FISIOCOMP Tools
Some of the computational tools developed at FISIOCOMP are available at our main GitHub repository at the following link: FISIOCOMP-UFJF. A brief description of some tools is given below.
MonoALG3D
Adaptive monodomain simulator using GPUs.
https://github.com/rsachetto/MonoAlg3D_C
Reference: A parallel accelerated adaptive mesh algorithm for the solution of electrical models of the heart.
OLIVEIRA, R. S.; ROCHA, B. M.; BURGARELLI, D.; MEIRA JUNIOR, W.; SANTOS, Rodrigo Weber dos.
International Journal of High Performance Systems Architecture (Print), v. 4, p. 89-100, 2012. https://doi.org/10.1504/IJHPSA.2012.050988
Cardiax
Cardiac electromechanics simulator based on finite element method. It solves monodomain and bidomain equations; cardiac mechanics using Holzapfel-Ogden and Guccione constitutive model; and coupled eletromechanics problem.
https://bitbucket.org/rochabm/cardiax
Reference: CAMPOS, J. O.; W. DOS SANTOS, R. ; SUNDNES, J. ; ROCHA, B. M. . Preconditioned Augmented Lagrangian formulation for nearly incompressible cardiac mechanics. International Journal for Numerical Methods in Biomedical Engineering, v. 10, p. 1-18, 2017. http://dx.doi.org/10.1002/cnm.2948
MyoMesh
Open-source pipeline for generating patient-specific biventricular heart meshes from MRI segmentations. It combines mesh processing, myocardial fiber assignment using the LDRB method, and scar labeling, producing final files ready for electrophysiology simulators (MonoALG3D, openCARP and FEniCS).
https://github.com/FISIOCOMP-UFJF/MyoMesh
Purkinje-Generator
Program to generate patient-specific Purkinje Networks within an endocardium surface given by triangles.
https://github.com/bergolho/Purkinje-Generator.git
ECGMARKER
ECGMARKER allows interactive viewing and manual annotation of ECGs, including QRS, QT intervals, extrasystoles, and arrhythmias.
https://github.com/SoaThais/ECG_MARKER.git
AGOS
AGOS is a CellML converter which allows the generation of C or Python code for solving the cell model.
https://github.com/FISIOCOMP-UFJF/agos
Reference: Ciro B. Barbosa, Rodrigo W. dos Santos, Ronan M. Amorim, Leandro N. Ciuffo, Fairus Manfroi, Rafael S. Oliveira, Fernando O. Campos. A Transformation Tool for ODE Based Models. Part of the Lecture Notes in Computer Science book series (LNCS, volume 3991).
https://doi.org/10.1007/11758501_14
OdeShell
An Interactive Tool and a Specific Domain Language to Develop Models Based on Ordinary Differential Equations. A simple compiler and an interactive shell to play with Ordinary Differential Equations (ODEs). The ODEs can be described using a very simple language and compiled to C code (more languages will be available). It is also possible to use the interactive shell to load, solve and plot the ODEs.
Rafael Sachetto Oliveira & Carolina Ribeiro Xavier
https://github.com/rsachetto/odecompiler
LVSpline
A pametrized approach for generating LV geometries and FE meshes using Python and Gmsh.
https://github.com/rochabm/lvspline
Reference: Campos, J. O., et al. “Uncertainty quantification and sensitivity analysis of left ventricular function during the full cardiac cycle.” Philosophical Transactions of the Royal Society A 378.2173 (2020): 20190381.
https://doi.org/10.1098/rsta.2019.0381