发表机构
University of Washington; Pacific Northwest National Laboratory; eScience Institute, University of Washington; Heidelberg University; Allen School of Computer Science, University of Washington（华盛顿大学; 太平洋西北国家实验室; 华盛顿大学电子科学研究所; 海德堡大学; 华盛顿大学艾伦计算机科学学院）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
针对实验生物学家使用建模工具困难的问题，开发了集成桌面与网页的交互式模拟器，支持Antimony语法编辑、实时参数调节、零安装及AI集成，并生成Python代码以增强模型可重复性。
AI 中文摘要
基于数学模拟（如常微分方程）的生物学模型对于理解生物过程和预测实验结果具有巨大价值。此类模型通常借助多种复杂的建模工具构建，然而，这些工具的复杂性往往成为实验生物学家使用的障碍。为提高生物学模型的可用性和影响力，我们创建了一个桌面平台（DeskIridium）和一个基于网络的模拟器（WebIridium，以GitHub页面形式托管），二者结合提供了促进实验生物学家易用性的功能，包括：通过Antimony语法进行人类可读的模型编辑；滑块实时调整参数值并同时显示模拟结果；零安装分发；集成AI聊天；以及生成SBML模型的独立Python实现以支持可重复性。桌面版本采用成熟的libroadrunner模拟包；基于网络的应用使用COPASI的Emscripten翻译版本。两个模拟器均兼容SBML，允许用户轻松导入先前构建的模型或使用易用的antimony语言编辑现有模型。我们采用现代AI方法进行软件开发，并分享了经验教训。二进制文件、源代码和网络界面可在以下网址获取：this https URL 和 this https URL。
英文摘要
Biological models based on mathematical simulations (e.g., ordinary differential equations) are hugely beneficial for understanding biological processes and predicting the outcomes of experiments. Such models are built using a variety of sophisticated modeling tools. Unfortunately, the complexity of these tools is often a barrier to use by experimental biologists. To improve the usability and impact of biological models, we have created a desktop platform (DeskIridium) and a web-based simulator (WebIridium, hosted as a GitHub page) that, in combination, provide features that promote ease of use by experimental biologists, including: human-readable editing of models via the Antimony syntax; sliders for adjusting parameter values while simultaneously displaying simulation results in real time; zero-install distribution; AI chat integration; and generation of standalone Python implementations of SBML models to support reproducibility. The desktop version uses the well-established libroadrunner simulation package; the web-based application uses an Emscripten translated version of COPASI. Both simulators are SBML-compatible, allowing users to easily import previously built models or edit existing models using the easy-to-use antimony language. We used modern AI methods for software development and share the lessons we learned. Binaries, source code, and the web interface are available at: https://github.com/sys-bio/IridiumSimulator and https://github.com/sys-bio/WebIridium.
