Towards scalable modeling of biology in Event-B
Towards scalable modeling of biology in Event-B
Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to check for model consistency step-by-step in an automated way. Our approach based on functions leads to an elegant and concise modeling method. We demonstrate this approach by constructing what is, to our knowledge, the largest ever built Event-B model, describing the ErbB signaling pathway, a key evolutionary pathway with a significant role in development and in many types of cancer. The Event-B model for the ErbB pathway describes 1320 molecular reactions through 242 events.
q-bio.MN, cs.CL
Sanwal, Usman
3651c8cf-23fe-4d75-8f89-db1fcbcacf88
Hoang, Thai Son
dcc0431d-2847-4e1d-9a85-54e4d6bab43f
Petre, Luigia
2a81e9f4-b9fd-4537-9e90-ff0d07562153
Petre, Ion
d942b378-d1e6-497c-b543-31366e9aeb2d
20 May 2021
Sanwal, Usman
3651c8cf-23fe-4d75-8f89-db1fcbcacf88
Hoang, Thai Son
dcc0431d-2847-4e1d-9a85-54e4d6bab43f
Petre, Luigia
2a81e9f4-b9fd-4537-9e90-ff0d07562153
Petre, Ion
d942b378-d1e6-497c-b543-31366e9aeb2d
[Unknown type: UNSPECIFIED]
Abstract
Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to check for model consistency step-by-step in an automated way. Our approach based on functions leads to an elegant and concise modeling method. We demonstrate this approach by constructing what is, to our knowledge, the largest ever built Event-B model, describing the ErbB signaling pathway, a key evolutionary pathway with a significant role in development and in many types of cancer. The Event-B model for the ErbB pathway describes 1320 molecular reactions through 242 events.
Text
2105.10344v1
- Author's Original
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Published date: 20 May 2021
Keywords:
q-bio.MN, cs.CL
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Local EPrints ID: 473034
URI: http://eprints.soton.ac.uk/id/eprint/473034
PURE UUID: 1efa2283-3c0d-4333-b6e9-acf396cd56a4
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Date deposited: 09 Jan 2023 18:21
Last modified: 17 Mar 2024 03:39
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Contributors
Author:
Usman Sanwal
Author:
Thai Son Hoang
Author:
Luigia Petre
Author:
Ion Petre
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