CTSA Tool Shop
The CTSA Tool Shop is a monthly webinar series hosted by C4 on behalf of the CTSA Consortium.
- Have you created novel tools to support research initiation, conduct, tracking, reporting, or other operational aspects of your CTSA?
- Might other sites benefit from using these tools?
- Can your tools be shared?
If so, C4 wants to help you introduce these tools to other sites for potential adoption.
This webinar series will focus on a single tool each session, highlighting its features and benefits, and how it can be transported and installed at another site.
Interested in giving a webinar? We ask that you post your tool on the Tool Awareness page first allowing you to share your tool with the consortium immediately, even before conducting your webinar. Once posted the Project Owner can request a webinar at any time.
EMERSE is a user-friendly search engine designed to help users search through the free text (e.g., dictated/typed) clinical notes in an electronic health record system. It provides numerous features to ensure efficient and reliable search results, including synonym suggestion, and the ability of searching in a case-sensitive manner (e.g., for distinguishing the cancer 'ALL' from the generic word 'all'). EMERSE has been in use at the University of Michigan since 2005 and has supported hundreds of IRB-approved studies. It is being used for cohort identification, data abstraction, as well as other quality improvement and hospital operational tasks. EMERSE should be able to work with documents from any type of medical record system. At the University of Michigan it searches documents from our legacy home-grown EHR as well as Epic. We have also built a plugin for the i2b2 Workbench so cohorts identified in i2b2 can automatically be sent to EMERSE for further searching.
BAT - Bleeding Assessment Tool
Graduate Tracking Survey System (GTSS)
Harvard Catalyst Profiles Research Networking Software
MURDOCK Study Community Registry & Biorepository
Optimizing the Practice of Mentoring
PRISM Online Training
Rapid Response Team Grant Proposal
Research Participant Registry
ShareCenter and CTSAconnect
TIES (Tissue Information Extraction System)
The MURDOCK Study Community Registry & Biorepository | July 18, 2014 at 11:00 am ET
The MURDOCK Study Community Registry and Biorepository of the Duke Translational Medicine Institute, a CTSA institution, is a valuable resource that enables the following: (1) population characterization with data on demographics, environmental exposures, and personal and family history of disease and banked samples; (2) linkage to electronic health records (EHRs) for more comprehensive information about patient diseases and treatments; (3) support of longitudinal health services and epidemiological research; (4) recruitment of volunteers into clinical trials, validation studies, and other epidemiologic studies; and (5) a research infrastructure that will accelerate sample and data collection. Opportunities for partnership are available with the MURDOCK Study including, but not limited to, access to samples and data as well as patient populations who have consented to be contacted for future studies and a site network available for the implementation of clinical research studies.
The online RRT Grant Proposal Management Software System is tailored for time and people management. This online tool includes automated, clear task assignments with deadlines and messaging (email notifications) for both scientists and grant administrators to ensure that key scientific and administrative tasks are completed at the optimal time. The system also includes shared document functionality to provide easy access to and storage for files and from which collaborators can access current versions of documents without digging through email and worrying about editing versions that are not current and month-formatted calendars with actions due for a given grant will be available to all of the team members involved in specific grant responses. The system is extremely customizable and can be altered to fit all grant proposals/projects.
PRISM Online Training is an hour-long Web-based workshop that helps researchers and other health care professionals use clear, audience-centered language in consent forms and other print materials for patients and study subjects. The training is based on well-documented health literacy principles and includes: back ground information on health literacy and readability, a detailed overview of plain language writing and editing strategies, before-and-after examples, editing exercises, and links to other helpful resources. The training is in the public domain and has reached more than 1000 users to date, with more than one-third completing a course evaluation and providing consistently high ratings. The National Institutes of Health, the Centers for Disease Control and Prevention (CDC), and Health Literacy Missouri are among dozens of organizations nationwide that drive traffic to PRISM trough links on popular resource pages.
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Open Proposals - UCSF has successfully experimented with using crowdsourcing tools to transform the process of generating ideas and building teams. We have taken the standard black box approach to the review and selection of proposals and reshaped it by adding a new pre-competitive phase that is open and collaborative.This open improvement phase allows the crowd to critique and build off others' ideas. The approach and accompanying tool (called 'Open Proposals') are now being assessed for readiness to share with other institutions.
Optimizing the Practice of Mentoring - The University of Minnesota Clinical and Translational Science Institute has developed a free, online, professional development course designed to prepare faculty in higher education to be effective research mentors for junior faculty, post-doctoral fellows, and graduate students. Content is organized into five modules that cover mentoring models, mentor roles and responsibilities, structure and dynamics of the mentoring relationship, and strategies for facilitating, and addressing challenges to, the mentoring process. The self-guided course (minimum of 90 minutes to complete) engages learners through text, audio, mini-presentations, self-assessments, and other interactive activities. Learners can proceed through the five modules sequentially or as self-selected topics to explore, with the option to stop and return to the course at any time. At the end of course, learners complete a Mentoring Action Plan and a Course Improvement Survey, and gain access to a mentoring toolkit containing helpful resources, including all those referenced during the course.
ResearchMatch has a simple goal - to bring together groups of people who are looking for one another: (1) people who are trying to find research studies, (2) researchers who are looking for people to participate in their studies, and (3) foundations / advocacy groups working to help individuals and families affected by specific medical conditions.. It is a free and secure registry that has been developed with input from major academic institutions across the country who want to involve you in the mission of helping today's studies make a real difference for everyone's health in the future.
Rockefeller University Bleeding History Phenotyping Tool and International Society on Thrombosis and Haemostasis Bleeding Assessment Tool (BAT) involves two electronic instruments which are available for obtaining standardized bleeding histories from individuals enrolled in a research study.
CR-Assist is designed to help ACTSI investigators/coordinators manage participants, track study visits and submit electronic appointment requests to our Clinical Research Site (CRS) schedulers, and print sample collection labels. Some of the features of the application are listed below. Excel-like participant lists which allows users to add/edit/sort/lookup participants with their visit information Study Calendar to help you plan your team's activities Realtime CRS availability calendar Electronic submission of CRS appointment requests and receipt of pager/email notification on the status of appointment Generation of recruitment report Data export to Excel for generating mailing labels and contact list Secured access from anywhere with internet connection
GATACA uses a vast array of data and knowledge to enable a user to build a model of a disease or disease area based on-genetic associations and abnormalities associated with clinical abnormalities. Enables systems medicine via systems biology
muStat (U-statistics for multivariate Data) provides a Web interface where investigators can upload multivariate data, e.g., from genome-wide expression and association studies, to a grid of several hundred computers for analysis using novel statistical approaches based on u-statistics for hierarchically structured data.
We would like to present an open-access research networking system called CUSP - Columbia University Scientific Profiles. CUSP allows anyone to search for CUMC people, departments, grants, and publications. CUSP can also visualize co-author or co-investigator networks in Google Earth. The CUSP profiles are updated on a monthly basis using PubMed and Columbia University's grants databases. We are also developing and pilot testing web services for selected schools to help them display current CUSP faculty profiles on their departmental web sites. In this way, faculty members can receive automatically updated PubMed publications from CUSP without manually updating their new papers.
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SMART Teams provide an innovative way to communicate the science of a CTSA to the surrounding community. In the SMART Team programs, a small team of high school students and their teacher work closely with a CTSA researcher to develop a physical model of a protein that is being investigated in the lab. While developing the model, the students read an original research paper and come to understand that science is a process whereby real people -- not unlike themselves -- come to understand an invisible molecular mechanism. The physical model that results from these modeling projects become useful communication tools that are used by the researchers to tell the story of their research to others.
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openSESAME (Search of Expression Signatures Across Many Experiments) is a web-based tool for using patterns of gene expression to discover relationships between experimental conditions, diseases, or biological states. openSESAME is unique in that it identifies connections between datasets based on expression patterns alone, without the need for prior knowledge of experimental groups or phenotypes. This web server is an interface to allow the scientific community to perform openSESAME queries using a repository of over 75,000 Affymetrix human gene expression profiles obtained from the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). A gene expression signature (sets of genes that are expected to be coordinately induced or repressed) is used as input, and openSESAME returns a list of datasets in which these genes are coordinately differentially expressed, as well as plots (heat maps) of the expression of the signature genes in these datasets.
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Harvard Catalyst Profiles Research Networking Software | February 15, 2013
Profiles Research Networking Software is an NIH-funded open source tool to speed the process of finding researchers with specific areas of expertise for collaboration and professional networking. Profiles RNS imports and analyzes "white pages" information, publications, and other data sources to create and maintain a complete searchable library of web-based electronic CVs. Built-in network analysis and data visualization tools allow administrators to generate research portfolios of their institution, discover connections between parts of their organization, and understand what factors influence collaboration.
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CES4Health.info is a free online tool for peer-reviewed publication and dissemination of products of community-engaged research that are in forms other than journal articles. Nearly every CTSA is producing such products - videos, training manuals, policy reports, curricula, digital stories, etc - and CES4Health.info is designed to have them "count" towards promotion and tenure if faculty are co-authors and get them into the hands of academics and community members who are working on similar issues and don't have to reinvent the wheel. The presenter is Cathy Jordan, Editor of CES4Health and faculty with the U of Minnesota CTSA; one of the products published through CES4Health is a community-engaged research curriculum developed at the U of Minnesota.
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The main Registry goal is to aid investigators with recruitment and to promote a research-informed community of potential research participants. The Registry will ultimately ask every patient who uses an outpatient service at UPMC, or who uses UPMC HealthTrak, if they would be interested in learning about research, and in being contacted to learn more about specific studies that may be of interest based upon medical record information and/or preference of health interests. The logistics of the Registry involve the consenting of patients by the clinical registrars or through UPMC HealthTrak (MyChart), matching patient ICD-9 codes in their medical records with inclusion/exclusion criteria for specific research studies, and contacting patients through a central Registry office. The Registry also includes individuals from the general community in Western Pennsylvania who are matched with studies based upon their stated preference of health interests. The goal of the Community Registry is to provide community members opportunities to receive educational materials about clinical research and to receive their permission to be contacted for study recruitment.
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CORES is a highly configurable, enterprise-wide software solution for research institutions which provides full central oversight while also allowing for flexible but consistent decentralized billing and usage functionality for core facilities.
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WebCAMP is a continually evolving ColdFusion-based system that has been developed to support various operational/administrative needs of CTSAs and other centers that provide resources to a broad spectrum of research studies. It has been available in the national community since approximately 2005 and grown steadily in its support of CTSA institutions since 2006. Its primary functions are protocol authoring/submission and review, utilization and regulatory tracking, billing, progress reporting and investigator surveys, and CTSA annual reporting.
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Science Exchange is a web-based platform to help researchers efficiently find and access research core facilities.
Since launching in August 2011, Science Exchange has gained significant traction in the US with core facilities from over 200 research institutes using the free platform to help get additional work and track usage of their facilities. The free software significantly reduces the administrative burden of managing core facilities and ensures payment from core facility users, reducing the amount of accounts receivable owed to facilities. Science Exchange software is free for facilities and researchers, the business model is based on a 5% transaction fee for facilitating payment across institutions.
Please join the webinar to learn more about Science Exchange and help create a centralized portal for efficient access to research and core facilities.
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The Graduate Tracking Survey System (GTSS), a web-based electronic questionnaire pre-populates the graduate's information on publications, clinical trials, grants, and patents by downloading the information in standardized format from public databases, which simplifies completion for graduates, insures a uniform format of important information, and facilitates aggregation of data.
The GTSS obtains information on whether trainees go on to improve human health, as well as related surrogate indicators of career development, and it is applicable to all training programs involving translational scientists. The Initial and Annual Survey are supported by a web-based system created by the Rockefeller University CTSA using open source technologies. When a graduate enters the web-based survey, she or he finds pre-populated fields for publications, grants, patents), and participation in clinical protocols, and need only confirm that the information from these sources is correct instead of entering the data manually.
If adopted broadly, the GTSS has the potential for aggregating standardized CTSA-wide data training for reporting to NIH and the public, providing benchmarks for assessing the success of individual training programs, and identifying opportunities to improve training programs.
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StudySearchTM is a web-based application designed to provide an easily readable publicly accessible searchable listing of IRB-approved protocols that are accruing study subjects. It was developed by the Regulatory Support and the Biomedical Informatics Cores of the Center for Clinical and Translational Science (CCTS) at The Ohio State University. Postings include basic descriptive information: study title, purpose of the study, eligibility criteria, and study personnel contact information. Any language concerning benefits and/or inducements are not included; therefore, while IRB approval for a study to be listed on StudySearchTM is required, IRB approval of the posted language is not. Studies are listed by one of two methods; one automated and one manual: (1). Studies registered on ClinicalTrials.gov with OSU-related location terms, are automatically downloaded at the beginning of each month; or (2). Studies are submitted directly by researchers to the CCTS Regulatory Core staff.
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The IRBshare System is a new shared IRB review model for multi-site studies comprised of Participating Institutions utilizing Shared Review Documents and a Shared Review Process, supported by a centralized, secure web portal and the IRBshare Master Agreement ("IMA"). IRBshare aims to optimize human research protections through building trust, enhancing communication, and sharing best practices between IRBs nationwide.
Presently, and based on extensive input from the OHRP, IRBshare is pertinent to only new multi-site studies funded by the National Institutes of Health (NIH) and undergoing the initial round of reviews conducted by the respective participating IRBs, inclusive of amendments to the protocol occurring during this initial review period.
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TIES (Tissue Information Extraction System) is an open-source, end-to-end system to de-identify, structure, code using controlled terminologies, and retrieve free-text pathology reports associated with bio-specimens. The tool enables users to query and analyze a large document repository, to use these documents to identify and obtain tissues for research, and to collaborate with other researchers. The tool is built on a foundation of research compliance, and provides template processes and policies for deployment.
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NUCATS Assist has been used at Northwestern to run more than 30 internally sponsored competitions, including young investigator awards, shared resource awards, and foundation awards. It is highly configurable and supports an NIH-style competition review process.
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PRISM supports the execution of multivariable prediction models with patient-specific characteristics so that personalized estimates of outcomes, often as a function of alternative treatments, can be generated within the routine flow of patient care. This can support evidence-based, shared medical decision-making to improve the safety, outcomes and cost-effectiveness of care. The current application is in the setting of generating individualized informed consent documents for PCI. However, the tool can support that translation of novel biomarkers, genetics and pharmacogenomic interactions into clinical care.
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eagle-i - Groundbreaking biomedical research requires access to cutting edge scientific resources; however such resources are often invisible beyond the laboratories or universities where they were developed. We have built a national research resource discovery platform that will help biomedical scientists search for and find previously invisible, but highly valuable, resources.
Open network. Open access. Open source.
After two years of intensive development, eagle-i is ready to leave the nest. The free software is now an open source project, and we welcome institutions to adopt it and participate in the network. The data in the system is also now open access; anyone — regardless of affiliation — is welcome to sign up for an account, or to download the Linked Open Data directly.
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SPARC (Services, Pricing, & Application for Research Center) is a web-based research management system that provides a one-stop-shop to researchers and their study teams to browse services and submit service and pricing requests to research service providers with a focus on billing compliance and proposal and budget development. Upgrades in process include work fulfillment data collection, invoicing and billing features, and outcome metrics using grant and publication data.
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ShareCenter and CTSAconnect | August 10, 2012
CTSAconnect Fact Sheet
CTSAconnect Questions and Answers
ShareCenter Fact Sheet
ShareCenter Questions and Answers
Give. Get. Do.
CTSA ShareCenter is a Consortium-wide resource that supports organic sharing across boundaries. It exists to reduce knowledge fragmentation and wasted effort. CTSA members and groups can use ShareCenter to seek help, share resources, and collaborate. Groups can be created and managed easily, discussion threads can track any subject, and CTSA members can find and follow one another. ShareCenter offers one-click synchronization with VIVO and LinkedIn, easy searching and tagging, and integration with CTSAconnect.
Reveal Connections. Realize Potential.
CTSAconnect addresses the problem of information fragmentation by coalescing the VIVO and eagle-i ontologies to create an Integrated Semantic Framework (ISF). The ISF is not a tool in itself — rather, it facilitates the production and consumption of Linked Open Data. CTSAs can use the ISF to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. Three example uses: (1) Find investigators who are best positioned to work on a drug-repurposing project, (2) Identify patient cohorts based on clinician expertise and encounter patterns, (3) Improve a renewal application by supporting better alignment and analysis of data on the outcomes of research investments.
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FURTHeR is a clinical cohort search tool used to search across the University of Utah clinical data warehouse and the Utah Population Database for people who satisfy various criteria of the researchers. It uses the i2b2 front end but has a set of terminology servers, metadata servers and federated query tool as the back end systems. FURTHeR does “on-the-fly” translation of search terms and data models across the source systems and returns a count of results by unique individuals. The set of databases that can be queried is currently being extended.
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cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source natural language processing system for information extraction from electronic medical record clinical free-text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context (family history of, current, unrelated to patient), and negated/not negated. The tool has been developed and deployed at Mayo Clinic since early 2000.
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