Building applications using MATLAB

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.

Getting Started

First download the project or clone it from GitHub here. To set up the toolchain, open the project in MATLAB.

Set Up Tooling

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.

filepath = biolib.getDirectory("SUPPORTPACKAGEROOT");
cd(filepath);
!git clone https://github.com/emscripten-core/emsdk.git --branch 1.39.8;

After this, install version 1.39.8 of the Emscripten tools in the selected directory.

switch true
    case ispc
        !emsdk\emsdk.bat install 1.39.8-upstream
    case isunix || ismac
        !./emsdk/emsdk install 1.39.8-upstream 
end

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.

biolib.generateToolchainFile();
RTW.TargetRegistry.getInstance("reset");

Depending on your machine's default shell, the generation of the toolchain might fail. If so, in +biolib/getToolchain.m line 81, try exchanging bash by source or vice-versa, to solve the problem.

Build Sample Function

Navigate to the example directory:

cd(fullfile(biolib.getDirectory("SUPPORTPACKAGEROOT"),"example"));

Create a single entry-point function called main(parameters). In the example below, this function takes in a DNA string and it calculates the proportion of Adenine, Thymine, Cytosine and Guanine.

% Example function
function out = main(arguments);
% Parse input arguments
args = split_arguments_by_space(arguments);
dna = upper(args{3});

adenine = int8(0);
thymine = int8(0);
cytosine = int8(0);
guanine = int8(0);

for i = 1:length(dna)
    if dna(i) == 'A'
        adenine = adenine + 1
    elseif dna(i) == 'T'
        thymine = thymine + 1
    elseif dna(i) == 'C'
        cytosine = cytosine + 1
    elseif dna(i) == 'G'
        guanine = guanine + 1
    end
end

fprintf('A:%d; T:%d; C:%d; G:%d', adenine, thymine, cytosine, guanine)

% Return code
out = 0;
end

% Helper function that reads the input arguments
function args = split_arguments_by_space(argument_string)
if any(isspace(argument_string))
    space_diff = diff(isspace(argument_string));
    start_positions = [1, find(space_diff == -1) + 1];
    end_positions = [find(space_diff == 1), length(argument_string)];
    number_of_args = numel(start_positions);
    args = cell(1, number_of_args);
    for i = 1 : number_of_args
        args{i} = argument_string(start_positions(i):end_positions(i));
    end
else
    args = {argument_string};
end
end

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.

cfg = coder.config("dll");
cfg.GenerateExampleMain = "DoNotGenerate";

cfg.TargetLang = "C";
cfg.Toolchain = "BiolibWasm";

cfg.BuildConfiguration = "Biolib Default";
cfg.CustomSource = "main.c";

codegen -config cfg main_biolib -args {"a",[1 inf]} main.c;

To view a full example of the required commands, see the setup.mlx file here.

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.

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:

You can find information about MATLAB based research notebooks and MATLAB Live Scripts here:

See code examples, introductory videos, and user stories:

Explore more MATLAB code examples at the MATLAB Code Examples page or discover how you can use MATLAB for Open Science.

Many faculty, staff, and students at universities already have access to MATLAB through their school. To see if you have access see this page: Does Your School Have a Campus License?

Building applications using MATLAB

Getting Started

Set Up Tooling

Build Sample Function

Further MATLAB Resources and Training

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