Search Results for: multi-experiment data integration

05/17/2022 - Metabolomic and multi-omic data are increasingly being collected in basic, preclinical, and clinical research studies. Interpretation of these data though remains challenging.  Common challenges include the difficulty in identifying metabolites and assigning unique identifiers, Read More...

05/13/2022 - About the Seminar Artificial intelligence and machine learning have the potential to greatly transform healthcare. Although these techniques have shown remarkable performance for many tasks including medical image analysis, we will share some of Read More...

05/04/2022 - For our next CDSL webinar we will have a guest lecture by  Dr. Julio Saez-Rodriguez from the Institute for Computational Biomedicine, Heidelberg. B io: Julio Saez-Rodriguez is Professor of Medical Bioinformatics and Data Analysis 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...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, 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...

04/03/2025 - The NCI Rising Scholars: Cancer Research Seminar Series is an opportunity to highlight the research and the important contributions made by NCI-supported postdoctoral fellows and early career investigators at NCI laboratories and NCI-funded institutions Read More...

01/23/2025 - The NCI Rising Scholars: Cancer Research Seminar Series , hosted by the Center for Cancer Training, highlights the research and important contributions made by postdoctoral scholars and early-career investigators funded via an NCI extramural fellowship Read More...

08/21/2023 - Xena can help you answer questions like: •    Is over-expression of this gene associated with lower survival in these two cancer types? •    Is this gene differentially expressed in TCGA tumor vs GTEx normal? •    What are Read More...

04/13/2023 - The NICHD DIR Tenure-Track Investigator Virtual Symposia Series provides tenure-track investigators within NICHD the opportunity to organize a virtual mini-symposium to showcase their area of science to the NICHD DIR and larger NIH intramural Read More...

03/17/2021 - Register/Join The focus of this webinar will be on two aspects of integrative analysis and translational research in the field of estrogen receptor-positive (ER+) breast cancer research. Namely, Dr. Meenakshi Anurag will discuss Read More...

This BTEP Coding Club session featured guest speakers and package developers, Ying Hu (CBIIT CGBB) and Chunhua Yan (CBIIT CGBB).

10/25/2023 - Partek Flow is your 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 analyzing Read More...

10/11/2023 - Partek Flow is your 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 analyzing Read More...

Multi-sample variant calling is an extension of single sample variant calling, where all samples are evaluated together, and the presence or absence of a variant is shown for all samples in parallel. We will perform Read More...

The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC 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...

Seurat v5 introduced the following new features: Integrative multi-modal analysis with bridge integration ‘Sketch’-based analysis of large data sets methods for spatial transcriptomics assay layers You can read about major changes between Seurat v5 Read More...

Combine multiple plots into a single figure Learn how to use aspects of cowplot and patchwork The primary purpose of this lesson is to learn how to combine multiple figures into a single multi-panel figure 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...

12/11/2023 - This presentation will provide a one-hour introduction to The AMARETTO software toolbox: multimodal and multiscale circuit-, network-, and graph-based fusion of multi-omics, clinical, imaging, and perturbation data across studies of patients, etiologies and model Read More...

09/27/2023 - Partek Flow is your 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 analyzing Read More...

Data Analysis Overview RNASEQ - Data Analysis WorkFlow Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Read More...

Let's draw an image on here, just to show that we can add one. There are two options. We can add an image as if it was another figure or we can simply draw Read More...

The Advanced Biomedical Computational Sciences (ABCS) group provides technology development, scientific consultation, collaboration and training, research, software development, and high-performance computing support. ABCS encompasses specialized groups focusing on machine learning applied to the interpretation of 2 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...

06/26/2025 - Join u for a webinar introducing MIRA, a Python oftware package de igned for the analy i of ingle-cell RNA- eq, ATAC- eq, and multimodal data. Di cover how MIRA help decode the ci Read More...

06/13/2025 - Dr. Fuhai Li,&nb p;A ociate Profe or at the chool of Medicine and Computer cience & Engineering, Wa hington Univer ity, will pre ent novel approache that combine large language Read More...

04/23/2025 - Dr. Ruppin's research is focused on multi-disciplinary, algorithmic, computationally driven analysis of large-scale biomedical omics and clinical data, with an emphasis on AI and machine / deep learning approaches. Overall, it centers on three 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...

07/24/2024 - As a cancer researcher, did you know that  data sharing  is now required by many funding agencies and journals? Join NCI CBIIT’s  Dr. Jill Barnholtz-Sloan & 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...

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...

The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were challenging or impossible into routine tasks. While QIIME began as a marker gene (e.g., 16S, Read More...

Lesson 1: Toward fully reproducible microbiome multi-omics bioinformatics with QIIME 2 Lesson 1 does not include a hands on component, but rather includes an introduction to QIIME2 by guest speaker, Dr. Greg Caporaso, a leading developer of the Read More...

10/03/2023 - Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Significant advances in the field now allow high-parameter data collection (60+ targets); however, considerable expertise and capital are needed to validate Read More...

09/13/2023 - Partek Flow is your 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 analyzing Read More...

Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...

These are considered appropriate if you are planning on doing all the data analysis yourself. High performance Linux computer (multi core, high memory, and plenty of storage) Familiarity with the “command line” and at least Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Start by activating the bioinfo environment. conda activate bioinfo Create a new directory for the multiqc data. mkdir multi cd multi Retrieve the Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Start by activating the bioinfo environment. conda activate bioinfo Create a new directory for the multiqc data. mkdir multi cd multi Retrieve the Read More...

We will be working with R from our /data/$USER directory. There is not much space in ~ (16 GB), so it is good practice to always cd to /data/$USER . cd /data/$USER Info $USER is Read More...

Can you speed up your code with parallelization? Considerations: levels of parallelization: multiprocessing vs multithreads The most common form of parallelism in R is multiprocessing. This is usually explicitly done by you or package you Read More...

developed as early as 1991 high-level, popular, general-purpose programming language that has a readable and easy to learn syntax Key features: easy to read easy to learn interpreted multi-platform wide community open source libraries (> 300,000) Two Read More...

06/14/2023 - Partek Flow is your 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 analyzing Read More...

05/03/2023 - Partek Flow is your 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 analyzing Read More...

04/27/2023 - Scientific journals almost always have limits on the number of figures that can be included in a publication. Don't fret, in the 6th and final lesson of the Data Visualization with R course 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...

04/12/2023 - Partek Flow is your 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 analyzing Read More...

03/30/2023 - Partek Flow provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers. Partek Flow software is available to NCI Read More...

03/08/2023 - Partek software provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers.  Partek Flow software is available to NCI Read More...

02/17/2023 - Dr. Brendan Miller is a post-doctoral research fellow at Johns Hopkins University in the Department of Biomedical Engineering. On Friday Feb 17, 1:00-2:00 PM, he will be discussing some tools he has recently helped develop Read More...

11/02/2022 - Do you need to strengthen your structural biology skills? The NIAID Bioinformatics and Computational Biosciences Branch (BCBB) is offering training sessions over the next few weeks. Current topics include three series of practical training Read More...

Back Services: Biophysics Facility offers ITC calorimeters as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes performing a test experiment and Read More...

OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR Read More...

OMAL focuses its research and development activities to quantitatively understand the molecular basis of three-dimensional (3D) cell organization, motility, invasion, and differentiation using fixed samples and live, 3D tissue culture models (i.e., translational models). 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 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 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...

Back Services: Biophysics Facility offers Tycho as an open-access instrument.  This instrument is very easy to use, and no formal training is required.  Core staff will help with their first experiment of new Read More...

Back Services: Biophysics Facility offers MP as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument training calendar.  Training includes mass distribution analysis of a Read More...

Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the difference Read More...

Back Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the Read More...

The NCI Research Flow Facility provides cell sorting and benchtop flow cytometry services to NCI investigators. Services are program-specific and are not available to all NCI or NIH investigators. Please inquire as to availability. Established Read More...

Bruker AVANCE 400 and 500 MHz NMR instruments. Helium Cryoprobe technology on the 500 MHz machine for added sensitivity, especially for Carbon-13 spectra. Access to a second 500 MHz instrument with Prodigy Liquid Nitrogen-cooled cryoprobe. User Accounts can be Read More...

Back Services: Biophysics Facility offers MDS as an open-access instrument. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Training includes the KD determination of a standard molecular 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 NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...

Back Services: Biophysics Facility offers DSC as an open-access instrument. First-time users must complete training before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: The differential scanning calorimeter measures the constant pressure Read More...

The Office of Collaborative Biostatistics, Office of the Clinical Director, is the statistical and data management component of CCR. The Section provides statistical leadership and data management consultation for CCR’s major clinical activities and Read More...

06/25/2025 - Join tony Brook Univer ity&r quo; Dr. Joel altz a he di cu e : the role of pathology artificial intelligence (AI) in the creation of pathology imaging biomarker , including tumor infiltrating lymphocyte 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...

01/10/2025 - NIH DIRECTORS SEMINAR SERIES In this presentation, Dr. Scholz will discuss the approach to tackling complex neurodegenerative diseases using modern genomic tools, focusing on Lewy body dementia, a major research area in her lab. 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...

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...

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...

07/18/2024 - 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...

Following Cell Ranger and/or other pre-processing tools, you will have a gene-by-cell counts table for each sample. The three most popular frameworks for analyzing these count matrices include: R ( Seurat ). Seurat, brought to you Read More...

03/05/2024 - This in-person, hands-on training will introduce participants to single cell RNA sequencing analysis using Partek Flow, a point-and-click software for analyzing high dimensional multi-omics sequencing data. At NIH, Partek Flow is hosted on the Read More...

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 analyzing sequencing 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...

VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create a "bwa index" Read More...

Create fastqc.swarm file with text editor (nano). fastqc -o output SRR10314042.fastq fastqc -o output SRR10314049.fastq fastqc -o output SRR10314054.fastq fastqc -o output SRR10314097.fastq fastqc -o output SRR10314043.fastq fastqc -o Read More...

This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes 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...

Lesson 2: Getting Started with R on Biowulf Learning objectives Understand how R can be deployed on Biowulf Understand how to access and use R modules Learn to create a custom R library on Biowulf Deploying Read More...

developed as early as 1991 high-level, popular, general-purpose programming language that has a readable and easy to learn syntax Key features: easy to read easy to learn interpreted multi-platform wide community open source libraries (> 300,000) Two Read More...

Scatter plots and plot customization Objectives Learn to customize your ggplot with labels, axes, text annotations, and themes. Learn how to make and modify scatter plots to make fairly different overall plot representations. Load a Read More...

04/14/2023 - This seminar will introduce the NIH Comparative Genomics Resource (CGR), an NIH-funded, multi-year NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms in collaboration with the genomics Read More...

04/11/2023 - Wondering why you should use R for data visualization? Lesson 1 of the Data Visualization with R course series will address this question and introduce the various plot types that will be generated throughout the Read More...

11/29/2022 - CIViC (Clinical Interpretation of Variants in Cancer, www.civicdb.org) is a free and open resource for curation and distribution of cancer variant knowledge which employs crowdsourced curation and expert moderation from published literature Read More...

11/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of 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...

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 Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative The STRIDES Initiative aims to help NIH and its institutes, centers, and offices (ICOs) accelerate biomedical research by reducing barriers in utilizing 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...

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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Extramural Common Fund Resources Metabolomics Workbench Developed by the NIH Metabolomics Common Fund's National Metabolomics Data Repository ( Read More...

The CCR Building 41 Flow Cytometry Core is a full-service facility within the Center for Cancer Research that supports over 150 users representing 26 laboratories. The Core Facility provides instrument and software training, technical expertise, assay development, and Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural CryoEM (NICE) Consortium NICE provides NCI, NIAID, NIEHS, NICHD, NIDCR, NEI, and NIA investigators with Read More...

September 8, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight Trans-NIH Intramural Sequencing Center (NISC) NISC is a multi-disciplinary genomics facility that 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 Biophysics Core’s mission is to provide support in the study of macromolecular interactions, dynamics, and stability by offering consultations, training, professional collaborations, and instrument access. General Services: Multi-technique molecular interaction studies, Kinetic and Read More...

Back Services: Biophysics Facility offers Octet as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes a full analysis of a Read More...

The LCBG Microscopy Core offers imaging technologies and training. The Core has established instrumentation for for 2D and 3D imaging of both fixed and living specimens.

The NIA Nonhuman Primate (NHP) Core Facility maintains a colony of rhesus macaques at the National Institutes of Health Animal Center. Established in 2012, the Core's mission is to offer research services supporting multi-disciplinary translational aging Read More...

Back Services: Biophysics Facility offers ZetaView as an open-access instrument. First-time users must complete a short training session before using it for the first time. Training includes instrument calibration and size analysis of a standard Read More...

Back Services: Biophysics Facility offers MST as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes the KD determination of a Read More...

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated 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...

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis 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...

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 Metabolic Clinical Research Unit (MCRU) opened in 2007 as a key component of the Strategic Plan for NIH Obesity Research . The NIDDK worked closely with the Clinical Center to design the Unit, which houses state-of-the-art 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...

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...

CREx News & Updates September 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 CCR 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...

As a multi-user facility, the different instruments provide a wide range of imaging modes for EIB scientists, from standard immunohistochemistry, through brightfield and wide-field epifluorescence imaging, to highly complex live cell confocal microscopy and super-resolution 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...

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...

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

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

Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of Read More...

The function of the SAIP is to collaborate with NCI investigators in the development of mouse models, new molecular imaging probes for early detection and therapy, monitor tumors in vivo, and perform drug efficacy studies Read More...

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to 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 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 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...

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 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 goals of the Bioinformatics Training and Education Program within NCI/CCR are: To make researchers aware of the bioinformatics resources available to them, To provide training and guidance on these resources regularly and at Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

What is Xenium? Xenium is a high-resolution, imaging-based in situ spatial profiling technology from 10x Genomics that allows for simultaneous expression analysis of RNA targets (currently in range of 100’s) within the same tissue section. Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural Core Resources NHGRI Flow Cytometry Core The Core performs high quality single cell analysis through the 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.

We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...

The AgingResearchBiobank was officially launched in January 2019 with a mission to provide a state-of-the-art inventory system for the storage, maintenance, and distribution of de-identified biospecimens and associated phenotypic, clinical, and imaging data from numerous NIA-funded Read More...

DTP maintains a repository of synthetic compounds and pure natural products that are available to investigators for non-clinical research purposes. The Repository collection is a uniquely diverse set of more than 200,000 compounds that have been Read More...

The centrally funded Statistics team within the Advanced Biomedical Computational Science group at the Frederick National Lab provides statistical consultation and data analysis support for NCI laboratories. We have broad-range expertise in biomedically relevant areas Read More...

What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and 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 bioinformatics, Read More...

The Staff Scientists/Clinicians (SSSC) Technical Enrichment Program (STEP) was established to provide SSSC’s an opportunity to compete for funding to gain comprehensive training in state-of-the-art techniques available through CCR Cores and Facilities. The Read More...

The Stem Cell Unit (SCU) has established a database to which hESC lines, adult stem cells and induced pluripotent stem (iPS) cells may be directly compared. These data give scientists the information they need when 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...

Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status, and enzyme activity levels. You can choose to search for a Read More...

CREx News & Updates November 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the NINDS Quantitative Magnetic Resonance Imaging Core. NINDS Read More...

Cores & Facilities From centralized laboratories to collaborative resources and technologies available to CCR Investigators. NCI Cores Centralized laboratories providing broad access to cutting-edge technologies and specialized expertise. Browse NCI Cores Collaborative Resources are technologies and 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 Center for Inherited Disease Research (CIDR)'s  mission is to support the genetics community by providing high-quality, cutting-edge genomics services and technologies in order to expand our understanding of disease and catalyze discoveries that Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

The NCI Clinical Research Correlatives Core provides non-CLIA-certified spectral flow cytometric assays to support clinical trials conducted in the CCR. The core specializes in immunophenotyping and immune monitoring assays. Established Technologies Spectral flow cytometry (Cytek), 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 News & Updates June 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Visit here to learn about services from Read More...

The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA Read More...

The mission of Human Brain Collection Core (HBCC) within the National Institute of Mental Health, Division of Intramural Programs (NIMH IRP) is to conduct and support research on brain and behavior, with the goal of Read More...

CREx News & Updates April 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...

With specimens that span neurological, neuropsychiatric, and neurodevelopmental diseases and disorders, the NBB serves as a central point of access to the world-class collections of our six biorepositories. In addition, the NBB provides researchers with 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...

Protein/Protein Interaction Database Through a license agreement with Elsevier, the CCR community has access to the largest Y2H data set available in the world (CCR Database of Antibodies and Protein Interactions, C-DAPI). This Read More...

CREx News & Updates May 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...

The core provides access to several different state-of-the-art 3D microscopes as well as computers to visualize and process image data. The facility houses equipment for 2D or 3D imaging of fixed and living specimens. High 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...

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 Crystallization Facility provides an automated environment for setting up crystallization experiments in a high-throughput format, storing the resulting plates under controlled conditions, and monitoring the status of prepared droplets remotely. The Facility is in 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 Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood Read More...

CREx News & Updates January 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NCI ANTIBODY CHARACTERIZATION LABORATORY (ACL) The ACL specializes in rigorously validating antibodies for signaling and 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...

Many established and emerging technologies are available to CCR scientists.  This technology-rich environment makes the CCR a unique place to conduct scientific research.  Through the OSTR, the CCR continues to find Read More...

Electron Microscopy Laboratory (EML) The EML offers investigators access to unique expertise and EM technologies that allow our partners to explore new avenues of research to enhance the knowledge of biological systems. To assist our Read More...

The EML offers investigators access to unique expertise and EM technologies that allow CCR Investigators to explore new avenues of research in order to enhance the knowledge of biological systems. To assist our customers, we Read More...

Total end-to-end system for single-cell research [embed]https://youtu.be/vMzhSzg1rUw[/embed] The BD Rhapsody Single-Cell Analysis system empowers and streamlines your research with a complete system of tools, including reagents and analysis software, Read More...

In support of Intramural Research Program (IRP) scientists, DOHS provides training, consulting, and resources to ensure that workers' risk to hazards and stresses in the laboratory environment is minimized. Our services include one-on-one consultation with 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...

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...

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 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...

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...

September 8, 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

CCR VOLUME Electron Microscopy (CVEM) aims to develop new techniques in volume electron microscopy (vEM) and, in collaboration with CCR Investigators, apply these techniques to research cell biological questions well-suited for study by high-resolution 3D Read More...

The Biophysics Resource (BR) was established in January 2001. Our mission is to provide CCR investigators with access to both the latest instrumentation and expertise in characterizing the biophysical aspects of systems under structural investigation. The Read More...

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The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management 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 Trans-NIH Metabolomics Core (TNMC) is a shared research resource that performs metabolomics analysis (and related small molecule research) for investigators at all Institutes and Centers across the NIH Intramural Research Program. The TNMC is 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...

The Division of Veterinary Resources Animal Surgery has supported large animal research and clinical care for more than 40 years. DVR surgeons provide outstanding and highly specialized large animal (rabbits, ungulates, etc.) research support in a 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 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...

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...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance 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...

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...

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...

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...

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...

This practice lesson is associated with Lesson 3 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on generating a feature table and representative sequences. We will continue working with the data Read More...

Practice Lesson 3 This practice lesson is associated with Lesson 3 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on generating a feature table and representative sequences. We will continue working with Read More...

Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...

Lesson 5: Working on Biowulf Lesson 4 Review Flags and command options Wildcards ( * ) Tab complete Accessing user history with the "up" and "down" arrows cat , head , and tail Working with file content (input, Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Generating VCF Files (Simulated data) VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create Read More...

To align FASTQ files for one sample, we construct the HISAT2 command with the following options. The "-x" flag prompts us to enter the base name (ie. without extension) of genome index. The Read More...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...

Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview Lesson 17 review In the previous class, we got an overview of functional and pathway analysis, which help to put RNA sequencing results into biological Read More...

Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...

Lesson 4: Submitting R Scripts via command line Learning Objectives Learn how to use R with less interaction Learn how to deploy sbatch R jobs, and learn about alternatives such as swarm . Learn about R job Read More...

Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...

Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language 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...