Use a Jupyter Notebook to model Michaelis-Menten Kinetics on experimental data
This Jupyter Notebook assists you in the analysis of initial rate experiments.
For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install
For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/
There are multiple tutorials online that help you to learn how to use a Jupyter notebook.
The notebook is provided as an .ipynb and as a .pdf file. The plots the script generates with the default input data are also given as .png files.
SEEK ID: https://fairdomhub.org/assays/1486
Modelling analysis
Projects: Towards Reproducible Enzyme Modeling
Investigation: On the reproducibility of enzyme reactions and kinetic modelling
Study: Analyse an Initial Rate Experiment
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 8th Oct 2021 at 15:30
Last updated: 28th Jan 2022 at 12:49
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https://orcid.org/0000-0001-9119-1778Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
Work of the Gygli group...
Projects: Test Project (dummy), Towards Reproducible Enzyme Modeling
Web page: Not specified
Investigation 1: An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure ...
Because enzyme activity depends very much on the reaction conditions, it is crucial to report all these metadata (see for example the STRENDA Guidelines:https://www.beilstein-strenda-db.org/strenda/public/guidelines.xhtml).
Another challenge in experiments to determine enzyme reaction parameters is the choice of suitable substrate concentrations to enable optimal kinetic fits and the informed choice of a kinetic model.
A Jupyter notebook is given to assist in the choice of substrate concentrations ...
Submitter: Gudrun Gygli
Studies: Analyse an Initial Rate Experiment, Design an Initial Rate Experiment, Progress Curve Analysis, Selwyn Test
Assays: Use a Jupyter Notebook to design an initital rate experiment, Use a Jupyter Notebook to model Michaelis-Menten Kinetics on experimenta..., Use a Jupyter Notebook to understand how a progress curve experiment can..., Use a Jupyter Notebook to understand how the Selwyn test works
This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.
NOTE THAT this pdf may be mangled when viewed on FAIRDOMHub, but should look fine when downloaded.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is a zip file containing all the files and folders needed to analyse raw data, fit initial rates and create a "Michaelis-Menten plot". Instructions on usage are added in the notebook.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
