Search Results for: click chemistry-based affinity enrichment of proteins

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

The overrepresented sequences graph is shown next. Presence of overrepresented sequences may indicate enrichment artifact or the sequencing library is not very diverse. On the other hand, overrepresented sequences could have biological significance. Click here 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...

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...

Citation: Arlova A, et al. Journal of Pathology Informatics 2022 Code Availability: https://github.com/ NIH-MIP/WSI_LungTumorSeg

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

Citation: Mehralivand S, et al. Academic Radiology 2022 Code Availability: https://github.com/Project-MONAI/research-contributions/tree/main/prostate-mri-lesion-seg

The Protein Expression Laboratory produces proteins to help CCR investigators achieve their research goals with the lowest possible cost in the shortest time. PEL is operated by Leidos Biomedical Research Inc. on behalf of NCI Read More...

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

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...

NCI scientists have many choices available to them for bioinformatic analyses of Next Generation Sequencing (NGS) data. While some require expertise in programming, others provide a more user-friendly, point-and-click interface. These options include programs for Read More...

Step 1 : Login to DNAnexus Step 2 : Once you login, you should see the Projects page. If you have used DNAnexus previously, you may see more than one project listed. If this is your first time using 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...

NoMachine Installation for Biowulf To run programs with a graphical user interface (GUI) in a unix environment like Biowulf, you need to connect via a terminal emulator such as NoMachine. For example, if you want Read More...

QC all reads K-mer length, if specified will generate a report for each sample of the positions for the most commonly occurring k-mers (or sequence of nucleotides) of the specified length - can hint at Read More...

Biowulf is the Unix-based high-performance compute cluster at NIH and houses thousands of bioinformatics analyses prorgrams. While most are used to working with point-and-click operating systems such as Windows or Mac, working in a command-line Read More...

Biowulf is the Unix-based high-performance compute cluster at NIH and houses over 900 softwares including those used for bioinformatics analysis. While most are used to working with point-and-click operating systems such as Windows or Mac, working Read More...

In addition to GSEA, over representation analysis is another method for determining which molecular biology functions, component, etc. are affected as a result of gene expression between biological conditions. Essentially, statistics such as Fisher Exact Read More...

06/24/2025 - Tran late gene li t into biological in ight u ing pathway enrichment tool . Thi training will provide an overview the current tatu of pathway tool , with focu on oftware available to NIH community.  Read More...

The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...

04/01/2025 - 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 Read More...

Alan K. Jarmusch, Ph.D., Director, Metabolomics Core Facility Core, NIEHS. “Metabolomics Research in the Intramural Research Program via the Trans-NIH Metabolomics Core and NIEHS Metabolomics Core Facility” Benjamin (Benji) Schwarz, Group Lead, Metabolomics and 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...

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 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...

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 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...

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...

The research conducted within the Synthetic Biologics Core (SBC) Facility has a dual role: Generate chemical biology tools and drug candidates for molecular targets identified by NCI research groups, Develop novel effective methods and tools 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...

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 August 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NCATS Functional Genomics Laboratory (FGL) FGL is designed to help NIH Investigators use the latest 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...

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...

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.

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...

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...

09/27/2024 - This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over 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...

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...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

12/06/2023 - NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform. The NIDAP platform hosts user-friendly bioinformatics workflows (Bulk RNA-Seq, scRNA-Seq, Digital Spatial Profiling) and other component analysis Read More...

11/17/2023 - This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over Read More...

Navigating DNAnexus DNAnexus is a Cloud-based platform for NextGen Sequence analysis for which CCR has a " site-license ". For this class we are using the platform to provide a uniform, stable, preinstalled interface for Read More...

Getting a DNAnexus account - every student should go to the main DNAnexus web page (https://dnanexus.com/) and apply for a "free account". The BTEP staff will associate each account with the Read More...

Navigating DNAnexus DNAnexus is a Cloud-based platform for NextGen Sequence analysis for which CCR has a " site-license ". For this class we are using the platform to provide a uniform, stable, preinstalled interface for Read More...

Getting a DNAnexus account - every student should go to the main DNAnexus web page (https://dnanexus.com/) and apply for a "free account". The BTEP staff will associate each account with the Read More...

06/24/2020 - Join us for a webinar:  How to Analyze Single Cell RNA-Seq Data: Point, Click, Done Register:  https://www.partek.com/webinar/how-to-analyze-single-cell-rna-seq-data-point-click-done/ Single cell mRNA sequencing allows for the identification of different cell subtypes Read More...

06/26/2018 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. A point-and-click web environment provides ready access to powerful tools for the analysis, integration Read More...

03/18/2015 - This workshop will cover basics of exome-seq analysis including downstream interpretation of variants using a variety of open-source and commercial webtools (Golden Helix, IGV, Ingenuity Variant Analysis, GeneGrid (Genomatix), MuPit/Cravat). Day 1 - AM (9:30 Read More...

Biowulf (https://hpc.nih.gov/apps/jupyter.html). Biowulf is the NIH Unix-based high performance computing system. Requires getting a Biowulf account Jupyter is available through Biowulf's Open On Demand. Open On Demand enables Read More...

Biowulf (https://hpc.nih.gov/apps/jupyter.html). Biowulf is the NIH Unix-based high performance computing system. Requires getting a Biowulf account Jupyter is available through Biowulf's Open On Demand. Open On Demand enables Read More...

Biowulf (https://hpc.nih.gov/apps/jupyter.html). Biowulf is the NIH Unix-based high performance computing system. Requires getting a Biowulf account Jupyter is available through Biowulf's Open On Demand. Open On Demand enables Read More...

Another quality assurance measure is to determine correlation between samples. It is expected that samples from the same biological condition will be highly correlated to each other based on gene expression. As expected, correlation plot Read More...

Mobaxterm is another open source and graphical based ssh client that Windows users can use to interact with Biowulf. To obtain Mobaxterm, goto https://mobaxterm.mobatek.net and click the Download tab at the top ( Read More...

Mobaxterm is another open source and graphical based ssh client that Windows users can use to interact with Biowulf. To obtain Mobaxterm, goto https://mobaxterm.mobatek.net and click the Download tab at the top ( Read More...

Partek Flow is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. Why Partek Flow? Partek Flow is compatible with all major genomic formats Read More...

Partek Flow is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. Why Partek Flow? Partek Flow is compatible with all major genomic formats Read More...

After generating and filtering out lower expressing genes from the median ratio normalized expressions data, it is time to perform differential expression analysis to see if there are genes or transcripts (trancripts will be used Read More...

Putty is an open source and grpahical based ssh client that is also capable of scp and sftp. It is one of the ways to interface with Biowulf for Windows users. To obtin Putty, goto Read More...

Putty is an open source and grpahical based ssh client that is also capable of scp and sftp. It is one of the ways to interface with Biowulf for Windows users. To obtin Putty, goto Read More...

NIDAP is cloud-based, expandable, and flexible. is collaboration-oriented; the workbook could be shared with other users. has point-n-click connections, requiring no coding experience to use. can be used with pre-built templates or you can build-your-own Read More...

To create a new Code Workbook, once again use the now-familiar green + New button, but this time please choose Code Workbook option. You may have to scroll down a little to see it. Feel free Read More...

The Chemical Synthesis Group is a component of the Chemical Biology Laboratory. This facility provides synthetic chemistry resources and expertise to the NCI Intramural community. The facility’s capabilities include: Providing expertise, consultation, and experience Read More...

Profile the entire transcriptome and more than 570 proteins on a single slide with the GeoMx Digital Spatial Profiler

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...

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...

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 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...

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...

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...

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...

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...

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...

Biomarker Discovery with Morphological Context:  Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial 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...

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 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...

CREx News & Updates June 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 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...

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...

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

Protein/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...

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...

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...

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...

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 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...

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...

The NIH MRI Research Facility (NMRF) is a shared, intramural resource for human imaging studies. The NMRF is supported by all Institutes at NIH and reports to the Shared Resources Subcommittee (SRS) of the Scientific Read More...

The Flow Cytometry Core (LGI) offers established technologies to support studies using flow cytometry and cell sorting. Established Technologies Applications that run on FACS Caliburs include: Immunophenotyping (up to 4-color), Intracellular markers, including cytokines and Read More...

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...

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.

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 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...

Biophysics Core Facility assists NIH investigators in measuring molecular interactions and in characterizing macromolecular properties. This includes binding studies of proteins, DNA, RNA, and their ligands in buffers, cell lysate, plasma, and other media. We 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 Department of Laboratory Medicine provides state-of-the-art laboratory testing in support of Clinical Center patient care and will serve as a center of excellence in research and training in laboratory medicine, particularly in areas which Read More...

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 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...

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...

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...

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...

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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . 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...

Functional annotation clustering works to cluster annotations that share similar genes. If we click on Functional Annotation Clustering in the Annotation Summary Results page then we can see the functional annotation clusters that our input Read More...

Plots condense complex and busy tabular data into a form that is easier to interpret. An expression heatmap is a common visualization used in RNA sequencing analysis. A heatmap shows numerical data on a color Read More...

We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Review the course syllabus and general structure of lessons to come. Introduce Unix and describe how it differs from other operating systems. Introduce and get set Read More...

Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Course overview. Introduce Unix and describe how it differs from other operating systems. Introduce and get set up on DNAnexus and the GOLD system. Discuss ways Read More...

In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that Read More...

Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and Read More...

Unix, what is it, and why should biologists take the time to learn it? The Unix operating system forms the basis of many bioinformatics analyses resources, such as the NIH High Performance Cluster (HPC) Biowulf/ Read More...

04/12/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/11/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/09/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

10/27/2014 - PLEASE NOTE: This 2 day workshop is  a BYOC (Bring your own Laptop Computer) class. In order to provide more flexibility with room scheduling we are experimenting with a new format that involves students brining Read More...

Plots condense complex and busy tabular data into a form that is easier to interpret. An expression heatmap is a common visualization used in RNA sequencing analysis. A heatmap shows numerical data on a color Read More...

Fugu is an open source and graphical based application for Mac users that can be used for data transfer between local and high performance compute systems such as Biowulf. To obtain Fugu, refer to the Read More...

Fugu is an open source and graphical based application for Mac users that can be used for data transfer between local and high performance compute systems such as Biowulf. To obtain Fugu, refer to the Read More...

08/14/2025 - Biowulf isthe 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 (NGS) Read More...

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

06/17/2025 - Explore tran cription factor binding ite analy i and peak calling. Thi training will introduce ChIP- eq data analy i followed by a tep-by- tep live demon tration of a ChIP- eq analy i Read More...

06/10/2025 - Under tand how to identify and interpret variant . Thi training will introduce Exome equencing data analy i followed by a tep-by- tep live demon tration of an exome equencing analy i workflow u ing Read More...

05/16/2025 - This one-day in-person NIH AI Symposium will bring together researchers from a broad range of disciplines to share their AI-related research, with the goal of disseminating the newest AI research, providing an opportunity to Read More...

This archive contains past and present issues of the &nbsp;BTEP BioInformatics Bulletin. The BTEP Bioinformatics Bulletin features select upcoming bioinformatics events offered across NIH and is distributed monthly via email to the Center Read More...

04/17/2025 - Cardinal Bernardin Cancer Center Virtual Grand Rounds Interested in learning about various cancer indicators, approaches for data integration , and how to leverage data to drive scientific discovery? Then join NCI CBIIT&rsquo;s 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...

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...

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...

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

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...

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...

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...

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...

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...

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...

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...

Clinical Support Laboratory – Cellular Immunology offers a spectrum of bioassays to assess cellular responses to antigens and mitogens including ELISPOT, cytotoxicity assays, and proliferation assays. Established Technologies Elispot Assays, Dual or Triple Color Fluorospot Assays, Read More...

The Bloomington Drosophila Stock Center (BDSC) collects, maintains, and distributes genetically defined strains of Drosophila melanogaster for research and education. The BDSC supports a large, worldwide community of scientists using Drosophila as a model organism 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 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...

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...

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 Molecular Targets Program (MTP) is an organizational entity within the Center for Cancer Research (CCR) at NCI. The MTP provides the focus and infrastructure to enable CCR tenured and tenure-track Principal Investigators to initiate 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...

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...

October 6, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NIH Center For Human Immunology, Inflammation, And Autoimmunity (CHI) CHI is a 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 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Cores on CREx NIBIB BEPS Micro Analytical Immunochemistry Unit The Micro Analytical Immunochemistry Unit employs a variety 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...

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...

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 Specimen Resource Locator (SRL) is a biospecimen resource database designed to help researchers locate resources that may have the samples needed for their investigational use. This publicly searchable database includes information about biospecimen banks 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 Center for Advanced Preclinical Research (CAPR) specializes in evaluating the efficacy of preclinical compounds, existing drugs, or biologics (therapeutics) in genetically engineered mouse models, GEM-derived allograft (GDA) models, or patient-derived mouse xenografts (PDX). We Read More...

The Mouse Modeling Core assists NIH investigators by generating and preserving genetically-engineered mouse strains. Services include scientific consultation, gene-targeting in mouse embryonic stem cells, micro-injection of nucleic acids, proteins, or ES cells into mouse embryos, 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...

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...

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...

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...

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

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

Protein Expression Laboratory The Protein Expression Laboratory develops, improves, and delivers protein-centric services. Our goal is to help client investigators achieve their research goals with the lowest possible cost in the shortest time. All PEL 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 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 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...

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...

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...

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 CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making 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...

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 News & Updates August 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...

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...

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...

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...

The Pan-Microbial Serology Facility (PMSF) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The PMSF focuses on determining individualized pan-microbial immune profiles associated with human diseases including immunological 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...

NCI LASP Animal Research Technology Support (ARTS) provides customized technical support for basic and translational animal-based research to the scientific community. We offer a wide array of services ranging from expert colony management to the 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...

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

The 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 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...

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

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 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...

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...

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 Biopharmaceutical Development Program (BDP) provides resources for the development of investigational biological agents. The BDP supports feasibility through development and Phase I/II cGMP manufacturing plus regulatory documentation.The BDP was established in 1993. We 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...

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

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

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

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, 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 15: Finding differentially expressed genes Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 14 review In the previous lesson, we learned to visualize RNA sequencing alignment results in the Integrative 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 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R Read More...

Learning Objectives Understand the components of an HPC system. How does this compare to your local desktop? Learn about Biowulf, the NIH HPC cluster. Learn about the command line interface and resources for learning. What 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...

Managing Bioinformatics Projects with Jupyter Lab Learning Objectives After this class, participants will have obtained the foundation needed to start using Jupyter Lab as an all-in-one place to maintain code, output, and other description of Read More...

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

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

04/17/2017 - Probing DNA-Protein Interactions This 2-day workshop, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics to be covered include: experimental design; read alignment; Read More...

09/01/2016 - This 2-day workshop, including a BYOD (Bring Your Own Data) exercise, will provide an introduction and hands-on training for Cytoscape, which is an open source software platform for visualizing  networks and integrating these networks Read More...

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

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...

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...

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