组织:交互式生物和生物物理模拟环境环境
T J Sego1, James P Sluka2, Herbert M Sauro3
1Department of Medicine, University of Florida, Gainesville, Florida, United States of America.
PLoS computational biology
|October 23, 2023
概括
组织造是一个开源的模拟环境,用于基于物理,化学和生物学的粒子建模. 它可以实时探索从分子到多细胞尺度的复杂生物物理系统.
科学领域:
- 计算生物学 计算生物学
- 生物物理学的生物物理.
- 软冷凝物质物理学 软冷凝物质物理学
背景情况:
- 建模复杂的生物系统需要多功能模拟工具.
- 现有的平台可能缺乏跨多个尺度 (从分子到多细胞) 的灵活性.
- 物理,化学和生物学模拟的桥梁是具有挑战性的.
研究的目的:
- 介绍Tissue Forge,这是一个基于粒子的建模的开源交互式环境.
- 提供一个统一的平台来模拟从分子到多细胞水平的生物物理系统.
- 支持从分子动力学到基于代理的多细胞系统的各种应用.
主要方法:
- 使用基于粒子的方法,重点是软凝聚物质物理学.
- 为模型构建和模拟提供交互式的实时环境.
- 支持内置和用户指定的模型,以及广泛的Python,C和C++ API.
主要成果:
- 组织造促进了虚拟实验的创建,模拟和探索.
- 能够实时与模拟进行交互,并在执行过程中对参数进行修改.
- 支持用于非屏幕和远程模拟的高性能计算环境.
结论:
- 组织造简化了复杂的生物物理问题解决在亚细胞,细胞和组织层面.
- 它的灵活架构支持广泛的应用和定制模型开发.
- 该环境可以在主要操作系统上访问,并可以通过conda.
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