2013 CTSI Annual Pilot Awards to Improve the Conduct of Research

To facilitate the development, conduct or analysis of clinical & translational research

Testing new Web-based software for increasing the speed of knowledge creation from translational and inter-disciplinary projects.

Proposal Status: 

NB: This Pilot proposal deals with several completely new ideas and related terminology.  To obtain explanations of these new ideas and terminology, please use the inserted Links to jump to WebSites, for descriptive information, and examples. 

OVERVIEW: Creation of useful knowledge from scientific investigations requires the collaboration of scientists usually separated by space, or both space and time.  Communications between scientists under these conditions could be enhanced by the use of the Web. Unfortunately, the minimum time required for an individual scientist to learn and utilize presently-available Web-tools is so great that communication-enhancement cannot take precedence over the other necessities for success in research: doing the work, publishing the results, and obtaining new grant monies.  Furthermore, the societal institutions of paper-based communications are hindering a paradigm-shift in scientific communication (e.g. the OpenAccess debates).  The project described below concentrates on reducing the minimum-time needed by an individual scientist to create a WebSite that provides a review of the scientist's research area in a way that combines both generality with specificity, thus accommodating readers with a range of different backgrounds and interests.  The project also provides an automated method of creating new inter-WebSite links that readers can use to more easily traverse the Web-based network that will be the basis of knowledge-creation and knowledge-storage in the coming era.  The active-archives created with this project's Web-tools will, unlike current passive-archives, gain value over time.  The project is designed so that all participants (Moderator-Scientists, Experts, Readers, and Archivists) act in their own self-interest when collaborating, thus providing independent motivation for use of the project-tools, which is a necessity for wide adoption of these enhancements to scientific communications.   ALSO, as aid to comparing  the proposal with present methods, there is a "Summary Table Overview" available in the Attachments portion at the end of the narrative portion. It is best to look at this Table NOW, when first reading this proposal. 

RATIONALE:  Under a grant from the National Library of Medicine, we have developed new Web-based OpenSource Software that will increase the speed of knowledge creation (CreateKnowledge-Link) out of research information from translational and inter-disciplinary projects.  The Pilot project proposed herein will test how well this software is accepted by a group of intended users at CTSI, and provide a path to making the software available to all other CTSI sites across the country.

PLAN:  Within the UCSF CTSI, this project will beta-test two software programs (described below): 1) Creating WebCompendia WebSites, and 2) Using the ForwardLink-Protocol.  Volunteer users will be recruited from within CTSI, from PostDocs and K scholars, by means of email, WebSites (including CTSI's WebSite and CTSI Blogs), lectures about the benefits of using the programs, and personal contact with CTSI mentors and research advisors.  The two software programs will be available on CTSI servers, and, at present, be limited to beta-test volunteers.  Volunteers who participate will be asked to inform us of any difficulties in using the programs and also be invited to suggest improvements or additional functionality that they could imagine would be useful.  All comments can be either signed or anonymous.  Under this Pilot Project, the OpenSource Software will be user-debugged and new functionalities may be added by the programmers who have worked on this project.  

   The volunteers and their mentors will also be requested to fill out an anonymous questionnaire about the factors that led them to volunteer. This information will help identify the most-effective communication means of informing scientists and academic clinicians about the capabilities and personal benefits of the new system.  If the pilot study is successful, and since the the methodology is clearly scalable to any number of servers, the OpenSource Programs would then be made available to all other CTSIs across the country, using these "most-effective means" to inform users at the other CTSIs about the benefits.

   The WebCompendia WebSite program will be used to create concise, yet comprehensive, OpenAccess, CreativeCommons WebSites that are basically stylized, highly-moderated blogs where, unlike a Wiki, no material can be posted without the explicit approval of the (scientist) Moderator.  Each WebCompendium will center on a topic of interest to the Moderator, and will, by the means of its structure (ExpandingOutline-Link), organize, out of the multi-dimensional research information that is accumulating, a narrow slice of information, together with an objective evaluation of the knowledge that can be derived from that slice of information (CreateKnowledge-Link).  WebCompendia will make it easy to address research questions using Strong-Inference, a method that "sharpens the cutting-edge" of scientific enquiry (ExpandingOutline-Link).  Each WebCompendium will be peer-reviewed by experts in the field, and each will automatically create an online-community of like-minded scholars interested in the same slice-of-available-knowledge, out of which new collaborations and/or jobs could arise (SelfInterest-Link).

   These WebCompendia (which will initially be found by Google or Yahoo searches) will also be inter-linked by means of the ForwardLink-Protocol, which codifies new non-semantic Web linkages (which are unlike Google or Yahoo searches).  The links will be automatically created by use of the WebCompendia program (ForwardLink-Link).  These Links will, to scholars, be much more informative and much easier to evaluate than present Web-links and Web-searches (see Sortable Table section in ForwardLink-Link), thus increasing the usage of WebCompendia for communication of scientific ideas and information. 

   The programs to create WebCompendia and their inter-linkages will use online pop-up instructions and easy-to-intuit clicks for ease-of-use without training.  Each user of these programs (whether as Moderator, Contributor-Expert, or Reader) will be motivated to participate based on their own self-interest (SelfInterest-Link), without need for external inducements.  We expect the use of WebCompendia to expand initially based on the needs and interests of students: 1) PostDocs, 2) Senior Residents in medical or surgical training, 3) PreDocs starting thesis work (SelfInterest-Link).

   The two programs are contained within a free OpenSource Content-Management System called TikiWiki CMS Groupware (Wikipedia; TikiWiki), which is maintained and updated by a team of volunteers, after functional OpenSource programs are made available to the team (as will occur after a successful beta-test).  The TikiWiki CMS provides a means of tailoring the System to the specific requirements of WebCompendia.

CRITERIA FOR SUCCESS: 1) As reported by the volunteers, the debugged programs are functional and usable without training; 2) From the anonymous questionnaires and feedback from seminar attendees, effective means are identified that can be used to inform and motivate scientists and academic clinicians to consider using the WebCompendia and ForwardLink programs that are made available on their local CTSI servers across the country. 3) Problems of installation of the TikiWiki CMS Groupware, WebCompendia, and ForwardLink-Protocol programs at other CTSIs are identified during the installation on CTSI servers, and predicted by CTSI IT personnel.  4)  A practical program is developed for promoting the usage of these programs at other CTSI sites, based on knowledge of previous interactions among CTSIs at the national level, and the information from volunteers on the best communication-means.

COSTS & JUSTIFICATION:  Costs are requested for the two programmers that have created the Software. They will correct errors and add new functionality that is described by the volunteers.  These programmers are in Indiana and Texas, and are experienced in adapting TikiWiki to new uses.  The PHP programmer earns $50/hr, and the Tiki WebSite designer earns $35/hr.  Budget = $40,000 for 12 months; the costs for each will depend on the debugging and types of additions suggested by the volunteers. The PI will not charge any salary to this grant.  For travel for the PI to East Coast CTSI, during promotion of the programs, Budget = $6,000.  For use of a WebLink facility to give seminars at other CTSIs during promotion, Budget = $4,000.  Total Budget = $50,000.

COLLABORATORS:  As part of this Pilot project, assistance is sought from several CTSI programs and experts.  We propose collaborations with the following: 1) IT personnel on ease or difficulty in setting up the software on the CTSI server. 2) Faculty and mentors within CTSI with regard to the usefulness of the programs to the volunteers. 3) Planning of the promotional campaign necessary to effectively spread the use of these programs both within and outside CTSIs.  4)  Critiques of the questionnaires to be filled in by the volunteers. 5) Statistics of program usages on the CTSI server.  6) Advice on how best to approach other CTSI programs for them to try out the program locally, with special reference to overcoming faculty and/or IT inertia at these other sites. 7) Collaboration with John Daigre's efforts to use established social media for scientific communications and collaborations. 


The proposal by Dr. Jewett represents a significant opportunity to advance the way clinicians and scientists (and especially their trainees) communicate with one another via the web.  The implications for translational research are profound.  The software has the potential to revolutionize they way data are shared, analyses are conducted, and results are evaluated and interpreted.   Following the links that have been inserted into the proposal, one can see that the platform is robust and very user-friendly.  The costs seem reasonable and well-justified.  The plan is straightforward and the outcome measures seem appropriate.  Overall, the proposal will enable the CTSI at UCSF to remain at the forefront of web-based communication, knowledge creation, and interdisciplinary collaborations.   I encourage you to support this proposal.


Thank you for the comments.  

You emphasize the importance of the proposal to the UCSF CTSI, and this again shows that the design is for a win-win.  In this case the UCSF CTSI can lead the other CTSI's, which in turn can lead other scientists AND clinicians.  The country-wide CTSI effort is uniquely positioned to enable this connection.

I'm having some trouble understanding the project. Are you trying to determine how best to convince biomedical researchers to write about their research using a new style of wiki software? Thanks in advance for breaking it down a little bit more.

I do thank you for this comment.  I've been TOO CLOSE to the development, so that I can't see the Forest!!  I'm slow in responding because your comment has led me to develop a TABLE that shows how WebCompendia differ from present publishing methods.  I will get this table up into the online WebSites by this week-end.  Each morning I awake with a NEW addition to the table.  


I will be very interested in your reaction to the table, and whether it clarifies many obscure points.


One thing-- WebCompendia are highly moderated BLOGS, NOT a WIKI.  A Wiki allows changes by anyone.  A moderated blog requires the Moderator's explicit permission for adding material.

The observation that the proposal is unclear is very important.  Writing is always improved by such honest comments.  Besides the SummaryTable described above (and in Attachments), I have now included an "Overview" section that does a better job of giving the context and goals of the project.  Only time will tell (as well as new readers) whether this is sufficient.

Please check the Summary Table Overview attachment, and let me know if this makes the project clearer.  Your opinion is very valuable.  Thanks.

Dr. Jewitt is on to something important here. As a scientist and educator, I believe we are going to see a paradigm shift in the way scientific knowledge is exchanged, integrated, and disseminated, and that Dr. Jewitt's software platform and vision for its potential uses represents a significant advance toward this paradigm shift.  The proposal will enable CTSI fellows and mentors to engage in useful  scholarship in areas of critical importance to their own respective fields, while simultaneously providing valuable feedback about the strengths and limitations of the sofware to facilitate its further refinemenet.   My only concern is how to ensure that busy post-docs and mentors can be enticed to spend time doing the writing and scholarship in this project, as opposed to the other scholarly tasks and obligations.  I suppose that the more the use of the software can be aligned with other academic or scientific goals of the mentee/mentor, the greater the chance of a "win-win" scenario in which study participation helps to move some other scholarly task forward, such as writing a book chapter, paper, grant, lesson plan or course curriculum.  I am optimistic about the potential success of this project, but amplification of the plan to ensure sufficient study recruitment would be helpful. 

Thanks for your summary-description of the project and what it may accomplish.  

With regard to having the participant's "finding time" to use the tools, early on in the planning I was told of how good ideas failed if participants were needed primarily for the project's goals.  This led me to objectively plan how the participants would gain from the project, even though it took some of their time.  First, we made one overall goal that the software would save time as compared with present methods.  Second, we examined how to self-motivate each participant (Moderator-Scientists, Experts, Readers, and Archivists).  This is described here: (http://selfinterest.webcompendia.org).  Of course, the CTSI project will test whether these descriptions are correct, and will provide a means to change them if the motivations aren't adequate.

This pilot proposal should be seriously considered by CTSI. It’s important to try new, online methods such as WebCompendia to disseminate research information. WebCompendia provides a new way for researchers to communicate their findings. Researchers are starting to see the value of micro-publications that can be published quickly to a wide audience. WebCompendia will give users immediate access to research and allow users to continue the conversation with new information. Since WebCompendia is based on an existing Open Source project (TikiWiki), it will be easier to expand the functionality of the application for the pilot rather than having to build an application from scratch.

We are in the midst of a revolution in the means by which we exchange ideas. Most current tools lack focus, often resulting in a free-for-all exchange. The WebCompendia tools that use the ForwardLink-Protocol have great potential to help us harness the power of communication the internet has brought us and provide a means of creating focused research communities. This proposed project would provide important feedback on how to fine tune the usability of the WebCompendia tools.


I share Dr. Mathalon’s concern that researchers may be hesitant to put in the time to use these tools, but this current proposal is an excellent way to address that very concern. At the very least, this project would point to changes that could increase the usability of these tools.


This is an important project, and funding it would help keep UCSF at the forefront of this new wave of researcher collaboration.


Add 3/14/13: I taught at a California State Unversity campus where the teaching load is very high, leaving almost no time for research. The same is true for Community College faculty. Hosting a WebCompendia would be an excellent way for such faculty to remain engaged in their field, even though they do not have the resources to maintain a full research project. This would keep them on the forefront of their field, thus having a very positive impact on the quality of science education.



Thanks for the review, and mentioning a new group of faculty (State-University and Community College) that could contribute to collaboration and benefit from using WebCompendia.

See my reply to Dr. Mathalon regarding motivating researchers to use these tools.

This Pilot project builds and promotes a collaboration platform where interdisciplinary data and information are shared by researchers and practitioners from different fields. One of the impressive features in WebCompendia is the scrutiny of the data to be published. Incorrect or misleading data won’t be published on WebCompendia without the explicit approval of the Moderator. This data filtering function can significantly reduce the search time and enhance the quantity of the search results in the meantime. The implementation of this project is feasible since the supporting software technologies have been developed.

In addition, this knowledge-sharing platform can potentially become a test bed for validation of data mining algorithms and social networking analysis, especially for document retrieval and text mining. Data and roles in this project are heterogeneous and the data will continuously grow with use of the system. This provides an excellent data source in the research of information retrieval, data mining and analysis of big data.

Last but not least, I agree with one comment by Dr. Robert Plantz that this project will assist researchers in teaching-oriented schools by facilitating collaboration and resources online. I look forward to using WebCompedia in the near future.

I am pleased to see all the comments expressing interest in this project. We definitely need new methods of communicating and collaborating about research. What strikes me about this idea is that it has the potential to makes the process of collaborative knowledge creation transparent and visible in a way that the traditionally published article is not. Why limit ourselves to the equivalent of a hand-scribed manuscript when we have the technology available to us today to create dynamic content that can be multi-dimensional and drive research in new directions?


I thank you for the comment, and especially for emphasizing that the vehicle for communication on the Web is basically different from paper-based methods.  This is clear with respect to Facebook and Twitter.  It is also true of WebCompendia that use the ExpandingOutline Format so as to organize and present information in a new way.  Then, the enhancements due to easy emails and replies are a further bonus over paper and snail-mail.

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