Competitive workflow: Novel software architecture for automating drug design

Current Opinion in Drug Discovery and Development

Volumn 10, Issue 3, 2007, Pages 347-352

  Cartmell, John ^a   Krstajic, Damjan ^b   Leahy, David E ^c  

^a CYPROTEX DISCOVERY LTD   (United Kingdom)

^b Research Centre for Cheminformatics

^c NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Agents; Automated decision making; e Science; Molecular design; QSAR; Workflow

Indexed keywords

DRUG;

AUTOMATION; COMPETITIVE BEHAVIOR; COMPUTER LANGUAGE; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA BASE; DECISION MAKING; DRUG ABSORPTION; DRUG DESIGN; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; HUMAN COMPUTER INTERACTION; INFORMATION PROCESSING; LABORATORY TEST; MODEL; PRODUCTIVITY; QUALITY CONTROL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; SKILL;

AUTOMATION; COMPUTER-AIDED DESIGN; DATABASES, FACTUAL; DRUG DESIGN; EXPERT SYSTEMS; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE; SYSTEMS INTEGRATION; TECHNOLOGY, PHARMACEUTICAL;

EID: 34249108530     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (30)

1. Cartmell J, Enoch S, Krstajic D, Leahy DE: Automated QSAR through competitive workflow. J Comput Aided Mol Des (2005) 19(11): 821-833.
2. van der Aalst WM, Barros AP, ter Hofstede AH, Kiepuszewski B: Advanced workflow patterns. In: Cooperative Information Systems: 7th International Conference, CoopIS 2000 Eilat, Israel, September 6-8, 2000 Proceedings. Etzion O, Scheuermann P (Eds), Springer, Berlin Germany (2000):18-29.
3. van der Aalst WMP, ter Hofstede AHM, Kiepuszewski B, Barros AP: Workflow patterns. Distributed Parallel Databases (2003) 14(1):5-51.
4. Hassan M, Brown RD, Varma-O'Brien S, Rogers D: Cheminformatics analysis and learning in a data pipelining environment. Mol Divers (2006) 10(3):283-299. •• Good description of the implementation of workflow approaches to data processing in drug discovery.
5. Mierswa I, Wurst M, Klinkenberg R, Scholz M, Euler T: YALE: Rapid prototyping for complex data mining tasks. 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, PA, USA (2006). •• Introduction and overview of the excellent open-source data mining system YALE.
6. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: A tool for building and running workflows of services. Nucleic Acids Res (2006) 34:W729-W732. • Examples of the application of Taverna, the leading open-source workflow management system for e-Science.
7. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics (2004) 20(17):3045-3054.
8. Oinn T, Addis, M, Ferris J, Marvin D, Greenwood M Carver T, Wipat A, Li P: Taverna, lessons in creating a workflow environment for the life sciences. Tenth Global Grid Forum, Berlin, Germany 2004.
9. Kawas E, Senger M, Wilkinson MD: BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics (2006) 7:523.
10. Sroka J, Kaczor G, Tyszkiewicz J, Kierzek AM: Xqtav: An XQuery processor for Taverna environment. Bioinformatics (2006) 22(10):1280-1281.
11. Romano P, Marra D, Milanesi L: Web services and workflow management for biological resources. BMC Bioinformatics (2005) 6(Suppl 4):S24.
12. Digiampietri LA, Medeiros CB, Setubal JC: A framework based on web service orchestration for bioinformatics workflow management. Genet Mol Res (2005) 4(3):535-542.
13. Tang F, Chua CL, Ho LY, Lim YP, Issac P, Krishnan A: Wildfire: Distributed, grid-enabled workflow construction and execution. BMC Bioinformatics (2005) 6:69.
14. Garcia Castro A, Thoraval S, Garcia LJ, Ragan MA: Workflows in bioinformatics: Meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics (2005) 6:87.
15. Seibel PN, Kruger J, Hartmeier S, Schwarzer K, Lowenthal K, Mersch H, Dandekar T, Giegerich R: XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 7:490.
16. Weiss G, Sen S: Learning in multiagent systems. In: Multiagent Systems: A Modern Approach to Distributed Artificial Intelligence. Weiss G (Ed), MIT Press, Cambridge, MA, USA (1999):259-298.
17. Karasavvas KA, Baldock R, Burger A: Bioinformatics integration and agent technology. J Biomed Inform (2004) 37(3):205-219.
18. Merelli E, Armano G, Cannata N, Corradini F, d'Inverno M, Doms A, Lord P, Martin A, Milanesi L, Moller S, Schroeder M et al: Agents in bioinformatics, computational and systems biology. Brief Bioinform (2007) 8(1):45-59. •• Excellent overview of current status and potential of multi-agent systems in bioinformatics.
19. Koutkias V, Malousi A, Chouvarda I, Maglaveras N: Constructing a semantically enriched biomedical service space: A paradigm with bioinformatics resources. Stud Health Technol Inform (2006) 120: 236-246.
20. Keele JW, Wray JE: Software agents in molecular computational biology. Brief Bioinform (2005) 6(4):370-379.
21. Nascimento LV, Bazzan AL: An agent-based system for re-annotation of genomes. Genet Mol Res (2005) 4(3):571-580.
22. Armano G, Milanesi L, Orro A: An agent architecture for predicting protein secondary structures. NETTAB 2002: Agents in Bioinformatics, Bologna, Italy (2002). • Reports early practical applications of agent approaches of software architecture to drug design.
23. Buhler PA, Vidal JM: Towards adaptive workflow enactment using multiagent systems. Inf Technol Management (2005) 6(1):61-87. • Interesting description of the adaptability provided by agent-workflow systems.
24. d'Iverno M, Luck M (Eds): Understanding Agent Systems. Springer, Berlin, Germany (2003). •• Highly recommended reading for those interested in agent technologies. Provides a thorough and thought out framework for understanding agents and agent taxonomy to the specification level.
25. Corkill DD: Collaborating software: Blackboard and multi-agent systems & the future. Proceedings of the National Lisp Conference, New York, NY, USA (2003).
26. Repetto M, Paolucci M, Boccalatte A: A design tool to develop agent-based workflow management systems. 4th AI*IA/TABOO Joint Workshop "From Objects to Agents": Intelligent Systems and Pervasive Computing, Villasimius, Italy (2003). • Describes agent-based workflow systems approaches that have been developed outside the drug-discovery domain.
27. Ramampiaro H, Wang AI, Brasethvik T: Supporting distributed cooperative work in CAGIS. In: Software Process Technology: 7th European Workshop, EWSPT 2000, Kaprun, Austria, February 21-25, 2000. Conradi R (Ed), Springer, Berlin, Germany (2000):115-130.
28. Lehtovuori PT, Nyronen TH: Soma-workflow for small molecule property calculations on a multiplatform computing grid. J Chem Inf Model (2006) 46(2):620-625.
29. Kovatcheva A, Golbraikh A, Oloff S, Xiao YD, Zheng W, Wolschann P, Buchbauer G, Tropsha A: Combinatorial QSAR of ambergris fragrance compounds. J Chem Inf Comput Sci (2004) 44(2):582-595. • Describes a combinatorial approach to QSAR modeling.
30. Olah M, Bologa C, Oprea TI: An automated PLS search for biologically relevant QSAR descriptors. J Comput Aided Mol Des (2004) 18(7-9):437-449.