The CalC ("Ca2+ Calculator") Reaction/Diffusion Modeling Software

CalC ("Calcium Calculator") is a modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. CalC is free software distributed under the terms of version 3 of the GNU General Public License.

Installation instructions:
README

• CalC version 7.0 implements cooperative (2-to-1) Ca²⁺ buffers: version fork into 6.x & 7.x
• CalC version x.4 implements binary file output
• CalC version x.6 implements non-linear membrane pump
• CalC version x.7 implements spherical enclosures and obstacles
• CalC version x.7.2 implements space-dependent calcium uptake
• CalC version x.8 implements arbitrary volume shapes and 2D surface plots
• CalC version x.8.4 improved and optimized adaptive time-step control
• CalC version x.9.1 important bug fix! (thanks to Christian Stricker!)
• CalC version x.9.2 bug fix in 1D data output (thanks to Morten G. Pedersen!)
• CalC version x.9.3 fixed program termination occurring before diagnostic output
• CalC version x.9.4 fixed problems with narrow off-center sources in polar variables
• CalC version x.9.6 cleaned up code to reduce compilation warnings and allow stricter compile flags
• CalC version x.9.7 allows to target membrane buffers to specific volume(s) or obstacles(s)

CalC versions 6.x.x mirror versions 7.x.x, but allow simple (1-to-1) Ca²⁺ buffers only, and therefore run faster; use them whenever cooperative buffers with two binding sites are not needed

NEW: CalC is now part of NeuroFedora open source Computational Neuroscience tools

Version		Ca²⁺ buffers:	Source:		Executables:
Release 7.9.7	Jan 15, 2021	Two Ca²⁺-binding sites	UNIX	MSDN C++	Win64	OS X 10.11.6
Release 6.9.7	Jan 15, 2021	One-to-one (faster code)	UNIX	MSDN C++	Win64	OS X 10.11.6

[ Link to full descriptions of all CalC release updates ]

Bug Alert! Bug in CalC versions x.8.0-x.8.9 affects some scripts defining more than one Ca²⁺ channel, reducing the current through the 2^nd and each consecutive Ca²⁺ channel. The bug was fixed in version x.9.1. Thanks to Christian Stricker for reporting. Click for detailed bug information

CalC Description and Features:
CalC uses a variation of the Alternating Direction Implicit (ADI) finite difference method, which is very CPU-time efficient, and accurate to 2nd order in time and space. Time-step is varied adaptively during the simulation.

CalC is CPU-time efficient and platform-independent (Windows, OS X, Linux, cygwin, etc.)
CalC is operated by a simple script language with non-trivial flow control, greatly increasing its flexibility.
CalC is easily combined with MATLAB without any special modifications (see demo).
CalC allows simulations in any geometry: cartesian 3D, 2D or 1D, polar, spherical, cylindrical, conical, etc.
CalC allows an arbitrary number of Ca²⁺ buffers, with 1-to-1 and 1-to-2 Ca²⁺ binding.
CalC scripts may include ordinary differential equations, for instance to model Ca²⁺-dependent exocytosis.
CalC results can be viewed in real time by piping the output into xmgrace (only on UNIX platforms).

CalC is provided on an as-is basis, but I will respond to any bug reports or technical questions, as soon as I can. If you use CalC in your published work, please cite our 2002 Biophys J article, and please send me a reference for inclusion in the CalC publication list upon publication.

CalC is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the license, or (at your option) any later version. CalC is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the license file for more details.

	Supported in part by the National Science Foundation grants 0417416, 0817703 and 1517085. However, NSF bears no responsibility for any findings, recommendations or conclusions provided by this material.
	Last modified: January 15, 2021 Maintained by Victor Matveev