Challenges to Open Science - Comments from Steven Brenner
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Challenges to Open Science - Comments from Steven Brenner

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Steven presented three slides with some critical commentary as an off the cuff introduction the panel session. This was not a formal presentation but some comments that he prepared during the ...

Steven presented three slides with some critical commentary as an off the cuff introduction the panel session. This was not a formal presentation but some comments that he prepared during the workshop.

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Challenges to Open Science - Comments from Steven Brenner Challenges to Open Science - Comments from Steven Brenner Presentation Transcript

  • Challenges to Open Science Thoughts from a skeptical supporter
  • An original quote
    • “If you can not measure it, you can not improve it.” – Lord Kelvin
  • Need to align incentives
    • Even students are attuned to career incentives
      • If they aren’t, then their mentor should train them
    • Incentive & evaluation change slowly
      • The prime criterion is a technology centuries old
  • Evaluation
    • Evaluations are most important for the scientifically-young (fellowships; postdocs labs; faculty position; tenure)
    • The short time between publication & evaluation makes citation analysis ineffective
    • Many evaluators will be unfamiliar with detailed field
  • Wiki Science
    • Been there
    • (not) done that
  • BCM Sequence Annotation Web Server Randall Smith rsmith at dot.bcm.tmc.edu Wed Aug 24 06:14:20 EST 1994 Announcing a new WWW Server: The BCM Sequence Annotation Server URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html Developed by Kanwal Gill, Brent Wiese, and Randall Smith Human Genome Center, Baylor College of Medicine, Houston TX USA We have created a "Sequence Annotation" WWW Server that allows researchers to add their own annotations to Entrez (NCBI) DNA and protein sequence reports. Our Annotation Server is intended as a method for investigators to easily share new information about sequences, e.g., new features, interesting sequence matches, domain identifications, etc. A user who wishes to make an annotation for an Entrez sequence will be given the chance to select an annotation type (eg coding region, variant, etc.). The user is then requested to enter a short annotation that will appear as an embedded link in an Entrez report. The annotator will then be prompted to enter an extended commentary which gives the further details about the annotation. The annotator may also enter some keywords that can be searched on and URL's that will lead to more information (eg, an entry in another database, a file of data on the annotator's home computer, etc). Only the annotations themselves are stored on our local server. When a user wishes to view an annotated record, our server requests a sequence report from the NCBI Entrez Server. The local annotations are then embedded within the returned report. As an initial entry, we have added several hundred annotations based on data kindly provided by Keith Robison. The annotations list probable coding regions within bacterial sequences that are not annotated as such in GenBank (see Table 2 of K. Robison, W. Gilbert and G.M. Church, "Large scale bacterial gene discovery by similarity search", Nature Genetics 7:205, 1994). We invite the biological community to use the server to view this data as well as to add data of their own. Users wishing to view the data need only the URL listed above and a graphical WWW browser such as Mosaic or Chimera. Users wishing to add data would be well-advised to also prepare the text of their annotation and extended commentary as well as to have their URL's (if any) in mind before beginning. Extensive on-line help is provided for both types of users. Suggestions and comments regarding how the server can best meet the needs of the biological community are welcome. There is a comments form provided in the server for typing in your comments. Comments may also be emailed to Randall Smith at rsmith at bcm.tmc.edu. ------------------------------------------------------------------------ Randall F. Smith Human Genome Center Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine Houston, TX 77030 USA rsmith at bcm.tmc.edu 713-798-4735; FAX: 713-798-5386 ------------------------------------------------------------------------
  • Wiki Molecular Biology any successes?
    • BCM annotation server http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html
    • eProtS http://eprots.pdbj.org/
    • WikiProteins 10.1186/gb-2008-9-5-r89 Barend Mons
    • Protopedia www.protopedia.org
    • Gene Wiki: 10.1371/journal.pbio.0060175
    • TOPSAN www.topsan.org
    • Rfam-Wikipedia link (Alex Bateman)
    • SNPedia.com
    • OpenWetware
    • Instructional Wiki by Cheryl Kerfeld for undergraduate student education in genomics (a successful example)
    • GeneTests.org – NON-wiki with hundreds of essays about genetic variation