Conference item
Experimental biological protocols with formal semantics
- Abstract:
- Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from data. However, integration between automated tasks in the process of biological discovery is still lacking, largely due to incompatible or missing formal representations. While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics. This makes it challenging to extract novel understanding by identifying when theory and experimental evidence disagree due to errors in the models or the protocols used to validate them. To address this, we formalize the syntax of a core protocol language, which provides a unified description for the models of biochemical systems being experimented on, together with the discrete events representing the liquid-handling steps of biological protocols. We present both a deterministic and a stochastic semantics to this language, both defined in terms of hybrid processes. In particular, the stochastic semantics captures uncertainties in equipment tolerances, making it a suitable tool for both experimental and computational biologists. We illustrate how the proposed protocol language can be used for automated verification and synthesis of laboratory experiments on case studies from the fields of chemistry and molecular programming.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 1.1MB, Terms of use)
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- Publisher copy:
- 10.1007/978-3-319-99429-1_10
Authors
- Publisher:
- Springer Verlag
- Host title:
- 16th International Conference on Computational Methods in Systems Biology (CMSB), 12th-14th September 2018, Faculty of Informatics, Masaryk University, Brno (CZ)
- Journal:
- 16th International Conference on Computational Methods in Systems Biology (CMSB) More from this journal
- Volume:
- 11095
- Pages:
- 165-182
- Series:
- Lecture Notes in Computer Science
- Publication date:
- 2018-08-24
- Acceptance date:
- 2018-06-08
- DOI:
- ISBN:
- 9783319994284
- Pubs id:
-
pubs:834334
- UUID:
-
uuid:a5604229-f042-44ee-855a-decfc7231a70
- Local pid:
-
pubs:834334
- Source identifiers:
-
834334
- Deposit date:
-
2018-06-21
Terms of use
- Copyright holder:
- Abate et al
- Copyright date:
- 2018
- Notes:
- © The Author(s) 2018.This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.
- Licence:
- CC Attribution (CC BY)
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