Open Source Java Molecular Science Software

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.

Agent-based multiscale model of cancer proliferation dynamics

Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear,

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.

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

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.

Optimal assignment-based similarity functions for chemical graphs. The approaches represent extensions of the Optimal Assignment Kernel of Fröhlich et al.

Octet is an object-oriented molecular representation framework written in Java.

PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. SPiM2Eclipse provides a bridge for those running SPiM from the command-line by allowing simulations to be completed by a single click, displaying an embedded plot of the results. Features: -As an Eclipse plugin you have all of the powerful features of Eclipse available to you. -Syntax color highlighting -One-click simulation with plotting For more information on SPiM see the offical project website at: http://research.microsoft.com/en-us/projects/spim/

A system for temperature and spectrum acquisition control in hyperfine interaction research.

This project is an interactive viewer for 3D virtual screening data.