CellCompiler Files

CellCompiler latest version: 0.3

<Abstract>
This system generates C or Java program code.
Any one of RelML, RelMLPDE, SimpleRecML, StructuredRecML and StructuredRecMLPDE can be 
considered as an input file. 
 
<GUI>
location: jp.ac.ritsumei.is.hpcss.cellMLonGPU.app 
 CellCompilerGUI.java
Note: The GUI only currently supports biological funtion simulation with ordinary differential equations (ODEs).

<Main>
location: jp.ac.ritsumei.is.hpcss.cellMLonGPU.app
 CellCompilerMain.java

  Arguments Information  
  1. -C or -J  			(-C outputs C code, while -J outputs Java code)
  2. RelML or RelMLPDE or SimpleRecML or StructuredRecML or StructuredRecMLPDE
  3. Input file directory	(example; ./model/RelML/fhn_BackwardEuler.relml)
  4. Output directory 		(example; ./output)
  5. Output file name 		(example;  fhn_BackwardEulerSimulation) 

Example run arguments for biological function simulations with PDE:

FitzHugh-Nagumo model simulation using FTCS method and 5x5 mesh: 

-C RelMLPDE ./model/RelMLPDE/FHN_FTCS_Diffusion_2DV5_5x5.relml ./output fhn_ftcs_5x5

FitzHugh-Nagumo model simulation using Crank-Nicolson method and 5x5 mesh:

-C RelMLPDE ./model/RelMLPDE/FHN_CN_Diffusion_2DV5_5x5.relml ./output fhn_cn_5x5

Luo-Rudy 1991 model simulation using FTCS method and 5x5 mesh:

-C RelMLPDE ./model/RelMLPDE/LR1_FTCS_Diffusion_2DV5_5x5.relml ./output lr1_ftcs_5x5

Hund-Rudy 2004 model simulation using FTCS method and 5x5 mesh:

-C RelMLPDE ./model/RelMLPDE/HR04_FTCS_Diffusion_2DV5_5x5.relml ./output hr_ftcs_5x5


<SubMain>
Code Generator for Non-linear Simultaneous Equation system
location: jp.ac.ritsumei.is.hpcss.cellMLonGPU.app 
 ProgramGeneratorMain.java @author n-washio

Equation Expansion for Recurrence Relation system
location: jp.ac.ritsumei.is.hpcss.cellMLonGPU.app 
 SimpleExpansionMain.java @author m-ara

************************************** version 0.3 ChangeLog ********************************

- Made optimization changes in the code generation. The time it takes to generate simulations with explicit PDE schemes were reduced by 98%. The code generation time is now 40 to 60 times faster.

************************************** version 0.2 ChangeLog ********************************

- Added implicit FDM method handling for biological function simulations with PDEs.
- PDE code generator creates separate C source and header files containing the Newton solver for implicit methods. 
- Added classes for reading and storing CellML file information. This might serve as API for using CellML files 
     in CellCompiler.


************************************** version 0.1 ChangeLog ********************************
version 0.1
   Introduced the automatic handling of boundary conditions for biological function simulations involving partial differential equations.


************************************** discontinued versions ********************************

CellMLCompiler latest version: 1.02

 CellMLCompiler(Java) latest version: 2.0

 ************************************** C++ Version ChangeLog ********************************
version 1.0
 Single cell simulation program generator

version 1.02
 Added 1D and 2D cell array simulation for C and Cuda program generator
 
 ************************************** Java Version ChangeLog ******************************** 
 version 2.0 
  Java version of the CellMLCompiler. This version is similar to the CellMLCompiler v1.02 (C++)