Prothrombin mutations: thrombophilic mechanisms and an unusual variant

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					Web-based Collaborative Computing
   Tools for Clinical Pathology

       Noah Hoffman, May 2006
• A bit about web-based applications
• Wiki as a tool for collaborative authorship
• Current projects
   – Test interpretation database
   – Lab medicine wiki
   – Micropedia
     Web applications made simple

persistence            logic
                                        webserver    Server

              client           client       client
Test interpretation database - Goals
• facilitate organization of custom
  interpretations for laboratory results
• include reference management with interface
  to PubMed
• permit collaborative authorship of contents
  (with restrictions)
    Existing interpretation repositories
• Filemaker
    – Serves primarily as patient database; test interpretation
      storage is just one feature
    – versatile
    – Requires Filemaker on client computer (expensive)
    – Being phased out for security reasons?
•   Hemepath database
    – Web-based, integrates sets of interpretive comments into
      report generation
    – Interpretive comments stored in drop-down menus - difficult
      to modify, requires configuration of client machine
    – Comments not searchable
• Word files
    – Versatile, ubiquitous
    – Difficult to search, maintain
    – Data unstructured, difficult to extract or manipulate
        Additional requirements
• stable and maintainable
• platform-neutral
• fast
• scaleable
• open source components = no direct cost for
• data easily backed up and manipulated
• No PHI
           interpretation database:
• Operating system
   – development: Mac OS X
   – operation: mixed architecture Linux/IBM AIX (C&C server)
• Webserver
   – Apache
   – SSL encryption
• CGI - Python (
• Database - MySQL
• Development tools
   – version control - CVS
   – file synchronization - Unison
•   Add a few additional fields
•   Authentication using UW NetID
•   Incorporate coded comments from LIS
•   Handle simultaneous edits

“A collaborative website whose content can be
edited by anyone who has access to it using
simple formatting rules.”

"Hypertext-based collaborative software that
enables documents to be authored
collectively using a web browser."
                         How wikis work
  • A wiki “engine” does the work
         – Retrieves content (typically stored as ASCII/plain text) and
           translates wiki markup to HTML (see below)
         – applies style to translated content
         – provides an online editor

       Wiki markup                              HTML
[“front page”]           <a href=“http://….front_page”>front page</a>
''bold face''            <b>bold face</b>

----                     <hr>

[[Attach(file.doc)]]     <a href="http://…file.doc">file.doc</a>
Wikipedia ranked #17th most-visited
           site, May 2006
OF WORKING (IFCC News, March/April)
Andrew Wootton, Chair, IFCC
Communication and Publications Division

  • Announced plans to implement new web services via
    the IFCC site in the coming year:
     – A wiki to serve the Laoratory Medicine community: "Each of
       us contributing to our pet analyte and sharing the workload
       to produce a sum far greater than any of the parts! Let’s try it
       and see how it works. We have the tools."
     – A web framework that would provide national societies with
       their own web pages on the IFCC website.
     Lab medicine residents’ wiki
• Goal: organize useful information
• Implementation
  – Modified version of a simple freeware wiki engine
    written in python (pikipiki)
  – Single CGI script
  – Data stored as plain text files
  – Runs on upper campus (Computing &
    Communications) servers
Wiki usage
• Conceived by Dr Ferric Fang
• Developmental version implemented using an
  open-source wiki engine written in python
• Goal - provide a quick reference of
  microorganisms of medical importance
  – Definitions
  – Protocols
  – Images
• Emphasis on usefulness for the clinical micro
          Micropedia wiki features
• Collaborative authorship/editing
• Fine-grained control over access and permission to
  modify content
• Tracking of changes is built in; old versions of data
  are saved
• Hierarchical formatting (ie, section headers, lists) is
  largely automated
• Intra-site (that is, page to page) linking is automated
  and stable
• Automated generation of indices, table of contents
• Markup is simple and intended for non-technical
  users; GUI editor available
• Content is searchable
• Content may be reformatted for print media
Reference management
Structured content permits
reformatting for print media
• There is no shortage of existing or easily
  created software solutions to the problem of
  creating and maintaining content as a group
• The success of any given implementation
  probably depends more on social and
  institutional factors than the software chosen

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