MEmilio - Software tools for the modular spatio-temporal modeling and simulation of infectious disease dynamics

为了加快流行病学模型的开发、分析和模拟，我们开发了研究软件MEmilio。这个模块化的软件工具箱是为了适应研究人员和用户的需要而设计的。在很大程度上，软件是用c++编写的，这是最快和内存效率最高的编程语言之一。模板用于实现各种通用结构，如模型、图形或参数模拟。该项目的目的是使研究软件MEmilio可重用，并可能在其原始环境之外进一步开发。它的模块化设计和Python接口的自动创建激励了其他研究人员模型的实现，以创建新的混合模型或建立模型性能的合理比较。为了实现这种影响的显著增加，我们将进一步使软件开发专业化。MEmilio已经包含了大量的单元测试、不同的持续集成（CI）管道和一个评审过程。我们将把c++和Python的代码覆盖率提高到100%，并更好地区分单元测试和集成测试。将通过专业团体和改进现有结构来进一步保证质量。我们将使MEmilio实现适应外部标准，以吸引新的用户和开发人员。我们将使MEmilio具备(i)基于基于规则的语言Kappa的标准化模型制定以及（ii）基于PEtab格式的模拟实验和数据集的标准化描述的可能性。我们将协调不同模型和编程语言之间的接口，以允许在c++和Python中以相同的方式执行所有MEmilio模型。图形或I/O等通用方法将进一步模板化，也将使用高级模板元编程。我们将重点关注有效的实现和可伸缩性，以充分利用可用资源。节能的实现将允许MEmilio模型的预测及时提供给科学家、政治家和决策者。此外，我们将通过扩展对社区标准的支持和实现通用输入格式来增加MEmilio的多功能性。为了支持以用户为中心的开发，我们将通过提供用户培训和开发人员研讨会，建立一个活跃的用户和开发人员社区。

To accelerate the development, analysis and simulation of epidemiological models, we developed the research software MEmilio. This modular software toolbox is designed to accommodate the needs of researchers and users. In large parts, the software is written in C++, which is among the fastest and memory-efficient programming languages. Templates are used to allow for various general structures such as models, graphs, or parameter simulations. The aim of this project is to make the research software MEmilio available for reuse and possible further development beyond its original context. Its modular design and automatic creation of Python interfaces incents the implementation of other researchers’ models to create new hybrid models or establish sound comparisons of model performances. To achieve this considerable increase in impact, we will further professionalize the software development. MEmilio already contains lots of unit tests, different continuous integration (CI) pipelines and a review process. We will increase code coverage in C++ and Python to 100% and better distinguish between unit and integration tests. Further quality assurance will be established through a professional community and improvement of the already existing structure. We will adapt MEmilio implementations to external standards to attract new users and developers. We will equip MEmilio with the possibility for (i) standardized model formulation based on the rule-based language Kappa as well as (ii) standardized description of simulation experiments and datasets based on the PEtab format. We will harmonize the interfaces between the different models and programming languages to allow identic execution of all MEmilio models from C++ and Python. General methods like a graph or I/O will be further templated, also using advanced template metaprogramming.We will focus on efficient implementations and scalability to make best use of available resources. Energy-efficient implementations will allow to provide predictions of MEmilio models on time to scientists, politicians, and decision makers. Furthermore, we will increase the versatility of MEmilio by extending the support of community standards and implementing general-purpose input formats. To support user-centered development, we will build an active community of users and developers by offering user training and developer workshops.