Language-oriented rule-based reaction network generation and analysis: Algorithms of RING

Srinivas Rangarajan; Ted Kaminski; Eric Van Wyk; Aditya Bhan; Prodromos Daoutidis

doi:10.1016/j.compchemeng.2014.02.007

Language-oriented rule-based reaction network generation and analysis: Algorithms of RING

Srinivas Rangarajan
, Ted Kaminski
, Eric Van Wyk
, Aditya Bhan
, Prodromos Daoutidis

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

Abstract

The underlying algorithms of the language interface and post-generation analysis modules in RING, a network generation and analysis tool, are discussed. The front-end is a domain-specific reaction language developed with Silver, a meta-language based on attribute grammars. The language compiler translates user inputs written as a program into internal instructions, catches syntactic and semantic errors, and performs domain-specific optimization to speed up execution. In addition to generating reaction networks, RING allows post-processing analysis options to: (a) obtain reaction pathways and overall mechanisms from initial reactants to desired products using graph traversal algorithms, (b) group together isomers to reduce the size of the network through a novel molecule hashing technique, (c) calculate thermochemical quantities through semi-empirical methods such as group additivity, and (d) formulate and solve kinetic models of the entire or lumped complex network based on a rule-based kinetics specification scheme.

Original language	English (US)
Pages (from-to)	124-137
Number of pages	14
Journal	Computers and Chemical Engineering
Volume	64
DOIs	https://doi.org/10.1016/j.compchemeng.2014.02.007
State	Published - May 7 2014

Bibliographical note

Funding Information:
Financial support from the National Science Foundation (CBET # 1307089 , IIS grant # 0905581 ) and from the University of Minnesota Digital Technology Center is gratefully acknowledged. The authors also acknowledge partial support from the Initiative for Renewable Energy (Large Grant: RL-0004-09 ), Digital Technology Center , and the doctoral dissertation fellowship at the University of Minnesota.

Keywords

Automated reaction network generation
Domain-specific languages
Extensible languages
Isomer lumping
Kinetic modeling
Reaction network analysis

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10.1016/j.compchemeng.2014.02.007

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title = "Language-oriented rule-based reaction network generation and analysis: Algorithms of RING",

abstract = "The underlying algorithms of the language interface and post-generation analysis modules in RING, a network generation and analysis tool, are discussed. The front-end is a domain-specific reaction language developed with Silver, a meta-language based on attribute grammars. The language compiler translates user inputs written as a program into internal instructions, catches syntactic and semantic errors, and performs domain-specific optimization to speed up execution. In addition to generating reaction networks, RING allows post-processing analysis options to: (a) obtain reaction pathways and overall mechanisms from initial reactants to desired products using graph traversal algorithms, (b) group together isomers to reduce the size of the network through a novel molecule hashing technique, (c) calculate thermochemical quantities through semi-empirical methods such as group additivity, and (d) formulate and solve kinetic models of the entire or lumped complex network based on a rule-based kinetics specification scheme.",

keywords = "Automated reaction network generation, Domain-specific languages, Extensible languages, Isomer lumping, Kinetic modeling, Reaction network analysis",

author = "Srinivas Rangarajan and Ted Kaminski and \{Van Wyk\}, Eric and Aditya Bhan and Prodromos Daoutidis",

note = "Funding Information: Financial support from the National Science Foundation (CBET \# 1307089 , IIS grant \# 0905581 ) and from the University of Minnesota Digital Technology Center is gratefully acknowledged. The authors also acknowledge partial support from the Initiative for Renewable Energy (Large Grant: RL-0004-09 ), Digital Technology Center , and the doctoral dissertation fellowship at the University of Minnesota. ",

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doi = "10.1016/j.compchemeng.2014.02.007",

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AU - Van Wyk, Eric

AU - Bhan, Aditya

AU - Daoutidis, Prodromos

N1 - Funding Information: Financial support from the National Science Foundation (CBET # 1307089 , IIS grant # 0905581 ) and from the University of Minnesota Digital Technology Center is gratefully acknowledged. The authors also acknowledge partial support from the Initiative for Renewable Energy (Large Grant: RL-0004-09 ), Digital Technology Center , and the doctoral dissertation fellowship at the University of Minnesota.

PY - 2014/5/7

Y1 - 2014/5/7

N2 - The underlying algorithms of the language interface and post-generation analysis modules in RING, a network generation and analysis tool, are discussed. The front-end is a domain-specific reaction language developed with Silver, a meta-language based on attribute grammars. The language compiler translates user inputs written as a program into internal instructions, catches syntactic and semantic errors, and performs domain-specific optimization to speed up execution. In addition to generating reaction networks, RING allows post-processing analysis options to: (a) obtain reaction pathways and overall mechanisms from initial reactants to desired products using graph traversal algorithms, (b) group together isomers to reduce the size of the network through a novel molecule hashing technique, (c) calculate thermochemical quantities through semi-empirical methods such as group additivity, and (d) formulate and solve kinetic models of the entire or lumped complex network based on a rule-based kinetics specification scheme.

AB - The underlying algorithms of the language interface and post-generation analysis modules in RING, a network generation and analysis tool, are discussed. The front-end is a domain-specific reaction language developed with Silver, a meta-language based on attribute grammars. The language compiler translates user inputs written as a program into internal instructions, catches syntactic and semantic errors, and performs domain-specific optimization to speed up execution. In addition to generating reaction networks, RING allows post-processing analysis options to: (a) obtain reaction pathways and overall mechanisms from initial reactants to desired products using graph traversal algorithms, (b) group together isomers to reduce the size of the network through a novel molecule hashing technique, (c) calculate thermochemical quantities through semi-empirical methods such as group additivity, and (d) formulate and solve kinetic models of the entire or lumped complex network based on a rule-based kinetics specification scheme.

KW - Automated reaction network generation

KW - Domain-specific languages

KW - Extensible languages

KW - Isomer lumping

KW - Kinetic modeling

KW - Reaction network analysis

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DO - 10.1016/j.compchemeng.2014.02.007

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JO - Computers and Chemical Engineering

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ER -

Language-oriented rule-based reaction network generation and analysis: Algorithms of RING

Abstract

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