Types for BioAmbients
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in wh...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Open Publishing Association
2010-02-01
|
| Series: | Electronic Proceedings in Theoretical Computer Science |
| Online Access: | http://arxiv.org/pdf/1002.4066v1 |
| _version_ | 1818085013986476032 |
|---|---|
| author | Sara Capecchi Angelo Troina |
| author_facet | Sara Capecchi Angelo Troina |
| author_sort | Sara Capecchi |
| collection | DOAJ |
| description | The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in which the ambient can stay. The type system ensures that, in a well-typed process, ambients cannot be nested in a way that violates the type hierarchy. Exploiting the information given by the group types, we also extend the operational semantics of BioAmbients with rules signalling errors that may derive from undesired ambients' moves (i.e. merging incompatible tissues). Thus, the signal of errors can help the modeller to detect and locate unwanted situations that may arise in a biological system, and give practical hints on how to avoid the undesired behaviour. |
| first_indexed | 2024-12-10T20:03:02Z |
| format | Article |
| id | doaj.art-08befa971d2541c4b011bfbbcd768b53 |
| institution | Directory Open Access Journal |
| issn | 2075-2180 |
| language | English |
| last_indexed | 2024-12-10T20:03:02Z |
| publishDate | 2010-02-01 |
| publisher | Open Publishing Association |
| record_format | Article |
| series | Electronic Proceedings in Theoretical Computer Science |
| spelling | doaj.art-08befa971d2541c4b011bfbbcd768b532022-12-22T01:35:28ZengOpen Publishing AssociationElectronic Proceedings in Theoretical Computer Science2075-21802010-02-0119Proc. FBTC 201010311510.4204/EPTCS.19.7Types for BioAmbientsSara CapecchiAngelo TroinaThe BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in which the ambient can stay. The type system ensures that, in a well-typed process, ambients cannot be nested in a way that violates the type hierarchy. Exploiting the information given by the group types, we also extend the operational semantics of BioAmbients with rules signalling errors that may derive from undesired ambients' moves (i.e. merging incompatible tissues). Thus, the signal of errors can help the modeller to detect and locate unwanted situations that may arise in a biological system, and give practical hints on how to avoid the undesired behaviour.http://arxiv.org/pdf/1002.4066v1 |
| spellingShingle | Sara Capecchi Angelo Troina Types for BioAmbients Electronic Proceedings in Theoretical Computer Science |
| title | Types for BioAmbients |
| title_full | Types for BioAmbients |
| title_fullStr | Types for BioAmbients |
| title_full_unstemmed | Types for BioAmbients |
| title_short | Types for BioAmbients |
| title_sort | types for bioambients |
| url | http://arxiv.org/pdf/1002.4066v1 |
| work_keys_str_mv | AT saracapecchi typesforbioambients AT angelotroina typesforbioambients |