Mesoscopic Reaction Diffusion Simulator
We have released a new version of MesoRD. Apart from bugfixing, this version updates the code for the microscopically treated bi-molecular reactions to also include reactants with different diffusion rates. See the manual for more details. Grab it here
We are proud to annonce the release of MesoRD version 1.0!. Please download it here. This new version of MesoRD handles high spatial resolution also for close to diffusion-limited bi-molecular reactions, which has not earlier been possible using conventional spatially discrete stochastic simulation softwares. This is accomplished by introduction of scale dependent reaction rates based on microscopic reaction parameters as described in [8]. The microscopic parameters can now easily be added to existing SBML model descriptions].
A new version of MesoRD has been released, MesoRD 0.3. Some of the new features of MesoRD 0.3 is that it adheres to the SBML version 2, level 4, has rewritten CSG module and supports libsbml-4.*.
Please note that these releases are now obsolete. Use MesoRD
version 1.0, which does automatic scaling of reaction rates
based on microscopic reaction parameters.
We have
developed a special release of MesoRD, which allows for
reaction rates to be calculated using nearest neighbour
subvolumes. This allows for a correct description of the
reaction rates when the size of the subvolumes are close to
the reaction radii of the molecules. There are two different
versions which support this extension. One 3D version with
corresponding documentation, and one 2D version with
corresponding documentation.
MesoRD-0.2.1 is not compatible with the latest release of libsbml. Please use version libsbml-2.3.4, which is known to work together with MesoRD. Old libsbml releases can be found here.
The report of the first Master's degree project is on-line link.
Noise induced Min phenotypes in E. coli published in PLoS Comp. Biol. link
Version 0.2.1 is out. This new release makes the SBML files created for MesoRD compliant with the SBML standard. They should now pass the validators available (for example http://sbml.org/validator). See documentation in categories Compartment Modelling and CSG Modelling for more information.
There seem to be some problems with the equations in the on-line documentation and Windows Internet Explorer. Until the bug is fixed use the PDF version.
Version 0.2.0 is out. This new release allows MesoRD to do deterministic simulations using the same input files as for stochastic simulation. New features have been added to improve usability, code has been rewritten and bugs have been fixed.
What a day! A toolbox has been developed to ease the tedious task of visualising the simulation data. The toolbox runs in MATLAB and has been tested on Windows XP and Linux. Check it out at the MesoRDToolBox homepage.
"Stochastic reaction-diffusion simulation with MesoRD" is published in Bioinformatics link.
Version 0.1.10 is out! This release fixes some large bugs in unit handling and some small bugs here and there. It is most recommended for all users. This release also supports the latest libSBML version (in fact it requires the latest version).
A patch that works around the build errors you get if you use libSBML version 2.1.0 rather than version 2.0.3 has been submitted. To apply it, download the patch to the source distribution root, and do patch -p0 < libsbml-2.1.0.diff.
With emphasis on early. Version 0.1.9 is out. Our first alpha release. Sources, binaries and user documentation are available at the file release page. The MesoRD User's Guide for this release is available on-line for browsing.