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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...

Clinical Support Laboratory – Flow Cytometry Section is a laboratory specializing in providing immunophenotyping support of NCI intramural clinical trials, though assessments may also be performed using cells from Non-human primates and other species. The CSL Read More...

In support of Intramural Research Program (IRP) scientists, DOHS provides training, consulting, and resources to ensure that laboratory equipment is used and maintained properly and safely. We provide expert safety and health consulting support for Read More...

The NIH Library is a biomedical research library, whose collection and services are available at no cost to NIH staff: Electronic Resources: Over 20,000 electronic journals, 190,000 eBooks, and 50 databases. , Training classes covering topics such as data Read More...

Clinical Support Laboratory – Cellular Immunology offers a spectrum of bioassays to assess cellular responses to antigens and mitogens including ELISPOT, cytotoxicity assays, and proliferation assays. Established Technologies Elispot Assays, Dual or Triple Color Fluorospot Assays, 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 Pathology Service, Division of Veterinary Resources (DVR), Office of Research Services (ORS), provides diagnostic gross and histopathologic evaluation of any species of laboratory animals used in the NIH Intramural Research Program due to morbidity, Read More...

The Biological Products Core provides the AIDS research community with high-quality purified preparations of various strains of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV), economically prepared by leveraging the economy of scale. Materials Read More...

Molecular Cytogenetics Core Facility facilitates the assessment of structural and numerical genomic changes in pre-cancer and cancer research models. This core provides comprehensive support for the cytogenetic analysis of cells from human and research animal Read More...

The Department of Laboratory Medicine provides state-of-the-art laboratory testing in support of Clinical Center patient care and will serve as a center of excellence in research and training in laboratory medicine, particularly in areas which Read More...

The Biomedical Engineering and Physical Science (BEPS) shared resource supports NIH’s intramural basic and clinical scientists on applications of engineering, physics, imaging, measurement, and analysis. BEPS is centrally located on the main NIH campus Read More...

CREx News & Updates July 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...

Protein and Metabolite Characterization Core (PMCC), formerly known as the Protein Characterization Lab (PCL),  offers various technologies to CCR investigators to characterize proteins and metabolites. The core develops and applies state-of-the-art analytical technologies, primarily mass Read More...

In order to meet increasing demands from both NIH intramural and extramural communities for access to a small angle X-ray scattering (SAXS) resource, the Center for Cancer Research (CCR) under the leadership of Drs. Jeffrey Read More...

10/25/2023 - Every week, thousands of biomedical research papers are published with a portion of them containing supporting tables with data about genes, transcripts, variants, and proteins. For example, supporting tables may contain differentially expressed genes Read More...

::: columns ::: {.column width="75%"} - No install of R or RStudio required. We will access RStudio server through the DNAnexus platform. Course documentation available at https://bioinformatics.ccr.cancer.gov/docs/rintro/index.html . ::: ::: {. Read More...

To participate in this class you will need your government-issued computer and a reliable internet connection. You do not need to download or install any software to participate in the class. However, at the end Read More...

To participate in this class you will need your government-issued computer and a reliable internet connection. You do not need to download or install any software to participate in the class.

To participate in this course, you will need a computer, a reliable internet connection, and a web browser. All classes and help sessions will be held virtually through Webex. In addition, this class will be Read More...

Two introductory lessons on Biowulf were presented in this course series. You can access those here and here . The first contains an introduction to Biowulf including information regarding storage space and the module system. The Read More...

To participate in this class you will need your government-issued computer and a reliable internet connection. You do not need to download or install any software to participate in the class.

To participate in this class you will need your government-issued computer and a reliable internet connection. You do not need to download or install any software to participate in the class. However, at the end Read More...

All material used for this course can be found in these pages. For hands-on lessons, we will explore this material using R on Biowulf. Requries a NIH HPC account. Tidyverse packages come pre-installed. Local R Read More...

This course will use R on Biowulf to avoid issues with R and package installations. To use R on Biowulf, you must have a NIH HPC account. If you do not have a NIH HPC ( Read More...

This course will be taught using R and RStudio on Biowulf. To use R on Biowulf, you must have an NIH HPC account. If you do not have Biowulf, this course can be taken using Read More...

We will use R on Biowulf for this course to avoid issues with R and package installations. To use R on Biowulf, you must have a NIH HPC account. If you do not have a Read More...

This course will use R on Biowulf. To use R on Biowulf, you must have an NIH HPC account. However, if you do not have Biowulf, this course can be taken using a local R Read More...

For a more detailed background on survival analysis as a statistical methodology, check out this related presentation ("Introduction to Survival Analysis") by Alexander Mitrophanov, PhD.

For a more detailed theoretical background on these topics, check out this related presentation ("Decision Trees, Survival Trees, and Random Forest") also by Brian Luke, Ph.D.

For a more detailed theoretical background on clustering, check out this related presentation ("Introduction to Clustering") also by Brian Luke, PhD.

This class is not hands-on. Experience using or access to Partek Flow is not required for participation. Tip For a review or introduction to RNA sequencing, see An Introduction to RNA-Seq: Overview of Expression Data Read More...

Submit a job using sbatch . Submit a multi-threaded job. Sumbit a swarm job.

04/22/2021 - Meeting link: https://cbiit.webex.com/cbiit/j.php?MTID=m2e54a1e4fca4e029e3691210f2422599 Meeting number: 160 936 5213 Password: Please obtain your meeting password from your host. Cohost: Leonard Freedman Presenter: Justin Read More...

Submit a job using sbatch. Submit a multi-threaded job. Sumbit a swarm job.

Much of the content for this presentation is from hpc.nih.gov. For more information and more detailed training documentation, see hpc.nih.gov/training/. Note This lesson will be demo-based only. Hands-on lessons will Read More...

Much of the content for this presentation is from hpc.nih.gov. For more information and more detailed training documentation, see hpc.nih.gov/training/. Note This lesson will be demo-based only. Hands-on lessons will Read More...

For this help session, you will be downloading the Golden Snidget data. Practice materials are located here .

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

01/28/2025 - This talk will cover how our group uses the resources of the FRCE cluster to process cryo-electron microscopy data collected in-house. This session is geared towards beginner users. This session will be recorded, and Read More...

12/19/2024 - ggplot2 is a popular R package for data visualization that uses layers to build high quality plots. In this lesson, you will learn to use ggplot2 to create and modify scatter plots including a Read More...

11/26/2024 - This talk will introduce quantum chemistry and how it is useful for the modeling of therapeutic and diagnostic agents. This session is geared towards beginners. This session will be recorded, and materials will be Read More...

11/12/2024 - We will discuss statistical considerations in planning, executing, and interpreting experiments using animals. Topics will include interpreting minimally powered pilot studies, dealing with complex time series, and maximizing knowledge gain from limited resources. This Read More...

10/08/2024 - We will cover recently developed statistical approaches to the classification of BRCA2 variants using the functional-assay data generated by our NCI collaborators (Dr. Sharan’s lab). Our main objective is to illustrate how statistical Read More...

08/13/2024 - NCI staff are welcome to register for an upcoming Childhood Cancer Data Initiative (CCDI) webinar titled, "CCDI Federated Data: Enhancing Data Discoverability," where you can learn about one of the newest advancements Read More...

08/13/2024 - This session will cover the basics of linear mixed-effects modeling as a method of regression analysis for clustered data. Special emphasis will be on the ideas behind random-intercepts and random-slopes modeling, and the discussion Read More...

07/23/2024 - In this presentation, we will demonstrate how to use enterprise data science platform to configure, run, share, and scale downstream bioinformatics and image analysis pipelines using cloud and HPC resources. This session is geared Read More...

06/11/2024 - This talk will cover the basics of statistical resampling methods such as bootstrap, Monte Carlo, and permutations for estimating parameters and testing hypotheses.  We will discuss when you might want to use Read More...

05/14/2024 - This presentation will explain the difference between the mean and standard deviation of a set of values and the standard error of the mean. The parameters involved in comparing two normally distributed populations relative Read More...

04/23/2024 - Crunching of large data requires large resources. Exploration of holobiont metagenomes is considered a “big data” project and here I’ll be describing how I used the FRCE Read More...

04/09/2024 - In this talk, we will cover what differentiates parametric and non-parametric statistics, tests/methods of both types for different data scenarios, when to use one vs. the other, and tradeoffs/pitfalls of each. This Read More...

03/26/2024 - In this session, we will discuss the potential of GPUs, and when and why to use GPUs on the Frederick Research Computing Environment (FRCE). We will explore the possibilities of GPU-accelerated AI applications and Read More...

02/27/2024 - This session will cover what are containers, and why and how to use them in your Bioinformatics workflows. We will review best practices, basic commands, and useful resources. This session is geared towards beginners.& Read More...

There are a number of Bioconductor events/conferences throughout the year including the annual BioC conference in North America and similar regional conferences throughout the world (e.g., BioC Asia, BioC Europe). Upcoming events (e. Read More...

To use the materials you generated on the RServer on DNAnexus on your local computer, let's export our files. To do this, let's select all files in our working directory. This will export Read More...

02/13/2024 - The first half of the session will briefly review statistics training resources available to the NCI based on feedback from previous Statistics for Lunch sessions. For the second half, we will have an open Read More...

01/23/2024 - In this session, we will discuss the potential of GPUs, and when and why to use GPUs on the Frederick Research Computing Environment (FRCE). We will explore the possibilities of GPU-accelerated AI applications and Read More...

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...

01/09/2024 - This talk will cover the basics of what affects and how to compute statistical power, sample size, and effect size. This is a beginner level talk. Some examples will be presented in the statistical Read More...

11/28/2023 - Recent advances in protein structure prediction methods such as AlphaFold2 and ESMFold has enabled protein structure prediction to achieve experimental accuracy in certain cases. In this talk, we will discuss the advantages and limitations Read More...

11/14/2023 - This talk will cover how to maximize the utility of your data by handling missing values and performing mathematical transformations. We will cover best practices, common pitfalls, and touch on data standardization methods. This Read More...

10/24/2023 - In this session, we will provide an overview of the Next-Generation Sequencing (NGS) capabilities and applications. We will present the workflows and analyses for Illumina short-read, PacBio, and Oxford Nanopore long-read sequencing on Frederick Read More...

10/10/2023 - In this talk we will discuss what is a p-value and examples of p-value hacking. We will also review the basics of several statistical tests and when to use them. This session will be Read More...

09/12/2023 - In this talk we will discuss how and why to minimize and correct for batch effects in our experiments. We will cover appropriate sample randomization and several computational methods to help uncover and mitigate Read More...

08/22/2023 - In this session, we will discuss conceptual overview of a computing cluster, how to get access to the NCI cluster in Frederick (FRCE) and how to connect and run basic programs. We will also Read More...

08/15/2023 - This talk will cover what to do when you first start looking at a new dataset. We will also discuss how to efficiently orient the data to avoid pitfalls and maximize knowledge gain in Read More...

No summary available.

02/12/2026 - Proteins mediate the critical processes of life and beautifully solve the challenges faced during the evolution of modern organisms. Dr. Baker’s goal is to design a new generation of proteins that 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...

04/16/2025 - Updated Location: ATRF, Frederick MD, Main Auditorium What to bring:  Laptop capable of connecting to internet via NIH wifi For questions or to register, please contact Amy Stonelake ( amy.stonelake@nih.gov ) Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

04/10/2025 - This one hour online training introduces participants to the tools and techniques for analyzing and quantifying microscopy images using MATLAB’s low-code algorithms. Participants will learn how to preprocess images, segment regions Read More...

BTEP strives to maintain links to resources that should be of interest to CCR Bioinformatics Community.  Some of the resources to will be accessible through more than one of these lists, but since the lists Read More...

01/14/2025 - In this talk, we will cover the basics of survival analysis as a statistical methodology developed for censored data. Special emphasis will be on visualizing survival data, comparing survival-time distributions for subject groups, and Read More...

10/22/2024 - Popular structure prediction program AlphaFold3 and its competitor Chai-1 recently added capabilities to predict 3D RNA structures straight from sequence input. In this talk, we will discuss some test cases for these programs and Read More...

Clinicians and bench scientists (a.k.a., wet lab researchers) are at the forefront of scientific achievement. However, most, if not all contemporary projects involve robust scientific analysis, where the tools of exploration aren’t Read More...

05/28/2024 - Frederick Research Computing Environment (FRCE) and Computational Sciences Series In this session, we will explore how machine learning can be used to analyze whole slide pathological images (WSIs). We will showcase how to utilize Read More...

04/19/2024 - In this webinar, attendees will learn the basics of using the All of Us Researcher Workbench’s point-and-click research tools, including how to create a workspace, how to build a cohort of All of Read More...

04/16/2024 - GitHub is a powerful platform for tracking, sharing, and collaborating on software projects of all kinds. Whether you’re a bioinformatics analyst, a software engineer, or a biologist who sometimes codes, GitHub Read More...

04/12/2024 - This session will outline the All of Us Researcher Workbench registration process for NIH researchers. Access to the Researcher Workbench is free, and all registered researchers are provided $300 initial computational credits. Some analyses in 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...

Course Overview Welcome to the R Introductory Series! A series of introductory lessons in R for scientists. This course will include a series of lessons for individuals new to R or with limited R experience . 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...

This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim sequences, denoise Read More...

Course Overview This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim Read More...

Course Overview Welcome to the Data Wrangling with R course series The purpose of this course is to introduce you to essential R packages and functions that will make your life easier when it comes Read More...

For today's practice, we are going to embark on a Unix treasure hunt created by the Sanders Lab at the University of California San Francisco. Note: the treasure hunt materials can be obtained directly Read More...

Lesson 4 Practice For today's practice, we are going to embark on a Unix treasure hunt created by the Sanders Lab at the University of California San Francisco. Note: the treasure hunt materials can be Read More...

As mentioned above, instructions for using the Biostar module on Biowulf can be found in the course documents . The Biostars module loads the software used in this course series. A list of the software included Read More...

Lesson 5 Practice The following can be used to practice skills learned in Lesson 5. Login to Biowulf If you are already logged in, exit the remote connection and reconnect. Remember, you must be on the NIH Read More...

Course Wrap-up This lesson concludes the Bioinformatics for Beginners course series. Please email us any time at ncibtep@nih.gov for help with your bioinformatics questions or concerns. Lesson Objectives Short course overview. Review BTEP Read More...

Bioinformatics for Beginners: RNA-Seq Course Description: This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focuses on RNA-Seq analysis. All steps of Read More...

Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...

06/22/2023 - Scientists and educators from many different fields need to find and understand chemical data to perform their work. As such, understanding PubChem, the world’s largest collection of freely accessible chemical information, Read More...

Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types and the code Read More...

R Course FAQs Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types Read More...

Course Overview Welcome to the Data Visualization with R Series A series of lessons designed to introduce learners to the R package ggplot2 This course will include a series of lessons for scientists with beginner Read More...

No summary available.

2024 Senatorov IS, Bowman J, Jansson KJ, Alilin AN, Capaldo BJ, Lake R, Riba M, Abbey YC, Mcknight C, Zhang X, Raj S, Beshiri ML, Shinn P, Ngyuyen H, Thomas CJ, Corey E, Kelly K. Castrate 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...

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...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...

Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end Read More...

We are going to download some bulk RNA-Seq test data and learn how to decompress it. First we will create a place to store the data. Go to the directory you've created for working Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to activate the bioinfo environment when working on Biostar class materials. conda activate bioinfo The bulk RNA-Seq test data we've Read More...

Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...

A common question posed to the Bioinformatics Training and Education Program (BTEP) is “How can I learn R and Python to analyze my data?”. First, it’s important to state that learning any programming language Read More...