Software:IBioSim
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| Initial release | August 16, 2017 |
|---|---|
| Stable release | 3.1.0
/ August 30, 2019 |
| Written in | Java,C++ |
| Operating system | Linux, macOS and Microsoft Windows |
| License | Apache License |
| Website | github |
iBioSim
iBioSim[1][2] is a computer-aided design (CAD) tool aimed at the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. The software runs on all major platforms, Windows, Mac OS, and Linux.
Capabilities
- Deterministic time-course simulation
- Stochastic time-course simulation
- Support for SED-ML
- Import and export of standard SBML to Level 3 Version 1
- Import and export of standard Synthetic Biology Open Language (SBOL)
Applications
The tool has been used in a number of research projects:
- Engineering production of resveratrol in E. coli[3]
- Part of a general workflow for the design, implementation and testing of synthetic genetic circuits[4].
Notability
iBioSim is one of the few tools that focuses on the simulation and design of genetic regulatory circuits[5]. As such, the tool is more actively used in the synthetic biology community. It uses a visual GUI environment that allows users to `draw' genetic networks on screen.
See also
- List of systems biology modeling software
References
- ↑ Watanabe, Leandro; Nguyen, Tramy; Zhang, Michael; Zundel, Zach; Zhang, Zhen; Madsen, Curtis; Roehner, Nicholas; Myers, Chris (19 July 2019). "iBioSim 3: A Tool for Model-Based Genetic Circuit Design". ACS Synthetic Biology 8 (7): 1560–1563. doi:10.1021/acssynbio.8b00078.
- ↑ Myers, C. J.; Barker, N.; Jones, K.; Kuwahara, H.; Madsen, C.; Nguyen, N.-P. D. (1 November 2009). "iBioSim: a tool for the analysis and design of genetic circuits". Bioinformatics 25 (21): 2848–2849. doi:10.1093/bioinformatics/btp457.
- ↑ Cotner, Michael; Zhan, Jixun; Zhang, Zhen (20 August 2021). "A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia coli". ACS Synthetic Biology 10 (8): 1992–2001. doi:10.1021/acssynbio.1c00163.
- ↑ Konur, Savas; Mierla, Laurentiu; Fellermann, Harold; Ladroue, Christophe; Brown, Bradley; Wipat, Anil; Twycross, Jamie; Dun, Boyang Peter et al. (20 August 2021). "Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation". ACS Synthetic Biology 10 (8): 1931–1945. doi:10.1021/acssynbio.1c00143.
- ↑ Yeoh, Jing Wui; Gomez-Carretero, Salvador; Chee, Wai Kit David; Teh, Ai Ying; Poh, Chueh Loo (2022). "Genetic Circuit Design Principles". Handbook of Cell Biosensors: 339–381. doi:10.1007/978-3-030-23217-7_171.
External links
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