Software tools for reproducibly simulating, analyzing, and visualizing biomodels

技术研究与开发3：项目总结 模型在一个可测试的数字框架中代表了我们的知识、观察和假设。因为 模型是数字化的，应该很容易重复使用模型并再现模拟结果。然而，许多人 动态生化模型不可重复使用，许多模拟结果也不可重现，包括 以系统生物学标记语言等标准格式报告的模型和模拟结果 (SBML)和仿真实验描述标记语言(SED-ML)。这种不可再生性限制了 通过禁止研究人员重复使用模型和模拟结果来进行其他建模的影响 研究单个生物过程的模型，并将其组合成整个生物系统的元模型。 目前，模型很难重复使用，模拟也很难重现，因为很少有研究人员报告 复制模拟所需的元数据，(B)有许多不兼容的模拟器，(C)没有 模拟结果储存库，(D)没有减少模拟结果的标准，(E)没有标准 用于描述结果可视化，以及(F)没有足够的工具来可视化模拟结果。 为了解决这些问题，我们将开发新的工具和公共服务器，以(A)使用现有的模拟器来 可重复地模拟各种模型，以及(B)存储和(C)可视化模拟结果： 1.我们将建立一个数据库，用于存储模型、模拟实验、结果及其元数据 它将生成DOI并支持对模拟结果的查询。该系统将帮助研究人员 共享和检索模拟结果，并将大数据分析应用于模拟结果。反过来， 该系统将帮助研究人员重用仿真实验并再现仿真结果。 2.我们将构建一个仿真系统，为多个仿真器提供通用接口，每个仿真器 支持单独的仿真算法和建模域。这将使研究人员更容易 无需安装特定于领域的模拟器即可重复使用模型和重现模拟。 3.建立一个基于Web的系统，利用仿真系统和仿真结果数据库来 在浏览器中交互模拟和可视化模型。这将使研究人员能够检索到 存储仿真结果，请求新的仿真，并直观地分析仿真结果。 为了确保我们的工具推进生物建模，我们将与几个CP和SP一起开发我们的工具 它将提供基于Web的模型存储库和日志工具，用于交互模拟和可视化 上报的模特。这些CPS将推动我们开发用户友好的工具，我们将把CPS拉到要求 模型作者对他们的模拟实验进行注释，以便它们是可重现的。 为了帮助研究人员使用我们的软件，我们将与tr&ds1和tr&ds2合作，将我们的软件合并为 可重现的建模工作流程。我们还将广泛记录我们的软件，并将其开源分发。 此外，作为培训和传播核心的一部分，我们将编写教程和组织研讨会。

TECHNOLOGY RESEARCH & DEVELOPMENT 3: PROJECT SUMMARY Models represent our knowledge, observations and hypotheses in a testable digital framework. Because models are digital, it should be easy to reuse models and reproduce simulation results. However, many dynamic biochemical models are not reusable and many simulation results are not reproducible, including models and simulation results reported in standard formats such as the Systems Biology Markup Language (SBML) and the Simulation Experiment Description Markup Language (SED-ML). This irreproducibility limits the impact of modeling by inhibiting researchers from reusing models and simulation results for additional studies and combining models of individual biological processes into meta-models of entire biological systems. Currently, models are hard to reuse and simulations are hard to reproduce because (a) few researchers report the metadata needed to reproduce simulations, (b) there are many incompatible simulators, (c) there is no simulation results repository, (d) there is no standard for reducing simulation results, (e) there is no standard for describing results visualizations, and (f) there are inadequate tools for visualizing simulation results. To address these problems, we will develop novel tools and public servers for (a) using existing simulators to reproducibly simulate a wide range of models and (b) storing and (c) visualizing simulation results: 1. We will build a database for storing models, simulation experiments, their results, and their metadata which will mint DOIs and support queries over simulation results. The system will help researchers share and retrieve simulation results and apply big data analytics to simulation results. In turn, the system will help researchers reuse simulation experiments and reproduce simulation results. 2. We will build a simulation system which provides a common interface to multiple simulators that each support individual simulation algorithms and modeling domains. This will make it easy for researchers to reuse models and reproduce simulations without having to install domain-specific simulators. 3. We will build a web-based system for using the simulation system and simulation results database to interactively simulate and visualize models in a browser. This will enable researchers to retrieve deposited simulation results, request new simulations, and visually analyze simulation results. To ensure our tools advance biomodeling, we will develop our tools in conjunction with several CPs and SPs which will provide model repositories and journals web-based tools for interactively simulating and visualizing reported models. These CPs will push us to develop user-friendly tools, and we will pull the CPs to require model authors to annotate their simulation experiments so they are reproducible. To help researchers use our software, we will work with TR&Ds 1 and 2 to combine our software into a reproducible modeling workflow. We will also extensively document our software and distribute it open-source. In addition, as part of the Training and Dissemination Core, we will develop tutorials and organize workshops.