From raw data to kinetic parameters: an EnzymeML-based workflow for reproducible enzyme kinetics (doi:10.18419/darus-3337)

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From raw data to kinetic parameters: an EnzymeML-based workflow for reproducible enzyme kinetics

doi:10.18419/darus-3337

DaRUS

2023-02-02

1

Häußler, Max, 2023, "From raw data to kinetic parameters: an EnzymeML-based workflow for reproducible enzyme kinetics", https://doi.org/10.18419/darus-3337, DaRUS, V1

From raw data to kinetic parameters: an EnzymeML-based workflow for reproducible enzyme kinetics

doi:10.18419/darus-3337

Häußler, Max (Universität Stuttgart)

DaRUS

Häußler, Max

Pleiss, Juergen

Häußler, Max

2023-01-30

https://doi.org/10.18419/darus-3337

Chemistry, Computer and Information Science, Biocatalysis, Data Management

Master thesis in the form of a JupyterBook with the title: "From raw data to kinetic parameters: an EnzymeML-based workflow for reproducible enzyme kinetics" <p></p> JupyterBook can be accessed via: <a href="https://haeussma.github.io/masterthesis/welcome.html">https://haeussma.github.io/masterthesis/welcome.html</a> <p></p> Goal of the thesis was the development of a workflow for enzyme kinetics parameter estimation workflow, which is based on raw measurement data and utilises the EnzymeML format. Furthermore, data management was a vital aspect of the thesis. Thus this dataset contains all raw measurement data in the "data" folder, as well as the written thesis in form of a JupyterBook in the "book" folder. In summary, all data analysis as well as the written report can be reproduced.

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README.md

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requirements.txt

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runtime.txt

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abstract.md

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acknowledgements.md

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conclusion.md

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declaration.md

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discussion.md

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introduction.md

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methods.md

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references.bib

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references.md

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requirements.txt

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results.md

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welcome.md

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_config.yml

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_toc.yml

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concept_workflow.png

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cover_master_thesis.jpg

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logo.png

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workflow_SLAC.png

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chymotrypsin_inhibition.ipynb

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enzyme_inactivation.ipynb

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glycosidase_inhibition.ipynb

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SLAC_kinetic_characterization.ipynb

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calibration_parser.py

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measurement_parser.py

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measurement_to_enzymeml.py

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plotter.py

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utility.py

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writeEnzymeInactivation.py

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__init__.py

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apastyle.py

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bracket_citation_style.py

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chymo_HSA(M3).xlsx

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chymo_HSAwt.xlsx

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pNA-standard.xlsx

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EnzymeML_CotA.xlsm

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Repetition CotA ABTS kinetics higher volumes 2nd time.xlsx

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Slide 2 - Activity effect of incubating CotA in MTP.xlsx

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experimental_data.xlsx

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experimental_data_real.xlsx

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p-NP_standard.xlsx

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EnzymeML_a-glucosidase_Acarbose.xlsm

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EnzymeML_a-glucosidase_E_maxima.xlsm

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EnzymeML_a-glucosidase_E_radiata.xlsm

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EnzymeML_a-glucosidase_F_vesiculosus.xlsm

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EnzymeML_a-glucosidase_S_elegans.xlsm

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EnzymeML_SLAC_pH3.xlsm

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EnzymeML_SLAC_pH3_5.xlsm

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EnzymeML_SLAC_pH4.xlsm

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EnzymeML_SLAC_pH4_5.xlsm

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EnzymeML_SLAC_pH5.xlsm

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EnzymeML_SLAC_pH5_5.xlsm

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2022-10-11 - SLAC pH 3.0 25 degrees C.txt

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