Search Results for: circular dichroism (CD) spectroscopy

This page uses information directly from the Biostar Handbook by Istvan Albert (PSU). Activate the bioinformatics environment and install some software as directed. conda activate bioinfo conda update -y blast conda install -y cd-hit pip Read More...

ls (list) pwd (print working directory) 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 Read More...

ls (list) pwd (print working directory) 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 Read More...

ls (list) pwd (print working directory) 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...

ls (list) pwd (print working directory) 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...

The mv command is a handy way to rename files if you've created them with a typo or decide to use a more descriptive name. For example: cd mv file2.txt README.txt ls 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 EML offers investigators access to unique expertise and EM technologies that allow CCR Investigators to explore new avenues of research in order to enhance the knowledge of biological systems. To assist our customers, we Read More...

setwd() Set working directory (equivalent to cd ) getwd() Get working directory (equivalent to pwd )

To access the NIH Partek Flow server, go to https://partekflow.cit.nih.gov/flow and enter the user's NIH username and then password. Note User may have selected a password different than that Read More...

pwd (print working directory) ls (list) nano (basic editor for creating small text files) rm (remove files) mkdir (make a directory) cd (change directory) mv (rename or move files) less (view files) man (manual) cp ( Read More...

Today, we will download data from the NCBI/SRA. Let's create a project directory named biostar_class and new folder within biostar_class named sra_data to store the data we are using today. Read More...

Today, we will download data from the NCBI/SRA. Let's create a project directory named biostar_class and new folder within biostar_class named sra_data to store the data we are using today. Read More...

For this portion of the review, let's create a directory in the ~/biostar_class folder called review1. Check your present working directory (PWD) pwd If you are not in the ~/biostar_class cd ~/biostar_ Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Use the "cd" command to change Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Use the "cd" command to change Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Change to your data directory as follows: 1. Use Read More...

Directories must be completely empty of all files and other contents before you can delete them. There are ways to "recursively" remove file and directories using the -r option, but these can be Read More...

Login to Biowulf. Make sure you are on VPN. Open your Terminal if you are using a mac or the Command prompt if you are using a Windows machine. ssh username@biowulf.nih.gov When Read More...

All Unix commands have a man or "manual" page that describes how to use them. If you need help remembering how to use the command ls , you would type: man ls There are Read More...

Go to your biostar_class directory. cd biostar_class Create a new directory named "refs" and go to that directory. mkdir refs cd refs Use the following command to retrieve data from NCBI. Read More...

Before getting started, let's create a folder called snidget within the ~/biostar_class directory to conduct our analysis. To do this, we need to first go to the ~/biostar_class folder, how do you 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...

Create a directory called golden and change directories. {{Sdet}} Solution{{Esum}} mkdir golden cd golden {{Edet}}

The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command line. Begin Read More...

Lesson 2 Practice The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command Read More...

Before getting started, let's create an output directory for the classification based analysis results in the ~/biostar_class/snidget folder. cd ~/biostar_class/snidget mkdir -p classification_based/salmon

In this lesson, we will continue to use the HBR and UHR dataset and focus on learning how to visualize the alignment outputs (both HISAT2 and Bowtie2) in IGV. Before getting started, change into the ~/ 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...

We can use the less command to view the contents of a file like this. cd less /data/sample.fasta You'll need to type q to get out of less and back to the 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...

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...

The Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...

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

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

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

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

The 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...

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...

Accessing Partek Flow at NIH and tips for data transfer Learning objectives Instructions for accessing Partek Flow NCI researchers can find instructions for accessing Partek Flow at https://bioinformatics.ccr.cancer.gov/btep/partek-flow-bulk-and-single-cell-rna-seq-data-analysis/ . But Read More...

Download the data using prefetch and fasterq-dump . {{Sdet}} Solution{{Esum}} cd raw_data cat ../sra_id.txt | while read sra_id; do prefetch $sra_id; fasterq-dump $sra_id; gzip ${sra_id}*.fastq;done {{Edet}} What Read More...

The data is available in the Sequence Read Archive (BioProject PRJNA803155 ), so the first step is to grab the data from the SRA. For your convenience, we have also created a compressed archive of the Read More...

According to the data availability statement, the data can be found in PRJNA803155 . Change to the Practice directory created above or make it now. Then make a new directory named raw_data . {{Sdet}} Solution{{Esum}} Read More...

We will need to use a manifest file to import. See the Import tutorial . Note: The manifest file can be comma separated depending on the format that you use at import , despite what is written Read More...

Practice Lesson 2 For the help sessions, we will work on processing sequences generated in Zhang Z, Feng Q, Li M, Li Z, Xu Q, Pan X, Chen W. Age-Related Cancer-Associated Microbiota Potentially Promotes Oral Squamous Read More...

As you can see from the image, there are several accessor functions to access the data from the object: assays() - access matrix-like experimental data (e.g., count data). Rows are genomic features (e.g., Read More...

For this exercise, go back to the ~/biostar_class/hcc1395 folder and create a new directory called trimmed_data. {{Sdet}} Solution{{Esum}} cd ~/biostar_class/hcc1395 mkdir trimmed_data cd trimmed_data {{Edet}} The adapters Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

Recall that the scripts used for differential expression analysis are in the folder /usr/local/code. We can also access this folder using the environmental variable CODE. How many scripts are in this folder (find Read More...

We will be downloading a FASTQ file from the Sequence Read Archive to learn about trimming. But first, go back to the ~/biostar_class folder and then create a new directory named trimming. cd ~/biostar_ Read More...

First we will obtain the SRA data from the biostar handbook web site curl http://data.biostarhandbook.com/sra/sra-runinfo-2019-01.tar.gz --output sra-runinfo-2019-01.tar.gz Now we can unpack the data. tar 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...

To align raw sequencing reads to a reference transcriptome, we will need a reference transcriptome (ie. the sequences of known transcripts in FASTA format). Fortunately, a reference transcriptome is included with the Golden Snidget dataset, Read More...

As with any language, the learning curve for Unix can be quite steep. However, to get started analyzing data you really need to understand the following: Directory navigation: what the directory tree is, how to Read More...

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

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

As with any language, the learning curve for Unix can be quite steap. However, to get started analyzing data you really need to understand the following: Directory navigation: what the directory tree is, how to Read More...

ssh -Y username@biowulf.nih.gov cd results_dir sinteractive --mem=8g --gres=lscratch:5 Open a connection to biowulf.nih.gov with "NoMachine". Minimize this window and work at the command line. module Read More...

Both fastq-dump and fasterq-dump are faster when following prefetch , and fasterq-dump paired with prefetch is the fastest way to pull the files from the SRA. There are alternative options, which we will mention later. prefetch Read More...

Both fastq-dump and fasterq-dump are faster when following prefetch , and fasterq-dump paired with prefetch is the fastest way to pull the files from the SRA. There are alternative options, which we will mention later. prefetch Read More...

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

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

An alternative to aligning raw sequencing data to a reference genome is to map them to a reference transcriptome. In this lesson, we will use the HBR and UHR datasets, and learn about this approach 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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be 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...

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...

Change into ~/biostar_class/snidget/snidget_hisat2/ when running featureCounts to obtain the expression counts table. The annotation file for this dataset is in ~/biostar_class/snidget/refs and is named features.gff. How would 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...

Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Activate the bioinformatics environment. conda activate bioinfo First let's make a place to store today's work. In your biostar_class Read More...

Where is the RNA sequencing data that we will be using for this course? Remember we will be demonstrating the steps of RNA sequencing in class using the Human Brain Reference (HBR) and Universal Human Read More...

In this lesson, we will identify genes that are differentially expressed between conditions. Here, we want to compare UHR samples to HBR samples, so we will be using existing applications to determine the ratio of Read More...

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...

Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home Read More...

Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home 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...

For this tutorial, you will be using either your own Biowulf account, or a student account. If you do not have a Biowulf account, see the instructor to get the login and password for a Read More...

Let's open IGV locally on our computer. Then we will copy the Golden Snidget refs folder to our public directory so we can download and use these locally. Remember the location on your computer Read More...

Let's go back to the biostar_class directory and create a folder called practice_trimming for this exercise. How do we do this? {{Sdet}} Solution{{Esum}} This depends on where you are currently (ie. 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...

Lesson 11 Practice Objectives In this lesson, we learned to merge multiple FASTQC reports into one perform data cleanup (quality and adapter trimming) to prepare our sequencing reads for downstream analysis. Here, we will put what Read More...

This data set is from the Griffith lab RNA sequencing tutorial and are kept at http://genomedata.org/rnaseq-tutorial/practical.tar. This dataset is derived from a study that profiled the transcriptome of HCC1395 breast Read More...

Due to time constraints, we will not be going over the creation of bigWig files in class. The information below is for your reference and you can view these during your spare time. In Lesson 9, Read More...

Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...

Lesson 12 Practice Objectives In this practice session, we will work with something new, which is a dataset from the Griffith lab RNA sequencing tutorial. Here, we will have a chance to practice what we have Read More...

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...

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...

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...

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

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...

The Neurorehabilitation and Biomechanics Research Section (also referred to as the NAB LAB) is a multidisciplinary group of highly qualified scientists, clinical and technical staff, and trainees with diverse backgrounds including medical, physical therapy, neuroscience Read More...

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...

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...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

This practice lesson is associated with Lesson 5 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on choosing a sampling depth to rarefy, running core-metrics, and comparing alpha diveristy between our Read More...

Lesson 5 Practice This practice lesson is associated with Lesson 5 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on choosing a sampling depth to rarefy, running core-metrics, and comparing alpha diveristy Read More...

This practice lesson is associated with Lesson 4 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on filtering our feature table and representative sequences, classify our features, and generate a phylogenetic Read More...

Practice Lesson 4 This practice lesson is associated with Lesson 4 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on filtering our feature table and representative sequences, classify our features, and generate Read More...

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

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

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To better understand S4 objects as they relate to the Bioconductor core infrastructure. To learn more about a popular Bioconductor S4 Read More...

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