Open Source Chemistry Software - 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.

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.

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

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

APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.

Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them

.Net based tools for AnIML formatted data files

This project supports ASTM E13.15 "Analytical Data Magement" in its work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry and biology data.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environ

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

BiMS (biclustering for mass spectrometry data) is a Java application designed to allow the application of biclustering algorithms to mass spectrometry datasets. Users can load their MS datasets and apply different clustering and biclustering algorithms (current version includes Bimax and BiBit). In adition, users can load raw datasets (in mzML or mzXML formats) and preprocess them using MALDIquant package and MassSpecWavelet.

BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

The Octet-CDK interoperability package.

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

Help us to improve Cell Culture. We want to hear your feedback! Request new Cell Culture feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Cell Culture is a highly specialized protocol-driven system designed to support development of the cell lines. Cell Culture manages activities related to the growth and maintenance of cell lines, provides stable cell lines development and incorporates laboratory methods facilitating faster and more accurate inventory lifecycle management: from the procurement of cell lines and request processing to tracking of tubes and other items in the laboratories. Cell Culture provides easy to follow, step-by-step protocols, with tips and notes and is of interest to researchers, technicians and process engineers using cell culture within the biotechnology, biomedicine and pharmaceutical industries.

CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.

CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.