TY - JOUR
T1 - The Reasoning Engine
T2 - A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models
AU - Yordanov, Boyan
AU - Dunn, Sara Jane
AU - Gravill, Colin
AU - Arora, Himanshu
AU - Kugler, Hillel
AU - Wintersteiger, Christoph M.
N1 - Publisher Copyright:
© Mary Ann Liebert, Inc.
PY - 2023/9/1
Y1 - 2023/9/1
N2 - We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT)-based methods within a unified computational environment to address diverse biological analysis problems. The Reasoning Engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain-specific languages and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization, and reasoning over models consistent with experimental observations to reveal novel biological insights.
AB - We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT)-based methods within a unified computational environment to address diverse biological analysis problems. The Reasoning Engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain-specific languages and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization, and reasoning over models consistent with experimental observations to reveal novel biological insights.
KW - Satisfiability Modulo Theories
KW - formal reasoning
KW - gene regulatory networks
KW - interaction networks
KW - synthesis
UR - http://www.scopus.com/inward/record.url?scp=85171958096&partnerID=8YFLogxK
U2 - 10.1089/cmb.2023.0117
DO - 10.1089/cmb.2023.0117
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C2 - 37733940
AN - SCOPUS:85171958096
SN - 1066-5277
VL - 30
SP - 1046
EP - 1058
JO - Journal of Computational Biology
JF - Journal of Computational Biology
IS - 9
ER -