References

References

Bis19

Ekaba Bisong. Google colaboratory. In Building Machine Learning and Deep Learning Models on Google Cloud Platform, pages 59–64. Apress, 2019. URL: https://doi.org/10.1007/978-1-4842-4470-8_7, doi:10.1007/978-1-4842-4470-8_7.

Bux15

Engelbert Buxbaum. Inhibition and inactivation of enzymes. In Fundamentals of Protein Structure and Function, pages 141–161. Springer International Publishing, 2015. URL: https://doi.org/10.1007/978-3-319-19920-7_6, doi:10.1007/978-3-319-19920-7_6.

Com20

Executable Books Community. Jupyter book. February 2020. URL: https://doi.org/10.5281/zenodo.4539666, doi:10.5281/zenodo.4539666.

Cro11

Mercè Crosas. The dataverse network®: an open-source application for sharing, discovering and preserving data. D-Lib Magazine, January 2011. URL: https://doi.org/10.1045/january2011-crosas, doi:10.1045/january2011-crosas.

HMvdW+20

Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, Robert Kern, Matti Picus, Stephan Hoyer, Marten H. van Kerkwijk, Matthew Brett, Allan Haldane, Jaime Fernández del Río, Mark Wiebe, Pearu Peterson, Pierre Gérard-Marchant, Kevin Sheppard, Tyler Reddy, Warren Weckesser, Hameer Abbasi, Christoph Gohlke, and Travis E. Oliphant. Array programming with NumPy. Nature, 585(7825):357–362, September 2020. URL: https://doi.org/10.1038/s41586-020-2649-2, doi:10.1038/s41586-020-2649-2.

HvHJF07

Dominic P.H.M. Heuts, Erik W. van Hellemond, Dick B. Janssen, and Marco W. Fraaije. Discovery, characterization, and kinetic analysis of an alditol oxidase from streptomyces coelicolor. Journal of Biological Chemistry, 282(28):20283–20291, July 2007. URL: https://doi.org/10.1074/jbc.m610849200, doi:10.1074/jbc.m610849200.

HSG+06

S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer. COPASI–a COmplex PAthway SImulator. Bioinformatics, 22(24):3067–3074, October 2006. URL: https://doi.org/10.1093/bioinformatics/btl485, doi:10.1093/bioinformatics/btl485.

HFS+03

M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, and et al. The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4):524–531, 2003. doi:10.1093/bioinformatics/btg015.

Hun07

J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science & Engineering, 9(3):90–95, 2007. doi:10.1109/MCSE.2007.55.

JBF+18

Project Jupyter, Matthias Bussonnier, Jessica Forde, Jeremy Freeman, Brian Granger, Tim Head, Chris Holdgraf, Kyle Kelley, Gladys Nalvarte, Andrew Osheroff, M Pacer, Yuvi Panda, Fernando Perez, Benjamin Ragan-Kelley, and Carol Willing. Binder 2.0 - reproducible, interactive, sharable environments for science at scale. In Proceedings of the Python in Science Conference. SciPy, 2018. URL: https://doi.org/10.25080/majora-4af1f417-011, doi:10.25080/majora-4af1f417-011.

KRKPerez+16

Thomas Kluyver, Benjamin Ragan-Kelley, Fernando Pérez, Brian Granger, Matthias Bussonnier, Jonathan Frederic, Kyle Kelley, Jessica Hamrick, Jason Grout, Sylvain Corlay, Paul Ivanov, Damián Avila, Safia Abdalla, Carol Willing, and Jupyter development team. Jupyter notebooks - a publishing format for reproducible computational workflows. In Fernando Loizides and Birgit Scmidt, editors, Positioning and Power in Academic Publishing: Players, Agents and Agendas, 87–90. Netherlands, 2016. IOS Press. URL: https://eprints.soton.ac.uk/403913/.

MRH+20

S. Malzacher, J. Range, C. Halupczok, J. Pleiss, and D. Rother. BioCatHub, a graphical user interface for standardized data acquisition in biocatalysis. Chemie Ingenieur Technik, 92(9):1251–1251, August 2020. URL: https://doi.org/10.1002/cite.202055297, doi:10.1002/cite.202055297.

NON+21

Matt Newville, Renee Otten, Andrew Nelson, Antonino Ingargiola, Till Stensitzki, Dan Allan, Austin Fox, Faustin Carter, Michał, Ray Osborn, Dima Pustakhod, lneuhaus, Sebastian Weigand, Glenn, Christoph Deil, Mark, Allan L. R. Hansen, Gustavo Pasquevich, Leon Foks, Nicholas Zobrist, Oliver Frost, Alexandre Beelen, Stuermer, azelcer, Andrew Hannum, Anthony Polloreno, Jens Hedegaard Nielsen, Shane Caldwell, Anthony Almarza, and Arun Persaud. Lmfit/lmfit-py: 1.0.3. October 2021. URL: https://doi.org/10.5281/zenodo.5570790, doi:10.5281/zenodo.5570790.

ORH04

B. G. Olivier, J. M. Rohwer, and J.-H. S. Hofmeyr. Modelling cellular systems with PySCeS. Bioinformatics, 21(4):560–561, September 2004. URL: https://doi.org/10.1093/bioinformatics/bti046, doi:10.1093/bioinformatics/bti046.

Ple21

Jürgen Pleiss. Standardized data, scalable documentation, sustainable storage – EnzymeML as a basis for FAIR data management in biocatalysis. ChemCatChem, 13(18):3909–3913, July 2021. URL: https://doi.org/10.1002/cctc.202100822, doi:10.1002/cctc.202100822.

RBS21

Jan Range, Frank Bergmann, and Neil Swainston. Pyenzyme 1.1.0-alpha. June 2021. URL: https://doi.org/10.5281/zenodo.5021263, doi:10.5281/zenodo.5021263.

RHL+21

Jan Range, Colin Halupczok, Jens Lohmann, Neil Swainston, Carsten Kettner, Frank T. Bergmann, Andreas Weidemann, Ulrike Wittig, Santiago Schnell, Jürgen Pleiss, and et al. Enzymeml—a data exchange format for biocatalysis and enzymology. The FEBS Journal, 2021. doi:10.1111/febs.16318.

SMRS+19

Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson L. Lister, and Milo Thurston. Fairsharing as a community approach to standards, repositories and policies. Nature Biotechnology, 37(4):358–367, 2019. doi:10.1038/s41587-019-0080-8.

Sna16

The Science Snail. A generalized model for enzymatic substrate inhibition. 2016. [Online; accessed 22. Januray 2022]. URL: https://www.sciencesnail.com/science/a-generalized-model-for-enzymatic-substrate.

TAB+14

Keith F. Tipton, Richard N. Armstrong, Barbara M. Bakker, Amos Bairoch, Athel Cornish-Bowden, Peter J. Halling, Jan-Hendrik Hofmeyr, Thomas S. Leyh, Carsten Kettner, Frank M. Raushel, Johann Rohwer, Dietmar Schomburg, and Christoph Steinbeck. Standards for reporting enzyme data: the strenda consortium: what it aims to do and why it should be helpful. Perspectives in Science, 1(1):131–137, 2014. Reporting Enzymology Data – STRENDA Recommendations and Beyond. URL: https://www.sciencedirect.com/science/article/pii/S2213020914000135, doi:https://doi.org/10.1016/j.pisc.2014.02.012.

VGO+20

Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, C J Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E. A. Quintero, Charles R. Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17:261–272, 2020. doi:10.1038/s41592-019-0686-2.

WDA+16

Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, and et al. The fair guiding principles for scientific data management and stewardship. Scientific Data, 2016. doi:10.1038/sdata.2016.18.

EuropeanOFNResearchOpenAIRE13

European Organization For Nuclear Research and OpenAIRE. Zenodo. 2013. URL: https://www.zenodo.org/, doi:10.25495/7GXK-RD71.

WesMcKinney10

Wes McKinney. Data Structures for Statistical Computing in Python. In Stéfan van der Walt and Jarrod Millman, editors, Proceedings of the 9th Python in Science Conference, 56 – 61. 2010. doi:10.25080/Majora-92bf1922-00a.

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