Open Source Java Molecular Science Software for ChromeOS

A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.

Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.

MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data.

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.

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

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

NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.

MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list.

Ninja is an object oriented toolkit for manipulating InChI identifiers.

Agent-based multiscale model of cancer proliferation dynamics

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.

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.

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.

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

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.

2-D chemical structure drawing program

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.

Janocchio is an application or applet for viewing 3D molecular structures and calculating NMR couplings and NOEs

LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.

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)