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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
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Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.
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
Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
Jpowder, http://www.jpowder.org, is a Java viewer of powder diffraction data, and is a collaborative project between the ISIS Facility of the STFC and the E-Learning and Software Develepment Unit of the Kasem Bundit University.
Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells
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.
The RNA Ontology Consortium proposed a translation the RNA backbone angles to 46 clusters ('suites') and hence unique names. This project calculates the suites from RNA 3D structures, and to search on a Java-based index structure of known folds.