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Bioinformatics
10/23/2012 - Learn the fundamentals in genomic data analysis of CGH and SNP arrays using BioDiscovery Nexus Copy Number software. In this hands-on training session, you will learn how to load, process, visualize, and analyze array Read More...
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Bioinformatics
10/16/2012 - Fundamentals of DNA copy number analysis using Nexus Learn the basics of copy number analysis and its application to genomic research. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/ Read More...
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Bioinformatics
12/03/2020 - Register Registration is required to join this event. If you have not registered, please do so now. It has been established that over half of all cancer types are driven by DNA Copy Number Read More...
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Bioinformatics
10/22/2020 - Register Presenter: Dr. Sam Dougaparsad Field Application Scientist It has been established that over half of all cancer types are driven by DNA Copy Number Variants (CNVs). In this presentation, we will demonstrate the Read More...
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Bioinformatics
05/28/2013 - Nexus Copy Number is a user-friendly desktop application for analysis and visualization of structural variation (copy number, allelic events, and small sequence variations) from CGH and SNP array- and NGS-generated data. The simple and Read More...
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Bioinformatics
06/06/2022 - Are you a cancer researcher or bioinformatician wanting to learn more about how the experts at NCI’s Genomic Data Commons (GDC) process a variety of molecular data types? This month’s GDC support Read More...
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Bioinformatics
08/10/2020 - Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted. Associated with being causal mutations for disease phenotypes, it is important in clinical and Read More...
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Bioinformatics
06/22/2022 - Cancer origination and progression is a complex process that can be viewed as a somatic evolutionary progression with clonal cellular expansion(s) driven by accumulation of survival-/evasion-beneficial genomic mutations, alongside constantly changing selective Read More...
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Bioinformatics
03/05/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/6c09064170554e54911e2a275cedcd11/playback
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Bioinformatics
02/26/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/a8032b731dee4058875d9a45b33ef376/playback
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Bioinformatics
Web Page
Bioinformatics
Nexus Copy Number (BioDiscovery) is a graphical user interface (GUI) based bioinformatics software that specializes in copy number detection using array or sequence derived data. Its analysis capabilities are listed below. {{Sdet}}{{Ssum}}List of Read More...
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Bioinformatics
While Nexus Copy Number is a GUI based copy number analysis tool and does not require knowledge with scripting, it is a good idea to consult with bioinformatics experts at the Center for Cancer Research Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * cd * mkdir * curl * tar * cat * grep * wc * outputting data * piping data from one command to another * cut Learn: * du * pip * csvkit * datamash Read More...
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Bioinformatics
This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...
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Bioinformatics
This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...
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Bioinformatics
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...
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Bioinformatics
Nexus Copy Number runs on the user's machine so it may be limited by local resources. By default, Nexus Copy Number comes with human (NCBI build 36.1, 37) and mouse (NCBI build 38) reference genomes. Additional reference Read More...
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Confocal
Multicolor imaging Fluorescence imaging is used for protein localization and colocalization in 3D. Multi-color imaging is necessary to observe colocalization of several proteins in the same cell. Many fluorescent proteins are now available for multi-color Read More...
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Bioinformatics
01/29/2024 - In the third lesson of the Introduction to Unix on Biowulf, January 2024 series participants will learn to copy, move, rename, and remove files and folder using Unix commands. Meeting link: https://cbiit.webex.com/ Read More...
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Bioinformatics
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...
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Bioinformatics
This is an NCI-licensed software with a 2 concurrent use license. To access Nexus Copy Number, submit a request at service.cancer.gov.
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Bioinformatics
Each version of R loaded as a module includes a number of installed packages . However, you may want to install additional packages, which will by default be stored in " ~/R/%v/library where %v Read More...
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Bioinformatics
touch creates an empty file nano basic editor for creating small text files rm remove files or directories. Be careful! mkdir make a directory and rmdir (remove a directory with NO files) mv rename or Read More...
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Bioinformatics
03/23/2023 - Learn how scientists are using ddPCR technology for absolute quantification of copy number variation, pathogen detection, detection of rare mutations, genome editing, and NGS data validation. We will go over ddPCR basics, and workflow Read More...
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Bioinformatics
04/10/2019 - BTEP Wednesday, April 10, 2019 9:00 am | Eastern Daylight Time (New York, GMT-04:00) | 2 hrs Meeting number (access code): 738 427 711 Meeting password: zPJpWP$6 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked Read More...
Web Page
Bioinformatics
06/19/2017 - Harvesting the Wealth of TCGA Data The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA Read More...
Web Page
Bioinformatics
Analysis reports from Nexus Copy Number can be exported as TXT. Visualizations can be exported as JPEG, PNG, TIFF, and SVG at various resolutions.
Web Page
Bioinformatics
Partek Genomics Suite (Partek) is a graphical user interface (GUI) based bioinformatics package. It hosts a range of work flows that allow for gene expression, epigenetic, and association analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{ Read More...
Web Page
Bioinformatics
Nexus Copy Number can take data from various arrays as input including Affymetrix CEl. To see the full list, click on "Load" -> "Load Data" -> " Read More...
Bethesda, MD
Collaborative
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...
Frederick, MD
Core Facility
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...
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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...
Frederick, MD
Core Facility
The Animal Diagnostic Laboratory (ADL) provides a full range of diagnostic capabilities, including microbiological cultures on various culture medium, microscopic screening for parasites such as mites and pinworms, molecular detection of pathogens, serological evaluation of Read More...
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Bioinformatics
03/20/2025 - This class will serve as a review for essential Unix commands needed for bioinformatics. It is suitable for those who took BTEP's recent Bioinformatics for Beginners course series ( https://bioinformatics.ccr.cancer.gov/ Read More...
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Bioinformatics
03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...
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Bioinformatics
01/22/2024 - Dear Colleagues, Optical Genome Maps (OGM) provide scaffolding information for large DNA molecules. In this talk, we describe the use of this technology for detecting structural variants and chaining them Read More...
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Bioinformatics
pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...
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Bioinformatics
We will create an alias for this command. sort | uniq -c | sort -rn The "sort" utility sorts text and binary files by lines. The "uniq" utility reads input, compares adjacent lines Read More...
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Bioinformatics
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...
Web Page
Bioinformatics
10/31/2022 - UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as well as Read More...
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Bioinformatics
10/14/2021 - The ISB Cancer Gateway in the Cloud (link is external) (ISB-CGC) offers multiple avenues for accessing and analyzing large-scale cancer datasets, including TCGA, TARGET, CPTAC and important references such as GENCODE and COSMIC. ISB-CGC Read More...
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Bioinformatics
10/12/2021 - Speaker : Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...
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Bioinformatics
09/28/2020 - Register/Join This webinar is intended for cancer researchers and bioinformaticians who are interested in learning more about the NCI Genomic Data Commons’ (GDC’s) bioinformatics pipelines for data harmonization. The GDC DNA-Seq analysis Read More...
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Bioinformatics
12/05/2018 - THIS EVENT HAS BEEN CANCELLED 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Read More...
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Bioinformatics
10/26/2018 - 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Walk through of 10x Genomics Read More...
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Bioinformatics
02/21/2017 - This BTEP Workshop will cover the fundamentals and best practices of Exome-Seq analysis, including downstream interpretation of variants using a variety of in-house and NCI-licensed software solutions. There will be hands-on training on CCBR Read More...
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Bioinformatics
01/07/2016 - REGISTRATION IS FULL FOR THIS WORKSHOP (25 ATTENDEES; 6 WAITLIST) The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number Read More...
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Bioinformatics
06/02/2015 - This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine Read More...
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Bioinformatics
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...
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Bioinformatics
03/18/2014 - The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA and miRNA gene expression, and DNA Read More...
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Bioinformatics
05/01/2013 - Intended Audience: This day-long training course is intended for Users who want to apply Next Generation Sequencing methodologies for DNA-Seq, Methyl-Seq, small RNA-Seq, RNA-Seq and ChIP-Seq studies. All analyses are done on the Genomatix Read More...
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Bioinformatics
{{Sdet}}{{Ssum}}Single nucleotide variants{{Esum}} CLC Genomics Workbench (sequencing based) What file types can I start my analysis with? FASTQ Geneious Prime (sequencing based) What file types can I start my analysis with? FASTQ Read More...
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Bioinformatics
Below is a list of licensed software available for use by CCR Researchers. Linked software pages include a brief description of each software, recommendations, things to know, input data types, output data types, access information, Read More...
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Bioinformatics
Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. It can perform the analyses listed below. {{Sdet}}{{Ssum}}List of Read More...
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Bioinformatics
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...
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Bioinformatics
Note that each section of the report is marked by color coded flags (i.e., green, yellow, red). Yellow and red flags, which indicate "warning" and "fail" respectively, may indicate a Read More...
Bethesda, MD
Core Facility
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...
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...
Frederick, MD
Core Facility
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...
Frederick, MD
Core Facility
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...
Frederick, MD
Core Facility
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...
Web Page
.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...
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Confocal
Contact the CCR Microscopy Core to discuss your experiment Thank you for your interest in using the CCR Microscopy Core. Please login to the Bookitlab with your NIH credentials and register Read More...
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Bioinformatics
04/16/2025 - Updated Location: ATRF, Frederick MD, Main Auditorium What to bring: Laptop capable of connecting to internet via NIH wifi For questions or to register, please contact Amy Stonelake ( amy.stonelake@nih.gov ) Read More...
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Bioinformatics
04/15/2025 - What to bring: Laptop capable of connecting to internet via NIH wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...
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Bioinformatics
Next, we need to generate the counts (ie. number of reads that map to a transcript). But first, change back into the ~/biostar_class/snidget folder and then take a moment to think about how Read More...
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Bioinformatics
Recall that the Golden Snidget data resides in ~/biostar_class/snidget folder. Can you change into the folder and find where the sequencing reads are (ie. in which folder they are located)? {{Sdet}} Solution{{Esum}} Read More...
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Bioinformatics
Lesson 16 Practice Objectives In this lesson, we learned about the classification based approach for RNA sequencing analysis. In this approach, we are aligning our raw sequencing reads to a reference transcriptome rather than a genome. Read More...
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Bioinformatics
Lesson 10 Practice Objectives In this lesson, we introduced the structure of the FASTQ file and learned to assess quality of raw sequencing data using FASTQC. Here, we will practice what we learned using the Golden Read More...
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Bioinformatics
One of the things we will be doing quite often is to visualize genomics data using some sort of genome browser. In this course series, we will use a popular one called Integrative Genome Viewer( Read More...
Web Page
Bioinformatics
One of the things we will be doing quite often is to visualize genomics data using some sort of genome browser. In this course series, we will use a popular one called Integrative Genome Viewer( Read More...
Web Page
Bioinformatics
Variant annotation means predicting the effects of genetic variants (SNPs, insertions, deletions, copy number variations (CNV) or structural variations (SV)) on the function of genes, transcripts, and protein sequence, as well as regulatory regions. The Read More...
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Bioinformatics
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...
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Bioinformatics
Lesson 9 Practice Objectives In this practice session, we will apply our knowledge to learn about the reference genome and annotation file for the Golden Snidget dataset visualize the Golden Snidget genome using the Integrative Genome Read More...
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Bioinformatics
“Gene set enrichment analysis” refers to the process of discovering the common characteristics potentially present in a list of genes. When these characteristics are GO terms, the process is called “functional enrichment.” Warning Overall GO Read More...
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Bioinformatics
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...
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Bioinformatics
Change in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder for this portion of the class. cd ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 Now that we have our SAM files generated for the Read More...
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Bioinformatics
Prior to differential expression analysis, we need to generate a design.csv file that contains the samples and their corresponding treatment conditions. Note that csv stands for comma separated value so the columns in these Read More...
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Bioinformatics
Here, let's change back in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder. cd $hbr_uhr_hisat2 To align FASTQ files for one sample, we construct the HISAT2 command with the following options Read More...
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Bioinformatics
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...
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Bioinformatics
Lesson 2: Navigating file systems with Unix Quick review Unix is an operating system We use a unix shell (typically bash) to run many bioinformatics programs We need to learn unix to use non-GUI based tools Read More...
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Bioinformatics
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...
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Bioinformatics
Before we can align the HBR and UHR raw sequencing data to human chromosome 22 transcriptome, we need to create an index of this transcriptome (like we did with the genome). This will make the alignment Read More...
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Bioinformatics
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...
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Bioinformatics
05/26/2021 - Register Description: This webinar will highlight UCSC Xena's newest features including genome-wide differential gene expression analysis, violin plots, and a simpler way to filter and subgroup. UCSC Xena ( http://xena.ucsc.edu/ ) is Read More...
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Bioinformatics
02/08/2021 - Dear colleagues, Coming Monday, Feb 8th, we'll be having a guest lecture by Prof. Vineet Bafna from UCSD. Abstract: Increase in the number of copies of tumor promoting (onco-) genes is a hallmark Read More...
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Bioinformatics
05/19/2020 - UCSC Xena ( xena.ucscedu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as Read More...
Web Page
Bioinformatics
02/08/2016 - BTEP Workshop on Data Visualization, Exploration and Analysis NOTE: This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) Read More...
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Bioinformatics
In Biowulf, we can create a swarm script to help with parallelization of tasks. For instance, we can use a swarm script to download multiple sequencing data files from the NCBI SRA study Zaire ebolavirus Read More...
Web Page
Bioinformatics
One of the things we will be doing quite often is to visualize genomics data using some sort of genome browser. In this course series, we will use a popular one called Integrative Genome Viewer( Read More...
Web Page
Bioinformatics
In Biowulf, a swarm script can help with parallelization of tasks such as downloading multiple sequencing data files from the NCBI SRA study Zaire ebolavirus sample sequencing from the 2014 outbreak in Sierra Leone, West Africa Read More...
Web Page
CRTP
How do I determine which EM technique should be used for my research? Schedule a free consultation with the Head of EML, Dr. Ru-ching Hsia, to discuss the aim of your research project. Dr.& Read More...
Web Page
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...
Frederick, MD
Collaborative
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...
Web Page
CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx Interested in imaging large scale biological samples? Volume electron microscopy allows for Read More...
Rockville, MD
Repositories
Trans NIH Facility
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...
Web Page
CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Technology Event Biophysical Methods for Protein Interactions Monday, May 15 – Friday, May 19, 2023 This workshop will review the strategies of Read More...
Web Page
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...
Web Page
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 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...
Web Page
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...
Web Page
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...
Web Page
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...
Bethesda, MD
Trans NIH Facility
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...
Web Page
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...
Web Page
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...
Web Page
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...
Web Page
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...
Web Page
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...
Web Page
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...
Rockville, MD
Trans NIH Facility
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...
Bethesda, MD
Trans NIH Facility
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...
Web Page
Confocal
Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...
Web Page
Confocal
WIDE-FIELD MICROSCOPY Nikon Ti 2000 wide-field microscope Capabilities: This microscope is suited for live cell imaging (4D) and fixed cells (3D) imaging. This microscope produces high quality wide-field images that may be improved by Read More...
Web Page
Confocal
Macro’s for Image Processing Dr. Wisniewski wrote a number of custom ImageJ Macros aimed at streamlining image processing tasks such as: Software Imaris The world’s leading Interactive Microscopy Image Analysis software company, actively Read More...
Web Page
Confocal
Research Mission The goal of OMAL’s research is to understand molecular mechanisms driving carcinogenesis and the reversal of this process through treatment, by utilization and advancement of optical microscopy techniques. These techniques include multiplex Read More...
Web Page
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
NIDAP , the N IH I ntegrated D ata A nalysis P latform, is an innovative, cloud-based, and collaborative data aggregation and analysis platform. The platform Read More...
Web Page
Bioinformatics
More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...
Web Page
Bioinformatics
More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...
Web Page
Bioinformatics
More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...
Web Page
Bioinformatics
Lesson 4: Useful Unix For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 3 Review Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
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Bioinformatics
Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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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...