Open Science with MATLAB

Jan Studnička
[email protected]

Jan Daněk
[email protected]

www.humusoft.cz
[email protected]

16.2.2024 MUNI www.mathworks.com

What is MATLAB and Simulink
• MATLAB Statistics a optimization

– Engineering tool for technical computing Signal Processing and Comm.

– Graphical and computational tools Image Processing and CV

– High-level programming language Computational Finance

– Intuitive user interface (GUI) Computational Biology

– Modular, open architecture Neural Network, Fuzzy

• Simulink Physical Modeling

– Modeling, simulation and analysis of multidomain Control System Design

dynamic systems Event-Based Modeling
– Block diagram environment Test and Measurement
– Model Based Design Application Deployment
– Integrated with MATLAB Code Generation and Verification
• Toolboxes
 MATLAB in the Industry

Aerospace and defense Automotive Biotech Pharmaceutical

Communications Earth and Ocean Electronics Energy Production

Industrial Automation Medical Devices Metals and Mining Neuroscience

Applied Physics Railway Systems Finance Software and Internet

3 https://www.mathworks.com/solutions.html#industries
 Applications specialized
autonomous systems and robotics

predictive maintenance and IoT

basic automotive systems and ADAS
image processing and data analysis and
computer vision data science
computational biology

aerospace and UAV

signal processing
MATLAB physical modeling
financial analysis
Simulink
test and measurement control systems
systems engineering
RF systems and antennas code generation and
real-time applications

wireless communication systems code verification and certification

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 Data Analysis Workflow

Access Explore & Discover Share

Files Reporting and
Data Analysis Documentation
& Modeling

Algorithm
Software Outputs for Design
Development

Code & Applications

Application
Development
Hardware Deployment

Automate
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 Workshop information

• MATLAB Online
– matlab.mathworks.com
• Examples
– humusoft.cz/muni
If you don’t have account,
create one with your
university’s email address

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 MATLAB desktop
Toolstrip Workspace
file and data management, APPS variables in MATLAB memory

Documentation
syntax, examples
Current Folder
folder browser

Command Window
interactive command prompt
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What is Open Science?
 FAIR Science
Open Infrastructure • MATLAB on Science Gateways
• MATLAB on Jupyter
• MATLAB on HPC infrastructure

• Diverse data formats

• Public open data sets
• Big Data

Open Data Interoperable Workflows

• Interoperable MATLAB code

• Deep Learning in MATLAB

• Open Source MATLAB Toolboxes Reproducable

• Runnable MATLAB on GitHub
• MATLAB on reproducibility portals
Results
• MathWorks support for community
Agenda
SHARE
–
Use case
Programmatically Access Open Data from MATLAB
Brain Observatory Toolbox for Allen Brain Data

Available via
• GitHub – Open with MATLAB Online

• Add-Ons drop-down in MATLAB

• Dandi Hub

Brain Observatory Toolbox

Brain Observatory Toolbox:
Data Source & Environment Use Cases

MATLAB Ease of Setup

Online
AWS S3
Bucket
DANDIHub
Science
Gateway
DANDI
Archive BOT
Local
Machine
Allen (remote data)
Institute
RESTful MATLAB on
Web API AWS for More Data
Neuroscience Capacity
Data Sources User Environments
Brain Observatory Toolbox
Cloud Workflow
No downloads
No installs
Accessible to anyone, anywhere
Make Your MATLAB Code Open

Open with MATLAB Online

SHARE -
Example
Programmatically Access Open Data from MATLAB
The Image Data Resource (IDR)

A MATLAB Live Script with accompanying

• Jupyter Notebook
• m file
• reproducible code capsule on Code Ocean
to access and analyze Microscopy image data
sets from the IDR database
Open-Microscopy-Data-MATLAB
MATLAB Live Script Notebooks
Tell a story… with code, words, pictures, equations, images, and controls…

Live Editor
Open Source MATLAB Community Toolboxes

1 click install via Add-Ons

• „Set and Forget“ for authors

• Automatically updates with new releases

Open Source Community Toolboxes

Link your GitHub repo
Open MATLAB Code on GitHub – Click and Run

DOI

200,000+ MATLAB
code repositories…

Including tools authored by

experts in their fields with
thousands of downloads per
year
Create Interoperable Workflows

Why researchers often need more than one tool

▪ Use functionality of one in another
▪ Run code available in another language (hybrid workflows)
▪ Collaborate

Call MATLAB from Python Call Python from MATLAB

$ pip install matlabengine

>>> py.math.sqrt(42)
>>> import matlab.engine
>>> py.importlib.import_module()
>>> m = matlab.engine.start_matlab()
>>> x = m.sqrt(42)

Using MATLAB with Python

Create Interoperable Workflows

Import DL models from other frameworks

MATLAB

Tensorflow Pytorch

Caffe2 ONNX MXNet

Cognitive
Core ML Chainer
Toolkit

importTensorFlowNetwork Deep Interpolation Toolbox

importNetworkFromPytorch
importONNXNetwork

Interoperable with DL frameworks

SCALE
UP
MATLAB Kernel on Jupyter
MATLAB Desktop via Browser on Jupyter
 EGI - Run MATLAB on EGI infrastructure

Data

Compute

Code

https://www.egi.eu/case-study/mathworks/
31
Parallelize Code with Minimal Changes

MATLAB

Workers

a = zeros(5, 1); a = zeros(5, 1);

b = pi; b = pi;
for i = 1:5 parfor i = 1:5
a(i) = i + b; a(i) = i + b;
end end
disp(a) disp(a)
 University of Cambridge Accelerates Neuroimaging
Data Analysis to Study Healthy Cognitive Aging

Challenge
Analyze terabytes of MRI and MEG imaging data for
a study on cognitive abilities in old age
Solution
Use MATLAB to process the data on a high-
performance computing cluster and to apply
advanced statistical, optimization, and machine
learning techniques Structural MRI images of the brain of a typical healthy 19-year old
(left) and typical healthy 86-year old (right).
Results
▪ Multistep image processing pipeline automated “MATLAB Parallel Server not only reduces processing time;
▪ Data analysis accelerated on a 1200-core cluster it also lowers the barrier to entry into parallel computing—an
▪ Key influences on late-life cognitive health important consideration given the wide range of technical
identified abilities among our scientists.”
- Richard Henson, University of Cambridge

Link to technical article

MATLAB Parallel Computing at IT4Innovations

• When you are ready to run your MATLAB application beyond your desktop,
IT4Innovations has powerful HPC resources that allow you to run MATLAB
to scale using MATLAB Parallel Server

GPU

Multi-core CPU
Parallel Computing Toolbox
MATLAB Parallel Server

• To get started:
– https://docs.it4i.cz/software/numerical-languages/matlab
– [email protected]
RE-USE
Code Ocean: Code from Papers for Sharing and Reuse

Code Ocean
Code Ocean: Code from Papers for Sharing and Reuse
Open any code in the browser
No license required
Reproduce and verify results
What Can You Do With MATLAB Code?

SHARE SCALE UP REUSE

MATLAB Campus-Wide a Institute-Wide licence v ČR a SR

https://www.humusoft.cz/univerzity/
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Questions?

[email protected]