This project aims to combining useful toolboxes in one cohesive package. Please note that some of these toolboxes have copyright. See below for how to cite them. All other scripts are written by me (William Lövfors) and are free to use (CC BY-SA).
## IMPORTANT: Working with submodules
To get up-to-date versions of some of the toolboxes, these are added as submodules. A submodule is essentially another git repo inside a git repo. Think of it as nested git repos. Because of this, you need to also clone/pull the submodule repos.
The easiest way is to clone with `git clone --recurse-submodules` (git version >= 2.13).
If you have already cloned without `--recurse-submodules`, you need to run `git submodule update --init --recursive`.
To later update the toolboxes (locally) run git `pull --recurse-submodules`.
## Copyright statements and citations:
Here the toolboxes that have non-free licenses are listed. Note that some toolboxes might not be listed here. If you want to use them, you **MUST** check if you are allowed to. For most toolboxes, the original webpage, and publications are listed.
#### Natsort (FEX)
Available at [MATLAB file exchange](https://se.mathworks.com/matlabcentral/fileexchange/47434-natural-order-filename-sort).
Stephen Cobeldick (2020). Natural-Order Filename Sort (https://www.mathworks.com/matlabcentral/fileexchange/47434-natural-order-filename-sort), MATLAB Central File Exchange. Retrieved December 9, 2020.
#### IQM tools/SBTOOLBOX
Available [here for SBtoolbox](http://www.sbtoolbox2.org/main.php) and [here for IQM tools](https://iqmtools.intiquan.com/)
Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515, 2006, doi:10.1093/bioinformatics/bti799
#### MEIGO
Available [here (project page)](http://gingproc.iim.csic.es/meigo.html) and [here (repo)](https://bitbucket.org/jrbanga_/meigo64/src/master/).
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR and Saez-Rodriguez J. (2014) MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics 15:136. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-136
#### Pesto
Available [here (repo)] (https://github.com/ICB-DCM/PESTO)
Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hross, S., Fröhlich, F., Hasenauer, J. (2018). PESTO: Parameter EStimation TOolbox. Bioinformatics, 34(4), 705-707. doi: 10.1093/bioinformatics/btx676
#### CasAdi
Available [here (project page)](https://web.casadi.org/) and [here (repo)](https://github.com/casadi/casadi).
J. A. E. Andersson, J. Gillis, G. Horn, J. B. Rawlings, and M. Diehl, “CasADi – A software framework for nonlinear optimization and optimal control,” Mathematical Programming Computation, vol. 11, no. 1, pp. 1–36, 2019, doi: 10.1007/s12532-018-0139-4.
