Search Results for "beta" - Page 3

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.

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.

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.

Janocchio is an application or applet for viewing 3D molecular structures and calculating NMR couplings and NOEs

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.

Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms.

MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list.

GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.

Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.

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

This project provides visual interactive interfaces to custom algorithms used in genomes research.

Synapsodel is an agent-based model of synaptic neurotransmission.

This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

SPAS (Structure Property Analysis Software) is a Quantitative Structure-Property Relationship (QSPR) software.

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database

Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.

LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.

IndelExtractor is a GUI and command-line application written in Perl that generates various molecular sequence alignment masks, including one to make identification and removal of Indels and their surrounding ambiguous alignment quick and simple.

Sage is a web-based stats system for your Folding@Home team. It is light, fast, and based on PHP and an assortment of SQL-based database management systems, so it is ideal for webservers.

md-utils is a set of command line tools written in C designed to perform certain operations and analysis on the molecular dynamics data. The supported operations involve trajectory coordinate transformation to the COM system, Cartesian coordinate transformation to selected internal coordinates and to projected normal mode coordinates, trajectory merging, selecting subsets of trajectory frames, selecting subsets of atoms, permuting atoms, etc. Analysis tools involve 1D, 2D and 3D data...