2013 CTSI Annual Pilot Awards to Improve the Conduct of Research

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

Printable Proposal Content

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Development of an Inter-departmental Shared Research Assistant Support Program for Translational Research

Proposal Status: 

Rationale: This proposal is based on two premises: First, it is well known that consecutive sampling is preferable to convenience sampling for essentially all prospective enrollment studies. One of the greatest obstacles to implementation of consecutive patient sampling, however, is the need to have 24/7 research assistant (RA) support for patient identification, enrollment, and data collection. Payment for RA support thereby commonly consumes over half of grant budgets for prospective studies, often rendering potentially meaningful studies impractical. Many worthwhile study ideas are abandoned early on and other fully fleshed out protocols get dropped because of lack of funding for 24/7 RA support.

The second premise behind this proposal is that RAs commonly have significant amounts of “down-time” in between enrollment of subjects. Review of four recent, extramurally-funded studies that were concurrently conducted with separate 24/7 RA support at SFGH showed enrollment of less than 2 subjects per day in one study and less than 1 subject per day in the other three. Discussion with investigators (and even the RAs themselves) has revealed frustrations with the inefficiency and cost associated with the need to have separate 24/7 RA study coverage in same site studies with prospective enrollment.

Plan: We propose the exploration and development of a shared RA program for translational research that we believe would lead to more efficient and cost saving research practice at UCSF. Although details of the development plan are beyond the scope of this one page proposal, we will begin by forming an interdisciplinary task force to perform a needs assessment and review funding and regulatory agency policies regarding shared resources. We will then develop shared RA network models, with CTSI review and input. We will test the approved model(s) through a pilot or feasibility study and report summary findings to CTSI.

Deliverables and Metrics for Success: The immediate deliverables from this work include:

1) A detailed analysis and summary recommendations of the feasibility and obstacles to the interdepartmental sharing of RA support.

2) Implementation of a pilot /feasibility study of a shared RA network based on CTSI review and approval of proposed models.

3) Determination of the potential cost and other resource savings from implementation of such a program.

The potential long-term deliverables of this project would include:

1) Campus-wide increase in the implementation of low-funded and unfunded research, especially by junior faculty and residents.

2) Increase in funded research: Investigators may be able to apply for more grants with low funding ceilings, and their budgets may be scored more competitively.

3) Promotion of an innovative climate of efficient research at UCSF, paving the way toward the development of sharing programs for other research resources.

Approximate Cost: We are asking for CTSI consultation support and $40,000 to conduct the pilot/feasibility study (RA support and administrative costs). Investigators will donate their time in kind.

Collaborators: The investigators have collaborated extensively and have substantial experience in this proposed arena: Dr. Rodriguez is the Department of Emergency Medicine Residency Research Director, has CDC funding and has served as an IRB chairperson. He has developed and maintained a robust ED RA program at SFGH for 7 years with prospective enrollment of over 4,000 subjects in various studies. Dr. Mitchell Cohen is an active trauma and general surgeon and serves as the Director of Trauma Research for the Department of Surgery. He is extensively funded by the NIH, CDC and DoD and is currently involved in several prospective trauma studies, as well as translation basic science work on similar topics. Dr. Hemphill is Chief of Neurology at SFGH and is the PI of the San Francisco hub of the NIH-funded NETT (Neurological Emergencies Treatment Trials) network. His group has conducted emergency and ICU studies related to stroke, status epilepticus, and neurotrauma.

The comments from other investigators have been very helpful. Although there may be slight overlap between this proposal and certain CRS efforts, this affords an opportunity for synergy and refinement of proposed models. Review of the CRS site and other discussion demonstrates that the current CRS model understandably has significant gaps, specifically in the area that we are trying to address with our proposal--  the issue of 24/7 RA support for emergency studies with need for timely response for enrollment (need for the RA to be in the ED within minutes at all hours). We look forward to collaborating with CRS (and others) in addressing this need, refinement of shared RA support proposals and ultimately field testing the CTSI approved final model. 



Commenting is closed.

Building a Searchable Online Library of Template/Example Language for Grant Proposals

Proposal Status: 

Rationale: One major hurdle faculty face in preparing grant proposals is in the drafting of the non-scientific components—that is, the Resource & Facilities, Resource Sharing Plan, biosketch personal statements, letters of support, and other regulatory sections (e.g., human subjects and vertebrate animals); this is especially true in the preparation of complex, multi-investigator and multi-institutional, Center-type grant proposals. Faculty may look at these sections as bothersome time-sinks, hardly worth time or effort, or as insurmountable challenges that prevent them from applying to a grant. In either case, the ability to procure the necessary funding to conduct of their research can be seriously affected by sub-par non-scientific components in their proposals.

The Research Development Office (RDO) supports the development of multi-component grant proposals and, since its inception in July 2012, has already amassed a collection of template/example language for the non-scientific components of large Center grant applications (e.g., P01, P30, P50, U19, and U54 mechanisms). Of particular importance, we have descriptions of many UCSF resources (general environment, schools, departments, core facilities, etc.); we also have collected Resource Sharing Plans, regulatory sections, letters of support, and biosketches. So far, we have deposited these documents on our office server and kept inventory on an Excel spreadsheet. This is not a viable, scalable, or sustainable way for us to accomplish our goal of creating, managing, and curating a database of template/example language and making it available to any UCSF faculty or staff member (Principal Investigators, Key Personnel, grant and research administrators, Research Management Services staff, Contracts & Grants staff, staff writers, etc.). This library will not replace any of our current functionality in the proposal development process—RDO personnel will continue to help draft personalized sections—but will instead allow us to expand our level of service and free up bandwidth. In particular, the templates/examples will be relevant for a large breadth of documents in addition to large Center grants, including R01s, training grants, and contracts. Sources for template/example language will include the internal RDO library, as well as RMS personnel, UCSF departments, and individual investigators willing to share their samples.  The creation of such a library has been enthusiastically supported by many faculty members, RMS and C&G staff, and administrators, and we look forward to working with them to continually adapt the library to best serve the needs of the UCSF community.


  1. Consult with a system administrator or web developer to identify an appropriate solution based on the following criteria:
    1. Ease-of-use: possible for any RDO staff member to be a site administrator in order to upload documents and update/manage content, overseen by Dr. Erin Bank, Research Development Specialist
    2. Searchability: keyword optimized for intuitive and easy searching by section title, keyword, and type of document
    3. Accessibility: open to UCSF faculty and staff via the UCSF network at any UCSF workstation or through a UCSF VPN account
    4. Connectability: able to link from the OSR/RDO website, currently under development to be hosted by the UCSF Office of Research using Drupal
    5. Adaptability: able to adapt to different types of documents and files as need dictates
    6. Trackability: count number of visits and downloads
    7. Capacity: room for hundreds of small-format .doc, .pdf, and .xcl files
  2. Work with a system administrator or web developer to implement the system
  3. Train Dr. Bank to be the primary manager of the database once it is up and running. Dr. Bank will also curate templates/examples contributed from outside the RDO

Criteria and metrics for success: We will track the visitors to the site and the number of times each document is downloaded, in addition to the number of text sections offered and the number of edits made to the stored text sections in order to keep them accurate.

Approximate cost and very brief justification: We request a budget of $20,000 to cover consulting fees; site building, authentication, and implementation; software installation; CMS costs (licensing fees, add-ons, hosting); training; and the UCSF server recharge.

Collaborators: A system administrator/web developer with experience working with UCSF; RMS, other staff, and faculty members will be both partners in contributing to the content of the database and users of the database after it is established.

Commenting is closed.

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. 

Commenting is closed.

Application Management System

Proposal Status: 

Application Management System

Rationale: There are several programs on campus that manage the dissemination, submission, review, and selection of applications for student positions, grant awardees, or other candidate selectees. The Research Allocation Program (RAP) is one such program where this process is perhaps the most complex due to the number of intramural funding mechanisms, the number of review committees, and the nature of the selection process. Currently, RAP applications are submitted online but the review and decision processes are done manually, thus limiting continued efficiency improvement and lowering the ease of program reporting. To remedy this situation for RAP and other related program processes on campus, we would like to develop a single electronic solution that will accommodate the processes for dissemination, submission, review, selection, and reporting. The solution may leverage parts of existing software such as NUCATS Assist (Northwestern University) or CTSI-ART, or be built completely customized with Drupal interfaces.

Plan: The overall goal is to develop a centralized application management system that would coordinate opportunity dissemination, application submission, application review, application selection, and follow-up processes for multiple programs across multiple agencies. Configurable application components and flexible workflows would accommodate changing business requirements and support process improvements. Such a process solution would result in significant longer terms savings for all collaborating programs.

Criteria and metrics for success: An automated application management system can decrease the amount of time and resources administrative staff spends on application processes and follow-ups, as well as on compiling and summarizing application information for program reporting. Designated administrators would have direct access into the system to customize forms and run reports. Communication with reviewers and applicants can improve through automated deadline reminders and standardized decision notices. Broader and deeper analysis of application and review processes would be possible through reporting measures that have not been available before. The system will be a central repository for applications and progress reports and will offer greater ability to measure programs and funding opportunity impact.

Advantages for all users

Applicants can find funding information, apply via a website that is open to the public, and can upload a single proposal PDF. The application can be saved until submission allowing to be built in stages. Potentially applicants could also use the system to enter and submit progress reports online.

Reviewers can find all materials in one place (proposals, review forms, previous reviews). They can receive automated notifications and reminders to complete tasks before deadlines. They can write their reviews in stages and assign initial scores. During the review meeting, they can score proposals “live” as they are discussed.

Administrators can replace uploaded PDF files, delete applications, and submit on applicant’s behalf. They will take advantage of automated messages/notifications/reminders to communicate with applicants and awardees. They will benefit from a system that tracks many variables, including applicant attributes (e.g., name, department, gender, award status, etc.), and reviewers’ attendance and productivity. Summarized financial award information will be available in the system. Administrators can use the system to manage progress reports starting with automated requests for project/progress report updates sent through the system at intervals designated by each funding agency.

Potential Collaborators Development team - Depending upon whether a system is developed from scratch or leverages an existing one, the system development responsibility will lay with Edwin Martin and ISU or our colleagues at CTSI Virtual Home or the SF Coordinating Center or potentially an outside contractor. Requirement owner - RDO [Emy Volpe (RAP), Gail Fisher (LSP)], Suya Colorado-Caldwell (EVC&P Committees), and many other campus programs that utilize application review and selection processes.

Budget: This project can be developed modularly. With the $50,000, we could plan the development of all modules and develop several of the modules. Our intention would be that matching funds be identified that would enable to the full development of the modular plan. Leveraging another existing system may enable the full system build for $50,000.

Commenting is closed.

MicroPub, A Publication Platform for Short Replication Studies

Proposal Status: 

1.    Rationale Modern basic science rewards large papers in highly cited journals.  However, it is difficult for translational and clinical researchers to assess the quality of a basic science paper.  A proxy is the number of citations, but that is a very inaccurate measure; some papers that cannot be replicated have hundreds of citations.  Given the lack of safeguards ensuring publication quality, the intense competition to produce high profile publications incentivizes publication bias (i.e. tendencies for journals to publish experiments confirming its original hypothesis or "positive" results).  An obvious way to affirm or dispute the quality of a paper is through replication.  Unfortunately, at present replication studies are not valued by the basic science community, and they typically go unpublished.  A large amount of translational and clinical research likely yields negative results because it was based on invalid basic science premises.  Our solution is MicroPub, a platform for soliciting and indexing “micro publications” that replicate data from published basic science articles.


2.    Plan 

We will create a website that publishes and indexes short replication studies.  Each “MicroPub” will contain an abstract, one figure, detailed methodology, and a short discussion.  Editorial moderation, rather than peer-review, will be used to evaluate the soundness of research. The short format will hasten the publication process.  Validation or refutation by independent investigators will serve as a high-quality measure of a finding’s reproducibility, and by extension, its validity.  This will be a critical resource for determining whether a basic science finding merits investigation at the translational/clinical level.  All papers will be Open Access. 


Initially, we will solicit MicroPubs from UCSF researchers.  We will utilize social media and traditional media outlets to popularize MicroPub.  Ultimately, we envision MicroPub being linked to the original article listings on PubMed, as well as related follow-up translational/clinical papers.   


2013-03-12 Addendum to Proposal:

We are discussing our goals with the UCSF Library, the Open Science Framework and the Reproducibility Initiative, and we have expanded our proposal as follows:

Many Small-Scale, Technical Basic Biological Experiments Can Only be Replicated by Academic Labs

Although core facilities and outside vendors are able to perform numerous specialized techniques at the same level or in some cases better than most academic labs, many high impact publications use novel methodologies that are technically challenging to replicate. These “artisanal” laboratories rely on apprentices (in the form of graduate students and postdocs), who learn from experts within the laboratory and then develop their own line of research. Thus, a paper can often only be replicated by members of the same academic lab or a competing academic lab.  There is no current outlet for publication of these replication studies, so they are very rarely published.  The scientific community misses out on this valuable information. MicroPub fills this niche.


MicroPub Re-aligns Cultural Incentives and Promotes Transparency

There are numerous reasons for the widespread lack of reproducibility in basic biomedical sciences.  But one reason is preeminent—you are not allowed to be wrong. This is institutional (NIH funding) and cultural. Given the current state of NIH funding, allowing the publication of a replication study that failed – admitting you are wrong – is to risk jeopardizing one's career.  And if many replication studies are never revealed to the wider scientific community, why do them? 


MicroPub aims to shift this culture.  It provides a venue that recognizes that irreproducibility often does not reflect scientific fraud or sloppiness, but may be due to other reasons.  Instead, irreproducibility is often due to subtle differences in experimental conditions or analyses, or publication bias.  Currently there is no published venue for discussion of these issues.  Although open access publications that utilize post-publication peer-review offer an avenue for online discussions, we feel that commenting per se does not carry the same strength as first-hand experimental data.  MicroPub provides a way to quickly publish first-hand data, and integrates it with open access and post-publication discussions.


Moreover, MicroPub provides a venue for scientists other than the initial authors to publish replication studies.  Right now, the peer-review barrier for doing so, particularly when a replication study contradicts the original study, is enormously high.  MicroPub is specifically devoted to studies of this type, so the barriers will be surmountable and the studies can be published and disseminated.


Of course, replication studies by initial authors will also be welcome.  It is often members of the same lab who replicate (or cannot replicate) each other’s results.  Again there are enormous disincentives (job security, NIH funding, reputation) against publishing such studies. MicroPub becomes a way for labs to publicly acknowledge and explore reasons for irreproducibility, and ultimately, to establish a reputation for honing long-term, course-correcting, scientifically valid results.  It is our hope that as cultural barriers against admitting error shift, so too will the institutional (NIH funding) barriers. 


2013-03-14 Addendum to Proposal:

MicroPub Keeps Track of Methodology Requests and Serves as a Detailed Methods Repository

One of the major barriers to replicating biological experiments is the unavailability of clear step-by-step methodologies and help with reagents and equipment. Due to journal space limitations, authors are unable to explain exactly how they did their experiments, and rely on citing previous publications that describe similar methods. However, methods are usually modified and these changes are often the key to getting the published results. As there is currently no accountability, requesting for protocols and reagents can be a slow, tedious process. MicroPub aims to solve this issue by providing a custom contact and tracking service that emails the first and the corresponding authors, explaining that a replicator wishes to replicate a particular figure in their publication. MicroPub will then announce this request on the website and keeps track of how long it has been since the original authors have been notified, and whether they have responded. These protocols are published onto MicroPub directly and become available to not only the replicator, but also to the wider community of scientists who may also wish repeat the experiment. To provide incentive, both the original authors and the replicator are credited for the methodology section. There are also cultural incentives, as collaborations are often predicated upon shared protocols and reagents. This act of sharing is one of the many benefits of attending scientific conferences, and MicroPub can provide a platform for these kinds of productive social interactions online.


3.    Criteria and metrics for success

MicroPub fits squarely within the mission of CTSI.  MicroPub “nurtures communication, encourages collaboration, fosters innovation, and catalyzes the successful conduct of research”.  Most importantly, MicroPub has potential to revolutionize translational and clinical research because it will ensure that researchers only pursue investigations on basic science findings that have been independently validated many times.  The success of the initiative will be measured by the total number of MicroPubs and by the number of MicroPubs used as justification for translational/clinical follow-up research.


4.    Approximate cost and very brief justification ($50K max)

The primary costs will be the development of a standardized publication format and of the website. Approximate initial cost: $35K


5.    Collaborators

We are a team of two, S.Y. Christin Chong, Ph.D., postdoctoral fellow, and Jonathan Russell, M.D.-Ph.D. student.  Both of us have extensive experience in scientific publication, science writing, and social media.  We will hire a developer experienced in creating web-based publishing platforms and social web services. 

Commenting is closed.

Tools and Infrastructure to Facilitate Compliance with ClinicalTrials.Gov Results Reporting

Proposal Status: 

Rationale:  US law requires researchers to register clinical trials within 21 days of enrolling the first participant (since 27Sep2007) and to report clinical trial results in the ClinicalTrials.Gov (CT.gov) online system within 12 months of the last participant visit.  Reporting results does not mean publishing in a peer reviewed journal, but rather entering information in CT.Gov’s standardized system.  Noncompliance can result in the following for institutions and individual PIs: fines of up to $10,000 per day, withholding future federal research funding, preventing study publication, and/or public notice of noncompliance.  Despite legal requirements and potential penalties, researchers still lag in mandatory reporting with only 22% compliance nationally (e.g. Prayle et al. BMJ 2012) and 73 UCSF trials campuswide currently overdue in reporting results.  In 2012, the US Office of Management and Budget increased their investigator burden estimate to 41 hours for results reporting in CT.Gov.  In short, compliance is hampered at least partly because CT.Gov is not an intuitive, user-friendly system.

Plan:  The UCSF Dental Data Coordinating Center (DDCC) has already partnered with the CTSI Regulatory Knowledge and Support (RKS) Program, UCSF Office of Ethics and Compliance (OEC) to develop a set of 5 SAS macros to summarize trial results data in a format suitable for CT.Gov Simple Results tables (http://hub.ucsf.edu/basic-results-sas-macros).  This funding would allow expanding those macros and developing other tools to meet the needs of UCSF investigators to comply with federal law.  The CT.Gov system is frequently updated and expanded, so this support would allow the tools to stay current with both required and optional reporting elements.  For example, one current macro allows 3 types of outcome measures: number (frequency), mean, or median; others such as geometric mean which CT.Gov allows will be added.  By developing and refining training materials and consultation, staff supported under this funding mechanism will provide technical assistance to UCSF investigators to help them use these free tools to meet compliance requirements.  Staff will also help troubleshoot the problems that UCSF CT.Gov Administrators identify.  The UCSF DDCC will set up a recharge for these technical assistance and training services.

Criteria and metrics for success:
•    Develop and disseminate additional training materials and tools to be posted on the ClinicalTrials.Gov webpage of the UCSF HUB website (http://hub.ucsf.edu/clinicaltrialsgov).
•    Reduce the noncompliant UCSF trials from 73 to 19 (i.e. slightly more than 1 per week over 52 weeks).
•    Establish a recharge mechanism to provide technical assistance and training to use results reporting tools.

Approximate cost and very brief justification ($50K max):
Most of the proposed budget of up to $50,000 (equivalent to just 5 days of possible federal fines) would be used to create a $48,000 fund from which the 73 current UCSF trials as well as future trials upon completion could draw to pay for technical assistance and advanced training in CT.Gov results reporting provided by the DDCC at rates similar to the CTSI biostatistics consultants.  (With an assistance fund this size, 54 UCSF trials could receive an average of 8 hours of technical assistance to attain compliance.  A smaller award would create a smaller assistance fund.) To make this project “shovel ready” prior to setting up a formal recharge mechanism, percent effort of staff will be allocated to the fund proportional to hours worked.  The remaining $2000 will be used to facilitate setting up the recharge mechanism.  Following this proposed CTSI grant, this service would remain as a sustainable service with a recharge mechanism and could serve other UC health science campuses (which are also struggling to comply with results reporting) and other institutions with CTSAs.

This proposed work is a collaboration between personnel affiliated with the UCSF DDCC and the CTSI RKS Program, UCSF OEC.  Steven Gregorich, PhD statistician, is Director of the DDCC which coordinates 4 large prevention trials for three U54 cooperative agreements (UCSF, Boston University, and University of Colorado—Denver).  Stuart Gansky, DrPH biostatistician, formerly directed the DDCC and now directs the UCSF U54 Center to Address Disparities in Children’s Oral Health (known as CAN DO).  Marlene Berro, MS, RAC of the OEC, as the UCSF administrator for ClinicalTrials.Gov, maintains the list of records with problems.  Nancy Cheng with master’s degrees in computer science and biostatistics has written SAS macros to produce Simple Results tables for ClinicalTrials.Gov.  Elaine Cooperstein, MS, CCRP and Sarit Helman, MPH are clinical trials specialists with experience with SAS, OnCore and ClinicalTrials.Gov.  Terri Sonoda is the budget analyst for CAN DO and the DDCC.

Commenting is closed.

Decreasing Time for CHR Approval of Full Committee Review Applications

Proposal Status: 

Rationale: There is currently an unacceptably long delay in the time required to obtain study approval by the UCSF Committee on Human Research (CHR). The CHR must review and approve all studies involving human subjects performed by UCSF faculty, staff, or students. Studies with more than minimal risk to participants, such as trials of diagnostic tests or treatments, require in-depth review by a faculty-led committee, a process referred to as Full Committee Review. Currently, the average time from submission to approval of these studies is 84 days. This long wait time can be a major obstacle to implementing a new study by compromising grant funding, industry contracts, research staff support, and the general progress of science by UCSF Investigators.

The major source of delay in approval of Full Committee Review applications is the process of “returns”, wherein the CHR requests that the investigator make a change or modification to the proposal. Among initial CHR submissions, 75% are returned for modification by a CHR analyst because they are unacceptable for review by the Full Committee. On average, the investigator response to this initial return takes 16 days. When applications are returned to the investigator after a Full Committee Review, the average time for the investigator to respond is 21 days. Many applications have multiple returns that collectively increase the time required for CHR approval.

The aim of this project is to significantly decrease the duration of CHR approval time for Full Committee Review studies by reducing the number of applications returned to the investigator for revision. UCSF approval time for Full Committee Review is significantly slower than the national average; the national target is <42 days for the duration of the approval process. An intervention to minimize or eliminate returns could meet this national goal for CHR excellence.

Plan: We will work in collaboration with John Heldens, Director of the CHR, and CHR staff to develop effective strategies that decrease the number of Full Committee Review application returns. In 2011, the CHR conducted a review of 700 applications and identified several broad categories of common investigator errors. Using these data, we will focus on improving 2 areas that require frequent returns:

1. Administrative Errors: 50% of initial applications are either incomplete or missing required attachments. These returned applications result in significant delays because an incomplete application cannot be submitted to for Full Committee Review.

Improvement Plan: We will review 100 randomly selected applications returned for missing or incomplete components to identify the most common errors (e.g. missing consent form or incomplete investigator descriptions). We will then work closely with CHR staff and the iMedRIS administrator to develop interventions that minimize these administrative errors, such as programmed iMedRIS alerts that prompt the investigator to complete required sections and attach required documents. We will then use logistic regression models to evaluate the proportion of returned applications among 100 that use the new interventions compared with 100 applications submitted with the current iMedRIS format.

2. Content Errors: The second most common cause of returns is significant deficits in the content of the application such as an inadequate description of study procedures or the data safety and monitoring plan, or an incomplete explanation of the study population or recruitment procedures.

Improvement Plan: In collaboration with CHR staff, we will create a “Content Score”, a summary score that reflects the overall quality of the application in terms of key content areas that when insufficiently addressed put the application at a high risk for return. To validate the use of the Content Score, we will use linear regression models to determine if a poor Content Score is associated with slower time to CHR approval among 100 randomly selected applications. We will track these applications for the number of returns, length of time for investigators to resubmit after each return, and the total number of days before CHR approval.

If the Content Score proves to be predictive of time to CHR approval, we will use the Content Score to develop targeted interventions to minimize returns. Possible strategies might include notifying investigators with poor Content Scores that there is a 90% likelihood of a return and recommending further review of specific sections prior to Full Committee review, or incentivizing investigators to provide high quality applications by allowing those with favorable Content Scores to be prioritized for review.

The Content Score will also highlight commonly misunderstood sections or questions of the CHR application. This will facilitate the development of targeted changes in the iMedRIS application to improve investigator responses and subsequently reduce return rates. Possible iMedRIS changes include questions being re-phrased or re-formatted, showing quick links to examples of high quality responses, or including links to other sources of information and help. 

Criteria and Metrics for Success: We will evaluate the success of our project based on significant changes in the time for CHR approval of Full Committee Review applications. In the first 3 months after completing the interventions developed in this project, we will calculate the proportion of applications with administrative errors, the mean number of returns per application, and the total time for CHR approval of all Full Committee Review applications. We will then compare these outcomes to all Full Committee Review applications submitted in the 3 months prior to initiating the new interventions. Metrics of success will be:

  1. A decrease in the proportion of applications with administrative errors to <20%
  2. A 20% decrease in the proportion of applications returned for content errors
  3. A decrease in the total time for CHR approval to <43 days

Budget: We request $50,000 to complete this project. The project involves significant data collection and analysis and iMedRIS programming and testing. Funds will be used to support a programmer/analyst to store, clean, manage and analyze data. Additional funds will support 5% effort for the clinical investigators, 2 CHR analysts, the iMedRIS adminstrator, and the CHR Director. These key personnel will work together to develop and test effective interventions to decrease CHR approval time.

Collaborators: Vanessa Jacoby, MD, MAS will be the principal investigator for this project. Dr. Jacoby is an Assistant Professor in the Department of Obstetrics, Gynecology, and Reproductive Sciences with a clinical research program focused on surgical treatments of common gynecologic conditions, such as uterine fibroids. She has advanced training in clinical research methods and has conducted multiple studies requiring Full Committee Review. Dr. Amy Gelfand, MD is a Clinical Instructor in the Department of Pediatric Neurology with clinical and research expertise in the care of children with chronic headaches. Dr. Gelfand is currently leading a project to simplify the CHR application process for low risk chart review studies. She will apply her expertise and experience from this project to assist Dr. Jacoby in completing the current proposal. John Heldens is the Director of the CHR with a focus on decreasing the number of returns among CHR Full Committee Applications. Dr. Jacoby and Dr. Gelfand have collaborated with John Heldens, the director of the CHR, on previous projects and they will work closely with Mr. Heldens on the proposed project as well.

Commenting is closed.

Search Engine to Directly Access EHRs without Data Warehouses or Loss of Unstructured Data

Proposal Status: 

Search Engine to Directly Access EHRs without Data Warehouses or Loss of Unstructured Data


Research hospitals, including UCSF, spend millions of dollars a year moving data from EHRs (electronic health records) to alternate data warehouses for analytics. Consultants are hired to map data to and from warehouses. As a result of this time and labor-intensive process, a search query can take up to two months until completion. A query does not even produce a complete set of patients matching the search criteria because data stored in hospitals’ legacy systems, or entered as physician notes in EHRs, lack clinical context and/or code association. Consequently, cohort identification and statistical correlations are severely limited in the conduct of clinical and translational research. As the adoption of EHRs grows, healthcare organizations need analytic tools that can aggregate data from disparate sources so that they have a more complete and comprehensive view of individual patients and patient populations.
Massive Minable Medical Data (M3D) is being developed as a search engine for clinical researchers at UCSF to search and analyze information directly from EHRs, without the laborious, time-consuming, and expensive mapping of data to new data warehouses. It offers fast and accurate data retrieval from natural language queries posed by the researcher. Natural language processing allows M3D users to ask intelligent questions to discover correlations, e.g. "how many patients with heart disease were taking Vioxx?" Direct integration with EHRs will save UCSF data moving expenses, which can potentially reduce cost by an order of magnitude. The specific difficulty with large EHR vendors, such as Epic,  is handling a system of many thousand database tables. To address this, M3D’s has developed an algorithm that uses machine learning to identify which tables contain relevant data- even when the researcher doesn’t.
Metrics for Success
1. Identify high priority query types
2. Secure access to representative datasets for validation
3. Pilot study/ adoption by clinical researchers
4. Expansion of capacities for physicians
5. Pilot study/ adoption by physicians

Success is the widespread adoption of M3D for accessing the wealth of information contained in EHRs at UCSF. We are currently seeking feedback from the medical community, specifically clinical researchers, regarding the the highest priority types of data/queries. Validation of the search engine on these query types are prerequisites to a pilot study with active researchers. Access to representative datasets for development and validation of the search engine is a prerequisite to a pilot study with active researchers. Once the design can be refined to satisfaction of clinical researchers, the process will be repeated with a broader set of physicians at UCSF.
Initial costs will be focused on securing the proper legal standing to work with patient data on Epic systems through either professional legal counsel or Epic certification. Important, but technically simplistic aspects of the search engine, such as the user interface, will be contracted out as needed.
Michael Sachs- UCSF BMS graduate student

Jingwei Zhang- UCSF/UCB BioEng graduate student

Sabrina Atienza- UCB CompSci

2013 George Ramonov- UCB CompSci 2013

Anil Sethi- Founded Sequoia Software, current CEO Gliimpse, 20+ years experience in Healthcare IT.

Commenting is closed.

Developing a Policy Roadmap for Research Outputs

Proposal Status: 


The information age has brought about incredible shifts in the dissemination of knowledge, and academic research is no exception. Research stakeholders including funding agencies, journals, researchers, and research institutions have all recognized the potential of Open Access to accelerate the scientific enterprise. Recent stakeholder policy revisions related to the demand for Open Access have become a source of uncertainty to the research community both in terms of traditional (academic articles) and non-traditional (data, software, etc.) research outputs. The creation of a policy roadmap that compiles and clarifies funder, publisher, and institutional policies regarding access to research outputs will help researchers navigate the Open Knowledge landscape, supporting compliance and encouraging openness in research.



1)   Identify any available resources that document research stakeholder policies regarding traditional and non-traditional research outputs. (For example the UK JISC JoRD Project is developing a central service on journal research data policies)

2)   Compile these resources in a web-based tool that allows researches to reconcile the complement of policies relevant to their work.

3)   Enhance the web resource with additional general information about licensing & copyright as they relate to research outputs, as well as international considerations.



-       A database of verified resources directly accessing stakeholder policies regarding research outputs

-       Full text documentation of these policies

-       Webpage providing access to the database & associated policy text


Success Metrics:

Success will be determined by visitation to the website. Web tracking metrics will include number of visitors (return and unique) and length of time spent on the site. Further indications of success will include any contacts initiated via the website, indicating community engagement.


Approximate Cost:

The proposed work will cost approximately $25K and will consist of 6 weeks of effort for an Analyst to compile the policy information, 3 weeks of effort for a web developer to setup a basic webpage to display the information, and some modest funds for promotional efforts.



Input for the proposed resource will be sought from personnel in the areas of research and research support, as well as policy. Council from relevant organizations, such as Creative Commons, will also be pursued.






Commenting is closed.

Completion of SID - A Database for Tracking of Spine Surgery Patient Interactions and Outcomes

Proposal Status: 


Over the past five years, Dr. Shane Burch, a UCSF spine surgeon, has developed a relational Filemaker Pro database solution (SID) for tracking all patients treated at the UCSF Spine Center.  The system tracks patient reported outcomes at clinical visits for both surgical and non-surgical patients over time, using hundreds of variables to enable both prospective and retrospective research projects. In 2011 over 25,000 patient reported outcome surveys were collected and SID is currently being used in an ongoing double blind prospective randomized FDA trial being run at the spine center. To our knowledge this represents one of the best data collection tools with the highest collection rates on campus. The database solution also offers integration of administrative data (cost) to be linked to patient reported outcomes allowing for economic analyses to be performed like cost minimization. This tool has greatly reduced our outcomes error rate and has helped us increase our outcomes collection rate to ~98% of eligible patients.


While the database is already proving to be very useful, there is still a significant amount of development work required to make the database integrate efficiently into a clinic setting with minimal research support.  We propose to hire a FileMakerPro specialist to help us complete the development of this database which will allow for additional functionality and the expansion of the spine database to other UC campuses. 


While the structure we've developed is specifically for the collection of spine surgery outcomes, this model could easily be adapted to other disciplines.  The true value of this model is in the ability to tie together diagnoses, procedures, and outcomes and produce very simple queries that are easily understandable to lay personnel.   



Identify and hire a FileMakerPro consultant/developer to complete the following functions:

  1. Develop and improve screen layouts for the use of SID on both stationary and mobile devices to expand the collection of patient reported outcomes.
  2. Develop an import function to merge outcome data collected via REDCap.
  3. Develop additional reporting and export functions to meet departmental needs such as cost analysis reporting, quality assurance reporting and accurate readmission rate reporting.
  4. Integration of data from a less versatile database such that the data from as far back as 2002 can be utilized through SID.
  5. Functional improvement of tracking patients for prospective studies through expansion of the “prospective study” feature:
    1. Patient preferences for completing outcomes (e.g., email, iPad, paper)
    2. Notifications to research staff triggering patient follow-up (collecting outcomes on patients who don’t return to clinic) to reduce the ‘lost to follow up’ error rate 
    3. Improve the reporting of complications to meet FDA or other societal requirements
  6. Roll out to other UC spine groups.
  7. Roll out to other UC non-spine groups.


Criteria and Metrics for Success

  1. Completion of all plans by 12/31/13 to include a single database containing all surgical and outcomes data from prior databases.
  2. Effortless “push of a button” function to import data from REDCap and queries to produce data reports for: outcomes by diagnoses, outcomes by procedure, cost, complication and follow up reporting.
  3. Distribution of SID as a turnkey solution for other spine clinics throughout the UC system.


Approximate Cost and Very Brief Justification

Total Budget: $49,500

We estimate that this project can be finished by a developer in 300 hours at a rate of $165/hour.



Dr. Shane Burch – Assistant Professor in Residence, UCSF Department of Orthopaedic Surgery, is an orthopedic surgeon who specializes in the treatment of spinal deformity, degenerative spine conditions and cancer involving the spine.

Linda Racine – Staff Research Associate II, UCSF Department of Orthopaedic Surgery, oversees the collection of outcomes and the management of multiple departmental databases.

Commenting is closed.

Partnering with Patients: Novel Data Sources for Comparative Effectiveness Research

Proposal Status: 


The Randomized Controlled Trial (RCT) has long been the gold standard for proving efficacy.  However, RCTs suffer from lack of generalizability to the broad population not merely because of strict patient inclusion/exclusion criteria, but because patients in these trials generally receive closer care than patients in the “real world.”  Observational and Phase IV studies were created to capture additional data in “real world” populations; however, they were not designed to elucidate comparative effectiveness of different treatments.  As a result, there have been limited tools to conduct medium to long-term comparative effectiveness research (CER) in real populations. However, with the concurrent evolution of electronic health tools and the concept of Patient Reported Outcomes (PRO) espoused by such organizations as the NIH and the Patient Centered Outcomes Research Institute, unprecedented opportunities in CER have emerged.  Orthopaedic Surgery, including Spine surgery and Arthroplasty represent compelling arenas for implementing pilot research modalities for several reasons.  First, a significant care gap continues to exist following elective orthopaedic interventions.  For example, in spine surgery,laminectomy and spinal fusion is the procedure with the highest costs associated with potentially preventable readmission, and among the highest rates of readmission.1 The Institute of Medicine in a 2009 report, targeted spine surgery as a top priority for CER.2,3  Readmission for arthroplasty is also highly variable between and within centers, and an evidence-based approach to reducing readmissions would have significant value in improving quality of care for elective joint replacement procedures. Despite this spotlight, there remain no widely accepted modalities for developing or implementing PRO measures in CER.4   The purpose of this proposal is to implement a mechanism for structured follow-up of patients after discharge to capture data, and detect potential complications early, at a stage that may permit treatment without readmission.


UCSF’s Department of Orthopedic Surgery has made significant strides in advancing the quality of patient care and safety following spinal surgery and arthroplasty, receiving the 2012 designations as a Center of Excellence for both services.  However, we continue to seek opportunities to innovate in this area and to become a national model of excellence.  The department has identified an innovative technology that can be scaled and generalized to all surgical specialties, that can open up a new arena in clinical research, and that is “shovel ready,” already in clinical use in several Bay Area orthopedic practices.  The tool captures rich data on signs/symptoms, health outcomes, and quality of life by engaging patients post-discharge, and allowing them to participate in their own outcome reporting. The specific aim of this proposal is to implement a pilot project that extends care beyond discharge by engaging patients in self-reporting of their health status at regular intervals during their own recovery.  Information from the resulting dataset may identify early signs of complication that will enable treatment in an outpatient setting rather than as a readmission.  The infrastructure for patient follow-up will begin with spine and arthroplasty services, and extend to surgical procedures throughout the UCSF campus.



We propose a pilot study using a novel HIPAA compliant SaaS platform called HealthLoop that is presently being piloted for clinical purposes by a large health plan.  Through a library of configurable electronic follow up protocols, orthopaedic surgery patients will be sent recurring automated email check-ins from their physicians after discharge with structured queries pertaining to their surgery.  A research database and a clinical dashboard will capture structured signs/symptoms, health outcomes, functional status, and impending complications using validated PRO tools. These will enable researchers to analyze a continuum of data throughout recovery and clinicians to intervene at any sign of impending complication.


Criteria and Metrics for Success

Metrics for success will include: Identification of practice patterns and/or follow up regimens that lead to superior outcomes; Reduction in complication rates; Reduction in ED visit and readmission rates; Reduction in total costs; Improved functional outcomes.


Approximate Cost and Justification

$50,000 is required for UC customization of clinical templates, provider training, implementation of the HealthLoop platform, execution of the pilot, as well as data analysis and reporting.



University of California Spine Surgery Consortium

Clinical and research staff at HealthLoop (Mountainview, CA) 


  1. Qasim M, Andrews RM. 2009. HCUP Statistical Brief #142. Sept 2012. AHRQ, Rockville, MD. http://www.hcup-us.ahrq.gov/reports/statbriefs/sb142.pdf.
  2. IOM (Institute of Medicine). Initial National Priorities for Comparative Effectiveness Research. Washington, DC: The National Academies Press. 2009.
  3. Numerof, Rita. Comparative Effectiveness Research in Spine Care in Defining the Value of Spine Care, Jeffrey A. Rihn, M.D., Alexander R. Vaccaro M.D., Ph.D., Todd J. Albert, M.D. and David B. Nash, M.D., editors, 2012.
  4. Basch et al, JCO December 1, 2012 vol. 30 no. 34 4249-4255.

Commenting is closed.

Assessment of Participant Health Literacy by Clinical Research Coordinators

Proposal Status: 

Rationale. Successful recruitment and retention of ethnically diverse research participants in clinical studies depends heavily on the comprehension, needs, and preferences of potential participants.  A critical influence on these outcomes is health literacy, the degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions.[i]  Since 30% of US adults have only basic health literacy,[ii] and Hispanic and African Americans are disproportionately concentrated among those of low health literacy,[iii] representation of these populations on clinical studies depends in part on the extent to which clinic and research staff can recognize patients of low or moderate literacy and communicate complex concepts to them in accessible and relevant terms. Tools that measure health literacy (commonly written questions that assess reading ability) have been criticized when used in clinical settings as alienating and stigmatizing to low literacy patients.[iv]  A recent review of health literacy research by the US Agency for Healthcare Research and Quality concluded that development of measures for spoken health literacy is a high priority.[v]

The proposed pilot study builds on a recently completed NCI RO1, Increasing Participation in Cancer Clinical Trials (2007-2012), that was a collaboration between the Kaiser Permanente (KP) Division of Research (DOR, C. Somkin, PI) and UCSF (R. Pasick, Co-I).  From in-depth analyses of 38 recorded nurse-patient clinical trial conversations, we elucidated 6 dimensions of patient utterances that we call “clinical trial health literacy” (CTHL), conversational indicators of a patient’s ability to understand basic concepts of trial participation: grammar, use of medical terms, knowledge of diagnosis and treatment, logic, initial clinical trial understanding, information seeking.  Our data show that these are closely inter-related and together serve as a strong indicator of health literacy.  Our long-term research plan includes development of a protocol for real-time assessment of these dimensions by Clinical Research Coordinators (CRC) and for corresponding messages tailored to high, medium, and low CTHL. This will be followed by a large-scale KP- and UCSF-based mixed methods study of protocol impact for participants (comprehension, satisfaction, needs fulfillment, decisional conflict), for CRCs (satisfaction, perceived efficacy), and on rate of clinical research study participation.

Plan. The purpose of this RAP grant is to conduct a feasibility test of CRC assessment of CTHL dimensions in the course of clinical research study recruitment conversations, and to further refine the dimensions for subsequent validation analyses.  Our specific aims are to: 1. establish a partnership between UCSF- CTSI Community Engagement Program faculty (Pasick), DOR (Somkin), and the UCSF CTSI Participant Recruitment Services (PRS, Nasser); 2. refine and pilot-test a CTHL screening tool for (a) ease of use by Clinical Research Coordinators and (b) reliability in recruitment attempts with 25 UCSF patients; 3. develop and pre-test a training protocol on CTHL assessment as one component of a new CRS curriculum on health literacy with 10-15 CRCs enrolled in the CTSI-initiated campus-wide CRC training program. Two focus groups will be conducted with CRCs at the outset to inform design of the feasibility test.  CRCs conducting the health literacy assessments will be interviewed following each encounter and patients will be queried briefly afterward as well.  

Criteria & Metrics for Success.  Long-term measures of success will include sustained collaboration among the above partners leading to incorporation of pilot study products in ongoing UCSF and KP CRC training, acquisition of NIH funding, and increased rates of participation in studies among those of low to moderate CTHL.  Intermediate measures are demonstration of the feasibility of CRC assessments as indicated by completion of 25 audio-recorded patient encounters that produce high ratings of satisfaction and comprehension by patients and of satisfaction by CRCs; a high degree of inter-rater reliability on encounter recordings rated by multiple CRCs; and training protocol pre-test results indicating that CRCs find the information and strategies useful, new for them, and easy to adopt.  

Approximate Cost/Brief Justification.  The project will be led by Dr. Pasick (5%) and Ms. Nasser (contributed, 5%) with project coordination by Ms. Allen (recipient of NCI Diversity Supplement to conduct the above NCI-funded Kaiser-based research, now a UCSF Research Analyst, 30%).  Dr. Somkin will represent KP needs and interests as a consultant ($5,000).  Patient incentives for study participation will be provided at $35 each ($875). PRS staff will devote 340 hours ($13,600) for focus groups, interviews, audio tape ratings, and training. Total cost: $46,336.  

Collaborators.  This study is a collaboration among Dr. Rena Pasick (Professor, Faculty of CTSI Community Engagement Program, with 25 years of NIH-funded research on cancer disparities and communication across cultures, including studies that involved training of service staff on health literacy); Ms. Nasser (Senior Director, CTSI Clinical Research Services Director); and Dr. Somkin (DOR, Research Scientist).




[i] Institute of Medicine Committee on Health Literacy. (2004). Health Literacy: A Prescription to End Confusion. L. Nielsen-Bohlman, A.M. Panzer, & D.A. Kindig (Eds). Washington, DC: The National Academies Press

[ii] Paasche-Orlow M, Parker, RM, Gazmararian, JA, Nielsen-Bohlman, LT, & Rudd, RR. (2005). The prevalence of limited health literacy. JGIM, 20, 175-184.

[iii] National Center for Education Statistics. National Assessment of Adult Literacy. Key Findings.  http://nces.ed.gov/NAAL/kf_dem_race.asp.  Accessed February 25, 2013

[iv] IOM (Institute of Medicine). 2009. Measures of Health Literacy: Workshop Summary. Washington, DC: The National Academies Press.

[v] Berkman ND, Sheridan SL, Donahue KE, Halpern DJ, Viera A, Crotty K, Holland A, Brasure M, Lohr KN, Harden E, Tant E, Wallace I, Viswanathan M. Health Literacy Interventions and Outcomes: An Updated Systematic Review. Evidence Report/Technology Assesment No. 199. (Prepared by RTI International–University of North Carolina Evidence-based Practice Center under contract No. 290-2007-10056-I. AHRQ Publication Number 11-E006. Rockville, MD. Agency for Healthcare Research and Quality. March 2011.

Commenting is closed.

Governance of Extant UC Biorepositories

Proposal Status: 

Rationale:  Each UC Biomedical campus contains tens to hundreds of biorepositories. These operations collect human biological samples (tissues and fluids) and associated data for use in research. UC biobanks traditionally have established their own governance structure, which includes rules for accessing, storing and sharing samples/data, including informed consent practices.  Governance, a complicated process, has myriad ethical implications including risk to individuals, identifiability, and data sharing. At UC and elsewhere, archived samples were not collected under current/emerging standards for informed consent. Decisions need to be made about the future appropriate use of these samples and data, especially in light of recent concerns about identifiability of “anonymous” genomic samples. Currently, there is little information about community perspectives on appropriate governance of extant biorepositories within UC. [Collections include samples that were initially collected as part of clinical care as well as collections done under research protocols.]




We will leverage an existing NIH-funded study, EngageUC; this study will develop an ethical, efficient, and sustainable system for biorespository research across the UC system. EngageUC includes a robust community engagement (CE) component in which community members who represent the diversity of California will be brought together to be educated about biobanking and to provide informed viewpoints on optimal consenting techniques. This input will then be used to inform a clinical trial of consenting mechanisms to develop an evidence base for prospective collection of biorepository samples. However, EngageUC is focused specifically on establishing policies for informed consent and governance for NEW collections moving forward, and does not examine how samples and data in existing biorespositories – including samples with varying forms of informed consent – should be governed.


This proposal leverages the EngageUC CE activities to develop and refine approaches for managing governance of extant biorepositories in the UC system. This project will: (a) extend planned CE activities by including an array of additional stakeholder groups who bring valuable insights on extant biorepositories; (b) work with community stakeholders, biorepository researchers, and UC institutional officials to develop consistent and comprehensive approaches for managing governance of UC’s extant biobanks; (c) and translate these approaches into policies that are feasible and acceptable for governance of existing biorepositories.


Criteria and metrics for success


Short term criteria for success will include conversations with diverse stakeholder groups to elicit perspectives about governance of extant biobanks and the recommendation of alternative governance approaches for adoption by the UC BRAID consortium including  how specimens will be stored, labeled, accessed, and shared; whether and how current perspectives on consent will be incorporated.  Long term we anticipate translation of approaches into UC policy.


Approximate cost and justification


The primary costs of the study will be salary support and administrative costs.  We require 15% effort for the program manager and 10% effort for one faculty member as well as RA support.  Administrative costs will be those associated with setting up meetings between community groups, researchers, and institutional officials.  We are requesting $50,000 total.




EngageUC team leaders bring expertise in biorepository research and management, informed consent research, community engagement, and ethical dimensions of informed consent. The team also has experience in mixed-methods research and the translation of research into policy. Jen Hult, MPH, is Senior Program Manager of EngageUC. Elizabeth Boyd, PhD, is Associate Vice Chancellor, Ethics and Compliance at UCSF and Program Director of the CTSI’s Regulatory Knowledge and Support program. Daniel Dohan, PhD, is Associate Professor of Health Policy and Social Medicine at the UCSF Institute for Health Policy Studies (IHPS), where he also serves as Associate Director for Training and Development. Sarah Dry, MD, is Associate Professor and Associate Chair for Research Services in the UCLA Department of Pathology. Arleen Brown, MD, PhD, is Associate Professor of Internal Medicine and Health Services Research and Leader of the UCLA CTSI Community Engagement and Research Program. Barbara Koenig, PhD, is Professor of Social and Behavioral Sciences at UCSF. An internationally-renown bioethicist, Dr. Koenig brings extensive experience in research on biobanking and community engagement and will be the primary faculty member involved in this project.

Commenting is closed.

Information Interface for Patients, Clinicians and Researchers

Proposal Status: 

Rationale:Taking findings from basic research to practical applications that enhance human health and well-being is the signification of translational research. Improvement in human health and well-being, however, does not necessarily involve the cure of a disease. Sometimes mere information transfer might help patients substantially in dealing with their medical condition. This is particularly true for patients with family history of yet unknown or contradictory diagnoses – in other words for patients with rare hereditary diseases. This point was emphasized very recently by Erika C. Hayden in Nature [1]. Providing information is the foundation of molecular genetic diagnostics and genetic counseling, which should readily be available for any inherited disease, even if no cure will be available in the foreseeable future. The provided information can answer basic questions of the patient, such as What do I have? Why my family? Is there a risk for my children? Is there anything I can do about it? And this will assist the patient in understanding their medical condition.

COL4A1 (OMIM: *120130) and COL4A2 (OMIM: *12090) encode for extra cellular matrix proteins that constitute basement membranes. Mutations in COL4A1 and COL4A2 cause multi–system disorders including porencephaly, cerebral small vessel disease with hemorrhage, Axenfeld-Rieger anomaly with glaucoma, and variable muscular dystrophy including muscle-eye-brain disease. To date, more than 50 different pathogenic sequence variances have been described in highly penetrant multi-system disorders. For ICH – the only disease so far that has been systematically screened for COL4A1 and COL4A2 sequence variants – we estimate that mutations in COL4A1 and COL4A2 may cause up to 10% of all cases of spontaneous ICH. The Gould lab identified the first COL4A1 mutations in mice and humans and recently published a comprehensive review on the topic. For these and other reasons, the Gould lab receives inquiries from researchers, clinicians and patients throughout the world interested in collaborations, clinical advice or participation in research. We recognize that many other labs at UCSF and around the world face these same types of requests. We propose that developing a centralized information management system (IMS) to promote and streamline interactions and communication between these three stakeholders will be an efficient and effective paradigm to enhance translational research.


Based up on the platform developed by the Leiden Open Variation Database (LOVD) we will generate a centralized information management system (IMS) that streamlines interchange of information between patients, clinicians, and researchers. The IMS will be tripartite in order to provide the relevant information to the appropriate target audience. We will develop the platform using COL4A1 and COL4A2 as a scalable model for any number of other groups.

  1. Patients will find a comprehensive overview on the different disorders associated with COL4A1 and COL4A2, as well as a platform to connect to medical doctors, researchers, and genetic counselors especially trained on these medical conditions.
  2. Medical doctors and genetic counselors will find a locus-specific database that collects all sequence variations in COL4A1 and COL4A2 with links to the according reference of their initial description, the latest literature on COL4A1 and COL4A2, as well as information on ongoing patient studies.
  3. Researchers will maintain the IMS and thereby find a useful research dataset for molecular diagnosis, large-scale mutation statistics, and the determination of genotype-phenotype correlations. Research will also benefit from a collaborations platform, which promotes discussion in the field. They will also identify patients willing to donate biological material for further investigations on multi-system disorders.


Criteria and Metrics for Success:

Immediate goals:

  1. Set-up a locus-specific database for COL4A1 and COL4A2 based on the format used for the Leiden Open Variation Database (June 1, 2013).
  2. Set-up a literature database on COL4A1 and COL4A2 based on the Mendeley open source reference manager (June 1, 2013).
  3. Write a comprehensive overview on the different disorders associated withCOL4A1 and COL4A2 and update all according NCBI datasets (July 1, 2013).
  4. Collect information on MDs and genetic counselors that are especially trained on medical conditions associated with COL4A1 and COL4A2 based on information provided by experts and databases, such as GeneTests(July 1, 2013).
  5. Create an interactive web-interface that links all the different resources by July 1, 2013.
  6. Go live by August 1, 2013.


Mid-term goals:

  1. This IMS will increase clinicians’ awareness of COL4A1 and COL4A2 as one possible cause for multi-system disorders and they will find necessary resources and information to help make decisions for their patients.
  2. Interested patients with multi-system disorders can arrange to donate biological samples, such as DNA or skin biopsies, to researchers listed on the IMS in order to promote research on multi-system disorders.
  3. The IMS can be a model for other inherited diseases and may lay the seed for an extended IMS that comprises also other genes and diseases.


Long-term goals:

  1. Once the platform is established we will use it as the model and continue to build this resource for other inherited diseases of the extracellular matrix.
  2. Establish this platform as a template for other UCSF researchers and clinicians to interface with each other and with patients to promote information transfer and patient recruitment.
  3. In summary, this proposal will improve the conduct of research on a devastating disease here at UCSF and worldwide.


Total Budget: $22,000

Cost estimations:

Summer student: $4000/mo for 3 months = $12,000

Web Developer: $50/hr for 1 month = $8,000

Postdoctoral Fellow to oversee project 15% effort for 3 months = $2,000



1.            Hayden EC: Data barriers limit genetic diagnosis. Nature 2013, 494(7436):156-157.

Commenting is closed.

Establishment of centalized freezer surveillance system to increase protection of human biospecimens

Proposal Status: 

Rationale: There are currently about 1000 mechanical – 80 degree Celsius freezers in use at UCSF. The majority of these freezers are used to store biomedical specimens for basic research, translational research, clinical trials, and prospective biobanking efforts.       

To protect clinical research material stored in these freezers the performance of the freezers has to be monitored 24/7, and alarm information systems need to be in place informing owners about freezer malfunctions. Currently a central freezer monitoring service is offered through the Alarm Management program of the UCSF police department. The system is based on connecting freezers via a phone line to the police department. This monitoring model has certain disadvantages, such as the fact that it relies on the temperature gauge of the freezer itself (instead of an independent measurement) and the system only triggers an alarm without generating ongoing temperature/performance reports.  

Protection of stored research biospecimens and human samples derived from clinical trials will be increased if a UCSF-wide monitoring system is made available to laboratories and investigators providing alarm surveillance services including constant temperature and energy reporting.  Such a system will also guide preventative maintenance decisions by recording changes in freezer energy consumption over time, further enhancing the protection of stored material by reducing the instances of unexpected freezer malfunctions, and extending the life of the freezer asset.


Plan: Pilot implementation and testing of a remote freezer monitoring/surveillance system enabling investigators/laboratories to connect their freezers independent of campus location to an alarm/monitoring system that provides instant emergency alarm message functions and constant reports about temperature and energy consumption.

Criteria and metrics for success:

  • Usability at all campus locations with Wifi access
  • Liability of the system in recognizing alarm situations and generating alarm messages
  • Liability in generation of data reporting (energy consumption) as guide for required preventative maintenance (further potential for energy-saving maintenance and repairs)

Approximate costs: Currently a system providing such services (klatu networks, TRAXX) is tested by the Facilities Management Group at UC San Diego. This application intends to leverage the ongoing UC San Diego to test whether the system is be suitable for UCSF and also to analyze whether this system could be recommend as standard to be used by all UCs. Estimated cost of establishing a pilot study at UCSF including surveillance and monitoring of 50 freezers are $50,000.

Additionally, implementing a technology that reports out on freezer energy consumption and that triggers maintenance and repairs could have a huge financial impact to UCSF’s bottom line (each low temperature freezer uses about as much energy in a year as a typical house) and part of these costs may be reimbursable in the long run if the system is approved by the California Public Utilities Commission as a viable energy efficiency measure under the UC/CSU/IOU Energy Efficiency Partnership program. The technology is currently under review by the SDG&E Emerging Technologies group, using data from UC San Diego as well as several other SDG&E customers.


Collaborators: Gail Lee (UCSF Facilities Services), Munn Maric (UCSF Facilities Services), Anna Levitt (UC San Diego Facilities Services), Jim Sobczyk (UCSF Campus Life Services “Freezer Farm”), Julie Auger (UCSF Research Resource Program), Britt-Marie Ljung (UCSF Pathology and Cancer Center Tissue Core), Hubert Stoppler (UCSF Cancer Center Tissue Core)

Commenting is closed.

Evaluation of Methods for Bioinformatics Tools Training

Proposal Status: 

Rationale – Background and training in bioinformatics tools is required for the research community at UCSF to remain at the forefront of biomedical research and successfully compete for funding.  Bioinformatics tools help translate our collective molecular understanding of disease into actionable insights and life-improving patient care innovations.  Application of bioinformatics knowledge can minimize persistent barriers to progress in the translational research workflow by providing a bridge between the domain expertise of the experimentalist and the world of computationally driven, information-based research methods (see Appendix Fig 1). 

Currently at UCSF, training on bioinformatics tools is decentralized.  Services, databases, and courses are hosted by Core Labs, the UCSF Library, and other departments.  Centers of data generation are not always integrated with the tools needed to gain insight from the data or place data in a disease-context. Navigating lists of bioinformatics tools can be a daunting task for researchers with no background in bioinformatics (see Appendix for current lists). 

This arrangement carries numerous risks:

  • Insufficient information about the best tools and platforms to address a particular research question.
  • Inability to accurately gauge the true investment needed in both time and money to gain full value from an experiment.
  • Poor return on investment from expensive experiments, and missed opportunities due to lack of awareness about tools available to translate raw data into findings and testable hypotheses. 

In keeping with the UCSF Library’s commitment to support the continuing educational needs of information resource users, and extend services to a wider audience of researchers, we propose a pilot project to evaluate web-based methods for bioinformatics training.  The UCSF Library will provide access to a centralized, web-based resource for training on well-adopted, authoritative bioinformatics resources by hosting the OpenHelix collection of bioinformatics tutorials on its website.  This new service would cross-reference with related services (Core Labs, Cores Search, MyCORES etc.) to provide centralized and coordinated access to bioinformatics tools training at UCSF. 

We are aware that there are a number of different groups at UCSF with expertise and interest in bioinformatics training and our aim with this proposal is to work with these groups to identify needs and develop solutions for translational medicine researchers.

Successful implementation of this new bioinformatics training service can:

  • Provide researchers with the skills needed to locate, learn about, and apply the information housed in bioinformatics databases.
  • Enable them to identify the right tool for their particular research question.
  • Improve collaborations between experimentalists and bioinformatics experts at UCSF.
  • Reduce time between data generation and insight by making bioinformatics training and tools available to those who generate data at the time it is generated.
  • Reduce the current burden on Core Labs that may not have time for basic bioinformatics training requests from researchers.
  • Establish an engaged user base through which the UCSF Library and Research Resource Program can continually evaluate services, identify unmet needs for training and resources, and design new services.


  • Collaborate with the UCSF Institute for Computational Health Sciences, leveraging their expertise in bioinformatics to identify researchers' training needs and develop solutions to meet those needs.
  • Form a Bioinformatics Tools User Group (user base for this pilot)
  • Survey user group to identify bioinformatics tools and training needs
  • Evaluate OpenHelix as an inexpensive, out of the box solution for bioinformatics training
  • Make Go/No Go decision on value of OpenHelix
  • Design and implement library-based home for resources such as OpenHelix:  Bioinformatics @UCSF Library
  • Collaborate with CTSI to create Marketing and Outreach plan for successful adoption of new service
  • Ongoing evaluation of web-based bioinformatics training service and development of a business model for continued support of the service.

 Criteria and Metrics for Success

  • Pilot user base includes bioinformatics subject matter experts as well as end users.
  • Good response rates on User-Needs and OpenHelix evaluation surveys
  • Steady increase in hits to library-based bioinformatics website 6 months after launch
  • Steady increase in utilization of OpenHelix tutorials 6 months after launch
  • Good response rate on User Satisfaction survey 1 year after launch of new service.  Metrics identifying most/least utilized bioinformatics tools.
  • Increase in User Satisfaction rating 2 years after launch of new service


Julie Auger, Executive Director of UCSF Research Resource Program (RRP)

Budget includes funding for:

  • 2-year license to OpenHelix
  • Programming resources to integrate with existing web infrastructure (UCSF Library, Core Labs and Cores Search)
  • Minimal in-kind CTSI support for survey development, marketing and outreach plan
  • External trainers for on-site training on most highly valued bioinformatics tools.



1. Hyperlinks to current lists of bioinformatics tools





2. Examples of Medical Libraries that host or are evaluating OpenHelix as part of their library-based bioinformatics services

  • Mt. Sinai School of Medicine Levy Library –successful implementation with 5-year renewal and fully booked on-site training classes
  • Becker Medical Library – Wash U
  • University of Illinois
  • Emory – Woodruff Health Sciences
  • University of Pittsburg
  • Weill Cornell Medical Library

3. Figure 1.  Awareness and training in bioinformatics tools can eliminate persistent roadblocks in the translational research workflow. 



Commenting is closed.

Biobank Inventory Software Evaluation

Proposal Status: 

Biobanking Inventory Software Evaluation

Rationale:  Access to high quality human biospecimens and associated clinical data is essential to translational and clinical research programs.  Effective and efficient use of human biospecimens is an important tenet of our role as community-entrusted stewards of these valuable resources.   These points are reflective of the conclusions of the CTSI funded (2008-9) Tissue Task Force that engaged Huron Consulting as well as a recent 2011 audit of UCSF tissue banks by UCSF Audit Services. 

It is estimated that UCSF currently maintains 50-200 biobanks – some of them program based (i.e. Cancer Center Tissue Core) and others are PI specific.  However, many researchers remain unaware of the breadth and depth of biospecimens available on campus. Ready access to available inventories would improve utilization and enhance our stated role as community-entrusted stewards of these valuable resources. The UC BRAID Biobanking Work Group, comprised of representatives from all 5 UC academic medical centers, has also identified inventory access as critical for building a UC Regional Research Network across all 5 UC centers; this Network would improve Californians’ access to clinical trials and support critical biomedical research on a broad array of health issues.  The largest access challenge is the variety of inventory software systems employed by the various banks.  The extent of this diversity and barriers to sharing information is not clear currently.  This proposal requests funds to: 1) Conduct a UC-wide assessment of the various inventories in use; 2) Identify the functional needs of each participating bank; 3) Evaluate the feasibility of a common interface that would allow biobanks to choose to share information while retaining their existing inventory software system (low-cost) or determine if broadly viewable inventories are only possible when using a common electronic tool (high-cost), and; 4) Understand biobankers perceived benefits and barriers to increasing researchers’ access to their biobank inventory.  An additional benefit would be a comprehensive list of UCSF Biobanks available for researchers to place deposits. 

Plan:  A Program Manager, hired through the UCSF PMO, will be employed to facilitate this assessment.  He/She would develop an assessment plan and interview UCSF biobank managers to establish current practices and inventory systems as well as to understand of the perceived benefits/barriers to increasing access to biorepositories.   This will inform the process to engage Biobankers at the other UC campuses through UC BRAID.  Additionally, information about the perceived benefits/barriers will help us to identify areas of concerns that must be addressed, and educational programs that may be developed, in order to create a system that will support greater sharing of biosamples at UCSF; this information can be used for similar purposes at other campuses as well.  In addition, the survey will provide a definitive list of biobanks for deposits and withdrawals, and will facilitate integration of biobank inventories with clinical data from the Electronic Medical Record in the Enterprise Data Warehouse, currently under development.

Criteria and metrics for success:  Deliverables from this project would include a list and description of all biobanks at UCSF including the availability of the specimens to the research community and identification of relevant information stored for each specimen; a technical assessment of each of the inventory software systems in use; and a compilation of identified benefits and barriers to opening access to inventories.   This would facilitate the determination of a common interface for the inventories to better mine the data stored. 

Project Total cost:  $53,150.  Request to CTSI:  $50,000.  The remainder of the project costs would come from Research Resource Program (RRP) funds. 

Program Manager to set up the program, identify needed information, conduct Biobanker interviews and write up the assessment:  2.5 days/week for 6 months at $175/hour:  $21,000

Program Staffer (Analyst II or III) to conduct Biobanker interviews and enter data into project database:  50% effort for 6 months $24,150 including benefits (base salary $69,000, median Analyst II salary)

Technical Assessment Staff:  2 weeks of technical assessment by programmer to determine potential inventory interfaces and provide recommendations:  $100/hr x 80 hours = $8,000. 


Collaborators:  Cancer Center Translational Informatics, directed by Sorena Nadaf, has significant experience with software assessment for use on an enterprise level. 

UC BRAID Biobanking Committee, chaired by Sarah Dry, UCLA, will provide insight into appropriate interview questions and UC-wide biobanking needs.

Commenting is closed.

Advocacy Impact on Research Agendas

Proposal Status: 

RATIONALE: Realizing that the benefits of the current revolution in biology and oncology would be enhanced by vigorous public support, for the past twenty years, the UCSF Breast Oncology Program (BOP) has implemented comprehensive strategies focused on leveraging advocacy engagements. To help transform the conduct of clinical and translational research, advocates support a wide range of NCI sponsored Specialized Programs on Research Excellence, (SPORE) and Physical Sciences and Oncology Center (PS-OC) Cancer Center projects, as well as multi-site grants sponsored by Department of Defense (DOD), Komen, California Breast Cancer Research Programs (CBCRP), Stand Up to Cancer (SU2C), and Translational Breast Cancer Research Consortium (TBCRC). Applying core principles that forge synergy with NCI Advocacy Research Working Group Recommendations: strategic innovation, collaborative execution, evidence based decision-making, and ethical codes of conduct, researchers and advocates interact across a broad spectrum of partnership modes at various levels of intensity. Participating in four areas: 1) research and programmatic support, 2) education and outreach, 3) policy and strategy, and 4) representation and advisory, UCSF breast cancer advocates are at the forefront of efforts to revamp translational research processes. For example, advocates involved in grants meet on an ad hoc basis with the study investigator and team. Infusing the patient lay perspective into discussions, trained research advocates vet hypothesis, define strategic priorities, address research challenges, and incorporate innovative science and study design into research projects/clinical trials. Importantly, promoting cross-sector and trans-network collaboration, advocates catalyze change in research practices by identifying systematic barriers to research efficacy, effectiveness, and expediency.

CHALLENGE: As champions of precision medicine, evidence based practices, Bayesian statistics, adaptive trial design, biospecimen standardization, biomarker validation, improved test result reproducibility, and informed consent reform, advocates are driving change in research practices as well as in FDA initiatives leading to new regulatory and interpretative mechanisms. Moreover, forging credibility, advocates now have a dramatic presence as authors in scientific papers, presenters at scientific conferences, voting members in scientific advisories, cooperative groups, data safety monitoring boards, planning committees, protocol/peer review committees, and informed consent working groups. Yet, despite the growing momentum of advocacy in the support and reform of clinical and translational research, collateral challenges remain. Because advocacy efforts often aim for outcomes that are hard to measure, capture, and operationalize, unique quantitative and qualitative approaches are needed to systematically assess the impact of advocacy messages and activities. Lessons learned from successes and failures will allow us to continuously optimize efforts and promote best practices to other UCSF advocacy groups.

PLAN & METRICS FOR SUCCESS: Three innovative methods are being developed specifically to respond to advocacy’s unique measurement challenges:

1.  A static table will be used to create an interactive model for measuring progress in real time.

2.  Stakeholder surveys that gather advocacy stakeholder perspectives and feedback will be used to assess the extent to which researchers support advocacy involvements and whether the support is changing over time.

3.  Logic models and systems mapping approaches will be developed by a committee of researchers and advocates to monitor performance, address challenges, and identify “best practices” and key entities to guide infrastructure improvements.

Arming stakeholders with the tools to make advocacy activities more transparent, recommendations more targeted, and outcomes more impactful, participants will formally assess the extent to which advocacy processes are improving the conduct of clinical and translational research.

JUSTIFICATION: Collaborative team science provides a starting point for comprehensive change and advocacy activities are being looked at as a shining example of how research advocacy will help spur medical innovation, democratize science, and expedite the incredible potential of future investments in bioscience. To sharpen and shape the vision for capacity building and bi-directional mentoring and transnetworking opportunities, advocates and other stakeholders will participate in two workshops specializing in evaluation and strategy development for advocacy and policy change efforts.

COST: A total budget of 50K is requested: Project coordinator 24K; Advocacy Training ProjectLEAD 5K; Workshops: 2 UCSF Workshops on Advocacy Impact Metrics 12K; Infrastructure:  Training Materials and Modules for UCSF Outreach 9K.

COLLABORATORS:  Susan Samson, Linda Vincent, Susie Brain, BOP science advocates, Hope Rugo (clinical lead PS-OC), Sarah Goins (coordinaor BOP), Laura van ’t Veer (Leader BOP), Susanne Hildebrand-Zanki (Associate Vice Chancellor Research), Elizabeth Boyd (Associate Vice Chancellor Ethics and Compliance)

Commenting is closed.

An Early Translational Researcher’s Framework for Health Economics Evaluation

Proposal Status: 


Economic considerations are important in determining the development and use of a new technology in any scientific field. This is particularly true in healthcare, where overall spending in the U.S. is at an unsustainably high rate, thus making cost consciousness imperative in the development of new technologies. Researchers who desire to translate new understandings of disease mechanisms into commercially viable methods of diagnosis, therapy and prevention often neglect or struggle to incorporate health economics into the assessment of the potential value of their innovations. We propose to develop a framework for health economics evaluation, with insights, tools and relevant case studies, specifically targeted to support the research and development goals of early translational researchers. The primary objectives of the framework are:

  • to highlight some key economic factors that lead to the adoption or rejection of new technologies into clinical practice, and
  • to help researchers better frame the potential economic value of their innovations

Supporting an Unmet Need

In the Catalyst Award Program at UCSF CTSI, early translational researchers receive targeted advice on product development and commercialization strategies, in addition to seed funding. These key insights, provided early in the translation process, have often led researchers to significantly recalibrate their research and development goals and approach to maximize the potential clinical and commercial success of their innovations. Health economics and cost-effectiveness are consistently raised as critical issues in the potential success of new technologies reviewed in the program. A complete economic evaluation of any proposed technology is far beyond the goals and capabilities of the program. However, an accessible framework that  provides key insights, tools and case studies to help researchers understand the contributing factors to the economic evaluation and adoption of new technologies, would be invaluable.


An Initial Pilot Project Focused on Medical Devices

Since the proposed framework will be driven by a limited number of case studies, we will maximize its value by initially developing and validating our approach for medical devices. If successful, a similar approach will be used to develop frameworks for therapeutics, diagnostics and digital health technologies, with the expectation of shared and technology-specific elements within each framework.

We will leverage the knowledge of key experts in health economics and policy as well as  technology adoption at UCSF. Additional independent experts in health economics, cost-effectiveness, reimbursement, and new technology assessment will also be identified and consulted.

  • Pilot Evaluation: A panel consisting of UCSF and external experts will initially be convened to discuss how early translational research projects can be best evaluated using the limited resources available to researchers. The panel will recommend and evaluate up to 5 medical devices whose development and successful (or failed) clinical adoption can be used to highlight important aspects of health economics.
  • Draft Development: The output of these reviews will be translated into the first draft of a framework for economic evaluation and is expected to include case studies, methodologies, templates, and resources.
  • Rapid Testing: This draft framework will be pilot-tested with 5 UCSF researchers involved in medical device projects that have been reviewed by the Catalyst Program. Their experience with the framework and their resulting economic evaluations will be assessed and discussed by the expert panel.
  • Finalize: The results and assessment of the pilot study will be used to develop a final framework for broader distribution.
  • Distribution: The final framework will be distributed through the Catalyst Award Program, The Center for Healthcare Value, and other CTSI and UCSF channels, other CTSA network channels, and outreach to relevant publishers, etc.

Short and Long-Term Success Metrics

The short-term success of this approach and of the framework will be determined by the results of the pilot study and the content of future Catalyst Award applications. Long-term success will be measured by the ability of researchers to better understand and incorporate economic factors into their translational projects. Project tracking and feedback mechanisms within the Catalyst Award Program will be used to monitor and evaluate such measures.



This project will be seeking to include a multidisciplinary group of health economics stakeholders, including key researchers at the Institute for Health Policy Studies at UCSF, health economists, reimbursement and technology evaluation experts. Lisa Schoonerman and Ruben Rathnasingham, who will lead the project, have extensive healthcare product development and commercialization experience. This pilot project, focused on medical devices, will require a budget of $15,000 for consultants, meeting expenses, production and promotion.

Commenting is closed.

Improving the consent process for complex studies: making the study understandable to subjects

Proposal Status: 

Rationale.  Consent forms for clinical trials have expanded and now often range from 25 – 30 pages, in spite of the fact that studies have documented the inability of most research participants to retain this amount of information.  In addition, many consent forms include technical, medical, and legal language that is difficult for a lay person to understand.  When these consent forms are reviewed by the Committee on Human Research (CHR), concerns about their length, readability and complexity are often raised.  Investigators may consequently spend a great deal of time editing consent forms to satisfy CHR requests.  However, much of this language is mandated by study sponsors, so investigators may struggle between meeting sponsor requirements and revisions requested by the CHR to improve readability.  Although investigators or study staff review study procedures and consent forms with patients, these long, complex forms are unlikely to be conducive to true informed consent, particularly among patients from vulnerable populations.


Plan.  We propose to test the feasibility, acceptability, and usefulness of a simple 2-page summary sheet, written in plain language, to improve the consent process, enhance subject understanding of the research study and its risks, and the CHR review process. 

This project has the following primary goals:

  • Develop a template and guide for investigators to use to create the research summary, and evaluate the ease of preparing the summary among a sample of investigators and their research staff.
  • Evaluate the readability and literacy level of summaries prepared by investigators and/or their staff.
  • Evaluate differences in subjects' understanding of the research protocol through use of the summary, using a short knowledge test after the standard consent procedure and then after reviewing the summary.
  • Assess research subjects’ evaluation of the summary in terms of comprehension of the research protocol and the study risks, and their satisfaction with the consent process.
  • Assess both investigators’ and CHR members’ satisfaction with the review process when the summary sheet is included.

An unintended effect of this process may be to heighten investigator awareness of using plain language in consent forms.


Criteria and metrics for success

  • A template for creation of a research summary is developed.
  • Using the template, creation of the research summary is judged by investigators to require little time.
  • Readability of research summaries is found to be at 8th grade level of lower.
  • Research participants report that the summaries improve their understanding of the research study and its risk and benefits.
  • Investigators and study staff report that the summaries improve the consent process and perceive that patients have a better understanding of the study.
  • Investigators report fewer difficulties with consent form review process.
  • Investigators report that sponsors did not object to the 2-page summary or delay the study as a result.
  • Investigators report that they would continue to use the summaries.
  • CHR members report that the summaries improve their understanding of research protocols and lessen their concerns about complex consent forms.


Approximate cost and justification

Total Budget: $48,854. Salary support for UCSF faculty and research assistant involved in developing and evaluating the materials.   Incentives for investigator, research staff, and research subject participation.


Collaborators.  Patricia Katz is Prof of Medicine, has been a member of the Laurel Heights CHR Committee for 10 years, and is currently Vice-Chair of that committee. John Heldens is the Director of UCSF’s Human Research Protection Program. Jennifer Barton is Asst Prof of Medicine whose primary research focus is health literacy.  We especially seek clinical trial investigators willing to test the new materials as collaborators.

Commenting is closed.

Mobilization of Clinical Research Services (CRS) – Pilot Project

Proposal Status: 


This pilot stems from the 2012 awarded project of ‘Improving CRS performance through application of Lean/6 sigma’, intended to maximize the efficiency and impact of CTSI’s Clinical Research Services (CRS) program across UCSF and other affiliated institutions.  Current CRS Services are restricted by the locations and often higher-than-needed skillset to serve researchers across campus, resulting in low utilization of resources towards serving research (<50% of research utilization for Nursing services).  “Mobilization”, or training a number resources to apply their skillset at any clinical location across campus, will not only maximize the utilization of CRS services, but will also maximize the number of researchers and studies serviced across UCSF.  This project will focus on building the training, legal, and technological infrastructure for mobilizing CRS resources that includes nurses, nurse practitioners, and phlebotomists, across clinical settings found under UCSF. 


* Survey of existing mobile outpatient team concepts to leverage best practices.

* Based on CTSI/CRS strategy and current needs for research studies, identify the appropriate department(s) across UCSF campus where the mobilized resources will be piloted. The preference is to identify two departments/groups, one of which is already affiliated with CRS. 

* Perform a gap-assessment on the requested skillsets by researchers and available skillsets under CRS to meet the research demand. 

* Select the appropriate number of CRS resources to enroll in the mobilization program, along with modifying their respective job descriptions and legal contracts (i.e. union).

* Identify the system for requesting, scheduling, and billing for the mobilized resources. 

* Select the appropriate technology (if needed) for the mobilized resources to record and complete needed documentations as requested by study teams.

* Identify the process for mobilizing medical supplies as needed based on their availability at the studies’ clinical site(s).

* Measure the utilization, impact, and ROI on the project throughout the pilot period to determine its success and potential expansion to remaining CRS resources or other programs. 

Criteria and metrics for success

The anticipated success for this project is to increase the research utilization of the mobilized resources by study teams when compared to their pre-mobilized performance.  This success will also be coupled with the increase in satisfaction of serviced PIs/study teams and patient participants.  Below are few metrics that will be measured to gauge the performance and success of the project throughout its lifecycle:

* Number of departments under UCSF serviced by CRS mobilized resources

* Number and type of studies serviced by CRS mobilized resources

* Number and title of PIs serviced by CRS mobilized resources

* Satisfaction of PIs/Study Teams/ and Patient Participants * Capacity and utilization of CRS mobilized resources

Approximate cost and very brief justification ($50K max)

The anticipated cost of this project is $50K to support a Project Lead at ~ 50% of her/his effort 


From PET: Fabrice Beretta, Adel Elsayed, and from CRS: Eunice Stephens (ops manager), Kathy Burkart (finance manager), Deanna Sheeley (Research Nursing Core Dir).

Commenting is closed.

The Brain Initiative Outreach Proposal

Proposal Status: 


The overall long term goal of The Brain Initiative is to create a large internet-based registry of subjects interested in participating in neuroscience research. At launch, we will be recruiting individuals 55 years and older living in the San Francisco Bay Area. The Registry will serve as a base for future recruitment of subjects for studies on prevention of Alzheimer’s, Parkinson’s and other Neurodegenerative diseases. This project has been designed in order to address a major challenge in the conduct of clinical research, the limitations on getting enough subjects for large prevention trials of neurodegenerative diseases. By utilizing online tools, including the registry, the website and a large outreach effort we expect to create a large pool of subjects in the San Francisco Bay Area that will be willing to participate in Prevention Trials. The Registry is innovative because it will include a consent form, a set of questionnaires, several on-line neuropsychological tests, and will be designed for longitudinal followup of registered subjects. We have already obtained funds for the creation of the registry. However, in order to enroll and longitudinally follow a large number of participants the project will require very substantial marketing, advertising and community outreach efforts. This application is to request funds for the marketing, advertising and outreach efforts.

The generalizability of The Brain Initiative applies in several areas:  First, this project is generalizable to all areas of neuroscience translational research, since the project will recruit subjects interested in participating in studies on all areas of brain research. Second, we will be working with CTSI to market and advertise The Brain Initiative to underserved minorities including African Americans, Hispanics, and Asians, as well to the LGBT community. Third, this project will serve as a template to other registries and recruitment outreach programs in cancer, cardiovascular disease, and other disorders. The scalability of The Brain Initiative will be achieved through the capacity of internet based registries to scale to large populations. Initially we will focus on recruitment in the Northern California area. However, we have already been in discussion with investigators in Los Angeles, New York, North Carolina and other areas who might be interested in using The Brain Initiative website/registry for recruitment of subjects in their regions. In addition, we are in discussions with Bruno Vellas (Toulouse, France), Simon Lovestone (London England), Merce Boada ( Barcelona, Spain) and Nikklas Mattsen (Gothenberg, Sweden) concerning the extension of The Brain Initiative to their countries, and more broadly internationally. 


We plan to complete The Brain Initiative’s website and registry by May 31st 2013.  Once all technical elements are finalized and thoroughly tested, the advertising and outreach efforts will commence. The plan is to perform the following activities: 1) Digital outreach: a. Facebook, Twitter and other social networking sites. b. Online banners, Google adwords and other online advertising. c. Print advertising including mass mailings. d. Press releases to various newspapers, radio and TV stations throughout the Bay Area. 2)Community Outreach. a. Large Community event (1). b. Small community event (1)

Criteria and metrics for success

With the effort and budget that we propose we anticipate that we will be able to register the first 2,000 participants into The Brain Initiative. Here are the milestones for the period of 6/1/13 – 5/31/14: Milestone 1: By 6/30/13, 100 subjects recruited in The Brain Initiative. Milestone 1: By 12/31/13, 750 subjects recruited in The Brain Initiative. Milestone 1: By 5/31/14, 2,000 subjects recruited in The Brain Initiative.

Cost and justification

We estimate that the overall costs will be $50,000 for both the Digital outreach and the Community outreach. The costs are as follows: 1)Outreach Coordination: $11,732 in personnel costs 2) Digital Outreach Costs: a. Personnel Costs: $8,978 for posting and engaging participants b. Vendor Costs: $13,000 for online advertising. 3) Community Outreach: a. Personnel Cost: $4,290 for coordination of events. b. Large Community Event: $10,000 in overall costs. C. Small Community Event: 2,000 in overall costs


Dr. Michael Weiner, Dr. Scott Mackin

Commenting is closed.

Integration of Clinical and Administrative Data to Measure the Value of Orthopaedic Care

Proposal Status: 


Disorders of the musculoskeletal system present a significant burden to our healthcare economy. Musculoskeletal disorders are the largest cause of disability in the United States, accounting for more than half of chronic disease in patients over age 50 in developed countries.[i] The sum of direct and indirect costs for patients with musculoskeletal disorders in the United States has been estimated to be $849 billion dollars, or 7.7% of the national gross domestic product.[ii]  In addition to the financial cost, orthopaedic disorders diminish health-related quality of life. The demonstration of quality and value of care is necessary for defining the role and effectiveness of orthopaedic surgery interventions in the health care economy.  The purpose of this proposal is to create an infrastructure to combine administrative data on cost and quality metrics with clinical data on patient-based health status to measure the value of orthopaedic interventions, and to guide changes in care pathways with a goal of optimization of the value of care.


Optimization of value is an important goal of healthcare.  Administrative datasets have been useful in measuring quality of care metrics including rates of complication and readmission and in detailing the cost of care.  However, administrative data offers little insight into patient preference for health states, change in health status, and the value of care. The approach of integrating clinical outcomes with cost data provides an opportunity for moving beyond the use of process measures alone for measuring quality to providing critical information about the true value of care. This model provides a rational approach to making critical health care decisions and will be an increasing priority as we move towards a value-based health care system.



The Department of Orthopaedic Surgery has the experience and an established infrastructure to routinely collect and analyze health related quality of life outcomes through the Surgical Information Datasystem (SID).  We have collected patient-based health status information on over 90% of our elective patients.  We have developed methodologies to estimate utilities of health states with the EuroQol 5D, Oswestry Disability Index and the Neck Disability Index.  These health status measures permit an estimation of outcome measured in quality adjusted life years (QALYs).  Combining administrative data that permits comprehensive identification of cases and costs with patient-centered data will enable us to measure cost per QALY uniformly on orthopaedic cases. Our goal is to develop an infrastructure to combine the clinical outcomes data with hospital administrative data to measure the value of care. This will be accomplished through the creation of a data registry system that integrates clinical outcome and hospital administrative data. The registry will be established in collaboration with a medical informaticist with expertise in creating and implementing integrated data repository architecture that facilitates registry queries for the reporting of quality of care outcomes.


Criteria and Metrics for Success

Processes for reporting value of care metrics will be established at weekly departmental research meetings. Metrics for success will include ability to identify low value interventions and services and establish initiatives to improve the value of these interventions. Assessment of the value of interventions will be guided by demonstration of improvement in outcomes and/or reduction in costs.


Approximate Cost and Justification

$50,000 for the establishment of an integrated registry, staff training, data analysis and reporting.



UCSF Department of Orthopaedic Surgery- Divisions of Arthroplasty and Spine

Kevin Bozic,MD

Sigurd Berven, MD

Steven Takemoto, PhD


[i] The Burden of Musculoskeletal Diseases in the United States. http://www.boneandjointburden.org/ Accessed 7/21/11

[ii] The Burden of Musculoskeletal Diseases in the United States. Chapter 9: Healthcare Utilization and Economic Cost.  http://www.boneandjointburden.org/ Accessed 7/21/11

Commenting is closed.

UCSF Social Media Boot Camp for Scientists

Proposal Status: 


The UCSF Social Media Boot Camp for Scientists (official name to be considered based on comment received) is designed to help researchers explore social media as a tool to achieve various goals, including wider exposure for their research, connecting with potential funding opportunities, cultivating collaborations, and increasing the impact of research, to name a few.

A NatureJobs blog post, Social Media Tips for Scientists, puts it well:

For many scientists, the thought of spending time on social media sites is distinctly unappealing. To some it’s just a question of time: why add to that to-do list which is already long enough? For others it’s more to do with social media itself, finding the idea of sharing thoughts and ideas with the whole world pointless or self-indulgent.

“If that sounds like you, it might be time to reconsider your options – social media includes much more than the usual suspects like Facebook and Twitter, and there are even sites dedicated to academics. Indeed, a vast number of scientists are using social media for tremendous gains – whether that be forming new contacts and collaborations, sharing ideas, communicating science, inspiring others or just entertaining them. Why not join them?”

A series on Science Marketing featured in Nature Materials notes:

Today, researchers have to make their publications stand out from the stack of nearly 800,000 science and engineering manuscripts that are published each year, recent PhD graduates and postdocs face historically low employment prospects in academia, and principal investigators compete over shrinking government funding.”

Beyond that, researchers are noting that the unique aspects of social media are changing the way science is talked about, and scientists have even noted that social media tools help to clarify thinking, demystify the scientific process, and spark new ideas.


The UCSF Social Media Boot Camp for Scientists will:

  1. Offer useful information about social media specifically targeted at scientific researchers and the academic community;
  2. Address the challenges, myths and potential misconceptions about social media within the scientific community;
  3. Support researchers in developing individual goals for social media, identifying tools that meet their needs, and establishing a social media presence;
  4. Support community building among those within the UCSF campus community who are actively engaged in social media;
  5. Create a “starter kit” and related resources for other academic institutions interested in a similar effort;
  6. Develop a publicly available online resource featuring all UCSF Social Media Boot Camp for Scientists sessions;
  7. Launch a social media consultation service as part of CTSI’s Consultation Services program, which already offers expert advice for researchers in 18 subject areas.


The CTSI Communications team (Communications Director John Daigre, and Communications Manager Nooshin Latour) will lead the effort to establish a Planning & Implementation Team that includes UCSF communicators, researchers already active on social media, other universities, external Bay Area companies involved in social media, and others. UCSF University Relations has agreed to be a primary partner in this effort. Additionally, an important component of the project will be to enlist UCSF researchers to share their personal experiences, challenges, and successes involving social media.

All related events will be free and open to all at UCSF (ideally events will be available via webinars or similar for a broader audience).

The format of the Social Media Boot Camp for Scientists will be finalized with input from the Planning & Implementation Team. Events may be organized into one primary event (i.e. a one-day boot camp), or spread out over several months depending on feedback from organizers and partners.

Will consider piloting with other groups, such as K Scholars, as suggested in comments.

Examples of potential types of presentations and panel discussions:

  1. Marketing for Scientists: Thinking Beyond Self Promotion
  2. Understanding the Social Media Landscape
  3. Demystifying Social Media
  4. Social Media 101: Getting Started
  5. Twitter: It May Be More Than You Think
  6. Social Media Rules of Engagement: Risks and Rewards
  7. Social Media Advice for Physicians
  8. Making the Most of Videos and Podcasts (UCTV, iTunes, etc)
  9. Your Online Profile: LinkedIn, ResearchGate, UCSF Profiles and more
  10. Social Media Networking: What Tools Are Right for You?
  11. Academic Blogging
  12. Speaking with One Voice: Integrating Your Social Media Efforts
  13. The Future of Crowdfunding Science
  14. Altmetrics and Non-Traditional Research Impact Measures
  15. Using Social Media for Clinical Research Studies (suggested via commenting)
  16. Connecting with Other Researchers vs. The Public (suggested via commenting)
  17. Smart Social Media: Tools for Better, Faster Communication (suggested via commenting)


The UCSF Social Media Bootcamp for Scientists will:

  1. Support researchers’ efforts to achieve their individual goals (including career development, as noted in comments);
  2. Support community building on campus;
  3. Provide ongoing support (i.e. videos, consultation service) available to researchers interested in social media;
  4. Support amplification of UCSF’s brand as a preeminent health sciences innovator;
  5. Provide tools for other institutions to use in the development of similar events;
  6. Strengthen UCSF ties with external partners (i.e. Bay Area companies).

Metrics for Success: (TBD based on finalized event format)

  1. Participation of faculty/staff (~250+)
  2. Collaboration with UCSF faculty active in social media (~10+)
  3. Collaboration with campus groups (~10+)
  4. Collaboration with other universities (~1+)
  5. Collaboration with Bay Area companies (~3+)
  6. Satisfaction survey (75%+ satisfied)
  7. Other metrics TBD

Proposed Budget:

A proposed budget of $19,500 includes costs for coordination, meeting space, recording events, printing, promotion, incentives, guest speakers, etc.

Potential Collaborators:

- UCSF University Relations (confirmed via comments)

- UCSF Library (confirmed via comments)

- UCSF School of Medicine

- UCSF researchers active on social media (Bradley Voytek confirmed via comments)

- CTSI Online Learning (as suggested in comments)

- Other campus groups via UCSF Communicators Network

- Bay Area companies working with Social Media

- Other academic institutions

Commenting is closed.

Publicly Searchable Database of Recruiting Studies

Proposal Status: 

Publicly Searchable Database of Recruiting Studies


1.    Rationale

There are multiple sources for clinical trial listings at UCSF that are available to the general public via the web. These sources draw their information from the national ClinicalTrials.gov registration system that is required prior to recruitment into an interventional drug, biologic or device clinical trial. While this is a trusted source of clinical trials information there is significant opportunity for improvement with regard to how potential research participants locate, search, and receive accurate and information that will lead to informed interest and participation in research studies at UCSF. By limiting searches for UCSF clinical studies to clinical trials registered with ClinicalTrials.gov the major deficiencies include:

  • Registration is only required for interventional drug, biologic or device clinical trials – representing a limited proportion of all UCSF clinical research studies
  • Post-registration updates to recruitment status and contact information not required or enforced and are therefore often outdated
  • Summaries presented to general public are not presented in lay terms as derived directly from registration form

We feel that by creating a UCSF-centric listing with the public’s interest in mind that we can not only provide a valuable service to our patients and potential research participants, but can facilitate increased interest and enrollment into UCSF clinical research studies.


2.    Plan

We propose to incorporate a searchable database of recruiting studies at UCSF in a simple web-based format that is uniform and appropriately written for the general public while leveraging existing and planned participant recruitment resources. We will focus on the following approach in an effort to improve accessibility to information on recruiting clinical studies at UCSF:

  • Create a basic website with educational information on clinical research participation and a current listing of all UCSF studies that are recruiting, with GoogleSiteSearch functionality
  • Develop a structured template for describing clinical studies at UCSF in lay language and provide examples and best practices to researchers on how to describe their study
  • Obtain monthly reports from iMedRis of studies approved for participant recruitment; provide investigators with the template and notification of listing opportunity
  • Upon receipt of completed study description, provide editorial by medical writer for approval by investigator
  • Post study to website for search by the general public, including contact information for study staff
  • Provide monthly updates to website listings and contact information for study staff

3.    Criteria and Metrics for Success

Metrics include number of studies engaged and posted to website (interventional clinical trial vs. non), number of searches per month, number of studies accurately reflective of currently enrolling studies at UCSF per iMedRis as compared to ClinicalTrials.gov listings at quarterly time points.


4.    Approximate Cost and Justification

$44,000 for costs of web programming, search capabilities, 30%FTE medical writer and 10%FTE technical coordinator.


5.    Collaborators

iMedRis administrators, ISU


Commenting is closed.

Sharing Success - Making Open Proposals Self-Serve and Open Source

Proposal Status: 

Abstract. Develop an open source edition of the UCSF Open Proposals software suitable for deployment at external institutions. This will make UCSF's version easier to host and manage, enable other CTSAs to benefit from UCSF's work, and help establish UCSF's thought leadership in the field.

Rationale. In July 2012, CTSI launched UCSF Open Proposals, a web application enabling an open and collaborative community-based proposal submission process. The tool uses a crowdsourcing model to help researchers get valuable input on their proposal before submitting it to the review committee. It helps projects find collaborators, contributors, and advisers, and makes it easy for those with relevant expertise to offer feedback. Finally, it provides a stable platform for ideas even after the opportunity is closed, making it possible for the research community to link to, discuss, and build on previous ideas.

We see four fundamental technical limitations with the current Open Proposals system:

  1. The current version of the Open Proposals application was built in a way that’s very tightly integrated with accelerate.ucsf.edu, CTSI’s services portal. While this allowed us to launch faster, it prevents a standalone deployment, and makes upgrades more difficult.
  2. The design of the system requires the services of a professional web developer to create and configure even the most simple open proposals. This prevents CTSI from making open proposal deployment a turnkey process. At the same time, the system is mature enough at this point that it allows to customize each open proposal forum to fit the initiative-specific needs, at a relatively low cost (but it does require professional resources).
  3. The system is designed in a way where UCSF-specific authentication and identity data access mechanisms are baked directly in, instead of via an open pluggable process. This means that even if the software were to be shared with an outside partner, they would not be able to deploy it at their institution without removing and rewriting UCSF-specific code.
  4. The software is not open source. This prevents UCSF from sharing its work with outside partners, and makes it more difficult to discuss it in venues like the CTSA Toolshop. (At least one major CTSA partner has approached UCSF, wanting to know about the Open Proposals process and software.)

We propose developing a fully standalone open source version of the software, with a flexible authentication and identity backend which can integrate with solutions already in use at UCSF and other institutions. This will allow us to improve usability, maximize national impact, and pay off technical debt.

The solution would fully address limitations 1,2 and 4 and will be a stepping stone on the way to a turnkey solution described in #3.

In order to convert UCSF Open Proposals to a portable open-source product we need to make the following changes to the application:

  1. Allow system to stand alone by removing dependencies on accelerate.ucsf.edu
  2. Repackage the application to a distributable set of Drupal modules
  3. Implement support for any common network identity provider to support single sign on to the customer’s organization network
  4. Obtain approval from the Office of Technology Management to offer the product under a suitable open source license
  5. Enable external code contributions by hosting the code on an open source version management platform like Github or Bitbucket
  6. Ensure discoverability by listing the product and supporting user documentation on relevant repositories, such as Drupal.org Projects

In parallel, we will be working with several research institutions to find at least one external partner interested in pioneering Open Proposals at their organization, and help initiate a pilot Open proposal opportunity at their institution.

Criteria and metrics for success
This project will be a success if:

  1. An easy to deploy, standalone open source application is made available for the public via the established open source distribution portals
  2. UCSF is able to use the open source application to host its own Open Proposals instance
  3. The application is easy to manage. Application administrator can configure and activate a standard open proposal forum with reasonably low amount of professional assistance from web developer.
  4. An interested partner is found who is willing to pilot an open proposals opportunity at their organization
  5. The partner has installed Open Proposals product and successfully configured a test forum
  6. We receive satisfactory feedback on product’s usability and performance from the partner’s implementation team

Approximate cost and very brief justification
Estimated cost of development: $18,000. This includes anticipated development effort and about 10% contingency.  There may be additional cost of managing communications with the partner (TBD).

Cynthia Piontkowski – Web Producer, User Experience Designer, front end developer for UCSF Open Proposals
Brad Bulger – Drupal and Web Development Expert, Solution Architect, back end developer for UCSF Open Proposals
Anirvan Chatterjee – Solution Architect, Open Source Technology Expert

John Daigre - Communications Director
Oksana Gologorskaya – Product/Project manager, User Experience Designer


Commenting is closed.

Create Personalized Connections to Research Interests via the UCSF Research Participant Registry

Proposal Status: 


The UCSF Research Participant Registry (Registry) collects self-reported health information from volunteers and queries against study eligibility criteria for those investigators using the Participant Recruitment Service to enroll participants in their research studies via the Regsitry. This leaves a large gap of research studies that are not made readily available to potential research participants through this resource. For instance, a person may not have a specific condition for which they would appear in study-specific eligibility queries but are interested in a particular area, such as weight loss or nutrition studies. Simply asking Registry volunteers what they therapeutic areas or study types they are interested in doesn’t go far enough to close the gap for willing volunteers being connected to research of interest that could otherwise stimulate continued or expanded research participation.


Combining the resources of the Registry with the information on research at UCSF available in Profiles and the connectivity possible through outreach we feel we can close this gap. By providing Registry volunteers with a biannual feedback survey that specifically asks them which therapeutic areas or study types they have an interest in, we can then search UCSF Profiles and contact investigators to let them know of the willing pool of potential research participants whom they could then contact.



We propose to develop brief web-based surveys bi-annually to collect feedback from current Registry participants about their experience with the Registry- inquiring specifically as to what therapeutic areas or types of research they are interested in.

  • Identify investigators and researcher via UCSF Profiles that are conducting research in therapeutic areas identified in the survey.
  • Use the data collected from UCSF Profiles to contact researchers notifying them of potential research participants for their studies.
  • The PRS outreach coordinator will liaise between investigator and participants to providing excellent customer service and general information on research participation.
  • Utilize and integrate UCSP Profiles API 

Criteria and metrics for success:

  • # Registry participants that respond to feedback survey
  • # different therapeutic areas identified as compared to those using the Registry
  • # connections/referrals made between Registry participants and researchers
  • Inter-departmental collaborations and satisfaction survey among UCSF researchers


Proposed Budget:

$25,000 includes costs for coordination, survey development and implementation, submission to CHR, collecting survey responses and reporting, querying and reporting database information on UCSF Profiles and UCSF Research Participant Registry, integrating  outreach and communication efforts with UCSF investigators, connecting potential participants directly with investigators.


Potential Collaborators:

Participant Recruitment Service

CTSI Virtual Home (UCSF Profiles)

UCSF HRPP (iMedris) -as suggested by comments

Commenting is closed.