Use a Jupyter Notebook to design an initital rate experiment
This Jupyter Notebook assists you in the design 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 values are also given as .png files.
SEEK ID: https://fairdomhub.org/assays/1485
Modelling analysis
Projects: Towards Reproducible Enzyme Modeling
Investigation: On the reproducibility of enzyme reactions and kinetic modelling
Study: Design an Initial Rate Experiment
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 8th Oct 2021 at 14:29
Last updated: 12th Oct 2021 at 06:54
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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 study explores how to design an initial rate experiment. It starts with a "zero-round" experiment, which is used to design a "first-round" experiment, which then leads to the design of a "gold-round" experiment.
Submitter: Gudrun Gygli
Investigation: On the reproducibility of enzyme reactions and ...
Assays: Use a Jupyter Notebook to design an initital rate experiment
Badly chosen substrate concentrations for an intital rate experiment give data that makes it difficult to fit with a kinetic model and judge the quality of the fit.
Well chosen substrate concentrations for an intital rate experiment give data that makes it easy to fit with a kinetic model and judge the quality of the fit and use it as a basis for the final gold-round experiment.
Very well chosen substrate concentrations for an intital rate experiment give data that makes it very easy to fit with a kinetic model and judge the quality of the fit.
An initial choice of 5 widely spaced substrates enables a first, rough estimate of Km to inform the design of first-round experiments.
This is the Jupyter Notebook to allow editing and working with the code.
Design an initial rate experiment in four steps
This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed:
- Estimate the enzyme reaction parameters
Input: estimates of Km and vmax
and indicate the enzyme concentration concentration you are planning to use. If you have no ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.
Design an initial rate experiment in four steps
This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed: 1. Estimate the enzyme reaction parameters
Input: estimates of Km and vmax
and indicate the enzyme concentration concentration you are planning ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
