To build an application using MATLAB code, you can use
the BioLib-MATLAB-Coder-Toolchain to compile the MATLAB
code to a BioLib-compatible WebAssembly executable.
First download the project or clone it from GitHub here. To
setup the toolchain, open the project in MATLAB.
Add the biolib-matlab-coder-toolchain and biolib-matlab-coder-toolchain/registry folders to the MATLAB path. You can
do this in MATLAB by right-clicking on the folder and selecting Add to Path. This is required for the toolchain to
be registered. Make sure that the root directory is a path without spaces and not a mapped network drive.
Next, run the following code to download the Emscripten tools into the Add-On directory.
After this, install version 1.39.8 of the Emscripten tools in the selected directory.
!emsdk\emsdk.bat install 1.39.8-upstream
case isunix || ismac
!./emsdk/emsdk install 1.39.8-upstream
If you have not already installed MATLAB Coder™, install instructions can be
found here. Now generate the BioLib
toolchain and register it with MATLAB Coder™. Your MATLAB code needs to be supported by MATLAB Coder in order to be
compiled using this toolchain.
In the above example, the input arguments are a string with the format -i [DNA_STRING] where -i is the key
and [DNA_STRING] the value. We split the parameter string in the example, and assign each position to a variable.
Note, that each argument to be entered in the final application need a key to be passed from BioLib.
To show the output, you can (1) print them as stdout or (2) write them to a file. Use the exit code out = 0; to
indicate that the application ran successfully.
Finally, run the below code to produce a WebAssembly file that runs on BioLib.
To view a full example of the required commands, see the setup.mlx
The last step is to upload the WebAssembly file, biolib_main.wasm, as an Emscripten module to a BioLib application.
You can see an example of this here and you can learn how to
create your first BioLib application here.
Further MATLAB Resources and Training
To learn more about MATLAB a number of useful resources are freely available online.
Getting Started with MATLAB is the central resource
page to learn how to use MATLAB. You can find a dedicated page for general tutorials at
the MATLAB and Simulink Tutorials page. And there
is also a number of free, self- paced, interactive MATLAB tutorials that run through the browser (no download required).
These “Onramp” courses offer approximately two hours of training on many topics. See for example: