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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
A sorting tool for Bioinformatics, Biochemistry and/or Molecular biology. This sorts nucleotide sequences aligned using "ClustalW". There may be a way to do this w/ original app, but someone I know couldn't figure out how - thus this project was born
SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
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This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
A novel stochastic simulation environment for biochemical modeling
UPDATE(2017-07-24) This repository has moved to BitBucket: https://bitbucket.org/parkinsonlab/cell-2017
Cell++ is a novel stochastic simulation environment which is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signaling.
A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement
RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
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.
Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.
easy to use sepctrography software. allow to display spectrography curves, and to overlay severals curves. you can create firste or second derivatives from the curves, or place marks to identify peaks.
finals drawings can be saved as png or pdf files.
ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
The Comparative Genomics Vocabulary (CGV) is a SKOS representation of comparative genomics containing terms, text definitions and synonyms of the domain. The vocabulary is structured with broader and narrower relationships between the concepts.
Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.