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Dynamic publication media with the COPASI R Connector (CoRC)
Johanna C J Daas1, Jonas D Förster2, Jürgen Pahle1
1Biological Information Processing Group, BioQuant, Heidelberg University; BQ47, INF267, 69120 Heidelberg, Germany.
Mathematical Biosciences
|April 22, 2022
Summary
Dynamic publication media and the COPASI R Connector (CoRC) offer a versatile approach to communicate biochemical models. This integration enhances reproducibility, teaching, and science communication through interactive documents.
Area of Science:
- Computational Systems Biology
- Biochemical Modeling
- Scientific Communication
Background:
- Dynamic publication media are increasingly used for composing and publishing scientific work.
- The COmplex PAthway SImulator COPASI is a widely adopted biochemical modeling toolkit.
- The COPASI R Connector (CoRC) facilitates R integration with COPASI.
Purpose of the Study:
- To demonstrate the synergistic combination of dynamic publication media and CoRC for communicating biochemical models.
- To explore applications in documentation, teaching, and science communication.
- To provide freely available examples of integrated dynamic documents.
Main Methods:
- Utilizing R programming environment with tools like R Markdown, Jupyter, and Shiny.
- Integrating COPASI functionality into R via the COPASI R Connector (CoRC).
- Developing six dynamic document examples (R Markdown, Jupyter notebooks) hosted on platforms like GitHub and shinyapps.io.
Main Results:
- Successful integration of dynamic publication media with CoRC for biochemical model communication.
- Demonstrated versatility in documentation (reproducible workflows), teaching (self-paced lessons), and science communication (engaging presentations).
- Creation of accessible, interactive, and template-based dynamic documents.
Conclusions:
- The combination of dynamic documents and CoRC provides a powerful and versatile tool for biochemical model communication.
- This approach enhances the accessibility and engagement of scientific content.
- Freely available example documents promote adoption and further development.
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