Open Source Python Molecular Science Software - Page 3

This software has moved to http://www.poissonboltzmann.org/

A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.

A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.

Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.

The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.

PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.

PyCancerDB is a source code distribution providing a Web-based interface for browsing and updating the Cancer Proteomics Database, together with scripts for maintaining the database.

PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/

QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.

Quantum Chemistry Import Tool is a django application that parses the output file of quantum chemistry software as NWChem, Octopus, Gaussian, etc. The result can be saved in relational database.

SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.

The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE.

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

:awsum: You lost the game.

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

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.

Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...).

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.

cnsFace is a GUI for the Crystallography and NMR System.

A laboratory information management system (LIMS) geared towards academic research groups in the life sciences. Written in Python and using the Django framework, you run this software on your own server.

Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.