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Bioinformatics
12/08/2022 - 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...
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Bioinformatics
05/10/2021 - Abstract: Deep learning is revolutionizing the prediction of protein tertiary structure and is close to solve this grand challenge hanging over the scientific world for many years. In this talk, I will describe how Read More...
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Bioinformatics
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 parallelization in the context of Biowulf We have organized Read More...
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Confocal
Software Image Acquisition Commercial imaging systems of LRBGE Optical Microscopy Core are controlled by acquisition software specifically designed for the appropriate microscope, such as ZEN (Zeiss confocal microscopes), Nikon Elements (Nikon), Imspector (Abberior). Custom-built HILO Read More...
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Bioinformatics
For package support and questions on related topics, there is an active Bioconductor support site that operates similarly to other forums (e.g., Biostars ). There is also a Slack workspace for general community interaction with Read More...
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Bioinformatics
As we learn more about R and start learning our first commands, we will keep a record of our commands using an R script. Remember, good annotation is key to reproducible data analysis. An R Read More...
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Bioinformatics
For package support and questions on related topics, there is an active Bioconductor support site that operates similarly to other forums (e.g., Biostars ). There is also a Slack workspace for general community interaction with Read More...
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Bioinformatics
As we learn more about R and start learning our first commands, we will keep a record of our commands using an R script. Remember, good annotation is key to reproducible data analysis. An R Read More...
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Bioinformatics
12/14/2022 - David Baker is the director of the Institute for Protein Design, a Howard Hughes Medical Institute Investigator, the Henrietta and Aubrey Davis Endowed Professor in Biochemistry, and an adjunct professor of genome sciences, bioengineering, Read More...
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Bioinformatics
The Lasergene Protein package includes Protean 3D (+1 prediction per Nova Application) and DNASTAR Navigator. The protein analysis and modeling workflow provides tools pertinent to antibody modeling, protein docking interaction prediction, epitome prediction, molecular motion visualization, Read More...
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Bioinformatics
If the autoSlide feature is set or if the audio-slideshow plugin is used, pre-recorded chalkboard drawings can be played. The slideshow plays back the user interaction with the chalkboard in the same way as it Read More...
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Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Cytoscape is an open source software platform Read More...
Frederick, MD
Core Facility
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...
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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.
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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...
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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...
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Confocal
2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...
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Bioinformatics
06/06/2025 - The la t decade ha demon trated the power of genomic to unravel the etiology of complex trait and di ea e . The va t majority of genomic tudie have been ba ed on Read More...
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Bioinformatics
05/20/2025 - In this talk, Dr. Hwang will discuss three examples of applying single-cell and spatial oncology approaches to the study of pancreatic cancer. First, he will explain how they utilized single-nucleus RNA-sequencing to uncover an Read More...
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Bioinformatics
If all R could do was function as a calculator, it wouldn't be very useful. R can be used for powerful analyses and visualizations. As we learn more about R and begin implementing our Read More...
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Bioinformatics
07/27/2023 - This new webinar will be covering and discussing the host responses to vaccines with invited speakers Dr. Oliver He and Dr. Guanming Wu. During the hour long webinar, Vaccine Induced Gene Expression Analysis Tool ( Read More...
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Bioinformatics
login node (head node) Used for submitting resource intensive tasks as jobs Editing and compiling code File management and data transfers on a small scale compute nodes (worker nodes) For computational processes Requires interaction with Read More...
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Bioinformatics
01/07/2022 - Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases including lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to Read More...
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Bioinformatics
11/23/2020 - Abstract: Mutational processes shape the genomes of cancer patients and their understanding has important applications in diagnosis and treatment. In this talk I will describe recent works in my lab to model mutational processes Read More...
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Bioinformatics
09/09/2020 - Each 90-minute microlab starts with an inspiring conversation between thought leaders from the Cancer moonshot and creative visualization experts, followed by an opportunity to engage new colleagues from other fields in a fascinating discussion Read More...
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Bioinformatics
08/28/2020 - Speaker: Dr. Luke Gilbert is an Assistant Professor in the Department of Urology, the Helen Diller Family Comprehensive Cancer Center and the Innovative Genomics Institute at the University of California, San Francisco. Dr. Gilbert Read More...
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Bioinformatics
As we learn more about R and start learning our first commands, we will keep a record of our commands using an R script. Remember, good annotation is key to reproducible data analysis. An R Read More...
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Bioinformatics
Request an interactive session using sinteractive with the following options. --gres=lscratch:5: to allocate 5gb of local temporary/scratch storage space --mem=2gb: to request 2gb of memory or RAM --tunnel: to open up a Read More...
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Bioinformatics
Login node (head node) Used for submitting resource intensive tasks as jobs Editing and compiling code File management and data transfers on a small scale Compute nodes (worker nodes) For computational processes Requires interaction with Read More...
Web Page
Bioinformatics
Login node (head node) Used for submitting resource intensive tasks as jobs Editing and compiling code File management and data transfers on a small scale Compute nodes (worker nodes) For computational processes Requires interaction with Read More...
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Bioinformatics
The yaml header or file allows us to control document level or project level options. Here, we can specify formats, themes, executable options, and others. --- title: "Volcano" author: "Alex Emmons, Ph. Read More...
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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...
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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...
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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...
Frederick, MD
Collaborative
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...
Bethesda, MD
Core Facility
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...
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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...
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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...
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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...
Bethesda, MD
Trans NIH Facility
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...
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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...
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Bioinformatics
09/09/2025 - Join&nb p;the National Heart, Lung, and Blood In titute (NHLBI)&nb p;for a hybrid work hop to explore how medicine will be tran formed by the current artificial intelligence ( Read More...
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Bioinformatics
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...
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Bioinformatics
03/20/2025 - Please note: Registration is required to get the Meeting Link for this event. Please pre-register. BTEP and the Single Cell and Spatial Transcriptomics Interest Group jointly present: Quantifying spatiotemporal dynamics during embryogenesis is crucial Read More...
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Bioinformatics
Register now for an upcoming seminar on January 22, 2025 , “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data” . This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will Read More...
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Bioinformatics
11/12/2024 - Join us at the upcoming hybrid NIH BRAIN NeuroAI Workshop on November 12 and 13, with virtual access to in-person panels and discussions at the NIH Campus in Bethesda, MD. Artificial intelligence (AI) is reshaping technology Read More...
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Bioinformatics
01/19/2024 - Trey Ideker, Ph.D., is a professor of medicine, bioengineering, and computer science, and former chief of genetics at the University of California San Diego (UCSD). Additionally, he is director or co-director of the Read More...
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Bioinformatics
Thus far we have: Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic . Aligned the raw sequences to a reference genome (human chromosome 22 Read More...
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Bioinformatics
There are many databases devoted to relating genes and gene products to pathways, processes, and other phenomenon. Again, the following is not meant to be a comprehensive list. Kyoto Encyclopedia of Genes and Genomes (KEGG) Read More...
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Bioinformatics
sbatch is used to submit batch jobs, which are resource provisions that run applications on compute nodes and do not require supervision or interaction . To submit a batch job, a job script containing a list Read More...
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Bioinformatics
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...
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Bioinformatics
10/19/2022 - Speaker: Ron Germain, M.D., Ph.D. NIH Distinguished Investigator NIAID, NIH Dr. Germain received his Sc.B. and Sc.M. from Brown University in 1970 and his M.D. and Ph.D. from Harvard Read More...
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Bioinformatics
02/11/2022 - The seminar is open to the public and registration is required each month. Dr. Hunter Mosely plans to discuss the richness of open data resources in biology and how they can support machine learning Read More...
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Bioinformatics
01/04/2021 - Abstract: Phenotypic heterogeneity in cancer is often caused by different patterns of genetic alterations. Understanding such phenotype-genotype relationships is fundamental for the advance of personalized medicine. In this talk, I will present a computational Read More...
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Bioinformatics
08/17/2020 - Speaker: Dr. Mary Carrington The exceptional influence of HLA and related genes located in the MHC on human disease relative to that of variation in the rest of the genome has now been clearly Read More...
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Bioinformatics
Thus far we have: Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic. Aligned the raw sequences to a reference genome (human chromosome 22 Read More...
Web Page
Bioinformatics
Request an interactive session using sinteractive with the following options. --gres=lscratch:5: to allocate 5gb of local temporary/scratch storage space --mem=2gb: to request 2gb of memory or RAM --tunnel: to open up a Read More...
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Bioinformatics
Stay in the /data/username/pies_2023 folder and request an interactive session using sinteractive with the following options. --gres=lscratch:5: to allocate 5gb of local temporary/scratch storage space --mem=2gb: to request 2gb of Read More...
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Bioinformatics
Step 1 to starting Jupyter Lab on Biowulf via command is to request an interactive compute session using sinteractive with the following options. The local temporary/scratch storage space and RAM allocation can be modified base Read More...
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Bioinformatics
There are many databases devoted to relating genes and gene products to pathways, processes, and other phenomenon. Again, the following is not meant to be a comprehensive list. Kyoto Encyclopedia of Genes and Genomes (KEGG) Read More...
Web Page
Bioinformatics
The yaml header or file allows us to control document level or project level options. Here, we can specify formats, themes, executable options, and others. --- title: "Volcano" author: "Alex Emmons, Ph. Read More...
Bethesda, MD
Core Facility
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...
Rockville, MD
Collaborative
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...
Bethesda, MD
Collaborative
The Mass Spectrometry Unit of the Collaborative Protein Technology Resource uses mass spectrometry for the study of proteins. We perform collaborative experiments with CCR researchers in areas such as: interactomes, quantitative global proteome analyses, and Read More...
Bethesda, MD
Trans NIH Facility
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...
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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...
Frederick, MD
Core Facility
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 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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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[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...
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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...
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Confocal
2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...
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Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...
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Bioinformatics
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...
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Bioinformatics
R Crash Course: A few things to know before diving into wrangling Learning the Basics Objectives 1. Learn about R objects 3. Learn how to recognize and use R functions 4. Learn about data types and accessors Console Read More...
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Bioinformatics
Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To generate high quality data reports using R Markdown to make data analysis more reproducible. Reminder: Uploading files from RStudio Server Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
09/22/2015 - Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Open Source Tools. As we walk though hands-on analysis of a cancer dataset, you will learn the principles of experimental design, Read More...