Portal-based knowledge environment for collaborative science

Concurrency and Computation: Practice and Experience

Volumn 19, Issue 12, 2007, Pages 1703-1716

  Schuchardt, Karen ^a   Pancerella, Carmen ^b   Rahn, Larry A ^b   Didier, Brett ^a   Kodeboyina, Deepti ^c   Leahy, David ^d   Myers, James D ^e   Oluwole, Oluwayemisi O ^f   Pitz, William ^g   Ruscic, Branko ^c   Song, Jing ^f   Von Laszewski, Gregor ^c   Yang, Christine ^b  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

^d STANFORD UNIVERSITY   (United States)

^e UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^g LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

Collaboratory; Informatics; Knowledge environment; Portal

Indexed keywords

COMPUTER AIDED SOFTWARE ENGINEERING; COMPUTER SUPPORTED COOPERATIVE WORK; GRID COMPUTING; INTEROPERABILITY; PORTALS;

COLLABORATIVE SCIENCE; INFORMATICS; INFORMATICS TOOLKIT; KNOWLEDGE ENVIRONMENT;

KNOWLEDGE ENGINEERING;

EID: 34548246469     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.1201     Document Type: Article

References (47)

1. Clery D, Voss D. All for one and one for all. Science 2005; 308(5723):809-824.
2. Kennedy D. Anniversary reflections. Science 2005; 309(5738): 1153-1158.
3. DOE National Collaboratory Program. http://www.doecollaboratory.org/ [18 December 2005].
4. Atkins DE, Droegemeir KK, Feldman SI, Garcia-Molina H, Klein ML. Messerschmitt DG, Messina P, Ostriker JP, Wright MH. Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure. http://www.communitytechnology.org/nsf_ci_report/ [18 December 2005].
5. NIH Roadmap. http://nihroadmap.nih.gov/ [18 December 2005].
6. Myers JD et al. A collaborative informatics infrastructure for multi-scale science. Challenges of Large Applications in Distributed Environments (CLADE) Workshop, Honolulu, HI, 7 June 2004. IEEE Press: Piscataway, NJ, 2004.
7. The Collaboratory for Multi-scale Chemical Science Web site. http://cmcs.org/ [18 December 2005].
8. Pancerella CM, Hewson J, Koegler W, Leahy D, Lee M, Rahn L, Yang C, Myers JD, Didier B, McCoy R. Metadata in the collaboratory for multi-scale chemical science. Proceedings of the 2003 Dublin Core Conference: Supporting Communities of Discourse and Practice-Metadata Research and Applications, Seattle, WA, 28 September-2 October 2003. DCMI, 2003; 121-130.
9. Myers JD, Pancerella C, Lansing C, Schuchardt KL. Didier B. Multi-scale science: Supporting emerging practice with semantically-derived provenance. Proceedings of the Workshop on Semantic Web Technologies for Searching and Retrieving Scientific Data, held at the 2nd International Semantic Web Conference, Sanibel Island, FL, 20 October 2003. Sun SITE Central Europe (CEUR): Aachen, 2003.
10. DARPA. BioSPICE Web site. U.S. Defense Advanced Research Project Agency, Washington, DC, 2005. https://biospice.org/ [18 December 2005].
11. Stevens RD, Robinson AJ, Goble CA. myGrid: Personalised bioinformatics on the information Grid. Bioinformatics 2003; 19(1):i302-i304.
12. The National Fusion Collaboratory Web site. http://www.fusiongrid.org/ [18 December 2005].
13. Earth System Grid Web site. https://www.earthsystemgrid.org/ [18 December 2005].
14. KnECS open-source software. http://sourceforge.net/projects/knecs/ [18 December 2005].
15. University of Michigan. CHEF Collaborative Portal Framework Web site, 2005. http://www.chefproject.org/ [18 December 2005].
16. Myers JD, Chappell A, Elder M, Geist A, Schwidder J. Re-integrating the research record. IEEE Computing in Science and Engineering 2003; 5(3):44-50. Available at: http://www.scidac.org/SAM/ [18 December 2005].
17. Apache Jakarta Project. Jakarta Slide Java Content Management System Web site, 2005. http://jakarta.apache.org/slide/ [18 December 2005].
18. Stein G. Web Digital Authoring and Versioning (WebDAV) Resources Community Web site, 2005. http://www.webdav.org/ [18 December 2005].
19. University of Chicago. Commodity Grid Kits, 2005. http://www-unix.globus. org/cog/ [18 December 2005].
20. Java Authentication and Authorization Service (JAAS). http://java.sun.com/products/jaas/ [18 December 2005].
21. Resource Description Framework (RDF). http://www.w3c.org/RDF/ [18 December 2005].
22. World Wide Web Consortium (W3C). XML Linking Language (XLink) Version 1.0, 2001. http://www.w3.org/TR/xlink/ [18 December 2005].
23. Apache Project. Lucene, Open Source search software, using Java, 2005. http://lucene.apache.org/ [18 December 2005].
24. DAV Searching and Locating (DASL) Web site. http://www.webdav.org/dasl [18 December 2005].
25. Data Format Description Language (DFDL) Web site. http://forge.gridforum. org/projects/dfdl-wg [18 December 2005].
26. Defuddle Web site. A parser implementation using the DFDL. http://defuddle.pnl.gov/ [18 December 2005].
27. Taatjes CA et al. Enols are common intermediates in hydrocarbon oxidation. Science 2005; 24:1887-1889.
28. Black G, Gracio D, Schuchardt K, Palmer B. The extensible computational chemistry environment: A problem solving environment for high performance theoretical chemistry. Proceedings of the International Conference on Computational Science (ICCS 2003) (Lecture Notes in Computer Science, vol. 2660), Sloot PMA, Abramson D, Bogdanov B, Dongarra JJ, Zomaya A, Gorbachev Y (eds.). Springer: Berlin, 2003.
29. Kendall RA et al. High performance computational chemistry: An overview of NWChem, a distributed parallel application. Computer Physics Communication 2000; 128:260-283.
30. Gaussian Web site. http://www.gaussian.com/ [18 December 2005].
31. Schuchardt KL, Myers JD, Stephan EG. A web-based data architecture for problem-solving environments: Application of distributed authoring and versioning the extensible computational chemistry environment. Cluster Computing 2002; 5(3):287-296.
32. Oluwole OO, Bhattacharjee B, Tolsma JE, Barton PI, William J, Green H. Rigorous valid ranges for optimally-reduced kinetic models. Combustion and Flame 2006; 146(1-2):348-365.
33. Schuchardt K, Oluwole O, Pitz W, Rahn LA, William J, Green H, Leahy D, Pancerella C, Sjvberg M, Dec J. Development of the RIOT Web Service and Information Technologies to enable mechanism reduction for HCCI simulations. Journal of Physics: Conference Series 2005; 16:107-112.
34. EMSL Gaussian Basis Set Order Form. http://www.emsl.pnl.gov/forms/ basisform.html [18 December 2005].
35. Ruscic B, Pinzon RE, Morton ML, von Laszewski G, Bittner S, Nijsure SG, Amin KA, Minkoff M, Wagner AF. Introduction to active thermochemical tables: Several 'key' enthalpies of formation revisited. Journal of Physical Chemistry A 2004; 108:9979-9997.
36. Ruscic B. Active thermochemical tables. 2005 Yearbook of Science and Technology. McGraw-Hill: New York, 2004.
37. Ruscic B, Pinzon RE, Von Laszewski G, Kodeboyina D, Burcat A, Leahy D, Montoya D, Wagner AF. Active thermochemical tables: Thermochemistry for the 21st Century. Journal of Physics: Conference Series 2005; 16:561-570.
38. International Union of Pure and Applied Chemistry. http://www.iupac.org/ projects/2003/2003-024-1-100.html [18 December 2005].
39. Ruscic B et al. IUPAC critical evaluation of thermochemical properties of selected radicals: Part I. Journal of Physical and Chemical Reference Data 2005; 34(2):573-656.
40. Song J, Sumathi R, Yu J, Green WH Jr. Next generation model construction software and new approaches to estimating rates and thermochemistry for combustion. Proceedings of the 228th ACS National Meeting, Philadelphia, PA, 2004. American Chemical Society: Washington, DC, 2004.
41. Java Portlet Specification, Version 1.0, JSR 168, October 2003.
42. Web Services for Remote Portlets Specification. http://www.oasis-open. org/committees/WSRP [18 December 2005].
43. Mueller KT, Garrison B, Giles CL, Mitra P. Cyberinfrastructure and research facilities: Developing collaboratory tools to facilitate multi-disciplinary, multi-scale research in environmental molecular sciences. Technical Report, Department of Chemistry, The Pennsylvania State University, University Park, PA, 2005.
44. Chemistry Research Instrumentation and Facilities. http://www.nsf.gov/ publications/pub_summ.jsp?ods_key=nsf04534 [18 December 2005].
45. The Collaboratory for MS3D Web site. http://ms3d.org/ [18 December 2005].
46. Young MM, Tang N, Hempel JC, Oshiro CM, Taylor EW, Kuntz ID, Gibson BW, Dollinger G. High-throughput structure determination: Rapid identification of protein folds using mass spectrometry and intramolecular cross-linking. Proceedings of the National Academy of Sciences of the United States of America 2000; 97(11):5802-5806.
47. Schilling B, Row RH, Gibson BW, Guo X, Young MM. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. Journal of the American Society for Mass Spectrometry 2003; 14(8):834-850.