Uses of SymPy in biology

[Aaron Meurer]

I am looking into potentially submitting a proposal for a CZI grant
for SymPy at some point in the future. However, in order to do this,
we need to demonstrate that SymPy is used in biology or biomedicine.

If anyone is aware of people or libraries that make use of SymPy in a
bio field, please let me know about it.

Aaron Meurer

[Gagandeep Singh (B17CS021)]

Hi, 

May be, http://pysb.org/

With Regards,
Gagandeep Singh
Github - https://github.com/czgdp1807
LinkedIn - https://www.linkedin.com/in/czgdp1807

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[thomas...@gmail.com]

Hello Aaron,

AMICI (https://github.com/ICB-DCM/AMICI) uses Sympy, for example for importing SBML (Systems Biology Markup Language). AMICI is often used in conjunction with PESTO (https://github.com/ICB-DCM/pyPESTO) for parameter estimation of biological models using differential equations. One such project is CanPathPro (http://www.canpathpro.eu/). If you want to go deeper, I suggest contacting Fabian Fröhlich at Harvard or Daniel Weindl at Helmholtz.

Tom
(Dr. Thomas S. Ligon)
thomas...@gmail.com
Frohnloher Str. 6a
81475 Muenchen
Germany
Tel. +49(89)74575075

[Nicolas Guarin]

Hi Aaron,

I think that we could ask in Twitter, maybe somebody know some application. Looking in the papers that we have collected I found the following:

Constantinescu, Dario, Gilles Vercambre, and Michel Génard. “Model-Assisted Analysis of the
Peach Pedicel–Fruit System Suggests Regulation of Sugar Uptake and a Water-Saving Strategy.”
Journal of Experimental Botany 71, no. 12 (June 22, 2020): 3463–3474. https://doi.org/10.1093/jxb/eraa103.

Giampieri, Enrico, Marco De Cecco, Daniel Remondini, John Sedivy, and Gastone Castellani.
“Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence.”
PLOS ONE 10, no. 6 (June 26, 2015): e0118442. https://doi.org/10.1371/journal.pone.0118442.

Weltman, Joel K. “Exclusive and Common Subsets of Zika Virus Polyprotein Mutants.”
Journal of Medical Microbiology & Diagnosis 06, no. 02 (2017). https://doi.org/10.4172/2161-0703.1000256.

Sturrock, Marc, Shiyu Li, and Vahid Shahrezaei. “The Influence of Nuclear Compartmentalisation on Stochastic
Dynamics of Self-Repressing Gene Expression.” Journal of Theoretical Biology, May 2017. https://doi.org/10.1016/j.jtbi.2017.05.003.

Lippolis, Davide Giosuè. “Stochastic Modeling of Fluctuations in the NF-KB Activity of Neoplastic Cells.” Tesi di laurea,
Università di Bologna, 2020. https://amslaurea.unibo.it/20550/.

Anane, Emmanuel, Diana C. López C., Tilman Barz, Gurkan Sin, Krist V. Gernaey, Peter Neubauer, and Mariano Nicolas Cruz Bournazou.
“Output Uncertainty of Dynamic Growth Models: Effect of Uncertain Parameter Estimates on Model Reliability.”
Biochemical Engineering Journal, May 2019, 107247. https://doi.org/10.1016/j.bej.2019.107247.

Vinje, Vegard. “Simulating Cerebrospinal Fluid Flow and Spinal Cord Movement Associated with Syringomyelia.”
Master, University of Oslo, 2016. https://www.duo.uio.no/handle/10852/51949.

Ceballos-Núñez, Verónika, Markus Müller, and Carlos A. Sierra. “Towards Better Representations of Carbon Allocation in Vegetation:
A Conceptual Framework and Mathematical Tool.” Theoretical Ecology, April 22, 2020. https://doi.org/10.1007/s12080-020-00455-w.

Nicolás