNA, *whatever* gels as long as a weight/size standard lane is present on the gel.

IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".

A web based information management system for macromolecular (protein) crystallography X-ray experiments. This project has moved to https://forge.ill.eu/projects/ispyb

IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).

2-D chemical structure drawing program

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. The information is structured according to the OECD validation principles. Download the QMRF Editor in order to describe your models in QMRF format and send the descriptions to JRC-COMPUTOX@ec.europa.eu to have them included in the database. More at http://qmrf.sourceforge.net/

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