denbi-modsim.github.io

Workshop Agenda

Please install/download the software tools and additional material prior to the workshop:

CellNetAnalyzer download: For the practical exercises on Day 1 you can download CNA from the following website.

For installation of CNApy follow the instructions on: https://github.com/cnapy-org/CNApy.
MATLAB: For the practical exercises with CNA you need MATLAB. If you do not have access to MATLAB you may download a 30 day trial version here:

For the hands on session with COPASI on the second day you may download COPASI from: http://copasi.org/Download/

for the modelling session, you will be asked to download BioModel #64, for your convenience it is also available here.
For the parameter estimation part, we have this archive, containing some models and data files to use during the tutorial.
To wrap things up we demonstrate how to use COPASI from a python Scripting interface. Here is the shared Colab Notebook, you can access it without Google account, however it will only allow you to make changes if you are logged in. All changes I make will be displayed there.
Slides:
- Intro Modelling
- Parameter Estimation

For the SABIO-RK hands-on session on the third day you will need Python and the Python library Requests: https://pypi.python.org/pypi/requests

For the SEEK API hands-on session you should either install Jupyter Lab or be allowed to use Google colab (Jupyter hosted by Google).