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Informatics tools for scientific discovery and collaboration.

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PDF grethe.pdf (3MB) Introduction to computing. Open source software tools. Wrappers. Introduction to supercomputers and parallel computers. Processing chips, graphic chips. Orders of magnitude in computation. The Grid. Amanda Grethe. pdf file of Powerpoint slides PDF
Microsoft PowerPoint cragin_hogan.ppt (213KB) Arrowsmith information diary: Linking your information activities to your research process. Melissa Cragin, Tim Hogan. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint palmer.ppt (176KB) Information-gathering and collaborative behavior of interdisciplinary scientists. Carole Palmer. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint smalheiser_morethanIR.ppt (358KB) More than information retrieval: The active role of the Arrowsmith grant in following-up searches with new experiments and new collaborations. Open source lab notebooks. Software to enhance collaborative thinking and creativity. Online knowledge environments. How can informatics lead to new models of experimental design and scientific collaboration? Neil Smalheiser. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint smalheiser_searchbasics.ppt (1MB) Basics of searching the biomedical literature. Medline fields, Medical Subject Headings, controlled vocabulary, UMLS, Metamap, semantic categories. Basics of PubMed. How it converts a user-typed query to the “real” query. Options for searches. Clinical queries. Augmenting PubMed: link-outs to the web (online papers, author/affiliation home pages, and links to Google searches); visualizing, clustering, filtering and mining search outputs. Searching other literatures besides Medline (Psychinfo, ERIC, EMBASE, Firstsearch, etc.). Alerting services: Pubcrawler. Other online search tools especially for biomedical information. Web of Science for citations. E-Prints and full access to the literature. Neil Smalheiser.Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint smalheiser_UICsite.ppt (530KB) The UIC Arrowsmith site. Different modes of (or reasons for) discovering information across two or more literatures. Examples. Existing B-term filters, planned filters and alternative output modes. Link by title words and phrases, vs. terms in abstract or full-text. Alternative ways of linking literatures: UMLS concepts, MeSH headings, affiliations. The open-ended (one node) search. Linking Medline to other bibliographic databases. Can one automate Arrowsmith searches, or automatically detect promising inferences? An alerting service to flag new papers that bridge disciplines. Neil Smalheiser.Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint smalheiser_welcome.ppt (43KB) Welcome. Information is Money. Earn it, save it, invest it; and retire rich! Neil Smalheiser. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint swanson.ppt (230KB) Strategies of searching the biomedical literature. Recall and precision. Techniques for broadening and narrowing searches. Relevance feedback, interactive search strategies. Don Swanson.Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint torvik_authorlinkage.ppt (259KB) Author linkages. Author disambiguation and linking literatures by author to study author publication behavior and collaborative networks. Monotone Boolean functions in information retrieval. Automatic recognition of types of web pages and extraction of information into database form. Vetle Torvik.Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint torvik_bioinformatics.ppt (98KB) Extensions of the Arrowsmith approach to bio-informatics: gene-gene associations, finding sequence overlap, using microarray data, images or other supplemental data to link literatures. Making inferences across linked research (basic and clinical) databases. Vetle Torvik. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint torvik_databases.ppt (617KB) Introduction to databases. Medline as a flat-file vs. Medline as a database suitable for querying. Why the WWW and even your own experiments can (and should) be thought of as a database. Databases for specialized data formats. What every neuroscientist should know about database design and data mining. Data and metadata. Ontologies. Visualizing massive datasets. Vetle Torvik. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint torvik_fieldtesters.ppt (112KB) How to record and evaluate Arrowsmith searches. Vetle Torvik. Powerpoint slides Microsoft PowerPoint
Microsoft PowerPoint yu.ppt (284KB) Basics of Information Retrieval, Natural Language Processing and Information Extraction. Overview of research in medical informatics to automatically extract biological information from full text of scientific papers. Structure of the Web. The semantic Web, the deep Web. How does Google work? Search engines, metasearch engines, query processing. Clement Yu. Powerpoint slides Microsoft PowerPoint
JPEG image workshop.jpg (140KB) Photo of participants JPEG image
HTML workshop.html (8KB) Outline of the workshop HTML
Title: Informatics tools for scientific discovery and collaboration.
Author(s): Smalheiser, Neil R; Swanson, Don R; Torvik, VI; Palmer, C; Cragin, M; Hogan, T; West, R; Bischoff-Grethe, A; Yu, C
Issue Date: 2003
Type: Learning Object
Description: Smalheiser NR, Swanson DR, Torvik VI, Palmer C, Cragin M, Hogan T, West R, Bischoff-Grethe A, Yu C. (presenters) Informatics tools for scientific discovery and collaboration. Arrowsmith Project short course, UIC Psychiatric Institute, September 3-5, 2003.
URI: http://hdl.handle.net/10027/41
Date Available in INDIGO: 2006-10-04
 

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