A tool for automated inference in rule-based biological models

Rule-based biological models help researchers investigate systems such as cellular signalling pathways. Although these models are generally programmed by hand, some research efforts aim to program them automatically using biological facts extracted from papers via natural language processing. However, NLP facts cannot always be directly converted into mechanistic reaction rules for a rule-based model. Thus, there is a need for tools that can convert biological facts into mechanistic rules in a logically sound way. We construct such a tool specifically for Kappa, a model programming language, by implementing Iota, a logic language for Kappa models. Our tool can translate biological facts into Iota predicates, check predicates for satisfiability, and find models that satisfy predicates. We test our system against realistic use cases, and show that it can construct rule-based mechanistic models that are sound with respect to the semantics of the biological facts from which they were constructed.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2016

Author dc:creator

• Voss, Chelsea (Chelsea S.)

Advisor dc:contributor.advisor

• Armando Solar-Lezama.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/106447

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/106447