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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.

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.

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use...

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

Java Native Interface wrapper for the IUPAC International Chemical Identifier (InChI)

this is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. The goal is to provide several cuda and c based functions which can be easily accessed using java, groovy and python.