U24HG011853

DOCKSTORE: THE COMMUNITY PLATFORM FOR REPRODUCIBLE BIOMEDICAL WORKFLOWS AND APPLICATIONS - DOCKSTORE - A PLATFORM FOR CREATING, SHARING, PUBLISHING AND REPRODUCING COMPUTATIONAL SCIENCE FOR SCIENCE TO WORK ANALYSES, TOOLS AND WORKFLOWS MUST BE REPRODUCIBLE; REPRODUCTION IS ESSENTIAL TO BUILDING CONSENSUS AND CONFIDENCE, AND IMPROVING THE STATE OF THE ART.

A LARGE AND GROWING SET OF SCIENTIFIC METHODS ARE COMPUTATIONAL IN NATURE, AND WE CAN MAKE THESE COMPUTATIONAL METHODS EXACTLY REPRODUCIBLE. DOCKSTORE IS A REPOSITORY FOR SCIENTIFIC TOOLS AND WORKFLOWS THAT PROVIDES THE MEANS PRECISELY TO CAPTURE THE CODE, PARAMETERS AND OPERATING SYSTEM ENVIRONMENT THAT ARE NECESSARY.

FOR TOOL USERS IT MAKES IT EASY TO FIND A GIVEN TOOL AND THEN RUN IT PRECISELY AS THE AUTHOR INTENDED. IT IS POSSIBLE TO EXPORT A TOOL FOR USE IN A CLOUD PLATFORM, SUCH AS NHGRI ANVIL, WITH A FEW CLICKS, OR SIMILARLY EASILY DOWNLOAD IT TO AN INSTITUTIONAL COMPUTE ENVIRONMENT, OR EVEN A LAPTOP.

FOR TOOL CREATORS IT PROVIDES AN INTEGRATED SYSTEM TO PUBLISH VERSIONED SCIENTIFIC TOOLS WITH A CITABLE DIGITAL OBJECT IDENTIFIER (DOI), LINKING TO CONTAINERS, EXISTING CODE REPOSITORIES AND CAPTURING VITAL PARAMETER CONFIGURATION INFORMATION.

DOCKSTORE, PREVIOUSLY FUNDED BY AN R01 FROM NHGRI GRANT, HAS GROWN TREMENDOUSLY OVER THE LAST FOUR YEARS. IT NOW HAS THOUSANDS OF USERS, HOSTS HUNDREDS OF TOOLS AND WORKFLOWS, AND IS USED AS THE METHODS FOR MULTIPLE MAJOR PLATFORMS AND PROJECTS.

THOUGH NOT TECHNICALLY A RENEWAL, THIS PROPOSAL WOULD PROVIDE THE CORE FUNDING TO CONTINUE THE DEVELOPMENT AND GROWTH OF DOCKSTORE, WHICH IS A FULLY OPEN SOURCE PLATFORM ENTIRELY RELIANT ON GRANT FUNDING. THIS PROPOSAL WOULD GROW DOCKSTORE AS A RESOURCE TO MAKE IT A HUB FOR BROADLY SHARING COMPUTATIONAL SCIENCE.

THE AIMS OF THE PROPOSAL COVER FOUNDATIONAL INFRASTRUCTURE DEVELOPMENT (AIM 1), SUPPORT FOR SHARING NEW, POPULAR CONTENT TYPES (AIM 2), THE EXPANSION OF PUBLISHING FEATURES TO MAKE DOCKSTORE MORE BROADLY USEFUL (AIM 3), AND A STRONG FOCUS ON TRAINING AND OUTREACH (AIM 4).

THE INFRASTRUCTURE DEVELOPMENT OF AIM 1 WILL INCREASE THE SCALING AND ROBUSTNESS OF DOCKSTORE AND SUPPORT DOCKSTORE AS A SECURE, COMPLIANT RESOURCE, ENABLING IT TO SAFELY HOST PRE-PUBLICATION TOOLS AND WORKFLOWS WORKING WITH MANAGED ACCESS DATASETS. IT WILL INTEGRATE DOCKSTORE MORE DEEPLY WITH SECURE CLOUD PLATFORMS, SUCH AS THE NHGRI ANVIL.

THE EXPANSION OF CONTENT TYPES BY AIM 2 WILL, FOR EXAMPLE, MAKE IT POSSIBLE TO PUBLISH PROGRAMMING NOTEBOOKS ON DOCKSTORE. SUCH ARTIFACTS ARE WIDELY USED BUT NOT YET ROBUSTLY SEARCHABLE BY ANY SCIENTIFIC RESOURCE.

AIM 3 WILL BRING ORCID INTEGRATION, ALLOWING USERS TO AUTHENTICATE THEMSELVES AND THEN SIGN AND ENDORSE THEIR WORK, AND TO PROVIDE OPEN PEER REVIEW OF PUBLISHED TOOLS.

AIM 4 WILL FOCUS ON GROWING AND EDUCATING THE USER BASE VIA AN EXPANSION OF ONLINE TRAINING MATERIAL, WEBINARS, IN PERSON WORKSHOPS AND COLLABORATIONS WITH TRAINING FOR PARTNER PROJECTS USING DOCKSTORE. WE WILL ALSO FURTHER DEVELOP MEANS TO CONTINUOUSLY ACQUIRE USER FEEDBACK.

Santa Cruz University Of California

NHGRI SUPPORTS THE DEVELOPMENT OF RESOURCES AND TECHNOLOGIES THAT WILL ACCELERATE GENOME RESEARCH AND ITS APPLICATION TO HUMAN HEALTH AND GENOMIC MEDICINE. A CRITICAL PART OF THE NHGRI MISSION CONTINUES TO BE THE STUDY OF THE ETHICAL, LEGAL AND SOCIAL IMPLICATIONS (ELSI) OF GENOME RESEARCH. NHGRI ALSO SUPPORTS THE TRAINING AND CAREER DEVELOPMENT OF INVESTIGATORS AND THE DISSEMINATION OF GENOME INFORMATION TO THE PUBLIC AND TO HEALTH PROFESSIONALS. THE SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM IS USED TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM IS USED TO FOSTER SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION.

93.172 - Human Genome Research

National Human Genome Research Institute (NHGRI) [HHS - NIH]

Santa Cruz, California 950641077 United States

Single Zip Code

Genomic Community Resources (U24 Clinical Trial Not Allowed) (PAR-20-100)

Amendment Since initial award the total obligations have increased 421% from $931,342 to $4,849,671.