nih intramural database nidb

4) dailybackup Runs nightly and copies all files and directories older than 24 h to a backup location from which they can be archived onto tape, online, or other media. NiDB can act as a central repository or as a node in a data sharing network. The most important improvements that we sought to address were ease-of-use, including installation, maintenance, and end-user support. A mask is created using bet, and only the previously calculated value from in-brain voxels are averaged to create a PV SNR. Each system has its strengths and weaknesses, which we will examine in relation to NiDB's features. Cross-project sharing will appear the same to the user in either model, but we found it easier to extend NiDB's pipeline features using a subject-centric model. Regular users of NiDB interact exclusively with the web based frontend, which is designed using HTML5 and JavaScript so that web pages are viewable on any modern browser. Projects are defined as Institutional Review Board (IRB) approved protocols and are associated with subjects at the enrollment level. The site is secure. XNAT installation was challenging and a significant knowledge of Apache tomcat was necessary to modify and redeploy the database. Non-DICOM data can be uploaded manually on the imaging study webpage or can be placed in the incoming directory for the parseincoming module to pick up. The sites mission is to improve the efficiency and effectives of business processes and information access between research communities. Project, toolkit, and database of neuroinformatics ecosystem: A summary of previous studies on "Frontiers in Neuroinformatics". Poline JB, et al. The fourth issue is one of standardized data definitions when sharing. Packages installed include PHP version 5.3.3, MySQL version 5.1, Python 2.7, ImageMagick 6.8. NIH Natcher Conference Center (Building 45) The National Heart, Lung, and Blood Institute (NHLBI) under the National Institutes of Health (NIH) is set to host the 2023 NHLBI Annual Sickle Cell Disease Research Meeting. 5) datarequests processes all data requests submitted via the website. Manually uploaded images will then be processed in the same way as automatically uploaded images. A unique identifier (UID) is assigned to each subject in the database, regardless of what project they are enrolled in. NIH Budget and Spending data from past fiscal years. LORIS: a web-based data management system for multi-center studies. Pipeline variables, Fig. Projects will not be created automatically, if a study has no corresponding project, it will be placed in the Generic Project (999999). Single or multiple files can be stored in each series. . Backup can be performed by a server secondary to the main NiDB server. Animated GIF files are created from 3D and 4D DICOM volumes using ImageMagick. Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA. Improved optimization for the robust and accurate linear registration and motion correction of brain images. Based on pipeline criteria, each analysis is performed on all imaging studies that have not already been run through that pipeline. Progress can be achieved through this multilateral partnership that might not be possible or timely without the synergistic effect this organization of information can bring to efforts. Subjects are then enrolled in projects, and multiple imaging studies are attached to each enrollment. The goal of these awards is to foster new or expand existing collaborations across the NICHD intramural program, stimulate projects that would not be possible to undertake with existing intramural funding, and encourage collaborations between basic scientists and clinicians or population health researchers. eCollection 2022 May. This answer was returned in 10.02 s, calculated from a sample of 2,799 subjects (31.18 years +/ 18.29, 1,415 female), based on data processed automatically with FreeSurfer. During installation a universally unique identifier is generated using the MySQL uuid function and is exported along with the subject's information to identify the originating site for data. By default, all searches are cross-project, with the only limitation being access permissions. The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods. A decentralized model is used for data sharing, which allows for individual sites to share with other sites without interacting with a central repository. 2). Disclaimer. Query times otherwise were 3 s. NiDB query times are much shorter, and only approached 3 s for very large query results, the bulk of that time is spent on transferring data over the network to the client and preparing it for display or download. Compared to centralized data repositories, NiDB may be appealing because it allows researchers to share data with only researchers they want to share with instead of an open-ended sharing agreement. Six terabytes of raw data is stored on the servers and 2TB of data has been requested for download in the previous 20 months. 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These systems are often highly customized to a site's particular data and to the preferences of the labs that built the systems. Design of the databases was another key difference when compared to NiDB. ET. NiDB is designed to store as little protected health information (PHI) or personally identifiable information as possible, and only uses PHI to identify duplicate subjects. Neuroinformatics. The Report Catalog is a menu driven interface geared for the NIH familiar user to provide customized reporting. COINS query times were reported as 5 min for data not included in their caching system, and only data older than 1 day was cached (Scott et al. Pipeline specification screen. Each pipeline, if run, creates a specific directory within the imaging study on which it is being run. 2021 Sep 17;38:223-244. doi: 10.1016/j.jare.2021.09.005. Portions of the reports are viewable at NIH Intramural Database (NIDB), the NCI Funded Research Portfolio, and NIH RePORTER tool. A useful feature of NiDB is the automatic QC of MRI data. NiDB also allows projects to be private so they will not show up in search results if they user does not have access. or https:// means you've safely connected to the .gov website. David C. Glahn, Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA. Access to additional report sources on biomedical and behavioral research programs, clinical trials, as well as broader science-related information resources are also referenced. Inclusion of Women and Minorities in Clinical Research, Physician-Scientist Workforce (PSW) Report 2014, ACD Biomedical Workforce Working Group Data, Data Book: The NIH-Funded Research Workforce, Data Book: NIH Research Training Grants and Fellowships, Data Book: Research Career Development Awards, Data Book: National Statistics on Graduate Students, Data Book: National Statistics on Postdocs, NIH Collaborations with Other HHS Agencies, The National Academies: NIH-Funded Reports, The Modernized ClinicalTrials.gov Website Is Here, OLAW Publishes Final Guidance on Flexibilities for Conducting Semiannual Program Review, July 4 (Tuesday), 2023: NIH Closed for the Federal Holiday, Making a Difference in Human Subjects Research: Empowering Participants, Engaging Communities, and Protecting Data, Find Your Fit at NIH: Funding Programs by Career Stage, U.S. Department of Health and Human Services. The greatest increase was seen in those who had underlying cardiovascular disease. Data querying was found to be difficult with COINS, but because of performance and reliability reasons rather than granularity of search criteria. Would you like email updates of new search results? Each time the pipeline is saved, a new version of the pipeline is created, so even if a pipeline changes, the exact commands run on previous analyses will be known. Installation varied from complex to simple with existing databases. Additionally the frequency of adding modalities is rare. Imaging studies are defined as a period of time during which data is collected from a subject on a piece of equipment. The hierarchy for raw data is Subject Enrollment Imaging Study Series, which is similar to the picture archiving and control system (PACS) storage definition (Fig. A publically accessible version of NiDB is available under the Demo link on the main NiDB website (http://nidb.sourceforge.net). Subjects, enrollments, imaging studies, and series are created if they do not exist, otherwise they are archived with existing objects. Modules are launched from cron, and status is recorded in the modules table in the database. National Library of Medicine Current research projects address areas such as: This intense concentration on hearing research and its genetic causes has enabled NIDCD intramural scientists to make significant research progress on this priority for the NIDCD. The NIDCDs distinguished scientists and fellows work at the forefront of research on communication disorders. COINS offers a power-user mode to allow people to run SQL queries to answer questions such across all projects on the system, which subjects have a particular MR scan sequence. 2008; Mueller et al. Evidence from a small-scale clinical trial suggests that a variation of the advanced blood cancer immunotherapy known as CAR-T could be adapted to treat myasthenia gravis, an autoimmune disorder of the nervous system.The modified CAR-T therapy, short for chimeric antigen receptor T-cell, used by scientists offers the potential for a longer-lasting reduction in myasthenia gravis symptoms and . Published in The Journal of Medicinal Chemistry by Emma Gogarnoiu, Caleb Vogt and Amy Hauck Newman, et al. Types of Research Training Funding Opportunities, Research Training in NIDCD Laboratories (Intramural), Congressional Testimony and the NIDCD Budget, U.S. Department of Health & Human Services, Clinical Studies at the NIH Main Campus in Bethesda, Maryland, Trainingat the NIDCD Main Campus in Bethesda, Maryland, Auditory Development and Restoration Program, Section on Genetics of Communication Disorders, Section on Sensory Cell Development and Function, Section on Sensory Cell Regeneration and Development, Section on Sensory Physiology and Biophysics, The Integrative Neuroscience of Communication Unit, U.S. Department of Health and Human Services. Notifying a user that a particular search yields data within a project to which they do have access can be both useful and potentially troublesome for some projects. With minor changes, the MySQL database could be exchanged for any other RDBMS, so focus will be paid to the web-based frontend and scripting and compiled program based backend. A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN). NIDB. A digital diary of scientific discovery in the Intramural Research Program. Kennedy DN, Haselgrove C, Riehl J, Preuss N, Buccigrossi R. Neuroinformatics. The task was awarded using the CIO-SP3 SB contract vehicle. Recent progress by UNITE includes advancing funding opportunities and publishing the results of outreach to the broad biomedical and behavioral research community. and transmitted securely. While the test site's hardware is large, NiDB can run on any system that can run CentOS 6.x, including desktops or laptops. The process for adding new modalities was simplified, and a new modular backend system was created to allow user-defined modules, but more importantly to ensure that a failure or bottleneck of one module does not impact other modules. Many ideas incorporated into NiDB originate from outside the neuroimaging community, but the combination of these ideas into one package is unique and makes the software extremely useful for neuroimaging data management. Fig. Motion estimation is computed on 4D data, such as fMRI time series, using FSL's MCFLIRT (Jenkinson et al. When you visit a health care provider for the first time, you will often be asked what medications and supplements you take. We hope to expand the number of operating systems that the installer can use in the future. 2021 Jun 17;12:682495. doi: 10.3389/fpsyt.2021.682495. A Staff Scientist is a NIH employee generally appointed to a time-limited, renewable position, or in extremely rare situations, to a permanent appointment (for retention or recruitment purposes). Data can be anonymized as well as having the output and directory formats selected during the download. Book, Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA. Secure .gov websites use HTTPS First Established: Wednesday, May 2, 2007. NiDB's peer to peer sharing of data is a novel application of the technique applied to neuroimaging data. A brief description of each module is as follows: 1) parsedicom archives all DICOM files received through the DICOM receiver. A large clinical trial found that daily multivitamins led to modest improvements in memory over a three-year period in older adults. 2012). Watch IRP researchers provide a quick taste of their scientific projects. This site needs JavaScript to work properly. In the process of creating a database that satisfies our local needs, we were able to create a database that we believe will satisfy many needs of other researchers and research groups, and solves some of the challenges to data sharing posed by the INCF. Project enrollment is also determined by checking the StudyDescription (0008,1030) DICOM tag. See how were doing it and more. ET DeWitt Stetten Jr. Lecture Genomic epidemiology has enabled critical insights during the COVID-19 pandemic. Object hierarchy of NiDB, showing, Fig. Marcus DS, et al. Depending on search type, results will be displayed as an HTML table, offered as a comma-separated value (csv) file, or displayed with checkboxes to allow downloading of data. Bethesda, MD 20894, Web Policies COINS contrasts this by offering no installation, since the database is hosted at the Mind Research Network. Both thumbnails are generated for every series, are displayed along with series information on the NiDB website and are provided to give a quick glance at the data so users can see gross motion or artifacts. These central repositories and consortiums do an excellent job of packaging large volumes of data in a consistent and understandable way. Das S, et al. Other than SQL table definitions, the middle tier is standard and the configuration is similar to many other web-based applications. Multi-site studies needed common databases to manage the data, and these were also often home-grown systems specific to the study under which they were developed. UNITE continues its commitment to fulfill NIH's pledge to identify and address structural racism where it may exist within the agency and the institutions it supports. As Acting DDIR, Dr. Schor will lead the NIH Intramural Research Program (IRP) and facilitate coordination and collaboration among the 24 NIH institutes and centers that are a part of NIH's distinct research community. Data request options such as DICOM anonymization or format conversion may take more time to process. For time series data, a mean intensity plot is calculated using FSL's fslstats function, as well as a mean temporal image, and variance of temporal image. The task was awarded using the This content is for members only. eCollection 2012. Since then, more than 600 million doses of the vaccine have been used to treat polio outbreaks in 28 countries. Clipboard, Search History, and several other advanced features are temporarily unavailable. A 7 character alphanumeric unique identifier (UID) format was chosen to allow large numbers of subjects, but also to make remembering and transcribing easier. eCollection 2021. The Laboratory Managers Interest Group was formed in June of 2003 to serve as an advisory group for NIH activities that impact research laboratory operations, share best practices for managing lab operations and resolving problems, and serve as a forum for professional development by hosting seminars and workshops on integral laboratory and NIH .

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