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Interactive Molecular Model Assembly with 3D Printing
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ModelBricks-modules for reproducible modeling improving model annotation and provenance.
Ann E Cowan1,2, Pedro Mendes1,3,4, Michael L Blinov1,5
11Center for Cell Analysis and Modeling, UConn Health, Farmington, CT USA.
NPJ Systems Biology and Applications
|October 12, 2019
Summary
Computational biology models are often single-use due to poor annotation. Introducing ModelBricks, small, annotated modules, enables reusable and understandable biological models through community contributions.
Area of Science:
- Computational Biology
- Systems Biology
- Bioinformatics
Background:
- Current biological models lack standardized annotations, hindering reusability and understanding.
- Recreating existing models or expanding them for new research is time-consuming and inefficient.
Purpose of the Study:
- To propose a novel concept for creating annotated, reusable computational biology models.
- To introduce 'ModelBricks' as modular, well-annotated components for building complex models.
Main Methods:
- Developing a framework for small, annotated modules (ModelBricks) using standard languages like SBML.
- Creating an open database for curated ModelBricks with unique identifiers and associated parameters.
- Designing ModelBricks to be flexible, encapsulating various biological mechanisms.
Main Results:
- ModelBricks facilitate the construction of new models that inherit annotations and provenance.
- This approach simplifies model understanding, reuse, and expansion.
- A flexible structure allows ModelBricks to represent diverse biological processes.
Conclusions:
- ModelBricks offer a solution to the reusability problem in computational biology.
- A community-driven database of ModelBricks will accelerate biological model development.
- Standardized, annotated modules enhance model transparency and facilitate scientific collaboration.
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