It will exit and disable the pipeline after submitting ten jobs successfully. The three-day conference, which will take place both in-person and online, offers a platform for researchers, health care providers, and other stakeholders who are interested in . Each system has its strengths and weaknesses, which we will examine in relation to NiDB's features. 2012). She will replace Michael M. Gottesman, M.D., who served as NIH DDIR for the past 29 years. When other sites download shared data, they can import it into their own database, examine the raw data, or import it into their own installation of NiDB, from which they can query, aggregate, and perform pipeline analyses. FOIA HHS Vulnerability Disclosure, NLM Support Center First and foremost is to be included in the NIH Intramural Database as a way to demonstrate progress and track dollars spent per research project. 3) mriqa Performs basic QC of MRI data including SNR calculation, motion correction, and motion estimation. Bookshelf Book GA, Meda SA, Janssen R, Dager AD, Poppe A, Stevens MC, Assaf M, Glahn D, Pearlson GD. COINS contrasts this by offering no installation, since the database is hosted at the Mind Research Network. As new MRI QC metrics are added to NiDB, those metrics are not automatically generated for existing series, only for new series. NSF National Center for Science and Engineering Statistics. Front Psychiatry. The NIH intramural sourcebook is a compendium of policies and resources for the NIH scientific research community. Animated GIF files are created from 3D and 4D DICOM volumes using ImageMagick. The https:// ensures that you are connecting to the An imaging study may include the collection of an MRI, an EEG, eye-tracking session, or any other data. 2012). This necessitates the recreation of all existing QC metrics to create the new metrics. A significant amount of work is required to organize diverse sets of data. 3. The NIH Intramural Database collects and disseminates information about research being performed in the Intramural Programs of the Institutes and Centers of the National Institutes of Health. Neuroimaging data sharing on the neuroinformatics database platform. To that end, the Research Portfolio Online Reporting Tools provides access to reports, data, and analyses of NIH research activities, including information on NIH . While the test site's hardware is large, NiDB can run on any system that can run CentOS 6.x, including desktops or laptops. NiDB maintains as little PHI as possible, using only the amount necessary to uniquely identify a subject. 7) pipelinetest processes any pipelines which have a testing flag set. Keator DB, et al. NiDB's approach to sharing is to allow all sites, small and large to share their data with any other site, in a peer to peer manner. In their latest study, the researchers created modified oral vaccines that target the other two polioviruses, types 1 and 3. Most neuroimgaging data imported into NiDB will be in DICOM format received from an MRI scanner in real-time, however any modality DICOM data can be imported into NiDB. Queries on NiDB perform well in almost all instances for general work, but performance for massive queries, such as those for analysis results can take time. The most important improvements that we sought to address were ease-of-use, including installation, maintenance, and end-user support. ExPORTER creates downloadable versions of the raw data for all research projects found in the RePORTER database for individual use and analyses. With minimal investment in time and resources, this model elevates data shared from a small one-person lab to the same level as data from large centers. First Established: Wednesday, May 2, 2007. Few support questions have been asked, but questions that have been asked are mainly related to installing NiDB on a non-CentOS 6.x platform. eCollection 2021. The format of 4 numbers followed by 3 letters (ex S1234ABC) is based on the license plate numbering used in several US states. Data sharing has traditionally been done through personal partnerships, but more recently large consortia such as LONI-IDA, BIRN, INDI, COINS NITRC-IR have sought out sources of data, packaged, and distributed them. ET DeWitt Stetten Jr. Lecture Genomic epidemiology has enabled critical insights during the COVID-19 pandemic. Direct links to the most widely used resources are below. Most fMRI tasks have a behavioral data file recorded during scanning, and these files can be uploaded manually to be associated with existing MR image series. Share sensitive information only on official, secure websites. Manually uploaded images will then be processed in the same way as automatically uploaded images. According to staff at the NIH Intramural Database (NIDB), 78.1 percent of NCI's publications were in compliance with the NIH Public Access Policy for fiscal year 2014. the contents by NLM or the National Institutes of Health. The correlation matrix embedded in the search results is provided because it provides a quick glance at the data to see if the results are sensible, however more in-depth analyses would be more appropriate for the second level pipeline. Included in the installer is the current version of NiDB web pages, Perl modules, database definition, and configuration files. No PHI will be received at the receiving site, but the MD5 hash will ensure that if a subject with duplicate name and date of birth exists, this duplicate will be flagged and the user can manually intervene to determine the nature of the duplication. Intramural Research Training Award (IRTA) Hiring Mechanism for Postdoctoral, Pre-Doctoral, Post-Baccalaureate, Technical, and Student IPDs. Neuropsychol Rev. A graphic depiction of some major funding mechanisms, and activity codes gives a hierarchical view of project organization. LORIS provides an installer for the LORIS code, but requires manual installation of the LAMP stack. XNAT: A software framework for managing neuroimaging laboratory data; organization for human brain mapping annual meeting; Toronto. The lack of databases was partly due to user focus on analysis methods over the organization of the data, and partly due to the complex and heterogeneous nature of neuroimaging data. Design of the databases was another key difference when compared to NiDB. NIDB. NiDB began as a repository to replace a DVD archiving system for MRI data. The task was awarded using the CIO-SP3 SB contract vehicle. SNP analysis using plink also requires a common file, which is only on the order of 20MB depending on the number subjects in the sample, so this file is stored along with each subject's SNP data (Purcell et al. Visit Website Making the QC system modular would allow new metrics to be created and stored independently. Query performance for searches of approximately 1,000 items at all hierarchy levels (subject, imaging study, series, pipeline analysis) was 1 s or less (Fig. Book, Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA. To add other quick analyses, like the correlation matrix, the search.php page could be edited and a function inserted to parse the existing search results prior to display. The NIH Intramural Database collects and disseminates information about research being performed in the Intramural Programs; Visit Website; Search the Sourcebook. Object hierarchy of NiDB, showing the subject-centric model, Fig. Gregory A. 2. Packages installed include PHP version 5.3.3, MySQL version 5.1, Python 2.7, ImageMagick 6.8. eCollection 2021. The purpose, participate requirements, location and contact details about each trial is available. Before 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. Studies on frequency of same-name/same-date of birth are uncommon, however a study by the Brennan Center for Justice found that only 289 of 3.6 million votes cast in New Jersey in the November 2004 elections were likely duplicates based on the same name and date of birth (McDonald 2005). Data can be anonymized as well as having the output and directory formats selected during the download. Features and ideas for the Neuroinformatics Database were conceived by many individuals over the course of its development. When downloading any type of data, the directory names by default contain the date and time of the scan, but this can be changed to only the subject UID. Our goal is to cultivate a workforce that better reflects the diversity of the U.S. population itself in order to most efficiently pursue the NIH mission. Imaging studies are defined as a period of time during which data is collected from a subject on a piece of equipment. Instead of the traditional method of having each site analyze a single modality of data, such as site A analyze MRI and site B analyze genetics, each site can analyze their own data or verify data from other sites. Backup can be performed by a server secondary to the main NiDB server. Front Neuroinform. This 8 (a) small business, with capabilities including IT infrastructure engineering and support; development and integration; and IT management and strategy, has been awarded a 3-year contract to support the National Institutes of Health CCR, the largest division of the NCI intramural research program comprised of nearly 250 basic and clinical . Within each imaging study are attached imaging series. Poline JB, et al. 1. Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA; Database, Neuroinformatics, Neuroimaging, Pipeline. The term frontend refers to any software with which a user has direct interaction, and backend refers to software which the average user does not directly interact with through web pages or command line. Simply selecting a year and an IC (or "All ICs") and entering a search term yields a list of related researchers and their projects. Lectures occur on most Wednesdays from September through June and begin at 2 p.m. Earlier this month, NIAID reissued the notice of funding opportunity (NOFO) NIAID New Innovators Awards (DP2, Clinical Trial Not Allowed).Rather than soliciting research on a particular scientific topic, this NOFO seeks investigators at a particular career stage; specifically, postdoctoral and other candidates in non-independent positions or newly independent investigators. The primary site for NIDB development has to-date stored 9,123 unique subjects with 19,594 imaging studies, in 139 projects, with 16,243 project enrollments. Front Neurosci. Accessibility 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. This real-world example shows the probability of same-name same-DOB to be 0.008 % in a sample of 3.6 million. 2005). Epub 2015 Apr 16. Beth M. Anderson, Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA. Basic information is extracted from the DICOM header such as patient weight, series description, series date time, and other modality and image specific parameters and recorded in the database. NiDB is primarily an imaging database, so PHI is used as little as possible, and in this case PHI is used solely to ensure data integrity. NiDB not only simplifies the local storage and analysis of neuroimaging data, but also enables simple sharing of raw data and analysis methods, which may encourage further sharing. However, it is possible to add modalities easily, which only involves adding a table, and this process could be automated with a web-based tool. XNAT provides a substantial vetting process for data before making it available to users, and COINS focuses on maintaining a large amount of data from different sites in a central location. National Library of Medicine 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. FSL is required for MRI QC and instructions are provided for the user to install the package. An increasing number of imaging centers have created a massive amount of neuroimaging data since fMRI became popular more than 20 years ago, with much of that data unshared. We fulfilled those requirements and in the process created a powerful database that other laboratories may find useful. Imaging studies can have multiple analyses run on them, but can only have one of each analysis run. Direct links to the most widely used resources are below. 2007; Scott et al. NiDB was developed at Hartford Hospital for the Olin Neuropsychiatry Research Center to store and manage multiple types of data analyses. We would like to show you a description here but the site won't allow us. 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Other than SQL table definitions, the middle tier is standard and the configuration is similar to many other web-based applications. 2008). An installer is provided to copy the NiDB files to their destinations and to configure and install requisite software. An official website of the United States government. Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA. This path becomes the analysis root directory, with all other analysis directories descendent from that. Data request sizes are frequently on the order of 100MB, but 100GB+downloads have been requested. Since XNAT's release, there are now a few large players in the neuroimaging database community such as LORIS, HID, and COINS (Marcus et al. Interactive 3D viewing of FreeSurfer surfaces can also be viewed using xtk, which offers more display options such as displaying multiple surfaces and changing surface colors. Other result display formats are available including: pipeline results, which shows images or values from pipeline analyses; longitudinal studies, which displays subjects which have had more than one imaging study for the specified search criteria; and debug mode, which displays the SQL statement used for the search without running it. NiDB not only simplifies the local storage and analysis of neuroimaging data, but also enables simple sharing of raw data and analysis methods, which may encourage further sharing. The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods. An official website of the United States government. The National Science Foundation (NSF) is an independent federal agency created by Congress in 1950.With an annual budget of about $6.9 billion (FY 2010), NSF is the funding source for approximately 20 percent of all federally supported basic research conducted by America's colleges and universities. A publically accessible version of NiDB is available under the Demo link on the main NiDB website (http://nidb.sourceforge.net). NiDB is built using open-source software and standard web application methodology, but it is closely tied to the operating system, requiring significant OS level configuration. 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. 2011; Keator et al. A decentralized model is used for data sharing, which allows for individual sites to share with other sites without interacting with a central repository. 2016 Jan 1;124(Pt B):1089-1092. doi: 10.1016/j.neuroimage.2015.04.022. Several MRI QC metrics are computed on data after archiving and are available to view on the website within 5 min after a series completes on the MRI scanner. NiDB was publically released on NITRC (http://www.nitrc.org/projects/nidb) and on SourceForge (http://nidb.sourceforge.net) in 2012, and to date have had 287 downloads in various formats and versions. Tracy Johnson, Ph.D. The third concern is over technical issues of data sharing, which NiDB solves by making the sharing process as simple as clicking export at the sending site and import at the receiving site. The Report Catalog is a menu driven interface geared for the NIH familiar user to provide customized reporting. The NIH Directors Wednesday Afternoon Lecture Series (WALS) is the highest-profile lecture program at the NIH. A DICOM receiver (dcm4che) is provided to run on the NiDB server to receive and store all DICOM images in a directory in preparation for NiDB to archive the images (Zeilinger 2013). The RAMB provides care and housing for rodent and aquatic species housed within this restricted-access, disease-free animal holding facility. Creation of new modalities is not as simple as would be preferred. If performed by an individual with Linux experience, NiDB can be installed and functioning within 1 h. The development site installation of NiDB runs on mirrored Silicon Mechanics servers, each with sixteen 2.4GHz cores, 12GB RAM, and 40TB disk space in a RAID6 configuration. Accessory modules are available such as parsevideo, which converts video files to ogg vorbis (www.vorbis.com) to allow inline viewing in the webpage. 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. A mask is created using bet, and only the previously calculated value from in-brain voxels are averaged to create a PV SNR. Within each imaging study, data is contained in ordered series. Subject data can then be recombined into a single file when downloading from NiDB, which allows only selected subjects to be included in the analysis. The task was awarded using the This content is for members only. The pipeline specification on the web interface has three parts: 1) basic information such as pipeline name, and whether it's a first or second level analysis 2) data specification including the exact series protocol names and details about where to store the data, and 3) the pipeline script to run. An example would be to answer the question, How do cerebral ventricle sizes correlate with age? By checking a box on the search page, a correlation matrix is added to the pipeline results display, so that question can be answered immediately (Fig. COINS: an innovative informatics and neuroimaging tool suite built for large heterogeneous datasets. 2011; Marcus et al. The Building 6 SZF supports NICHD and NHGRI with 15,000 two-liter tanks with a total capacity of over 330,000 . Dr. Dale Graham, Project Leader of the NIH Intramural Database Dr. Michael Gottesman, Deputy Director for Intramural Research Dr. Joan Schwartz, Assistant Director, Office of Intramural . The NIH Intramural Database collects and disseminates information about research being performed in the Intramural Programs; Visit Website The NIH Intramural Database collects and disseminates information about research being performed in the Intramural Programs; Visit Website; Search WALS. PHP is used as the clientserver based language to generate web pages viewed by the user. All functions of the backend of NiDB are performed by independent modules. To calculate the hash, all spaces and special characters (commas, hyphens, underscores) are removed from the two fields leaving only alphanumeric characters; all alphabetic characters are converted to upper case and the fields joined, name first. 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. Search. Science.gov searches over 50 databases and over 2100 selected websites, offering 200 million pages of authoritative U.S. government science information. Users report no problems or slowness during normal operation. An official website of the United States government. NiDB also allows projects to be private so they will not show up in search results if they user does not have access. Only XNAT, HID and LORIS are open-source, and none are as ubiquitous as the fMRI analysis tools, so while improvements have been made in availability of databases, only a small number of comprehensive open-source systems exist. Therefore, motion estimation in structural images can only be compared with images taken from the same person, preferably during the same imaging session. Hall D, et al. The most novel application of technology in NiDB is coupling of the data repository and the pipeline system. COINS, XNAT, and XCEDE are project-centric, meaning the parent object in the hierarchy is a project, while the parent object in NiDB is the subject (Gadde et al. Huguet J, Falcon C, Fust D, Girona S, Vicente D, Molinuevo JL, Gispert JD, Operto G; ALFA Study. David C. Glahn, Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA. NiDB goes a step further than LORIS by allowing simple sharing with data packages being exported and imported between installations, and integrates a powerful pipeline system. The sites mission is to improve the efficiency and effectives of business processes and information access between research communities. Towards Portable Large-Scale Image Processing with High-Performance Computing. eCollection 2022. The NIH has undertaken the practice of making raw data available from its funded studies, from which NDAR was created. The directory structure of analyzed data is similar to that of the raw data structure, which is subject-centric. Specifications for the tarball format are available on the NiDB website (http://nidb.sourceforge.net). Michal Assaf, 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. A publication for and about the NIH intramural research community; Visit Website; NIDB. 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. Pipeline specification screen. Real-time communication between instances of NiDB would be an interesting extension, which opens the door to automatic distributed analyses. We feel NiDB can speed the process of scientific discovery by making data and analyses available to researchers more easily than using other systems. Data can be queried by using several criteria and results returned can be grouped by subject, imaging study, and series. 2021 Apr 15;15:633438. doi: 10.3389/fnins.2021.633438. The NIH Data Management and Sharing (DMS) policy will take effect next month. NiDB can act as a central repository or as a node in a data sharing network. This simplicity has allowed massive analyses to take place with a significant reduction in user time required to setup the analysis. NiDB uses a subject-centric model to organize data. An example scenario might be that a site has 1,000 FreeSurfer jobs to process, that typically take 2030 h to complete a single job, the site would need 20,00030,000 h of processor time. NIDB. NiDB solves these problems by 1) minimizing PHI use, providing a cost effective simple locally stored platform, 2) storing and associating all data (including genome) with a subject and creating a peer-to-peer sharing model, and 3) defining a sample, normalized definition of a data storage structure that is used in NiDB. The fourth and current iteration of NiDB was rewritten from the ground up to reflect a new storage architecture which is blind to data-type, meaning any imaging modality, or other data, can be stored in the system and all searching, sharing, and pipeline processes are datatype neutral. The mission of this site is to provide a science gateway to a global audience. Reorganizing the rows by subject took an additional 30s on the web server, for a total time of 90s. . In order to complete an annual report, you will need . Data requests are recorded in the database and the datarequest module will process requests as they are received. Interplay of gut microbiota and oxidative stress: Perspective on neurodegeneration and neuroprotection. 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. official website and that any information you provide is encrypted A useful feature of NiDB is the automatic QC of MRI data. 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 . Please note that the primary policy source for the NIH IRTA Fellowship program is located within NIH Policy Manual 2300-320-7.. The site is secure. Scripts have been created to import eye-tracking, EEG (neuroscan), and SNP data. Object hierarchy of NiDB, showing, Fig. Six terabytes of raw data is stored on the servers and 2TB of data has been requested for download in the previous 20 months. August 2, 2022 Awards DMI, a global digital transformation solutions company, today announced it has been awarded a five-year task order to continue to provide support for the National Institute of Health's (NIH), National Institute of Health's Intramural Database (NIDB) enterprise-wide system. No method currently exists to anonymize non-DICOM data that contains PHI or identifying information, however few research data storage formats other than DICOM have the capability to store such PHI. Because of the large amount of PHI and IRB related data, and data from multiple sites stored on COINS, user access is tightly controlled with permissions leaning toward restrictive to prevent unintentional loss of PHI.
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