About

What is Pasmopy?

Pasmopy is a scalable toolkit to identify prognostic factors for cancers based on intracellular signaling dynamics generated from personalized kinetic models. It is compatible with biomass and offers the following features:

  • Construction of mechanistic models from text

  • Personalization of the model using transcriptome data

  • Prediction of patient outcome based on in silico signaling dynamics

  • Sensitivity analysis for prediction of potential drug targets

License

The software is released under the Apache License 2.0. For details, see the LICENSE file in the pasmopy repository.

Author

Hiroaki Imoto

Citation

If you use Pasmopy in a scientific publication, please cite the following papers:

  • Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient -specific modeling for classification of cancers. iScience 25, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944

    @article{imoto2022text,
  title = {A text-based computational framework for patient-specific modeling for classification of cancers},
  author = {Imoto, Hiroaki and Yamashiro, Sawa and Okada, Mariko},
  journal = {iScience},
  volume = {25},
  number = {3},
  pages = {103944},
  year = {2022},
  doi = {10.1016/j.isci.2022.103944},
}

  • Imoto, H., Yamashiro, S., Murakami, K. & Okada, M. Protocol for stratification of triple-negative breast cancer patients using in silico signaling dynamics. STAR Protocols 3, 101619 (2022). https://doi.org/10.1016/j.xpro.2022.101619

    @article{imoto2022protocol,
  title = {Protocol for stratification of triple-negative breast cancer patients using in silico signaling dynamics},
  author = {Imoto, Hiroaki and Yamashiro, Sawa and Murakami, Ken and Okada, Mariko},
  journal = {STAR protocols},
  volume = {3},
  number = {3},
  pages = {101619},
  year = {2022},
  doi = {10.1016/j.xpro.2022.101619},
}

When presenting work that uses Pasmopy, feel free to use Pasmopy logo.

_images/pasmopy-project-logo.png

Contact

If you discovered an error or need help, please contact me via GitHub Issues. Please head over to GitHub Discussions if you have any questions or would like to start a new discussion. In either case, you can also always send me an email.

Any contributions to Pasmopy are more than welcome!