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Comparison of software for molecular mechanics modeling. This is a list of computer programs that are predominantly used for molecular mechanics calculations. GPU – GPU accelerated. I – Has interface. Imp – Implicit water. MC – Monte Carlo. MD – Molecular dynamics. Min – Optimization. QM – Quantum mechanics.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Infectious disease dynamics. Mathematical models need to integrate the increasing volume of data being generated on host - pathogen interactions. Many theoretical studies of the population dynamics, structure and evolution of infectious diseases of plants and animals, including humans, are concerned with this problem.
BioWatch is a United States federal government program to detect the release of pathogens into the air as part of a terrorist attack on major American cities. Reportedly operating in Philadelphia, New York City, Washington, DC, San Diego, Boston, Chicago, San Francisco, Atlanta, St. Louis, Houston, Los Angeles and 21 other cities, the BioWatch program was created in 2001 in response to the ...
iBioSim [5] [6] is a computer-aided design (CAD) tool for the modeling, analysis, and design of genetic circuits. GUI/Scripting tool [7] for building and simulating multicellular models. Yes, but only for reactions. GUI tool [8] [9] for analyzing and simulating SBML models.
Manual Curation. The Pathogen-Host Interactions database ( PHI-base) [1] is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005.
MS Windows. Java. Free to use software to digitize geological cross-sections, and display and edit borehole logs. Geoscience ANALYST [30] Free 3D visualization and communication software for integrated, multi-disciplinary geoscience and mining data and models, which also connects to Python through geoh5py, its open-source API. Mira Geoscience Ltd.
This is a list of software used to simulate the material and energy balances of chemical process plants. Applications for this include design studies, engineering studies, design audits, debottlenecking studies, control system check-out, process simulation, dynamic simulation, operator training simulators, pipeline management systems, production management systems, digital twins.