Search Results for: database management

.contrast_primary_button{margin-bottom: 29.124px;margin-top: 0px;} Established in 2016, CREx is an NIH-exclusive online research resource marketplace designed to increase transparency around the advanced technologies and technical expertise available within the Intramural Research Program (IRP). Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

The Laboratory Animal Sciences Program (LASP) of the Frederick National Laboratory operates a Gnotobiotics Facility (GF) to support research focused on the role of microbiota in cancer inflammation, pathogenesis, and treatment response. The GF can Read More...

The Mouse Metabolic Phenotyping Center (MMPC)Live Program provides standardized, high quality, unique, and hard to find phenotyping services for mouse models of diabetes, obesity, and related metabolic disorders. Emerging as the next iteration of Read More...

The Optical Microscopy Analysis Core (OMAC), formerly known as the Optical Microscopy Analysis Lab (OMAL),  focuses its research and development activities to quantitatively understand the molecular basis of three-dimensional (3D) cell organization, motility, invasion, and Read More...

The Animal Diagnostic Laboratory (ADL) provides a full range of diagnostic capabilities, including microbiological cultures on various culture medium, microscopic screening for parasites such as mites and pinworms, molecular detection of pathogens, serological evaluation of Read More...

The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...

The CCR Microscopy Core provides NCI investigators access to state-of-the-art imaging tools and techniques, including light sheet fluorescence, high-resolution confocal, multi-photon, and super-resolution microscopy. The mission of the CCR Microscopy Core Facility is to support Read More...

The Central Repository provides the research community at the NCI with various cryogenic services, including low-temperature storage from +4° C to -196° C, controlled-rate freezing, computerized inventory and distribution of samples. The Central Repository is operated Read More...

The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

The Frederick Sequencing and Genomics Core (FSGC) was established through the integration and consolidation of the former Sequencing Facility (SF) and the Genomics Technology Laboratory (GTL). The new FSGC eliminates redundancy and provides cutting edge Read More...

The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for Read More...

The Division of Veterinary Resources’ (DVR) mission is to contribute to the advancement of NIH biomedical research programs by providing excellence in animal care, customer service, and specialized research services to support intramural research efforts. Read More...

The Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...

The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

CCR Office of Science and Technology Resources (OSTR) The Center for Cancer Research (CCR) Office of Science and Technology Resources (OSTR) explores and evaluates the latest technologic advancements and then makes them available to all Read More...

The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

CREx News & Updates February 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight ORS Division of Veterinary Resources (DVR) DVR is the central NIH lab animal support program Read More...

The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...

CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

02/10/2026 - This one-hour and thirty minute online training is part one of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

10/27/2025 - This one-hour and thirty minute online training is part one of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

06/26/2025 - This one-hour and half minute online training is part one of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

09/12/2024 - This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. Read More...

09/11/2024 - This one-hour and thirty minute online training is part one of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

05/17/2024 - This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. Read More...

05/16/2024 - This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. Read More...

01/26/2024 - This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. Read More...

01/25/2024 - This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. Read More...

Another way to run BLAST is to create your own custom database, and search against it with query sequences. Usually you will not have to create your own blast database, you can download prebuilt databases Read More...

07/24/2025 - NIDDK Biostats Seminar Series: From Research Study Design to Collecting, Managing, and Analyzing Data. Learning Objectives: 1. To delineate features of REDCap to support project management for research studies. 2. To outline steps to create detailed Read More...

01/16/2024 - This class focuses on data and project management using R and RStudio. RStudio makes it possible to work on a complete research project in a more efficient, integrated, and organized manner. This course is Read More...

01/10/2020 - In this introductory course, you will learn about AWS products, services, and common solutions. You will learn the fundamentals of identifying AWS services so that you can make informed decisions about IT solutions based Read More...

02/11/2026 - This hour and half online training is part two of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in a Read More...

10/28/2025 - This one-hour and fifteen minute online training is part two of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

06/27/2025 - This one-hour and fifteen minute online training is part two of an introductory two-part series for those who want to learn about research data management and sharing, or for those who are interested in Read More...

The NCI CCR Sequencing Facility will send researchers a link to the data, which is stored in their Data Management Environment (DME). Again, instructions for connecting DME to a Globus endpoint on Biowulf are in Read More...

No summary available.

01/16/2024 - About this talk: In this presentation we will go through the rich variety of database types, from traditional relational to cutting-edge NoSQL, uncovering how each 'flavor' adds its unique spice to the world of Read More...

10/23/2024 - CellMinerCDB is an interactive public web application ( https://discover.nci.nih.gov/cellminercdb/ ) that simplifies access and exploration of cancer cell line pharmacogenomic data across different sources such as the National Cancer Institute (NCI), Read More...

Data organization is extremely important to reproducible science. Consider organizing your project directory in a way that facilitates reproducibility. All inputs and outputs (where possible) should be contained within the project directory, and a consistent Read More...

While bracket notation is useful, it is not always the most readable or easy to employ, especially for beginners. This is where dplyr comes in. The dplyr package in the tidyverse world simplifies data wrangling Read More...

01/21/2026 - This one-hour online training offers an overview of the NIH-sponsored Generalist Repository Ecosystem Initiative (GREI) (Dataverse, Dryad, Figshare, Mendeley Data, Open Science Framework, Vivli, and Zenodo), and the role of participating in these repositories Read More...

11/20/2025 - This one-hour online training offers an overview of the NIH-sponsored Generalist Repository Ecosystem Initiative (GREI) (Dataverse, Dryad, Figshare, Mendeley Data, Open Science Framework, Vivli, and Zenodo), and the role of participating in these repositories Read More...

10/29/2024 - In this presentation, you will get an overview of the Cancer Digital Slide Archive (CDSA) platform. CDSA is an open source, web-based platform for storage, visualization, and management of digitized whole slide images.& Read More...

Closed reference OTU picking uses a reference database to cluster OTUs against reads that fail to cluster with a reference sequence due to real variation or sequence error variation are dropped subject to biases or Read More...

07/31/2025 - NIDDK Biostats Seminar Series: From Research Study Design to Collecting, Managing, and Analyzing Data. Learning Objectives: Be able to identify, load, and use R resources/packages based upon needs and experience level with R. 1. Read More...

04/08/2025 - Reactome is a free, open-source, curated and peer-reviewed pathway database that includes bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. This lesson will showcase the capabilities of Reactome in garnering biological Read More...

04/03/2025 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

02/11/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

02/06/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

02/04/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

01/30/2025 - This lesson is part of a course,  B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

01/28/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

12/11/2024 - This session of the BTEP Coding Club introduces NIH CloudLab, a free 90-day sandbox environment partnered with AWS, Google Cloud, and Azure, and demonstrates how to run Nextflow pipelines, a powerful workflow management system Read More...

10/09/2024 - This one-hour online training will provide detailed information and demonstrations on how to manage data in Excel.    By the end of this training, attendees will be able to:   Filter data by text, numbers, and Read More...

09/10/2024 - The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context Read More...

08/07/2024 -  Generalist repositories are a flexible, trusted resource for sharing research data for which there is no appropriate discipline specific repository as well as many other research outputs valuable for reproducibility and open Read More...

RStudio is an integrated development environment for R, and now python. RStudio includes a console, editor, and tools for plotting, history, debugging, and work space management. It provides a graphic user interface for working with Read More...

03/27/2024 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

03/18/2024 - Electronic lab notebooks (ELNs) are digital tools that allow researchers to record, manage, and share their data and results in a secure and efficient way. The virtual roundtable discussion will cover various aspects of Read More...

After consulting this guide, participants will Know how to access Partek Flow at NIH. Be able to transfer data from NCI CCR Sequencing Facility Data Management Environment to their Biowulf Partek Flow folder.

02/16/2024 - This one-hour training will provide detailed information and demonstrations on how to manage data in Excel. By the end of this course, the participants will recognize how to filter data by text, numbers, and Read More...

RStudio is an integrated development environment for R, and now python. includes a console, editor, and tools for plotting, history, debugging, and work space management.\ provides a graphic user interface for working with R.\ freely Read More...

To take full advantage of R, you need to install R packages. R packages are loadable extensions that contain code, data, documentation, and tests in a standardized shareable format that can easily be installed by Read More...

RStudio is an integrated development environment for R, and now python. RStudio includes a console, editor, and tools for plotting, history, debugging, and work space management. It provides a graphic user interface for working with Read More...

Love Data Week 2024 is quickly approaching! What is Love Data Week?  Love Data Week is an international week of celebrating all things data related, with an emphasis on data management, sharing, and security. Read More...

In addition to clasifying our organisms, we also want to reconstruct their phylogenetic relationships by generating a phylogenetic tree. We often assume that phylogenetic closeness can elucidate commonalities in phenotypic properties / functions, so it is Read More...

11/06/2023 - UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. The database is regularly augmented with additional data and is globally accessible Read More...

09/22/2023 - The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context of pathways, Read More...

09/13/2023 - Sometimes the data you need is not available in a .csv or a SAS7BDAT format, or maybe it is not available on your computer or within your organization at all. This intermediate class Read More...

02/25/2026 - Streamlining Data Sharing: Practical Tools and Researcher Stories from the NIH GREI A clear and comprehensive Data Management and Sharing (DMS) Plan is essential for meeting NIH policy requirements. This session introduces GREI’s Read More...

09/10/2025 - The National Center for Biotechnology Information (NCBI) is hosting a workshop at the NIH Research Festival 2025! This hands-on workshop, led by experts from the NIH Sequence Read Archive (SRA), will guide researchers through the Read More...

07/29/2025 - Globus is a GUI-based software suitable for efficiently transferring large datasets such as those generated from Next Generation Sequencing (NGS) to and from high performance computing systems (ie. NIH’s Biowulf). This demonstration only Read More...

07/24/2025 - QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data Read More...

07/23/2025 - This presentation will explore the next emerging stage where biobanking is characterised by being part of system - Biobanking 4.0. Biobanking has always been about data generation with tissue specimens providing the biological and genomic Read More...

nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...

11/04/2024 - This one-hour interactive training will cover how to use the ScHARe cloud and Terra platform focusing on how to utilize over 260 social determinants of health (SDoH) data sets and analytic notebooks containing ready-to-use code. Read More...

10/23/2024 - Please send any questions and/or specific topic areas that you’re interested in hearing about for this presentation by Friday, 10/18 to Kayla Strauss . QIAGEN Ingenuity Pathway Analysis (IPA) is the leading Read More...

10/22/2024 - Generalist repositories offer NIH researchers a flexible, trusted resource to share data for which there is no appropriate discipline specific repository as well as to share many other research outputs valuable for reproducibility and Read More...

Congratulations, your experiments have been completed and you have a large amount of data. Now, it’s time to analyze these data. But where do you begin? How can you gain the most meaning from Read More...

Partek Flow enables scientists to build comprehensive workflows for analyzing multi-omics high throughput sequencing data including DNA and variant calling, bulk and single cell modalities for RNA, ChIP, and ATAC, spatial transcriptomics, CITE, and immune Read More...

06/26/2024 - This in-person hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA), which is  available to access from the NIH Library . IPA can be used identify biological relationships, mechanisms, pathways, functions, and diseases Read More...

06/11/2024 - Large language models (LLMs) are artificial intelligence (AI) algorithms that employ deep learning and extensive data sets to create new content. LLMs offer many possible applications in the biomedical field, such as the development Read More...

The NIH Library provides expert guidance on bioinformatics, biostatistics, data visualization, and data curation throughout the research process. Explore a variety of classes, on-demand trainings, resources, and services related to data science and bioinformatics available Read More...

05/15/2024 - Generalist repositories offer NIH researchers a flexible, trusted resource to share data for which there is no appropriate discipline specific repository as well as to share many other research outputs valuable for reproducibility and Read More...

04/26/2024 - Webinar attendees will hear tips and tricks to code efficiently in the Researcher Workbench using R and RStudio. Although Python and SAS are alternative programming languages available on the Researcher Workbench, this session will Read More...

03/22/2024 - This 3-hour seminar is tailored for biologists, data analysts, and researchers who are eager to dive into the essentials of computational flow cytometry analysis using R. Flow cytometry is a crucial technique in cell Read More...

03/06/2024 - Please join us on Wednesday, March 6 when Daniella Lowenberg from the University of California, California Digital Library will present “Defining the Need for Open Data Metrics.”   Widespread adoption Read More...

03/06/2024 - The NCI Cancer Diagnosis Program in the Division of Cancer Treatment and Diagnosis is hosting a workshop, “Digital Pathology Imaging (DPI) in Cancer Clinical Trials and Research.” This workshop will Read More...

After this class, participants will Become familiar analyzing single cell RNA sequencing data using Partek Flow including Importing of data into a Partek Flow project QA/QC, filtering, and normalizing of single cell RNA data Read More...

Accessing Partek Flow at NIH and tips for data transfer Learning objectives After consulting this guide, participants will Know how to access Partek Flow at NIH. Be able to transfer data from NCI CCR Sequencing Read More...

Those researchers who used the NCI CCR Sequencing Facility to get sequencing done will receive a link to their data. This data can be transferred to the "PartekFlow" folder on Biowulf using Globus. Read More...

Course Overview Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with Read More...

Tidy data is an approach (or philosophy) to data organization and management. There are three rules to tidy data: (1) each variable forms its own column, (2) each observation forms a row, and (3) each value has its Read More...

In genomics, we work with a lot of tabular data - data organized in rows and columns. The data structure that stores this type of data is a data frame . Data frames are collections of Read More...

01/24/2024 - Dear colleagues,   Please join us on Wed., Jan. 24 when Dr. Avi Ma’ayan from the Icahn School of Medicine at Mount Sinai will demonstrate how to use these tools to access hundreds of thousands Read More...

By targeting 16S rRNA, we want to target bacteria and archaea. Therefore, we can exclude sequences that are unexpected such as those from chloroplasts or mitochondria. By setting --p-include p__ , we are retaining only sequences Read More...

The recommended method involves applying a scikit-learn multinomial naive Bayes classifier. This uses machine learning to train a classifier on a referene database and then use the trained classifier to classify your ASVs. These classifiers Read More...

Lesson 4: Feature table filtering, taxonomic classification, and phylogeny Learning objectives learn how to apply different types of filtering to your ASV table and representative sequence data. classify your ASVs. Generate a phylogenetic tree. Now that Read More...

12/07/2023 - This hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA) and CLC Genomics Workbench tools, which are available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, Read More...

10/23/2023 - QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data Read More...

09/19/2023 - This workshop is part of the  2023 NIH Research Festival  schedule . Data Sharing in Generalist Repositories  Generalist repositories offer NIH researchers a flexible, trusted resource to share data for Read More...

09/19/2023 - The NIH is home to a number of groups aimed at supporting bioinformatics, genomics, computational biology and various related topics. Many of these groups meet regularly to host talks or provide training opportunities, while Read More...

09/18/2023 - The NIH is home to a number of groups aimed at supporting bioinformatics, genomics, computational biology and various related topics. Many of these groups meet regularly to host talks or provide training opportunities, while Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

This lesson will introduce data wrangling with R. Attendees will learn to filter data using base R and tidyverse (dplyr) functionality. Learning Objectives Understand the concept of tidy data. Become familiar with the tidyverse packages. Read More...

Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...

Introduction to R and RStudio IDE Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help 3. Read More...

Introduction to Data Wrangling with the Tidyverse Objectives Wrangle data using tidyverse functionality (i.e., dplyr ). To this end, you should understand: 1. how to use common dplyr functions (e.g., select() , group_by() , arrange() , mutate() , Read More...

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...

General questions or comments about the BTEP program or classes should be addressed to: NCIBTEP@nih.gov Amy Stonelake, Ph.D . BTEP Program Manager and Bioinformatics Analyst amy.stonelake@nih.gov I am an experienced Read More...

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

04/01/2024 - Embark on a journey of visionary insights! Join us for the launch of the NEI Informatics & Data-Driven Insights: Seminars & Dialogue Opportunities for Vision Health series, hosted by the National Eye Read More...

Welcome! Welcome to the R Introductory Series! Who: Novices and beginners\ What: A course series introducing R and RStudio. This course will introduce the foundational skills necessary to begin to analyze and visualize data in Read More...

Learning Objectives Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment Data Read More...

This practice lesson is associated with Lesson 4 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on filtering our feature table and representative sequences, classify our features, and generate a phylogenetic Read More...

Practice Lesson 4 This practice lesson is associated with Lesson 4 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on filtering our feature table and representative sequences, classify our features, and generate Read More...

Lesson 3: Creating a feature table Lesson Objectives Check for primers Generate an ASV count table and representative sequence file Understand the difference between OTU picking and denoising The two primary files that will be used Read More...