PHARMACOLOGY:

Pharmacokinetic routines in Excel

Detailed spreadsheets on Pharmacokinetics compiled by Minto (Sydney, Australia) and Schnider (St. Gallen, Switzerland) at the Second World Congress in Total Intravenous Anesthesia.

http://pkpdtools.com/excel/downloads/

On-Line Pharmacokinetic Simulations

Pharmacological simulations online or under Excel developed by Ned Phillips, Hartmut Derendorf and Guenther Hochhaus: models of one and two compartments, IV bolus, single or multiple doses, metabolism, oral absorption, PK / PD, hepatic and renal action. Excel Add-in.

http://copnt13.cop.ufl.edu/pat/pha5127/simulatn.htm

ADAPT

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Autor: The Biomedical Simulations Resource (BMSR) at the University of Southern California.

https://bmsr.usc.edu/software/adapt/

Ethanol PD

Pharmacodynamics of ethanol, application and calculation of various metabolization models and mathematical methods. Author: Holford, Universidad Auckland, New Zeland.

http://holford.fmhs.auckland.ac.nz/research/ethanol

CLINICAL:

AIDA

AIDA contains a simple model of glucose-insulin interaction in the human body. It is intended for simulating the effects on the blood glucose profile of changes in insulin and diet for a typical insulin-dependent (type 1) diabetic patient (IDDM).

http://www.2aida.org/

ECGSIM

ECGSIM is an interactive complete ECG simulator, 3D model, conventional ECG, MAP, VCG, electrical activity maps for different parameters, PQRST wave forms as well as body surface potential maps.

https://www.ecgsim.org/

SKILLSTAT

Electrocardiography Simulator, the 26 most important patterns of the human ECG.

https://www.skillstat.com/tools/ecg-simulator

Neurological Eye Simulator

Online eye movement simulator demonstrating the effects of single or multiple injuries of 12 eye muscles and 6 cranial pairs related to eye movement. Generated at the University of California (Davis).

https://somapp.ucdmc.ucdavis.edu/eyerelease/Interface/TopFrame.htm

VisionSimulation

Online simulator of visual refractive disturbances, multiple scenarios and disorders.

https://visionsimulations.com/index.htm

Anestesia Simulation Portfolio

More than 45 simulation modules in anesthesia for physiological and clinical analysis, oximetry, blood flow, oxygen saturation, Qp / Qs, fractional saturation, respiration, treatments. Produced by the University of Florida.

http://vam.anest.ufl.edu/simulations/simulationportfolio.php

Neuma

PNEUMA are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. Cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. Author: The Biomedical Simulations Resource (BMSR) at the University of Southern California

https://bmsr.usc.edu/software/pneuma/

The Cardiovascular System

Simulator for up to 60 variables of the cardiovascular status of a simulated patient. Vasoactive drugs, assess patient status for up to 10 days. Provides graphical and analytical results. Authors: Min, de Goeijen, Sikken (University of Twente) and Coleman (University of Mississippi).

http://www.rikmin.nl/Java/Simulaties/CardioP1/Cardio.htm

CVSim

Cardiovascular simulator for preload, afterload, contractility, heart rate as viewed by pressure-volume relations, Drugs effects, clinical case of heart failure. Authors: Burkhoff, Kass, Maughan, Cardiology División, The Johns Hopkins Medical Institutions, USA.

http://oac.med.jhmi.edu/cvsim/index-Original.html

A Cardiovascular Simulator for Research

The model is capable of generating reasonable human pulsatile hemodynamic waveforms, cardiac function and venous return curves, and beat-to-beat hemodynamic variability.

https://physionet.org/content/rcvsim/1.0.0/

Web-HUMAN

Modeling of normal and pathological cardiovascular, respiratory, renal, acid-base balance, temperature regulation, fever, hydroelectrolytic, endocrine, neurological, and muscular balance. It handles more than 60 variables. Skidmore University, Florida, USA.

http://webhuman.us.es/human/

CARDIOWEB

Graphical calculation of the relationships between cardiac output, venous pressure, arterial volume, right atrial volume, arterial pressure, right atrial arterial pressure, venous volume vs time. With more than 20 parameters to define.

http://www.shodor.org/ssep/lessons/heart/cardioweb.html

CC3D

Multiscale multicellular modeling of tissue function and disease using CompuCell3D: A simplified computer simulation of acute primary viral infection and immune response in an epithelial tissue.

https://compucell3d.org/FrontPage

Infection Simulator

This program is designed to simulate the spread of HIV/AIDS across a population, as well as the spread of narcotics such as Pot, Cocaine, and Heroin. It shows real-time in OpenGL graphics how people interact with each other and accumulate various diseases.

https://sourceforge.net/projects/infection/

TRANSCRANIAL DOPPLER (TCD)

Cerebral hemodynamics, Doppler and cerebral monitoring model.

http://www.transcranial.com/downloads/index.html

VIRTUAL AUTOPSY

Interactive presentation of 18 cases of pathological anatomy very well documented with macro and microscopic pieces. The cases are oriented according to the user's criteria to reach a diagnosis (correct or wrong). Complementary documentation on anatomy and physiology, and the patient's medical history. Author: J Naylor, Dpt. Pathology, School of Medicine, University of Leicester, UK.

https://www.le.ac.uk/pathology/teach/va/titlpag1.html

Riesgo Cardiovascular

Universidad de Talca

http://pifrecv.utalca.cl/htm/simulador/simulador.php

Bacterial Growth

Amrit Vishwa Vidyapeetham University.

https://vlab.amrita.edu/?sub=3&brch=272&sim=1485&cnt=4

PHYSIOLOGY:

Nernst / Goldman Simulator

Diffusion potentials, equilibrium, concentrations and ionic permeabilities, temperature, graph and number. Authors: Branch and Wright, College of Medicine, University of Arizona, USA.

http://www.nernstgoldman.physiology.arizona.edu/

HumMod

Quantitative clinical physiology simulation, multiparametric situations such as circulation, respiration, kidney function, hormones, nervous system, metabolism, acid-base balance, thermoregulation, all integrated in a model.

http://hummod.org/agreement/

CVSim

CVSim is a lumped-parameter model of the human cardiovascular system that has been developed and used for research and for teaching quantitative physiology courses at MIT and Harvard Medical School since 1984. These include a six-compartment cardiovascular model with an arterial baroreflex system. Authors: Heldt et al., 2010.

https://www.physionet.org/content/cvsim/1.0.0/

Virtual Rat

Rat cardiovascular system by John Dempster (Strathclyde University, Glasgow). Dynamic simulation of the spinalized rat model with continuous recording of blood, left ventricular and venous pressures, heart rate and ventricular contractile force. It allows to apply more than 22 different drugs in various doses and define up to 10 new drugs. Includes vagal, renal or adrenal nerve stimulation, with or without spinalization. http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

Virtual Cat

The Virtual Cat is a simulation of an anaesthetised cat experiment - a whole animal preparation which is used as a tool for screening the actions of pharmaceutical compounds on the cardiovascular and skeletal muscle systems. The simulation displays the effects of drugs on the cat's blood pressure, heart rate, skeletal muscle and nictitating membrane contractions. John Dempster (Strathclyde University, Glasgow).

http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

Virtual Organ Bath

Simulated contractile properties of Ilium, Jejunum, arterial and biventer muscles, agonists, antagonists, electrical stimulation, export data. Author: Dempster J, Department of Physiology & Pharmacology, Strathclyde Institute for Biomedical Sciences, University of Strathclyde, Glasgow, UK.

http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

PhysiCell

Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal “virtual laboratory” for such multicellular systems simulates both the biochemical microenvironment (the “stage”) and many mechanically and biochemically interacting cells (the “players” upon the stage). PhysiCell was developed to work in concert with BioFVM to fill this role as a virtual laboratory.

http://physicell.org/about-2/

Human Ventricular Cell Model

Applet that simulates the activation of human epi -, endo - and myocardial cells, Calculate and graph various excitation cycles with more than 16 parameters, ionic currents, gates, etc. Authors: Tusscher, Noble, Noble and Panfilov (J Physiol 2004; 286: H1573-H1589). CellMC model at:

https://royalsocietypublishing.org/doi/suppl/10.1098/rsta.2011.0127

MCELL: A MONTE CARLO SIMULATOR OF CELLULAR MICROPHYSIOLOGY

Simulator of metabolism and subcellular physiology with both analytical and graphic results, offers great power and precision, 2D / 3D graphics. Author: MCell Team, Computational Neurobiology Lab, The Salk Institute for Biology Study, San Diego, USA.

https://mcell.org/

The Respiratory System

Eleven models for respiratory, mechanical, respiratory physiology, gas exchange, ventilation / perfusion ratio, and acid / alkali balance. Authors: Modell and Modell, Physiology Educational Research Consortium, Seattle, and various U.S.A. universities.

http://www.interniche.org/en/alternatives/simulations-physiology-respiratory-system

CELL BIOLOGY:

Cell Illustrator

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

http://www.cellillustrator.com/home

University of Colorado Simulations

Basic biology simulation suit

https://phet.colorado.edu/en/simulations/filter?subjects=biology&sort=alpha&view=grid

SimBio

SimBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic β cells. SimBio is written in Java, uses XML and can solve ordinary differential equations.

http://www.sim-bio.org/index.html

IMMUNOLOGY:

Enteric Immunity Simulator (ENISI)

Simulator of the gastrointestinal (GI) tract mucosal immune responses created for generating and testing hypothesis of mechanisms of immune regulation in response to the presence of resident commensal or pathogenic bacteria. Author: The NIMML Institute.

https://nimml.org/tools/enisi-suite

SIMMUNE

Immunological package consisting of three components: a) Modeler: molecules and properties, enzymatic transformations, properties and cellular behavior, extracellular compartments, parameters and simulation protocols, molecular complexes with properties and interactions; b) Simulator: molecular movements, gradients, reactions and molecular dynamics; c) Search engine of the intracellular signaling network. Institute for Theoretical Physics (Uni-Hamburg), Laboratory of Immunology (National Institute of Allergy and Infectious Diseases, NIH, USA) and NIAID, USA.

http://simmune.org/simmune/i_sim.html

C-ImmSim

Powerful Server-based simulator for dynamic modelling of Immune Response. Antigen and vaccine definitions, injection times, host haplotype, extortable results. From Center for Biological Sequence Analysis as the bioinformatic unit at Technical University of Denmark .

http://www.cbs.dtu.dk/services/C-ImmSim-10.1/

BIOCHEMISTRY:

COPASI

Application for simulation and analysis of biochemical networks and their dynamics.

http://copasi.org/

Biological systems modelling

JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.

https://jjj.biochem.sun.ac.za/

GHEMICAL

Computational chemistry software for quantum mechanics (semi empirical and ab initio) and molecular mechanics, reduced protein models, geometric optimization, molecular dynamics. It has a large number of visualization tools. Produced by Acton, Banck, Bréfort et al. From the University of Finland.

http://bioinformatics.org/ghemical/ghemical/index.html

Electrophoresis

Protein electrophoresis simulator, allows to run patterns, vary the % of acrylamide and the voltage of the run. Migration graph vs. molecular weight, performs goodness of fit statistics. Authors: Craig and Mix, Chemistry Dept. of the Rochester Institute of Technology, USA.

http://biomodel.uah.es/en/lab/SDS-PAGE/inicio.htm

Simul 5

Simulation of the movement of ions in liquid solutions in an electric field. It solves sets of nonlinear partial differential equations and nonlinear algebraic equations describing acid-base equilibria. Simul is useful for people engaged in electromigration separation methods, e.g., capillary electrophoresis, isotachophoresis, isoelectric focusing. Its mathematical model of electromigration accounts for any number of multivalent electrolytes or ampholytes, even in the hundreds. It includes a database of ions based on Takeshi Hirokawa's tables. Author: Bohuslav Gaš, Faculty of Science, Charles University, Prague.

https://web.natur.cuni.cz/gas/simul.html

Calcium Ion Selective Electrode Simulation

Simulation of calcium concentration measurements by ion selective electrodes, uses the standard addition method. University of Maryland, USA. https://terpconnect.umd.edu/~toh/models/CaElectrode.html

Worksheets for Analytical Calibration Curves

Excel and OpenOffice Calc Version.

https://terpconnect.umd.edu/~toh/models/CalibrationCurve.html

CellDesigner

Modeling of biochemical networks of regulatory genes, visual representation of biochemical semantics, comprehensive graphic notation, process diagrams, databases, export data and graphics in PDF / SVG. Author: A Funahashi, Systems Biology Institute and Keio University, Tokyo, Japan.

http://www.celldesigner.org/

BIOPHYSICS:

QuB

Quantify Unknown Biophysics to explore the dynamics of hidden states in a memoryless system. Simulate the output from a model system responding to a voltage / pressure / concentration ladder, or recover the most likely transition rates from noisy data.

https://qub.mandelics.com/

Virtual Molecular Dynamics Laboratory Suite

Set of molecular dynamics simulators: large-scale thermodynamics (Lennard-Jones model), molecular interactions, behavior of microscopic particles, molecular video player, simple polymer models using the IGSAW method that avoids self-intersection.

https://getwinpcsoft.com/The-Virtual-Molecular-Dynamics-Laboratory-8146/

NEUROPHYSIOLOGY:

NEURON

Gold standard simulation environment used in laboratories and classrooms around the world for building and using computational models of neurons and networks of neurons.

https://www.neuron.yale.edu/neuron/

XNBC

Biological neural network simulation package. Neural segments, neurons, neural clusters, networks, nuclei, synapses, conductances, simultaneous records. Neuronal discharges are analyzed by traditional, point process and time series methods.

http://ticemed-sa.upmc.fr/xnbc/

SNNAP

Simulator for Neural Networks and Action Potentials is a tool for rapid development and simulation of realistic models of single neurons and neural networks. It includes mathematical descriptions of ion currents and intracellular second messengers and ions. In addition, you can simulate current flow in multicompartment models of neurons by using the equations describing electric coupling. Also includes mathematical descriptions of intracellular second messengers and ions, and simulate the modulation of membrane currents and synaptic transmission, either enhancement or inhibition. University of Texas.

https://med.uth.edu/nba/snnap/

SPATCH

an open source virtual laboratory designed to perform simulated electrophysiological experiments without the technical difficulties inherent to laboratory work. It provides the core equipment necessary for recording neuronal activity and allows the user to install the equipment, design their own protocols, prepare solutions to bathe the preparation or to fill the electrodes, and gather data. Authors: Cannona and Hammond (UK & France).

https://www.brains-minds-media.org/archive/1403/index_html#d57e109

EONS

(Elementary Objects of the Nervous System) the focus consists in modeling hippocampal synaptic nonlinear dynamics and understanding their challenging complexity. Such modeling consists in understanding the role of the elements that comprise a synapse and participate in the transmission of information from the presynaptic terminal to post-synaptic density and more generally from a neuron to another. Author: The Biomedical Simulations Resource (BMSR) at the University of Southern California.

https://bmsr.usc.edu/software/eons/

Abstracted Protein Simulator

Model for the post synaptic density, a complex assembly of ion channels and cytoskeleton which is a critical part of learning and memory in the synapse, self assembly of simple viruses from their constituent proteins, since more complete molecular data sets are available for viruses than neurons.The model specification is an XML file which includes details of protein shapes, binding sites, interaction and state change probabilities. The simulation algorithm is based on monte-carlo techniques and 3D animation.

http://www.neurogems.org/protSim/

HHsim

Graphical Hodgkin-Huxley Simulator, excitable membranes using the Hodgkin-Huxley equations. Full access to the parameters of the equations. Written by Touretzky, Albert, Daw, Ladsariya of Carnegie Mellon University.

http://www.cs.cmu.edu/~dst/HHsim/

Virtual NMJ

The Virtual NMJ is a simulation of an experiment recording the electrical potentials associated with neuromuscular transmission at the skeletal neuromuscular junction. The simulation allows you to observe the muscle action potential (AP) and endplate potentials (EPPs) evoked by either nerve stimulation or by direct current stimulation of the muscle fibre. The effects of a variety of drugs and of changes to ionic composition of the extracellular solution on the AP and EPPs can be studied.

http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

Virtual Twitch

The Virtual Twitch is a simulation of the rat phrenic nerve-hemidiaphragm preparation, used to the study the actions of neuromuscular blocking and reversal agents, and other drugs which affect neuromuscular transmission. The hemidiaphraghm is a large, focally innervated, respiratory skeletal muscle, composed of fast-type muscle fibres. Electrical stimulation of the phrenic nerve evokes fast, shorting-lasting muscle twitches.

http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

Virtual Nerve

Axon simulator, local and action potentials, extracellular ionic concentrations of sodium and potassium, stimulation settings (frequency and intensity), effects of TTX, Lidocaine or Aminopyridine at adjustable concentrations. Records data and images from the oscilloscope screen. Author: J Dempster, University of Strathclyde, UK.

http://spider.science.strath.ac.uk/sipbs/page.php?page=software_sims

Stuttgart Neural Network Simulator

Neuronal network simulator for Backpropagation, forward networks, vanilla, BP momentum term / flat spot elimination, Counterpropagation, Quickprop, Backpercolation Rprop, RBF, ART1-2-MAP, Cascade Correlation, Recurrent Cascade Correlation, Dynamic LVQ, Backpropagation through time, Quickprop through time, Kohonen maps, TDNN, Jordan networks, Elman, Associative Memory. Uni-Stuttgart & Uni-Tübingen.

https://www.inf.ufsc.br/~aldo.vw/patrec/SNNS/index.html

CESE

Cell Electrophysiology Simulation Environment package for electrophysiological simulation in any type of (unique) cells, action potentials, ion currents, effects of ionic concentrations, temperature, I-Vs, Markovian currents, can use FitzHugh-Nagumo, Hodgkin-Huxley, Beeler-Reuter, Luo models -Rudy Model I and II and more than 15 additional models. Author: S Missan, Biotech / Pharma Professionals Network member, Canada.

https://sourceforge.net/projects/cese/

SpikeShaper

SpikeShaper is a Windows program for exploring and fitting parameters to Hodgkin-Huxley-type single compartment neural models. It provides an off-the-shelf generalized HH simulator that allows rapid construction of models, and easy exploration of the effects of changing the ionic and kinetic properties of models. The program also provides a facility for fitting the parameters of such models to template waveforms.

https://www.st-andrews.ac.uk/~wjh/spikeshaper/

NANS: Neuron And Network Simulator

Package of four graphic neuronal and network simulators. Ease building models, for teaching and research. University of Harvard, USA.

http://vlsi.eecs.harvard.edu/research/nans.html

ELECTROPHYSIOLOGY and The Molecular Basis of Excitability

Simulates two compartments (finite or infinite) connected by an ion channel (selective or not). It allows to define the concentrations of the solute (charged or neutral) in each compartment. Calculate the flows and the potential difference vs. time. F. Bezanilla´s Lab, Universidad de Chicago, USA.

http://nerve.bsd.uchicago.edu/

NEUROSIM 5

Neural simulator primarily designed for teaching neurophysiology at both undergraduate and graduate level. Fast high level model building including several measurent and display modes. Neurosim contains seven models, each of which simulates a particular aspect of neural function. The models operate independently of each other, but share many user interface features. Hodgkin-Huxley, Goldman, Membrane patch, Passive conduction, Network, Advanced HH, Wilson-Cowan. Design by Dr. W. J. Heitler, University of St. Andrew, Scotland.

https://www.st-andrews.ac.uk/~wjh/neurosim/

GENETICS

SELSIM

Simulates population genetic data in where natural selection occurs. Indicates patterns of genetic diversity suggestive of a particular form of natural selection. These data allow detecting genomic regions with historical selective pressures.

https://popmodels.cancercontrol.cancer.gov/gsr/packages/selsim/

Evolve

Simulation of artificial life, with a two-dimensional universe that evolves according to definable rules that includes processes of replication and cumulative selection. Author: K Stauffer.

https://labs.minutelabs.io/evolution-simulator/#/s/10/viewer?intro=

Evo Tutor

Evolution simulator able to natural selection, mutation, gene flow, genetics, reproduction, genetic drift, adaptation, speciation, extintion, phylogenetics, sexual selection, etc.

http://www.evotutor.org/index.html

Population Calculator

Population growth simulator with 11 control parameters, including number of young, mature and old, decades to simulate, birth rate, steady state, slow growth, Malthusian growth, influence of gender distribution. Author: Francis Turner.

http://www.di2.nu/pop_sim.html

TARGETgene

A major goal of cancer research is to find specific therapies directed at molecular disease targets. High-throughput technologies can now be used to identify hundreds or even thousands of candidate genes (e.g., genes with genomic alterations or differentially expressed genes) in a cancer. However, it is difficult to prioritize potential therapeutic targets from such a large amount of candidate genes. The vast array of in silico resources currently available in life sciences research offers the possibility of aiding the drug discovery process. Aimed to identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. Author: The Biomedical Simulations Resource (BMSR) at the University of Southern California.

https://bmsr.usc.edu/software/targetgene/

Hit Cancer

Evaluation of the mutations effect on the incidence of population cancer. Maintained by NIH, USA.

https://science.education.nih.gov/customers/HS_Cancer_Activity3_Simulator.html

POPULUS

The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models may be chosen from a menu, and students can move among the parameter boxes of an input window, changing initial defaults to values of their own choosing. Most modules offer several graphical outputs of model dynamics, and their computational algorithms are detailed in an Acrobat-based help system packaged with the program.

https://cbs.umn.edu/populus/download-populus

BEAST2

Cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analyzing the results.

http://www.beast2.org/

SimSoup

SimSoup is a project for the investigation of non-genetic mechanisms of evolution, especially evolution of chemical networks in the context of the Origin of Life. I am using an artificial chemistry approach, and SimSoup is also the name of the simulation program that I have developed to investigate the dynamic behavior of chemical networks and the molecular structures that determine the properties of these networks.

http://www.simsoup.info/SimSoup.htm

BIOGENESIS

Biogenesis is an artificial life program that simulates the processes involved in the evolution of organisms. It shows colored segment-based organisms that mutate and evolve in a 2D environment. Biogenesis is based on Primordial Life.

https://sourceforge.net/projects/biogenesis/

SOCIOLOGY:

QPAWN

This is a world simulation where people can join up as the nation of their choice and perform the foreign, economic, military, and political policies that they wish. Qpawn is a web-based simulator is a nation-simulation game in which players take the roles of leaders of nations or organizations. Qpawn differs from a government simulator in that it simulates a group of nations or the entire world, whereas a government simulator simulates a single nation or part of a single nation.

https://www.pbm.com/~lindahl/pbm_list/descriptions/1178799053.15965.html

ALL PORPUSE SIMS:

DIZZY

Dizzy is a tool for stochastic and deterministic simulation of chemical reactions. Faster stochastic simulation algorithms such as the optimized direct method, the sorting direct method, and the logarithmic direct method. Users can compare the effectiveness of the stochastic simulators on the problems which interest them. Developed by the Bolouri institute in Seattle, this version of the Dizzy tool has been extended at the Laboratory for Foundations of Computer Science, Edinburgh.

http://homepages.inf.ed.ac.uk/stg/software/Dizzy/

MCSIM

Suite of simulation software. Design one's own statistical or simulation models, Monte Carlo simulations, and Bayesian inference through (tempered) Markov chain Monte Carlo simulations. Parallel computing of Monte Carlo or MCMC simulations.

https://www.gnu.org/software/mcsim/

EPIDEMIOLOGY

GLEAMviz

Pandemic simulator, simple, intuitive and visual way to set up simulations, develop disease models, and evaluate simulation results using a variety of maps, charts and data analysis tools.

http://www.gleamviz.org/simulator/

InfluSim

A deterministic pandemic influenza simulator. Computes the effect of interventions like antiviral treatment of cases and social distancing. To be used for pandemic preparedness planning by health care offices. OS-independent Java/SWT/RCP/Applet.

https://sourceforge.net/p/influsim/wiki/Home/

QuickFlu

Outbreak simulator, uses parameters described by Longini et al. (Am. J Epidemiol. 159 (2004): 623-33) to calculate the average of secondary infections generated by the index case, visualization and rapid calculation of the consequences of the application of antiviral drugs as an intervention against influenza. Authors: Eichner and Schwehm of ExploSYS and Uni-Tübingen University Hospital, Department for Medical Biometry (IMB).

https://epimos.com/index.php?id=22&L=0

COVIDsim

Pandemic COVID-19 simulator. Development by Martin Eichner (Epimos GmbH) and Markus Schwehm (ExploSYS GmbH) supported by University of Tübingen and IMAAC NEXT Association and the German Federal Ministry of Education and Research.

http://covidsim.eu/

SISPREAD

Sispread allows to simulate the dynamics of an hypothetic infectious disease within a contact network of connected people. It is intended to help people concerned by public health to easily perform epidemic simulations and to analyze their results. Author: P Crepey, Softpedia.

http://sispread.sourceforge.net/

RADIOLOGY:

CTSIM

CTSim simulates the process of transmitting X-rays through phantom objects. These X-ray data are called projections. CTSim reconstructs the original phantom image from the projections using a variety of algorithms. Additionally, CTSim has a wide array of image analysis and image processing functions.

http://ctsim.org/

X-Ray Simulation (DEMO)

Fast and accurate character animation technique so that the user can import any kind of anatomic models, move the joints of the virtual patient into the required position, and deform the skin surface and the internal soft tissues accordingly. We also developed gVirtualXRay, an open source library to simulate X-rays, to generate the corresponding radiographs in real-time. Parameters of the X-ray machine, e.g. beam collimation, beam spectrum, etc. can also be changed by the user and the effect of the changes are visualized without delay.

https://gmrv.es/gmrvvis/xraysim/#screenshots

IMMUNOLOGY:

IMMSIM

Immune system simulator with the ability to generate interactions between cells of the immune system: B, T cells, macrophages, as well as antigens, antibodies, lymphokines and any other factor depending on the researcher's needs. It also allows to make clonal selection models and humoral response. Use the computer technique of the hypercellular automaton.

http://www.cbs.dtu.dk/services/C-ImmSim-10.1/