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PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.
Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.
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A repository of Python extension scripts for use with the Sparky (http://www.cgl.ucsf.edu/home/sparky) NMR assignment package. No packaged releases yet, but there are scripts in the Sourceforge CVS@ http://sparkyscripts.cvs.sourceforge.net/sparkyscripts
Brabosphere is a multiplatform application with two main uses: a 3D molecular visualisation tool and a graphical frontend for the quantum chemical program BRABO.
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
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ProtoFit is software for modeling the acid/base behavior of surfaces. The software is used for parameterizing surface protonation models and for visualization of potentiometric titration data.
PyDespike is a cross platform (Windows, Mac, Linux) program written in Python using the PyQt and PyQwt libraries used to graphically process (despike) raman or other spectroscopic data in an efficient manner.
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.
GAST-Viz is a toolkit allowing for the creation of OpenGL atomistic simulation applications using discrete element modeling methods. A number of sample applications are included.
MSQuant is a tool for quantitative proteomics/mass spectrometry and processes
spectra and LC runs to find
quantitative information about proteins and peptides. Though
automated it also allows manual inspection and change.
COMSPARI (COMparison of SPectral And Retention Information) is being developed to 1) visualize mass spectrometric data and, more importantly, to 2) visualize 2 sets of mass spectral data simultaneously in a format that easily allows for comparison.
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).
ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
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