Search Results for: Animal MRI System

Citation: Belue M, et al. Academic Radiology 2024 Code Availability: https://github.com/NIH-MIP/Prostate-MRI_T2W_Quality

Citation: Lay NS et al. Medical Physics 2023 Code Availability: https://github.com/ NIH-MIP/WSI_LungTumorSeg

Radiology and Imaging Sciences provides imaging services for National Institutes of Health (NIH) Clinical Center patients participating in research protocols conducted by the various NIH institutes. Services include X-rays, fluoroscopy, ultrasound, magnetic resonance imaging (MRI) Read More...

The Clinical Image Processing Service (CIPS) offers timely and accurate advanced image processing of diagnostic radiology images for clinical care, research, and training. CIPS’ functions include clinical services and scientific researches. Established Technologies CIPS can Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx Program Manager The CREx Team is happy to announce Deepika Velampati as the new CREx Program Read More...

The Molecular Pathology Unit is intended to spearhead opportunities for bridging basic and clinical research efforts by more precisely optimizing the development, characterization, and utilization of models of human disease. The initiative approach includes both Read More...

.row { display: flex; justify-content: space-around; align-items: flex-start; margin: 20px; } .column { text-align: center; padding: 10px; width: 30%; } .column img { display: block; margin: 0 auto; width: 150px; height: 150px; } .column strong { display: block; margin-top: 10px; } Background: Intravital microscopy (IVM) Read More...

OSTR offers two distinct supplemental funding mechanisms for CCR PI’s to request additional funds for technologies and research services requiring exceptional costs. Eligible expenses include services from Cores and outside vendors.  A third program ( Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...

The Neurorehabilitation and Biomechanics Research Section (also referred to as the NAB LAB) is a multidisciplinary group of highly qualified scientists, clinical and technical staff, and trainees with diverse backgrounds including medical, physical therapy, neuroscience Read More...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, 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 Magnetoencephalography (MEG) Core Facility specializes in MEG, a non-invasive procedure similar to electroencephalography (EEG), and aims to support research to better understand of the functioning of the brain. Established Technologies Magnetoencephalography (MEG) is a 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...

CREx News & Updates March 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NIA Nonhuman Primate Core The NIA Nonhuman Primate Core supports multi-disciplinary translational aging projects for Read More...

The FNLCR Molecular Histopathology Laboratory (MHL) provides comprehensive veterinary pathology support for animal health monitoring, biomarker discovery and validation, drug development, genomics, and proteomics on a cost recovered basis. The MHL is organized into multiple Read More...

TCIA is a service which de-identifies and publishes medical images of cancer for download. New data proposals are reviewed by an Advisory Group on a quarterly basis. The data are organized as “collections”; typically, patients’ 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 primary objective of the Protein Technology Core (PTC) is to establish an experimental screening pipeline for single-domain antibodies termed nanobodies. Nanobodies are antibody fragments consisting of a single monomeric variable antibody domain. The PTC, Read More...

The Chemistry and Synthesis Center (CSC) of the National Heart, Lung, and Blood Institute (NHLBI) provides IRP scientists with targeted imaging probes and chemical tools that help accelerate cell-based assays, in vivo imaging studies, and 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...

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...

October 6, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Science & Technology Seminars and Training Events Upcoming Seminars and Educational Opportunities The following Read More...

Mouse models of human cancer have had a profound impact on our current understanding of the mechanisms of tumorigenesis and the pathways regulated by cancer-related genes. These models hold the promise of serving as critical Read More...

Supplemental Technology Award Review System (STARS) Overview STARS Request Form STARS System The Supplemental Technology Award Review System (STARS) is a web-based interface for submission and review of S&S supplement requests by CCR Read More...

Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

The NHLBI Transgenic Core’s main mission is to keep up with the latest advancements in genome engineering technologies and to provide state-of-the-art services to assist NIH scientists in generating genetically engineered animal models. In Read More...

OSTR offers two distinct supplemental funding mechanisms for CCR PI’s to request additional funds for technologies and research services requiring exceptional costs. Eligible expenses include services from Cores and outside vendors.  A third program ( Read More...

OSTR offers two distinct supplemental funding mechanisms for CCR PI’s to request additional funds for technologies and research services requiring exceptional costs. Eligible expenses include services from Cores and outside vendors.  A third program ( Read More...

Large STARS can be used to request supplemental funding exceeding $8,000 to offset experimental costs (e.g., core or vendor services or specialized reagents).  Applications require detailed scientific and budgetary justification and must be proposed in Read More...

CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...

Small STARS can be used to request supplemental funding to offset exceptional costs (e.g., core or vendor services or specialized reagents).  All requests must be approved for funding before work can commence. Provides 50% cost 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...

CREx News & Updates December 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the STRIDES Initiative. VIEW STRIDES INITIATIVE NIH Cores 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NIH NeuroBioBank (NBB) The NBB provides researchers with access to human post-mortem brain tissue Read More...

Home About the Biophysics Core Biophysics Core Technologies We provide consultations and advice on the applications of biophysical methods. If you would like to discuss the requirements of a particular technique or consider selecting the 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 NHLBI Murine Phenotyping Core carries out physiologic and behavioral testing in a diversity of mouse models for NHLBI and other NIH institutes.Established TechnologiesCardiovascular Phenotyping, Metabolic Phenotyping, Pulmonary Phenotyping, Behavioral Phenotyping, Exercise Physiology, Echocardiography, Read More...

NCI maintains a low temperature repository of implantable in vivo-derived tumors and in vitro-established tumor cell lines from various species, which are available to qualified investigators as a service to the cancer research community. The Read More...

The COP evaluates novel therapies in pet dogs with cancer to improve outcomes for human patients and established the Comparative Oncology Trial Consortium (COTC), a collaborative effort of NCI and extramural comparative oncology centers at 24 Read More...

The NIH Biowulf Cluster provides researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations, deep learning to model protein structures, and PET brain Read More...

Back Services: This instrument is not user accessible.  We provide both data collection and data analysis services. Location: Building 50, room 3331 Description: An analytical ultracentrifuge is equipped with absorption and interference optical systems that monitor Read More...

Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols.  This service is intended for the occasional users of this system.  Researchers who expect to use this instrument Read More...

Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols.  This service is intended for the occasional users of this system.  Researchers who expect to use this instrument Read More...

The Mid-Atlantic CHTN is one of six participating divisions of the Cooperative Human Tissue Network (CHTN) and is based in the Pathology Department at the University of Virginia. While primarily a resource for cancer researchers, Read More...

NCI LASP Genome Modification Core (GMC) is a CCR-dedicated facility that provides advice, training, and reagents to NCI scientists seeking to utilize CRISPR and other nucleases to generate genome modifications in primary cells, cell lines, Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx Interested in imaging large scale biological samples?  Volume electron microscopy allows for 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...

The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and 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...

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

The NMR Facility for Biological Research operates six NMR spectrometers with proton resonance frequencies from 850 to 500 MHz. Three of the highest field spectrometers (850, 700, 600) are equipped with higher sensitivity cryoprobes optimized for high-resolution multi-dimensional and relaxation Read More...

The NIH Clinical Center Pharmacy Department provides pharmaceutical care to inpatients and outpatients on NIH intramural research protocols at the NIH Clinical Center. The Clinical Center facility encompasses 200 inpatient beds, 93 day-hospital stations, and 15 clinics. Clinical Read More...

The rapid advancement of single-cell technology has provided new powerful tools to answer many biological questions, such as identifying new or rare cell populations and characterizing the complexities of tumor heterogeneity. Realizing the great potential Read More...

NCI established the Nanotechnology Characterization Laboratory (NCL) to support the extramural research community to accelerate the progress of nanomedicine by providing preclinical characterization and safety testing of nanoparticles. It is a collaborative effort between NCI, Read More...

NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of protein, macromolecular complexes, membrane receptors, cellular organelles, and 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...

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 Antibody Engineering Program (AEP) is located at the Laboratory of Molecular Biology, which is part of the Center for Cancer Research (CCR), an intramural program at the National Cancer Institute (NCI). AEP focuses on Read More...

The PPS encompasses all scientific analyses related to pharmacology, once the specimen has been collected and stored. There is a multi-step process to evaluate how the drug is being handled by the body after administration. Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Spotlight The NIH Lab Managers Working Group have developed a new NIH-wide database of cold Read More...

Back Services: Biophysics Facility offers fluorometers as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3226 Description: Some substances reemit light after Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our Read More...

LCMB Microscopy Core offers live cell imaging technologies as well as super-resolution, fluorescence lifetime and confocal imaging systems for immunofluorescence. Our confocal instruments are a Leica SP8 laser scanning confocal microscope and a Nikon spinning Read More...

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

The Antibody Engineering Program (AEP) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The program focuses on generating therapeutic antibodies by phage display technology, including human antibodies and Read More...

[tabby title="Home"] About NICE-NIH Intramural CryoEM Consortium  NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of Read More...

Back Services: Biophysics Facility offers DLS as an open-access instrument. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Training includes DLS analysis of small- and large-molecular size 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...

10/15/2024 - This one-hour online training will cover techniques on locating biomedical research articles, patents, NIH-funded research projects, genetic information, and print and electronic books related to animal models and model organisms. This training will also Read More...

05/13/2025 - In this one hour and half hour online training, attendees will apply deep learning to brain MRI images.   By the end of this training, attendees will be able to:& Read More...

07/17/2024 - In this one hour and half hour online training, attendees will apply deep learning to brain MRI images.    By the end of this training, the attendees will be able to :    Read More...

11/17/2025 - Simple Questions Your RAG System Can't Answer

05/19/2025 - Immunotherapy has the potential to revolutionize the way we treat cancer, but a key challenge has been finding ways to tailor that therapy to the right patient at the right time. Attend this webinar, 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...

03/11/2021 - Abstract: Targeted quantitative proteomics using multiple/parallel reaction monitoring (MRM, PRM) is already being applied by many researchers in biology, biochemistry, and clinical research laboratories. These methods allow rapid and precise quantitation of proteins Read More...

01/13/2026 - The past decade has witnessed thriving cell atlas research activities in elucidating human cell types and their organization principles. The NIH BRAIN Initiative launched a pilot 3-year BRAIN Initiative Cell Census Consortium (BICCC) in 2014, Read More...

03/26/2025 - Developing artificial intelligence (AI) schemes to assist the clinician towards enabling precision medicine approaches requires development of objective markers that are predictive of disease response to treatment or prognostic of longer-term patient survival. The Read More...

01/27/2025 - NCI CCR Liver Cancer Program Seminar Series Dr. Sethupathy is professor of physiological genomics and chair of the Department of Biomedical Sciences at Cornell University. He leads a research lab focused on genome-scale and Read More...

08/09/2024 - We cordially invite you to attend the upcoming Data Sharing and Reuse Seminar featuring Dr. Robert Schuler and Dr. Jifan Feng. Dr. Schuler, a Senior Computer Scientist and Lead Scientist at the University of 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...

ggplot2 uses a default coordinate system (the Cartesian coordinate system). This isn't super important until we want to do something like make a map (See coord_quickmap() ) or create a pie chart (See coord_ Read More...

02/26/2026 - If you use AI tools even occasionally, you’ve probably spent more time than you’d like rewriting prompts, tweaking outputs, or trying to remember “that one prompt Read More...

01/16/2026 - Part of the Childhood Cancer Data Initiative (CCDI) Webinar Series During this webinar, experts from the USC Norris Comprehensive Cancer Center (NCCC) and Children's Hospital Los Angeles (CHLA) will present: An overview of Read More...

01/16/2026 - Speakers: James Amatruda, M.D., Ph.D. David Buckley, Ph.D. Jennifer Cotter, M.D. Alexander Markowitz, Ph.D. Moderator: Warren Kibbe, Ph.D., FACMI During this webinar, experts from the USC Norris Comprehensive Read More...

08/25/2025 - This one hour and half online training is designed for those who create reproducible projects and also want to extend the basics of R Markdown and apply those skills in  Quarto . Quarto Read More...

08/14/2025 - Biowulf is the NIH Unix-based high-performance computer (HPC). Unix is a command driven computer operating system. Biowulf has more computational power than the average laptop, which makes it ideal for analyzing Next Generation Sequencing ( Read More...

07/23/2025 - The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were once challenging or impossible into routine tasks. While QIIME began as a marker gene (e. Read More...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...

03/21/2025 - Partek Flow is a point-and-click software for analyzing multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. Input options include FASTQ, BAM, or expression tables, thus enabling scientists Read More...

03/20/2025 - This class will serve as a review for essential Unix commands needed for bioinformatics. It is suitable for those who took BTEP's recent Bioinformatics for Beginners course series ( https://bioinformatics.ccr.cancer.gov/ Read More...

03/18/2025 - This class is not hands-on and will demonstrate to participants the use of IGV for visualizing alignment results from Next Generation Sequencing using RNA as an example. After this class, participants will be able Read More...

03/13/2025 - This session will introduce participants to visualizing alignment results from Next Generation Sequences using the Integrative Genomics Viewer (IGV). This step is important as scientists may want to highlight results from certain genomic locations Read More...

03/11/2025 - In this class, participants will get hands-on experience with generating and interpreting differential gene expression analysis results from bulk RNA sequencing. In addition, participants will learn to generate common plots used to visualize bulk Read More...

03/06/2025 - This class introduces participants to the first steps to differential expression analysis in bulk RNA sequencing which involves filtering out noise from (ie. genes without expression across samples) and performing QC on the gene Read More...

03/04/2025 - Alignment of RNA sequencing data enables researchers to identify where in the genome each sequence came from. However, it does not inform of how many sequences aligned to each genomic feature such as a Read More...

02/27/2025 - NGS produces millions of sequences per sample and the challenge is to identify where in the genome each sequence came from. Fortunately, there are aligners that help scientists with this task. After this class, Read More...

02/25/2025 - Quality assessment may reveal low quality sequences and/or contaminations such as adapters in NGS data. Therefore, it is important to perform cleanup to ensure that the input for downstream analyses tools is of Read More...

02/20/2025 - This class will introduce the first step in analyzing NGS data using bulk RNA sequencing as an example. After attending, participants will be able to describe the file format in which NGS data is Read More...

02/18/2025 - This class will introduce basic experimental and analytical considerations for bulk RNA sequencing, a technique that is used to profile gene expression at the tissue level. Information taught serves as the foundation for participants 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...

01/21/2025 - About the Speaker: Hari completed his PhD in Cell Biology at the University of Toronto, where he used single-molecule imaging techniques to reveal how multimolecular interactions govern early signaling events in individual immune cells. Read More...

01/14/2025 - Join us for a webinar on EMERSE, a text processing system designed specifically for non-technical users, featuring David Hanauer, M.D., M.S. from the University of Michigan Medical School. EMERSE (Electronic Medical Record Read More...

12/12/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require 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...

11/20/2024 - ggplot2 is a popular R package for data visualization that uses layers to build high quality plots. There are over 100 packages that extend the functionality of ggplot2. This session of the BTEP Coding Club Read More...

11/19/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is a point-and-click software hosted on Biowulf, the NIH Read More...

11/14/2024 - The accessibility of artificial intelligence/machine learning (AI/ML) tools has taken off in recent years. This democratization of advanced analytics has the potential to revolutionize predictive toxicology, especially for applications that generate massive, Read More...

11/07/2024 - Dr. Blackshaw's work investigates the molecular mechanisms controlling neurogenesis and cell fate specification in the vertebrate forebrain, with a particular focus on the retina. He currently focuses on the use of comparative S 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...

10/09/2024 - This session will give an overview of the NCI Cancer Research Data Commons and the variety of available cancer data such as RNA expression and protein abundance. These data are hosted in openly accessible Read More...

09/24/2024 - This class will introduce beginners or those looking for a refresher to Jupyter Lab, a platform used to organize code and analysis steps in one place. Jupyter Lab can be easily installed or run Read More...

09/18/2024 - This one-hour online training will cover several integration points between SAS and open-source tools to empower the developer and the organization to integrate the benefits of both SAS and open source. & Read More...

09/12/2024 - Telomere to telomere (T2T) genome assemblies represent a paradigm shift in comparative genomics, offering insights into chromosome structure, evolution, and function at the highest resolution. Dr. O'Neill's lab has made recent Read More...

09/11/2024 - Qlucore Omics Explorer is a point-and-click package available to NCI CCR scientists that enables visualization-based analysis of multi-omics data including RNA-seq, scRNA-seq, proteomics, metabolomics, as well as enabling the use of machine learning classification Read More...

08/29/2024 - Dr. Mardis is an internationally recognized expert in cancer genomics, with ongoing interests in the integrated characterization of cancer genomes, defining DNA-based somatic and germline interactions and RNA-based pathways, and immune microenvironments that lead Read More...

08/15/2024 - Qiagen’s CLC Genomics Workbench is a point-and-click software for analyzing multi-omics sequencing data including variant analysis, RNA sequencing, and ChIP sequencing. This class will demonstrate variant analysis using this software. Participants will be Read More...

08/08/2024 - The Elemento lab combines Big Data analytics with experimentation to develop entirely new ways to help prevent, diagnose, understand, treat and ultimately cure disease. Our research involves routine use of ultrafast DNA sequencing, proteomics, Read More...

07/24/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...

07/24/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is hosted on Biowulf, the NIH high performance computing Read More...

07/10/2024 - Qlucore Omics Explorer is a point-and-click software for analyzing various omics data including RNA sequencing (bulk and single cell), proteomics, and metabolomics. Participants will learn to perform QC, construct visualizations (ie. PCA, heatmap, volcano, Read More...

06/27/2024 -   Alternative Meeting Information:  Meeting number: 2310 497 7985 Password: mjPjjmi$473 Join by video system Dial  23104977985@cbiit.webex.com You can also dial 173.243.2.68 and enter your meeting number. Join by phone 1-650-479-3207  Call-in number (US/Canada) Read More...

06/20/2024 - Dr. Irizarry will share findings demonstrating limitations of current workflows that are popular in single cell RNA-Seq data analysis. Specifically, he will describe challenges and solutions to dimension reduction, cell-type classification, and statistical significance Read More...

06/20/2024 - Clustered heat maps are widely used for visualizing patterns in molecular profiling data. But traditional, static heat maps have significant limitations when applied to large datasets (1000s of elements per axis). Presented in this Read More...

06/06/2024 - The Brooks Lab developed a computational tool called FLAIR (Full-Length Alternative Isoform Analysis of RNA) to produce confident transcript isoforms from long-read RNA-seq data with the aim of alternative isoform detection and quantification. With Read More...

help() and ? "provide access to the documentation pages for R functions, data sets, and other objects". help.search() "allows for searching the help system for documentation matching a given character string in Read More...

05/23/2024 - An exciting opportunity at the intersection of the biomedical sciences and machine learning stems from the growing availability of large-scale multi-modal data (imaging-based and sequencing-based, observational and perturbational, at the single-cell level, tissue-level, and Read More...

05/23/2024 - Versioning enables researchers to track changes in coding projects. This Coding Club introduces Git (https://git-scm.com), an open-source software used to perform versioning on a personal computer. At the end of this class, Read More...

04/11/2024 - Informaticians aim to bring the right information to the forefront at the right time to improve decision-making. Dr. Greene's  lab develops computational methods that integrate distinct large-scale datasets to extract the rich and Read More...

04/04/2024 - Although generative artificial intelligence (AI), a’la ChatGPT, is receiving a lot of “attention” these days, there are many other options for using AI to support biomedical research. In order to help analyze and Read More...

03/21/2024 - Context-aware AI implemented to facilitate data discovery and harmonization has significantly accelerated some of the common bottlenecks in the collaborative research process. Pilot work has shows major time and cost savings compared to current Read More...

03/04/2024 - This class is designed for those who want to extend the basics of R Markdown and apply those skills in Quarto. Quarto is an open-source scientific and technical publishing system that offers multilingual programming Read More...

02/29/2024 - Artificial Intelligence (AI) is becoming increasingly ubiquitous in biomedical research, enabled by large datasets, new algorithms, and hardware improvements. In this session, Dr. Brian Ondov will introduce the basic principles of AI and describe Read More...

02/28/2024 - Versioning enables researchers to track changes in coding projects. This Coding Club session will introduce Git (https://git-scm.com), an open-source software used to perform versioning locally and enables users to upload code to Read More...

02/21/2024 - Versioning enables researchers to track changes in coding projects. This Coding Club session will introduce the versioning tool GitHub (https://github.com). At the end of this class, participants will Become familiar with options Read More...

The lattice package is another prominent graphic system in R. Like ggplot2 this is also based on the grid package. For more information comparing the three plotting systems, see this chapter from Exploratory Data Analysis Read More...

Quarto® is an open-source scientific and technical publishing system built on Pandoc --- https://quarto.org/ What does this mean? Quarto allows you to combine code, commentary, and other features to tell a story about Read More...

According to Wikipedia, a path is "a string of characters used to uniquely identify a location in a directory structure." Therefore, a file path simply tells us where a file or files are Read More...

Last lesson we discussed the three basic components of creating a ggplot2 plot: the data , one or more geoms , and aesthetic mappings . ggplot(data = ) + (mapping = aes()) But, we also learned of other features that greatly Read More...

02/26/2026 - Scientific discovery is increasingly limited not by data availability, but by our ability to integrate evidence, generate hypotheses, and iteratively test them at scale. Recent advances in foundation models and large language models suggest Read More...

02/12/2026 - The NLM Division of Intramural Research (DIR) is pleased to welcome Tiarnán Keenan, MD, PhD, Stadtman Tenure-Track Investigator and Director of the Medical Retina Fellowship Program at the National Eye Institute 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...

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...

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...

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...

Recently, the NIH HPC Team has provided on demand access to HPC resources via web browser through integration of Open OnDemand , an open source project supporting "nearly 400 HPC centers around the world" . This 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...

12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...

11/26/2024 - Dr. Daniel Orringer received his M.D. from The Ohio State University, completed his residency in neurological surgery at the University of Michigan Health System, and fellowship training in neuro-oncology at the Massachusetts General-Brigham Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

10/15/2024 - On October 15th-16th, 2024, the NCI Office of Data Sharing (ODS) is hosting the Annual Data Sharing Symposium titled  Driving Cancer Advances through Impactful Research  inside the Clinical Read More...

09/19/2024 - Qiagen Ingenuity Pathway Analysis (IPA) is a point-and-click software that enables scientists to discern how genomic, transcriptomic, proteomic, and metabolomic changes influence molecular biology pathways and networks. This software is available to NCI investigators, Read More...

07/18/2024 - Long read sequencing holds an advantage over short read sequencing in areas such as structural variant and transcript isoform discovery.  This class will demonstrate long read analysis using Qiagen’s CLC Genomics Workbench, a Read More...

06/13/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...

06/12/2024 - Join us for an engaging training session where we will examine the similarities and differences between machine learning and statistical differential gene expression (DGE) analysis using Qlucore Omics Explorer. Qlucore Omics Explorer is a Read More...

Many experiments look to compare to distinct populations, and scRNASeq is no exception. The two populations being compared can vary wildly from experiment to experiment; some look to draw comparisons based on the experimental condition, 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...

1. Introduction and Learning Objectives This tutorial has been designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples that Read More...

05/28/2024 - The symposium's goals are to explore the integration of AI in understanding and managing immunological data, foster a paradigm shift in how immunologists leverage AI to propel their research forward, and inform NIAID Read More...

05/16/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...

05/08/2024 - Qlucore Omics Explorer is a point-and-click software that enables analysis of RNA sequencing (bulk and single cell), proteomics and metabolomics data. It’s machine learning capabilities also allow for classification of cell types. This Read More...

05/02/2024 - The explosion of biomedical big data and information in the past decade or so has created new opportunities for discoveries to improve the treatment and prevention of human diseases. As such, the field of 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...

03/01/2024 - Jens Rittscher is Professor of Engineering Science at the University of Oxford with his appointment held jointly between the Institute of Biomedical Engineering and the Nuffield Department of Medicine. He is a group leader Read More...

02/21/2024 - https://cap-lab.bio (link is external) https:// (link is external) qiime2.org (link is external) The QIIME platform, including QIIME 1 and QIIME 2 ( https://qiime2.org (link is external) ), has been extensively applied in microbiome Read More...

Let's look a bit into our RStudio layout. Source : This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View() ) will appear as a Read More...

ggplot2 is an R graphics package from the tidyverse collection. It allows the user to create informative plots quickly by using a 'grammar of graphics' implementation, which is described as "a coherent system for Read More...

The following represents the basic ggplot2 template: ggplot(data = ) + (mapping = aes()) We need three basic components to create a plot: the data we want to plot , geom function(s) , and mapping aesthetics . Notice the + symbol Read More...

Objectives Review the grammar of graphics template. Learn about the statistical transformations inherent to geoms. Learn more about fine tuning figures with labels, legends, scales, and themes. Learn how to save plots with ggsave() . Review Read More...