Department of Bioengineering, University of Washington, Seattle, Washington, United States of America.
Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany.
PLoS Comput Biol. 2018 Jun 15;14(6):e1006220. doi: 10.1371/journal.pcbi.1006220. eCollection 2018 Jun.
The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system for model authoring, simulation, and teaching that facilitates building reproducible dynamical models and reusing models by 1) providing a notebook environment which allows models, Python code, and narrative to be intermixed, 2) supporting the COMBINE archive format during model development for capturing model information in an exchangeable format and 3) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying model dynamics, variants and test cases. Tellurium Notebook, a Python-based Jupyter-like environment, is designed to seamlessly inter-operate with these community standards by automating conversion between COMBINE standards formulations and corresponding in-line, human-readable representations. Thus, Tellurium brings to systems biology the strategy used by other literate notebook systems such as Mathematica. These capabilities allow users to edit every aspect of the standards-compliant models and simulations, run the simulations in-line, and re-export to standard formats. We provide several use cases illustrating the advantages of our approach and how it allows development and reuse of models without requiring technical knowledge of standards. Adoption of Tellurium should accelerate model development, reproducibility and reuse.
在重现已发表动力学模型的结果时遇到了相当大的困难，这限制了对这一日益庞大的生物医学研究资源的验证、探索和再利用。为了解决这个问题，我们开发了 Tellurium Notebook，这是一个用于模型创作、模拟和教学的软件系统，通过以下方式促进可重现动力学模型的构建和模型的重用：1）提供一个笔记本环境，允许模型、Python 代码和叙述混合在一起，2）在模型开发过程中支持 COMBINE 存档格式，以便以可交换的格式捕获模型信息，3）使用户能够轻松模拟和编辑来自公共存储库的公共 COMBINE 兼容模型，以方便研究模型动态、变体和测试用例。Tellurium Notebook 是一个基于 Python 的 Jupyter 风格的环境，旨在通过在 COMBINE 标准公式和相应的内联、人类可读表示之间自动转换，与这些社区标准无缝协作。因此，Tellurium 将其他文学笔记本系统（如 Mathematica）所使用的策略引入到系统生物学中。这些功能允许用户编辑符合标准的模型和模拟的各个方面，在线运行模拟，并重新导出到标准格式。我们提供了几个用例来说明我们的方法的优势，以及它如何允许在不要求了解标准的技术知识的情况下开发和重用模型。采用 Tellurium 应该会加速模型的开发、可重现性和重用。
