Is Fortran used in medicine, vaccine research, or epidemic studies?

I am looking for any information about the use of Fortran in the medical field, in vaccine research, or in epidemic studies. Any pointers to code or mentions about usage in research papers or even general news will be useful.

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Amber molecular dynamics is one example popular Fortran software for drug interaction and discovery simulations.


It is used indirectly to the degree that medical researchers use R. R currently cannot build without Fortran.

Source: Will R Work on Apple Silicon? (link)

Much regulatory work uses Stata, but I don’t know much at all about it.


Fortran has long been one of the primary languages of statistical computing, although nowadays many algorithms are implemented in C, C++, Matlab, Python/Numpy, and R. Statistics includes biostatistics, and much of the biostatistics software of the MD Anderson Cancer Center is in Fortran.

Time series methods have been applied to EEG, for example in Multi-channel EEG analyses via dynamic regression models with time-varying lag/lead structure. Two of the authors of that paper also wrote the book Time Series: Modeling, Computation, and Inference, which analyses EEG time series using a Fortran code for time-varying vector autoregression. The latest version of the software is in Matlab. All important Matlab software should be translated to modern Fortran and sped up :slight_smile:


Googling “epidemic fortran” gets some relevant links:

The epirecipes project has Fortran code that a user can run in a Jupyter notebook for a SIR model from the book Modeling Infectious Diseases in Humans and Animals. Other programs from the book, in C++, Python, Fortran, and Matlab, are here.

The 2020 paper A Simulation of a COVID-19 Epidemic Based on a Deterministic SEIR Model refers to a Fortran code for simulated annealing.

The 2020 paper Simulation of the COVID-19 epidemic on the social network of Slovenia: Estimating the intrinsic forecast uncertainty has downloadable Python code calling Fortran 90 using F2PY.

Delay differential equations have applications in biology, and there are Fortran codes for them.


A naïve approach to identify Fortran in medicine would be to access journals relevant to the topics mentioned, and to hope «Fortran» is indexed as such, as a keyword. Without background in medicine, I tested New England Journal of Medicine, and The Lancet (on occasion mentioned in the radio’s science corner). A consultation of a research librarian and dedicated literature database likely is more suitable for such a query.

Given the age of Fortran, and chemometrics, one one hand, and the rise of «chemical mapping / imaging» of a sample to record spatial composition of e.g., a tissue, by means of MS and IR / Raman spectroscopy in histology (an open access review), on the other, I speculate the pixelwise processing (each pixel is about a whole spectrum) benefits from Fortran when it comes to cluster analysis / principal component analysis (a commercial example). This however suggests to complement abovementioned search by a consultation of databases about chemistry / physics / optics (e.g., this open access publication about cellular stress on SPIE).

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A lot of molecular simulation for drug discovery is done using density-functional theory (DFT) [1], and most of the widely-used DFT codes are written in fortran. See in particular ONETEP and other O(N) codes for the simulation of large molecules.


There are lists like here to appreciate Fortran’s contribution. On occasion, the extent sometimes is quantified, e.g., for NWChem:


(loc. cit.)

W.E. Schiesser and coworkers have written books with Fortran code

Computational Transport Phenomena: Numerical Methods for the Solution of Transport Problems

The Numerical Method of Lines: Integration of Partial Differential Equations

Ordinary and Partial Differential Equation Routines in C, C++, Fortran, Java, Maple, and MATLAB

His book Time Delay ODE/PDE Models: Applications in Biomedical Science and Engineering uses R. Maybe the R packages call Fortran code.

I don’t know what language his ODE/DAE/PDE software is written in, but many of the applications are in medicine:

Magnetic resonance imaging (MRI) guidance of radio frequency tumor ablation

Distributed compartment models for positron emission tomography (PET) receptor studies

Response of muscle and lung tissue to transient heating in vivo

Analysis of atherosclerotic lesion development

Intracellular calcium wave propagation linked to cardiac arrhythmia

Antigen-antibody reactions on chemically treated silicon wafers

Arterial endothelium permeability

Density equalizing maps of neural data

Thrombus dynamics

Acid-mediated tumor growth

Retinal oxygen transport

Rapid oxygen purge in a medical oxygen concentrator

Hemodialyzer dynamics

Epidermal wound healing

Drug distribution from a polymer matrix

Quantum efficiency of pigment molecules in cone photoreceptors

Method of lines applied to the discrete ordinates method for radiative heat transfer

Propagation of laser beams in polymer particles

Laser light propagation through Bose-Einstein condensates

Stimulated Brillouin scattering dynamics

Identification of free radical polymerization parameters

Dynamic analysis of polymer blown-film extrusion

Polymer swelling in fiber optic sensors

Drying of granular food particles

Droplet drying with moving boundary

Simulation of cement production units

Radial dispersion in Fischer-Tropsch reactors

Performance of membrane reactors

Methane combustion with CO2 separation

Diffusion and reaction of H2 in multilayer containment vessels

Spatial probabilistic model for steel corrosion in reinforced concrete structures

Reaction-diffusion in metallic systems

Oxygen grain-boundary transport

Dynamics of cryogenics refrigeration plants

Cryogenic (liquid helium) cooling of superconducting magnets

Heat transfer dynamics in rapid, thermal swing adsorption

Hydrotreating and naphtha reforming

Dynamics of a monolith loop reactor system

Methylation kinetics of Hg in aquatic sediments

Settling of particles in drilling fluids

Soil hydrology

Soil internal drainage and short furrow redistribution

Eutrophication and pH calculation

Dynamics of a karst aquifier

Coastal dynamics

Shoreline sediment evolution

River pollutant transport

Release control of toxic nanomaterials to the environment

Sinkhole dynamics

Solute transport in karst conduits

Adaptive grid solution of electrochemical kinetic equations

Evaluation of effective diffusivities for porous catalysts

Physics of organic light emitting diodes (LEDs)

Plasma turbulence

Integro partial differential equations in plasma physics

Josephson electrodynamics

Solution of 1-D Euler equations for cavitations and one-fluid two-phase flow problems

Longitudinal vibrations of Rayleigh-Bishop and Rayleigh-Love rods

Analysis of black hole singularities in general relativity

Relativistic wavepackets in chaotic quantum cosmology

Sun’s magnetic field

Fokker-Planck equations for time evolution of velocity probabilty distributions

Collapse of the World Trade Center towers

Black-Scholes options pricing models (e.g., for convertible bonds)

3D Convolusional Filtering

This program reads 3-Dimensional scalar fields out of STRUCTURED-POINTS *.vtk files and filters them according to specific convolutional matrices/Kernels.
It’s tested with up to 160 Processors (4 nodes) on Vulcan. Turnaround time of roughly 200 Seconds while reading/computing/writing to storage on 18.5E09 Voxels of kind INTEGER2.

HLRS - NUM - Convolusional Filtering of Computed Tomography scans. Intended to get a clear separation between bone marrow and cancellous bone for subsequent binarization and calculations.

This program, under current development by Johannes Gebert, uses Fortran 2003 (at least) and MPI.