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Cyberscience: Computational Science and the Rise of the Fourth Paradigm Honors 352, Class #0.5 August E. (Gus) Evrard, PhD Fall 2010

today * reading quiz * lecture – infrastructure and cyberinfrastructure * first blog posts – reactions * group projects – timeline, aims, google site as collaboration space * v0.2 syllabus next Monday

infrastructure Please see original image and quote from New York Times article at orks. orks

infrastructure characteristics and lifecycle lifecycle: invention development and innovation technology transfer, growth and competition consilidation splintering or fragmentation decline P. N. Edwards, Vast Machine, Ch. 1

Edwards on scientific knowledge P. N. Edwards, Vast Machine, Ch. 1

cyberinfrastructure vocabulary * ontology * taxonomy * workflow * scientific application * virtual organization...

ontology def’n: Tom Gruber (Stanford) Please see the rest of the original article on Ontology at ksl.stanford.edu/kst/what-is-an-ontology.html. ksl.stanford.edu/kst/what-is-an-ontology.html Ontologies as a specification mechanism A body of formally represented knowledge is based on a conceptualization: the objects, concepts, and other entities that are assumed to exist in some area of interest and the relationships that hold among them (Genesereth & Nilsson, 1987). A conceptualization is an abstract, simplified view of the world that we wish to represent for some purpose. Every knowledge base, knowledge-based system, or knowledge-level agent is committed to some conceptualization, explicitly or implicitly. An ontology is an explicit specification of a conceptualization. Tom Gruber, From Wikipedia article on Ontology Wikipedia

ontology components: wikipedia Wikipedia

example: geopolitical ontology in OWL Wikipedia

example: geopolitical ontology in OWL Wikipedia

taxonomy def’n: from Drupal.org Drupal.org

cyberinfrastructure elements * hardware – processors/cores – memory/storage – ports/routers – power sources * software – operating systems (OS) – languages: compiled, scripted, commercial, open source graphical history – – database * network – transfer protocols (http, ftp, tcp/ip,...) – authentication/authorization – quality of service: bandwidth, error control,...

goal: realize this graphic Regents of the University of Michigan

Additional Source Information for more information see: Slide 5: Please see original image and quote from New York Times article at Slide 6: P. N. Edwards, Vast Machine, Ch. 1 Slide 7: P. N. Edwards, Vast Machine, Ch. 1 Slide 9 Quote (top): Tom Gruber, “What is an Ontology?” Slide 9 Quote (bottom, left): Please see the rest of the original article on Ontology at Slide 9 Image (bottom, right): “Ontology (Information Science),” Wikipedia, CC: BY-SA 3.0, Slide 10: “Ontology (Information Science),” Wikipedia, CC: BY-SA 3.0, sa/3.0/. sa/3.0/ Slide 11: “Geopolitical Ontology,” Wikipedia, CC: BY-SA 3.0, Slide 12: “Geopolitical Ontology,” Wikipedia, CC: BY-SA 3.0, Slide 13: “About Taxonomy,” Drupal, GPL v3.0, Slide 15: Regents of the University of Michigan, “Knowledge-Driven Research Infrastructure,” CC: BY 3.0,