Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
- Submitting institution
-
Manchester Metropolitan University
- Unit of assessment
- 11 - Computer Science and Informatics
- Output identifier
- 2348
- Type
- D - Journal article
- DOI
-
10.1093/bioinformatics/btv660
- Title of journal
- Bioinformatics
- Article number
- -
- First page
- 908
- Volume
- 32
- Issue
- 6
- ISSN
- 1367-4803
- Open access status
- Out of scope for open access requirements
- Month of publication
- November
- Year of publication
- 2015
- URL
-
https://e-space.mmu.ac.uk/620006/
- Supplementary information
-
-
- Request cross-referral to
- -
- Output has been delayed by COVID-19
- No
- COVID-19 affected output statement
- -
- Forensic science
- No
- Criminology
- No
- Interdisciplinary
- Yes
- Number of additional authors
-
9
- Research group(s)
-
C - Machine Intelligence
- Citation count
- 8
- Proposed double-weighted
- No
- Reserve for an output with double weighting
- No
- Additional information
- The paper is the first to propose a formal way to annotate rule-based computational models, a process that is critical for the generation of automatic genetic circuits with “parts” extracted from curated databases. The work has been used to implement a genetic compiler for rule-based models (W.Waites et al. ACS Synthetic Biology, 7, 2018). The approach has been referenced in several papers in computational synthetic biology and systems biology, including (L.A Harris et al., Bioinformatics, 32, 11, 2016) describing BioNetGen, a well-known package for modelling biological systems.
- Author contribution statement
- -
- Non-English
- No
- English abstract
- -