TY - GEN
T1 - An SMT-Based Framework for Reasoning About Discrete Biological Models
AU - Yordanov, Boyan
AU - Dunn, Sara Jane
AU - Gravill, Colin
AU - Kugler, Hillel
AU - Wintersteiger, Christoph M.
N1 - Publisher Copyright: © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.
PY - 2022
Y1 - 2022
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 (DSLs) 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 (DSLs) 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.
UR - https://www.scopus.com/pages/publications/85147847512
U2 - 10.1007/978-3-031-23198-8_11
DO - 10.1007/978-3-031-23198-8_11
M3 - Conference contribution
SN - 9783031231971
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 114
EP - 125
BT - Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings
A2 - Bansal, Mukul S.
A2 - Cai, Zhipeng
A2 - Mangul, Serghei
PB - Springer Science and Business Media Deutschland GmbH
T2 - 18th International Symposium on Bioinformatics Research and Applications, ISBRA 2022
Y2 - 14 November 2022 through 17 November 2022
ER -