BioSimulators：用于推荐特定工具的仿真引擎与服务中央注册库
定量方法
2022-03-15 v1 计算工程、金融与科学
分子网络
摘要
计算模型在加速生物科学、生物工程与医学方面具有巨大潜力。然而，重现和重用仿真仍然具有挑战性，部分原因是用于模拟不同子系统与尺度的众多格式和方法仍被不同软件工具孤立。例如，每个工具必须通过不同的接口执行。为帮助研究者查找并使用仿真工具，我们开发了 BioSimulators（https://biosimulators.org），这是一个仿真工具能力中央注册库，并为每个工具的每个版本提供一致的 Python、命令行与容器化接口。BioSimulators 的基础是 CellML、SBML、SED-ML 与 COMBINE 归档格式等标准，以及确保这些标准被一致使用的仿真项目与仿真工具验证工具。为帮助建模者查找特定项目的工具，我们还利用该注册库开发了推荐服务。我们预期 BioSimulators 将帮助建模者交换、重现并组合仿真。
引用
@article{arxiv.2203.06732,
title = {BioSimulators: a central registry of simulation engines and services for recommending specific tools},
author = {Bilal Shaikh and Lucian P. Smith and Dan Vasilescu and Gnaneswara Marupilla and Michael Wilson and Eran Agmon and Henry Agnew and Steven S. Andrews and Azraf Anwar and Moritz E. Beber and Frank T. Bergmann and David Brooks and Lutz Brusch and Laurence Calzone and Kiri Choi and Joshua Cooper and John Detloff and Brian Drawert and Michel Dumontier and G. Bard Ermentrout and James R. Faeder and Andrew P. Freiburger and Fabian Fröhlich and Akira Funahashi and Alan Garny and John H. Gennari and Padraig Gleeson and Anne Goelzer and Zachary Haiman and Joseph L. Hellerstein and Stefan Hoops and Jon C. Ison and Diego Jahn and Henry V. Jakubowski and Ryann Jordan and Matúš Kalaš and Matthias König and Wolfram Liebermeister and Synchon Mandal and Robert McDougal and J. Kyle Medley and Pedro Mendes and Robert Müller and Chris J. Myers and Aurelien Naldi and Tung V. N. Nguyen and David P. Nickerson and Brett G. Olivier and Drashti Patoliya and Loïc Paulevé and Linda R. Petzold and Ankita Priya and Anand K. Rampadarath and Johann M. Rohwer and Ali S. Saglam and Dilawar Singh and Ankur Sinha and Jacky Snoep and Hugh Sorby and Ryan Spangler and Jörn Starruß and Payton J. Thomas and David van Niekerk and Daniel Weindl and Fengkai Zhang and Anna Zhukova and Arthur P. Goldberg and Michael L. Blinov and Herbert M. Sauro and Ion I. Moraru and Jonathan R. Karr},
journal= {arXiv preprint arXiv:2203.06732},
year = {2022}
}
备注
6 pages, 2 figures