OpenWetWare:Respond to NSF

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(Framework for thinking about OpenWetWare's mission)
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#Other?
#Other?
*'''[[Sri Kosuri]] ([[User talk:Skosuri|talk]])''': It's somewhat silly to consider this question now.  Currently, Jot/Apple is not available to us; and Mediawiki seems to be the best software for what we are doing.  As opportunities arrive for better software in the future, the Steering Committee (w/ support by technical people hired by the grant) have already shown they are well positioned to make such decisions (i.e., private wikis, moving servers, user management system).
*'''[[Sri Kosuri]] ([[User talk:Skosuri|talk]])''': It's somewhat silly to consider this question now.  Currently, Jot/Apple is not available to us; and Mediawiki seems to be the best software for what we are doing.  As opportunities arrive for better software in the future, the Steering Committee (w/ support by technical people hired by the grant) have already shown they are well positioned to make such decisions (i.e., private wikis, moving servers, user management system).
 +
*'''[[User:Skoch3|Skoch3]] 16:08, 23 January 2007 (EST)''':  I was drawn to OWW by use of MediaWiki.  I worried about setting up my lab on some framework that would not be available down the road.  That is: I wanted longevity.  I had looked into some other options.  [http://www.socialtext.com Social Text] actually is a really great product.  They do have an opensource version, but that is too complicated for me to deal with.  But OWW was just almost perfect for me.  Jot/Google lost out because, amazingly, while they do the merger you cannot access jotspot or even evaluate it at all.  Sort of long winded, but I think you are doing the best thing by leveraging MediaWiki.  I think the most likely wiki experience for a scientist to have is with wikipedia at this point.
==What should be the relationship between OWW and publishers?==
==What should be the relationship between OWW and publishers?==
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#Semantic web tools for annotating data enhancing machine readability
#Semantic web tools for annotating data enhancing machine readability
#Tools for conversion of word documents to wiki format
#Tools for conversion of word documents to wiki format
 +
#Personalized content, for instance suggested papers/grants (partnership with SciLink?)
===Fostering a community that values sharing===
===Fostering a community that values sharing===
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#Creating videos of protocols on OWW
#Creating videos of protocols on OWW
#[[OpenWetWare:Nature Methods article|Pushing through articles on OpenWetWare]]
#[[OpenWetWare:Nature Methods article|Pushing through articles on OpenWetWare]]
 +
#Organize an annual conference/retreat
 +
#Advertizing, marketing, and recruiting users within the biological science and engineering community.
 +
#Enable users to easily find other researchers in their field (e.g searchable categorized DB of scientists)
 +
#Start a 'reprint journal' where the articles are selected by voting within a community (for instance, the OWW synthetic biology journal where articles from the OA literature are nominated for re-publication by voting on syntheticbiology.org)
 +
#More 'social networking' tools (profiles, message boards, colleague lists, IMing) to make it easier to communicate and collaborate within your community.
 +
#Better tracking of site analytics, user surveys, etc.  Monthly reports on what communities are growing, how researchers are using the site, etc.
===Incentivizing sharing via the scientific reward structure===
===Incentivizing sharing via the scientific reward structure===
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#Promote publishing of supplementary information to papers on OWW (not large datasets but rather protocols and details of experimental setup)
#Promote publishing of supplementary information to papers on OWW (not large datasets but rather protocols and details of experimental setup)
#Getting an "impact factor" for OWW (inclusion in the Thomson Scientific index)
#Getting an "impact factor" for OWW (inclusion in the Thomson Scientific index)
 +
#Promote the development of unique author IDs in order to tie online contributions (e.g. edits on OWW) to your paper publication record.
 +
#Pioneer giving awards / recognition for contributing quality content in a non-peer reviewed, open, online resource.
 +
#Partner with a journal to publish short time scale (potentially non-peer reviewed) publications.
 +
#Pilot a curator role, for instance there could be 'always up to date reviews' curated by an expert in the field.  This person should get credit at least equivalent to writing a paper review.
 +
#Make it easy to move OWW pages to a DOI server so they can become part of the 'citeable' literature base.  We could partner with an existing DOI server, or start our own.
===Sustainable governance for OpenWetWare===
===Sustainable governance for OpenWetWare===
In order to promote the above three approaches, OWW needs organization and leadership.  How do we put into place this organization?
In order to promote the above three approaches, OWW needs organization and leadership.  How do we put into place this organization?
 +
 +
'''[[User:Jasonk|Jasonk]] 08:44, 19 January 2007 (EST):''' In previous discussions we [[OpenWetWare:Steering committee/Long term planning discussion|outlined this organization:]]
 +
#Steering Committee (volunteer)
 +
#*Primary responsibility: Ensure an active, vibrant user community.
 +
#Administrative (paid?)
 +
#*Keep track of money, organize meetings.
 +
#Technical (paid?)
 +
#*Primary responsibility: Keep the site software/hardware up-to-date. Implement new software and analysis suggested by the steering committee/user community.  Organize volunteer software development efforts. 
 +
#Lead Evangelist/"CEO" (paid)
 +
#*Primary responsibility: Manage/raise funds and ensure that the admin/tech and steering committee are working well together
 +
#Community facilitator (short term paid position or volunteer?)
 +
#*Dedicated effort to recruit/facilitate new users and set best practices for the community
 +
 +
This still leaves open the question of the best mechanism to achieve this organization, and on what time scale we expect to have it in place.
 +
 +
 +
*'''[[User:Vincent|Vincent]] 07:53, 19 January 2007 (EST)''': Would it be useful to try to define a '''Performance measure''' for each of the items above. It could help to monitor the progress of the OWW community as a all but also to guide and evaluate any hired person. I would suggest to specify for each item:
 +
** when the item is supposed to be available as a service to OWW community. <font color=green>(OPEN_DATE)</font>
 +
** what is the performance measure to be used to monitor progress of this specific item <font color=green>(PERFORMANCE)</font>
 +
** what is the target for this performance in 1 year, 3 years, 5 years. <font color=green>(TARGETS)</font>
 +
Example on previously listed items: {{hide|1=
 +
===Fostering a community that values sharing===
 +
Efforts that may help promote community growth and involvement include
 +
#Developing tutorials for <font color=green>'''OPEN_DATE''': NA  // '''PERFORMANCE''': nb tutorials created  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
##Starting a userpage <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb visits  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
##Starting a class <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb visits  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
##Starting a lab <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb visits  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
##Starting a research community <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb visits  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Developing and piloting norms for categorization of pages <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb of documented categories + usage stats on OWW pages  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Establishing good examples of consensus protocols as a model for others to follow <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb consensus protocols created + nb visits  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Creating videos of protocols on OWW <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb video created  + nb visits//'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#[[OpenWetWare:Nature Methods article|Pushing through articles on OpenWetWare]]
 +
#Organize an annual conference/retreat <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb events organized + nb attendees  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Advertizing, marketing, and recruiting users within the biological science and engineering community. <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb ads dessiminated  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Enable users to easily find other researchers in their field (e.g searchable categorized DB of scientists) <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': ???  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#Start a 'reprint journal' where the articles are selected by voting within a community (for instance, the OWW synthetic biology journal where articles from the OA literature are nominated for re-publication by voting on syntheticbiology.org) <font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb papers + nb feedbacks  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
#More 'social networking' tools (profiles, message boards, colleague lists, IMing) to make it easier to communicate and collaborate within your community.<font color=green>'''OPEN_DATE''': XXX  // '''PERFORMANCE''': nb tools available + measure of traffic  //'''TARGETS''':  (2007)XXX (2009)XXX  (2011)XXX</font>
 +
}}

Current revision

Contents

High Level Comments from NSF

  1. Wants to see a 3-year plan (willing to hear case for 5 years, w/ evaluation point at EOY3)
  2. Wants to see money spent on actual stuff (e.g., code) not project management
    • Jasonk 19:16, 16 January 2007 (EST):What are the chances we can convince them a community developer (the position we outlined for the NIH $) is doing 'stuff'? This is not project management (e.g. not dealing with funding, strategic decisions, etc), but rather a person supporting the growth of various communities on OWW - communities that in the end will do more "stuff" then a couple paid programmers could ever do. Also, those communities will be persistent when the grant money ends in 3 years, while the programmers won't. Plus we'd really like to get a volunteer software developer community off the ground, since new code will need support when the 3 years is over as well.
    • Vincent 13:01, 17 January 2007 (EST): Is there any possibilities to spend money on bringing face to face this virtual community in order to stimulate interactions/collaborations:
      • OWW annual conference
      • OWW workshops on hot OWW topics (characterization of parts, optimization of protocols, ethical issues ...)
      • OWW twinning (money available for some OWW user to visit some other(s) on a specific OWW project )

What user types should OWW target for focused development support? What are the needs of these communities?

  1. Individual researcher
  2. Research lab
  3. Research community
  4. Educator
  5. Journal
  6. Organization
  7. Other?
  • Sri Kosuri (talk): The focus here should not be on user types, but on any of the above categories that are willing to share information openly on biology research.

How should OWW best leverage existing software development efforts?

  1. MediaWiki
  2. Jot/Google
  3. Apple OS Next (e.g., an OS with a built-in wiki)
  4. Other?
  • Sri Kosuri (talk): It's somewhat silly to consider this question now. Currently, Jot/Apple is not available to us; and Mediawiki seems to be the best software for what we are doing. As opportunities arrive for better software in the future, the Steering Committee (w/ support by technical people hired by the grant) have already shown they are well positioned to make such decisions (i.e., private wikis, moving servers, user management system).
  • Skoch3 16:08, 23 January 2007 (EST): I was drawn to OWW by use of MediaWiki. I worried about setting up my lab on some framework that would not be available down the road. That is: I wanted longevity. I had looked into some other options. Social Text actually is a really great product. They do have an opensource version, but that is too complicated for me to deal with. But OWW was just almost perfect for me. Jot/Google lost out because, amazingly, while they do the merger you cannot access jotspot or even evaluate it at all. Sort of long winded, but I think you are doing the best thing by leveraging MediaWiki. I think the most likely wiki experience for a scientist to have is with wikipedia at this point.

What should be the relationship between OWW and publishers?

  1. None
  2. Sell-out
  3. Destroy
  4. Creative partnership
  5. Other?
  • What does OWW get from working with publishers?
    1. Increased legitimacy
    2. Opportunity to subvert existing merit structure in science
    3. Push forward more rapid publication options / technologies
    4. others?
  • Why publishers anyway? What should OWW's relationship be with facebook/myspace? or with slashdot/reddit/digg, or Google? There are other groups that could be considered for partnerships as well.

Framework for thinking about OpenWetWare's mission

in progress, please contribute

OpenWetWare's stated mission is to promote the open sharing of information in biological science and engineering research. There are three primary approaches to achieving this goal.

Developing tools and technologies

Example tools and technologies that reduce the barriers to sharing information include

  1. Publish to OWW button for private wiki pages
  2. Publish to DSpace button for public wiki pages
  3. Mediawiki extension that allows auto import of information from existing scientific databases (analogous to the Biblio extension).
    1. Genbank
    2. PDB
    3. Genome databases
  4. Tools for visualization of scientific information on the wiki (note these would likely rely on permitting users to use existing viewers inside OpenWetWare)
    1. Sequence viewer
    2. Structure viewer
    3. Genome browser
  5. Image editor for generating graphics in OWW
  6. Tagging of wiki pages
  7. Wiki forum
  8. Dynamic ranking of pages (like Reddit or Digg but using your OWW account)
  9. Introduction of WYSIWYG wiki interface and/or switchover to alternate wiki implementation
  10. Semantic web tools for annotating data enhancing machine readability
  11. Tools for conversion of word documents to wiki format
  12. Personalized content, for instance suggested papers/grants (partnership with SciLink?)

Fostering a community that values sharing

Efforts that may help promote community growth and involvement include

  1. Developing tutorials for
    1. Starting a userpage
    2. Starting a class
    3. Starting a lab
    4. Starting a research community
  2. Developing and piloting norms for categorization of pages
  3. Establishing good examples of consensus protocols as a model for others to follow
  4. Creating videos of protocols on OWW
  5. Pushing through articles on OpenWetWare
  6. Organize an annual conference/retreat
  7. Advertizing, marketing, and recruiting users within the biological science and engineering community.
  8. Enable users to easily find other researchers in their field (e.g searchable categorized DB of scientists)
  9. Start a 'reprint journal' where the articles are selected by voting within a community (for instance, the OWW synthetic biology journal where articles from the OA literature are nominated for re-publication by voting on syntheticbiology.org)
  10. More 'social networking' tools (profiles, message boards, colleague lists, IMing) to make it easier to communicate and collaborate within your community.
  11. Better tracking of site analytics, user surveys, etc. Monthly reports on what communities are growing, how researchers are using the site, etc.

Incentivizing sharing via the scientific reward structure

Ways for OWW to push back on the existing system

  1. Getting journals to permit citations of OWW pages in papers
  2. Promote publishing of supplementary information to papers on OWW (not large datasets but rather protocols and details of experimental setup)
  3. Getting an "impact factor" for OWW (inclusion in the Thomson Scientific index)
  4. Promote the development of unique author IDs in order to tie online contributions (e.g. edits on OWW) to your paper publication record.
  5. Pioneer giving awards / recognition for contributing quality content in a non-peer reviewed, open, online resource.
  6. Partner with a journal to publish short time scale (potentially non-peer reviewed) publications.
  7. Pilot a curator role, for instance there could be 'always up to date reviews' curated by an expert in the field. This person should get credit at least equivalent to writing a paper review.
  8. Make it easy to move OWW pages to a DOI server so they can become part of the 'citeable' literature base. We could partner with an existing DOI server, or start our own.

Sustainable governance for OpenWetWare

In order to promote the above three approaches, OWW needs organization and leadership. How do we put into place this organization?

Jasonk 08:44, 19 January 2007 (EST): In previous discussions we outlined this organization:

  1. Steering Committee (volunteer)
    • Primary responsibility: Ensure an active, vibrant user community.
  2. Administrative (paid?)
    • Keep track of money, organize meetings.
  3. Technical (paid?)
    • Primary responsibility: Keep the site software/hardware up-to-date. Implement new software and analysis suggested by the steering committee/user community. Organize volunteer software development efforts.
  4. Lead Evangelist/"CEO" (paid)
    • Primary responsibility: Manage/raise funds and ensure that the admin/tech and steering committee are working well together
  5. Community facilitator (short term paid position or volunteer?)
    • Dedicated effort to recruit/facilitate new users and set best practices for the community

This still leaves open the question of the best mechanism to achieve this organization, and on what time scale we expect to have it in place.


  • Vincent 07:53, 19 January 2007 (EST): Would it be useful to try to define a Performance measure for each of the items above. It could help to monitor the progress of the OWW community as a all but also to guide and evaluate any hired person. I would suggest to specify for each item:
    • when the item is supposed to be available as a service to OWW community. (OPEN_DATE)
    • what is the performance measure to be used to monitor progress of this specific item (PERFORMANCE)
    • what is the target for this performance in 1 year, 3 years, 5 years. (TARGETS)

Example on previously listed items:

Fostering a community that values sharing

Efforts that may help promote community growth and involvement include

  1. Developing tutorials for OPEN_DATE: NA // PERFORMANCE: nb tutorials created //TARGETS: (2007)XXX (2009)XXX (2011)XXX
    1. Starting a userpage OPEN_DATE: XXX // PERFORMANCE: nb visits //TARGETS: (2007)XXX (2009)XXX (2011)XXX
    2. Starting a class OPEN_DATE: XXX // PERFORMANCE: nb visits //TARGETS: (2007)XXX (2009)XXX (2011)XXX
    3. Starting a lab OPEN_DATE: XXX // PERFORMANCE: nb visits //TARGETS: (2007)XXX (2009)XXX (2011)XXX
    4. Starting a research community OPEN_DATE: XXX // PERFORMANCE: nb visits //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  2. Developing and piloting norms for categorization of pages OPEN_DATE: XXX // PERFORMANCE: nb of documented categories + usage stats on OWW pages //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  3. Establishing good examples of consensus protocols as a model for others to follow OPEN_DATE: XXX // PERFORMANCE: nb consensus protocols created + nb visits //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  4. Creating videos of protocols on OWW OPEN_DATE: XXX // PERFORMANCE: nb video created + nb visits//TARGETS: (2007)XXX (2009)XXX (2011)XXX
  5. Pushing through articles on OpenWetWare
  6. Organize an annual conference/retreat OPEN_DATE: XXX // PERFORMANCE: nb events organized + nb attendees //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  7. Advertizing, marketing, and recruiting users within the biological science and engineering community. OPEN_DATE: XXX // PERFORMANCE: nb ads dessiminated //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  8. Enable users to easily find other researchers in their field (e.g searchable categorized DB of scientists) OPEN_DATE: XXX // PERFORMANCE: ??? //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  9. Start a 'reprint journal' where the articles are selected by voting within a community (for instance, the OWW synthetic biology journal where articles from the OA literature are nominated for re-publication by voting on syntheticbiology.org) OPEN_DATE: XXX // PERFORMANCE: nb papers + nb feedbacks //TARGETS: (2007)XXX (2009)XXX (2011)XXX
  10. More 'social networking' tools (profiles, message boards, colleague lists, IMing) to make it easier to communicate and collaborate within your community.OPEN_DATE: XXX // PERFORMANCE: nb tools available + measure of traffic //TARGETS: (2007)XXX (2009)XXX (2011)XXX
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