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https://github.com/computationalphysiology/uio-digital-scholarship-days

Material for workshop on Digital Scholarship Days at UiO

https://github.com/computationalphysiology/uio-digital-scholarship-days

Science Score: 36.0%

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Material for workshop on Digital Scholarship Days at UiO

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Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

Bad luck, bad drug or bad heart: Computer models to the rescue

Workshop on Digital Scholarship Days at UiO Friday January 13th 2023

Binder DOI

  • Documentation: https://computationalphysiology.github.io/uio-digital-scholarship-days
  • Link to workshop: https://www.ub.uio.no/english/courses-events/events/all-libraries/2023/digital-scholarship-days/bad-luck-drug-heart.html

Run notebooks with binder

In this document, you will see the launch binder badge Binder. If you click on this it will open the main repo in jupyterlab using Binder. This will give you a notebook environment where you can run the notebooks in this repo.

Run notebooks directly from the documentation page

If you visit the documentation at https://computationalphysiology.github.io/uio-digital-scholarship-days then you will see a rocket icon at the top of the page for the pages that contain an interactive notebook

_

Clicking on the binder icon will also launch the current notebook in Binder.

Running the notebooks locally

To run the notebooks locally you need to have python version 3.8 or newer installed. You also need a working C compiler. Next, you can create a virtual environment python3 -m venv venv and activate it. On Linux/Mac you can activate the environment as follows . venv/bin/activate and on Windows, you can use the following command . venv\Scripts\activate Now you can install the requirements using the command python3 -m pip install -r requirements.txt You should also make sure to install jupyterlab python3 -m pip install jupyterlab Now you should be able to run the jupyter notebooks locally by starting jupyter lab jupyter-lab

Authors

  • Ilsbeth Gerarda Maria van Herck
  • Henrik Finsberg
  • Hermenegild Arevalo

License

License: CC BY 4.0

This repo is licensed using a CC-BY 4.0 so you are free to use, remix, and share so long attribution is provided to the original author.

Owner

  • Name: Computational Physiology at Simula Research Laboratory
  • Login: ComputationalPhysiology
  • Kind: organization
  • Location: Fornebu, Norway

GitHub organization for the computational physiology department at Simula Research Laboratory

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Dependencies

.github/workflows/build_docs.yml actions
  • actions/checkout v3 composite
  • actions/configure-pages v2 composite
  • actions/deploy-pages v1 composite
  • actions/setup-python v4 composite
  • actions/upload-pages-artifact v1 composite
.github/workflows/pre-commit.yml actions
  • actions/checkout v3 composite
requirements.in pypi
  • cmake *
  • drug-database *
  • gotran *
  • matplotlib *
  • numpy *
requirements.txt pypi
  • click ==8.1.3
  • cmake ==3.25.0
  • commonmark ==0.9.1
  • contourpy ==1.0.6
  • cycler ==0.11.0
  • drug-database ==0.1.3
  • fonttools ==4.38.0
  • gotran ==2022.2.1
  • kiwisolver ==1.4.4
  • matplotlib ==3.6.2
  • modelparameters ==2022.2.0
  • mpmath ==1.2.1
  • networkx ==3.0
  • numpy ==1.24.1
  • packaging ==23.0
  • pillow ==9.4.0
  • pint ==0.20.1
  • pygments ==2.14.0
  • pyparsing ==3.0.9
  • python-dateutil ==2.8.2
  • rich ==13.0.1
  • scipy ==1.10.0
  • six ==1.16.0
  • typer ==0.7.0