Search Results for: PRM parallel reaction monitoring

First we need to create the indices for Chr22. hisat2-build refs/22.fa refs/22.fa where "refs/22.fa" is the reference genome, and also the prefix we will use for the index created. Read More...

First we need to create the indices for Chr22. hisat2-build refs/22.fa refs/22.fa where "refs/22.fa" is the reference genome, and also the prefix we will use for the index created. Read More...

First we need to create the indices for Chr22. hisat2-build refs/22.fa refs/22.fa where "refs/22.fa" is the reference genome, and also the prefix we will use for the index created. Read More...

Make a directory called Lesson6_practice and change directories. {{Sdet}} Solution{{Esum}} mkdir Lesson6_practice cd Lesson6_practice {{Edet}} Navigate to the NCBI website and grab the accession information for the associated BioProject. Download the 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...

Lesson 6 Practice The following was designed to practice skills learned in lesson 6. Find the data Here is a paper examining the relationship between the oral microbiome and nasopharyngeal carcinoma. Where can you find the associated Read More...

Recall in the lesson that SAM files are human readable so we will need to convert these to sorted and indexed BAM files, which are machine readable for downstream steps in our analysis. How do Read More...

After the index file for the genome has been created, we will use a tool called bedGraphToBigWig to generate bigWig (bw) files from bedGraph (bg). Again, we use cat and parallel where cat reads/ids. Read More...

After the index file for the genome has been created, we can go ahead and run the following to create the bigWig files for both the HISAT2 and Bowtie2 alignments. Generate bw files for the Read More...

To help us align all of the FASTQ files in one go, we should create in the reads directory a file with the sample IDs names for the Golden Snidget. First, change into the ~/biostar_ Read More...

Slurm system: batch jobs, swarms jobs, interactive sessions Introduce parallel command Retrieve data from NCBI Trouble shooting jobs and job failures Help session: submitting jobs on Biowulf

Slurm system: batch jobs, swarms jobs, interactive sessions Introduce parallel command Retrieve data from NCBI Trouble shooting jobs and job failures Help session: submitting jobs on Biowulf

For RNA sequencing studies, we need to use a splice aware aligner to account for reads that map across exons. Bowtie2 is a commonly used aligner for DNA sequencing and is not splice aware. Let' Read More...

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

Flags and command options ( - ) are used to alter program functions Wildcards (e.g., * ) Tab complete for less typing Accessing user history with the "up" and "down" arrows on the keyboard Read More...

10/11/2021 - This course uses lectures, demos, and hands-on labs to give you an overview of Google Cloud products and services so that you can learn the value of Google Cloud and how to incorporate cloud-based Read More...

The NCI Clinical Research Correlatives Core provides non-CLIA-certified spectral flow cytometric assays to support clinical trials conducted in the CCR. The core specializes in immunophenotyping and immune monitoring assays. Established Technologies Spectral flow cytometry (Cytek), Read More...

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

The 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...

11/12/2024 - In this hour and half online training, attendees will learn how to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The training covers common pitfalls in writing MATLAB Read More...

09/14/2023 - In this 90-minute session, participants will learn to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The course covers common pitfalls in writing MATLAB code, explores the use Read More...

For RNA sequencing studies, we need to use a splice aware aligner to account for reads that map across exons. Bowtie2 is a commonly used aligner for DNA sequencing and is not splice aware. Let' Read More...

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...

Module 1 Week 1 Introductions and File systems L1 Why bioinformatics? L2 Intro to statistics? Lesson 1 Intro to Course, learning objectives Intro to Unix operating system What is a shell (how to proceed Windows vs Mac) What Read More...

Lessons focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading data from NCBI. Lesson 1 - Introduction to Unix and the Shell ( Recording ) Lesson 2 - Navigating file Read More...

To complement this course, we have created a Biostars module on Biowulf. The following programs have been included in that module: Apps/Dependencies: bbtools bcftools bedtools bio bioawk blastn bowtie2 bwa cd-hit csvkit csvtk cutadapt Read More...

Download data from the SRA with fastq-dump split files into forward and reverse reads download part, not all, of the data Compare fastq-dump to fasterq-dump Introduce prefetch Look at XML-formatted data with sra-stat Grab SRA Read More...

Download data from the SRA with fastq-dump split files into forward and reverse reads download part, not all, of the data Compare fastq-dump to fasterq-dump Introduce prefetch Look at XML-formatted data with sra-stat Use e-utilities ( Read More...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph file that contains coverage along genomic regions. Enchancing your vocabulary: BED file - this is also known as Browser Extensible Read More...

Biostars Software Description To complement this course, we have created a Biostars module on Biowulf. The following programs have been included in that module: Apps/Dependencies: bbtools bcftools bedtools bio bioawk blastn bowtie2 bwa cd-hit Read More...

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

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

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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * downloading data from SRA * decompressing tar files * e-utilities * fastq-dump Learn: * sra-stat * XML format * automating SRA downloads * working with comma-separated values (csv) format * Read More...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph (with extension bg) file that contains coverage along genomic regions. Enhancing your vocabulary: BED file - this is also known Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

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...

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...

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...

11/17/2022 - Join Icahn School of Medicine at Mount Sinai’s Dr. Zeynep Gümüş to learn about a user-friendly tool she and her team are developing to enable researchers of all computational skill levels to Read More...

11/10/2022 - R on Biowulf: a set of short case studies that will demonstrate the usage of R on the NIH Biowulf cluster We will focus on: 1) migrating/reinstalling R packages from your laptop to the Read More...

09/22/2022 - The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. In this lecture, new discoveries from Read More...

04/28/2021 - Register/Join In this public workshop, participants will have the opportunity to discuss the challenges and opportunities involved in establishing effective data management and sharing practices. The organizers encourage anyone working with data to Read More...

12/02/2020 - Register Visualizing biological data can be challenging. Heat maps are useful for showing the basic distribution of gene expression but interactivity is needed for additional, in-depth analysis. Clustergrammer2 is a visualization tool that allows Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private 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...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...

The 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...

The Crystallization Facility provides an automated environment for setting up crystallization experiments in a high-throughput format, storing the resulting plates under controlled conditions, and monitoring the status of prepared droplets remotely. The Facility is in Read More...

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

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

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...

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 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...

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

In support of Intramural Research Program (IRP) scientists, DOHS provides training, consulting, and resources to ensure that laboratory equipment is used and maintained properly and safely. We provide expert safety and health consulting support for Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NCI CLIA Molecular Diagnostics Laboratory (CMDL) The NCI CMDL is available to assist all Read More...

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

The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core Read More...

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 User Survey The CREx Team is carrying out a CREx User Survey. We would greatly appreciate 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...

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...

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...

Lesson 13 Practice Objectives In this lesson we learned how to align raw sequencing reads to reference and to process alignment results for downstream analysis. Here, we will test our knowledge by continuing with the Golden Read More...

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

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

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

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...

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...

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...

Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain Read More...

Module 1 Week 1 Introductions and File systems L1 Why bioinformatics? L2 Intro to statistics? Lesson 1 Intro to Course, learning objectives Intro to Unix operating system What is a shell (how to proceed Windows vs Mac) What Read More...

“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...

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...

Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain 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...

Now that our HISAT2 indices have been built and the text file with the sample IDs has been generated, we can do the actual alignment. First, change into the ~/biostar_class/snidget/snidget_hisat2 folder Read More...

From the publication REDO: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak First we get the project (PRJN) number from the publication: PRJNA257197 Next we're going to query the "sra& Read More...

Let's submit a batch job. We are going to download data from the Sequence Read Archive (SRA) , a public repository of high throughput, short read sequencing data. We will discuss the SRA a bit Read More...

How can we better automate downloads from the SRA? For example, what if we want the sequence files from the publication Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak First we need Read More...

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...

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...

The bulk RNA-Seq test data we've been working with is in FASTQ format. We'd like to do a BLAST search on a couple of these sequences. Data must be in FASTA format to Read More...

Bioinformatics for Beginners: RNA-Seq Course Description: This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focuses on RNA-Seq analysis. All steps of Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to activate the bioinfo environment when working on Biostar class materials. conda activate bioinfo The bulk RNA-Seq test data we've Read More...

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

09/22/2022 - The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. In this lecture, new discoveries from Read More...

11/19/2021 - High-resolution, whole-brain microscopy provides unprecedented new insights into the brain’s structural organization, molecular diversity and connectivity. The Brain Image Library (BIL) provides infrastructure that facilitates the sharing of this valuable data, enabling investigators Read More...

06/04/2021 - Speaker: Rangan Sreenivas Sukumar Distinguished Technologist Hewlett Packard Enterprise (HPE) Abstract: In March of 2020, the “Force for Good” pledge of intellectual property to fight COVID-19 brought into action HPE products, resources and expertise to Read More...

04/22/2021 - Abstract: Single-cell RNA-sequencing has emerged as a popular technique for dissecting temporal processes such as tumor development and cell differentiation from snapshots of asynchronous ensembles of cells. Ongoing efforts in this area are now Read More...

04/21/2021 - Register Here Inherited and environmental influences can put people at greater risk of cancer and impact their response/resistance to treatment. In this presentation, Dr. Eliezer Van Allen will describe how a patient’s Read More...

03/05/2021 - Overview: The Human Cell Atlas (HCA) is an ambitious global initiative that aims to create a comprehensive reference map of all human cells—the fundamental units of life—as a basis for both understanding 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...

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...

Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) 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 CCR-Frederick Flow Cytometry Core Facility provides research support to the Frederick-CCR community, including cytometry analysis and sorting services, instrument maintenance, new user training, and technical consultation. Typical Assays Performed by Core Instruments Immunophenotyping of 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...

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...

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

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

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

CREx News & Updates 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 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...

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...

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...

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 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...

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 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 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...

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...

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

The 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...

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

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

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...

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...

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

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

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...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

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

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

Lesson 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...

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...

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...