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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.
COVID-19 simulation models are mathematical infectious disease models for the spread of COVID-19. [1] The list should not be confused with COVID-19 apps used mainly for digital contact tracing . Note that some of the applications listed are website-only models or simulators, and some of those rely on (or use) real-time data from other sources.
The AMRFinderPlus tool from the National Center for Biotechnology Information (NCBI) is a bioinformatic tool that allows users to identify antimicrobial resistance determinants, stress response, and virulence genes in bacterial genomes. [2] This tool's development began in 2018 (as AMRFinder) and is still underway.
Open Bioinformatics Foundation. BioPHP. PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools. Cross-platform. GPL v2. Open Bioinformatics Foundation. Biopython. Python language toolkit. Cross-platform.
Name Description Knots Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that that the automated predictions by ...
The Phylogenetic Assignment of Named Global Outbreak Lineages ( PANGOLIN) is a software tool developed by Dr. Áine O'Toole [2] and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. [3] Its purpose is to implement a dynamic nomenclature ...
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.