An open-source java platform for automated reaction mapping

Journal of Chemical Information and Modeling

Volumn 50, Issue 9, 2010, Pages 1751-1756

  Crabtree, John D ^a   Mehta, Dinesh P ^b   Kouri, Tina M ^b  

^a UNIVERSITY OF NORTH ALABAMA   (United States)

^b Department of Geology and Geological Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; JAVA PROGRAMMING LANGUAGE; MAPPING; OPEN SYSTEMS;

CHEMINFORMATICS; END USERS; JAVA PLATFORMS; MODULAR ARCHITECTURES; OPEN SOURCES; PROGRAMMING SKILLS; SOFTWARE APPLICATIONS; SOFTWARE LIBRARIES;

OPEN SOURCE SOFTWARE;

EID: 77957237619     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100061d     Document Type: Article

References (33)

1. Muharam, Y.; Warnatz, J. Kinetic Modelling of the Oxidation of Large Aliphatic Hydrocarbons Using an Automatic Mechanism Generation Phys. Chem. Chem. Phys. 2007, 9, 4218-4229
2. Matheu, D.; Grenda, J. A Systematically Generated, Pressure-Dependent Mechanism for High-Conversion Ethane Pyrolysis. 1. Pathways to the Minor Products J. Phys. Chem. 2005, 109, 5332-5342 (Pubitemid 41004270)
3. Buda, F.; Bounaceur, R.; Warth, V.; Glaude, P.; Fournet, R.; Battin-Leclerc, F. Progress Toward a Unified Detailed Kinetic Model for the Autoignition of Alkanes from C4 to C10 Between 600 and 1200 K Combust. Flame 2005, 142, 170-186 (Pubitemid 40779923)
4. Nemeth, A.; Vidoczy, T.; Heberger, K.; Kuti, Z.; Wagner, J. MECHGEN: Computer Aided Generation and Reduction of Reaction Mechanisms J. Chem. Inf. Comput. Sci. 2002, 42, 208-214 (Pubitemid 35355295)
5. Cartensen, H.; Dean, A. Rate Constant Rules for the Automated Generation of Gas-Phase Reaction Mechanisms J. Phys. Chem. 2009, 113, 367-380
6. Kovacs, T.; Zsely, I.; Kramarics, A.; Turanyi, T. Kinetic Analysis of Mechanisms of Complex Pyrolytic Reactions J. Anal. Appl. Pyrolysis 2007, 79, 252-258 (Pubitemid 46589590)
7. Shi, Y.; Ge, H.; Brakora, J.; Reitz, R. Automatic Chemistry Mechanism Reduction of Hydrocarbon Fuels for HCCI Engines Based on DRGEP and PCA Methods with Error Control Energy Fuels 2010, 24, 1646-1654
8. Sun, W.; Chen, Z.; Gou, X.; Yiguang, J. A Path Flux Analysis Method for the Reduction of Detailed Chemical Kinetic Mechanisms Combust. Flame 2010, 157, 1298-1307
9. Nagy, T.; Turanyi, T. Reduction of Very Large Reaction Mechanisms Using Methods Based on Simulation Error Minimization Combust. Flame 2009, 156, 417-428
10. Liang, L.; Stevens, J.; Raman, S.; Farrell, J. The Use of Dynamic Adaptive Chemistry in Combustion Simulation of Gasoline Surrogate Fuels Combust. Flame 2009, 156, 1493-1502
11. Pepiot-Desjardins, P.; Pitsch, H. An Efficient Error-propagation-based Reduction Method for Large Chemical Kinetic Mechanisms Combust. Flame 2008, 154, 67-81
12. Straube, R.; Flockerzi, D.; Muller, S.; Hauser, J. Reduction of Chemical Reaction Networks Using Quasi-Integrals J. Phys. Chem. 2005, 109, 441-450 (Pubitemid 40206801)
13. Akutsu, T. Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data J. Comput. Biol. 2004, 11, 449-462 (Pubitemid 38901672)
14. Goto, S.; Nishioka, T.; Kanehisa, M. Ligand: Chemical Database for Enzyme Reactions Bioinformatics 1998, 14, 591-599 (Pubitemid 28461580)
15. Crabtree, J.; Mehta, D. Automated Reaction Mapping J. Exp. Algorithmics 2009, 13, 1.15-1.29
16. McGregor, J.; Willett, P. Use of a Maximum Common Subgraph Algorithm in the Automatic Identification of Ostensible Bond Changes Occurring in Chemical Reactions J. Chem. Inf. Comput. Sci. 1981, 21, 137-140 (Pubitemid 12521950)
17. Arita, M. In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia Coli Intermediary Metabolism Genome Res. 2003, 13, 2455-2466 (Pubitemid 37428270)
18. Masaaki, K.; Yasushi, O.; Masahiro, H.; Susumu, G.; Minoru, K. Computational Assignment of the EC Numbers for Genomic-Scale Analysis of Enzymatic Reactions J. Am. Chem. Soc. 2004, 126, 16487-16498
19. Felix, L.; Valiente, G. Efficient Validation of Metabolic Pathway Databases. In Proceedings of Sixth International Symposium on Computational Biology and Genome Informatics; World Scientific Press, Inc.: Salt Lake City, UT, 2005.
20. Felix, L.; Valiente, G. Validation of Metabolic Pathway Databases Based on Chemical Substructure Search Biomol. Eng. 2007, 24, 327-335 (Pubitemid 47380453)
21. Pemmaraju, S.; Skiena, S. Algorithmic Graph Theory. In Computational Discrete Mathematics: Combinatorics and Graph Theory with Mathematica, 1st ed.; Cambridge University Press: New York, 2003.
22. Morgan, H. L. The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service J. Chem. Doc. 1965, 5, 107-113
23. Representation of Chemical Compounds. Chemoinformatics: A Textbook; 1st ed.; Gasteiger, J.; Engel, T., Eds.; Wiley: Weinheim, Germany, 2003.
24. Faulon, J.-L.; Collins, M. J.; Carr, R. D. The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences J. Chem. Inf. Model. 2004, 44, 427-436
25. McKay, B. Practical Graph Isomorphism Congr. Numer. 1981, 30, 45-87
26. Hattori, M.; Okuno, Y.; Goto, S.; Kanehisa, M. Development of a Chemical Structure Comparison Method for Integrated Analysis of Chemical and Genomic Information in the Metabolic Pathways J. Am. Chem. Soc. 2003, 125, 11853-11865 (Pubitemid 37175419)
27. Gamma, E.; Helm, R.; Johnson, R.; Vissides, J. Creational Patterns. Design Patterns: Elements of Reusable Object-Oriented Software; 1st ed.; Addison-Wesley Professional: Reading, MA, 1994.
28. Randolf, K.; Dean, A. Hydrocarbon Fuel Effects in Solid-oxide Fuel Cell Operation: An Experimental and Modeling Study of n-hexane Pyrolysis Phys. Chem. Chem. Phys. 2007, 9, 4245-4258
29. Naik, C.; Dean, A. Detailed Kinetic Modeling of Ethane Combust. Flame 2006, 145, 16-37
30. Cheon, Y.; Leavens, G. A Simple and Practical Approach to Unit Testing: The JML and JUnit Way. In ECOOP 2002-Object-Oriented Programming; Springer-Verlag: Berlin, 2002.
31. Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (cdk): An Open-source Java Library for Chemo- and Bioinformatics J. Chem. Inf. Model. 2003, 43, 493-500
32. Herraez, A. Biomolecules in the Computer: Jmol to the Rescue Biochem. Mol. Biol. Educ. 2006, 34, 255-261 (Pubitemid 44087130)
33. Friedman-Hill, E. Writing Rules in Jess. Jess in Action: Java Rule-based Systems, 1st ed.; Manning Publications Co.: Greenwich, CT, 2003.