Search Results for: editing

Nano is a basic file editor that is built into Unix and enables editing of plain text files including txt, csv, fasta, genbank, gtf, and fastq. To edit a file using Nano, just use nano Read More...

Jupyter Notebook utilizes markdown for text editing. "Markdown is is a lightweight markup language for creating formatted text using a" -- https://en.wikipedia.org/wiki/Markdown We can use different size headings Read More...

What is the first step to editing a new or an existing file using nano. {{Sdet}}{{Ssum}}Solution{{Esum}} If you are editing a new file, then the command below will open a blank editor Read More...

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...

One of the great things about Quarto is that you do not really need to know markdown to use it. You can use a "What you see is what you mean (WYSIWYM)" editing Read More...

I am familiar with markdown and use it regularly, so I deselected "Use visual markdown editor". However, one of the great things about Quarto is that you do not really need to know Read More...

I am familiar with markdown and use it regularly, so I deselected "Use visual markdown editor". However, one of the great things about Quarto is that you do not really need to know Read More...

Introduce the RNA-Seq data Use wget and curl to download files Learn to compress / decompress and unarchive files Learn sed and awk for file editing

08/28/2020 - Speaker: Dr. Luke Gilbert is an Assistant Professor in the Department of Urology, the Helen Diller Family Comprehensive Cancer Center and the Innovative Genomics Institute at the University of California, San Francisco. Dr. Gilbert Read More...

Ipywidgets - to create interactive notebook elements MyST - provides more text editing features including admonitions such as notes, warnings, and cautions

Once you have your Biowulf account, you can connect remotely to Biowulf using a secure shell (SSH) protocol. If you have a macbook, you will need to open the terminal application. If you are using Read More...

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...

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...

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...

05/07/2013 -   This 2 hour seminar will be an interactive discussion and demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies ( Read More...

After you are done editing, what is are the steps to exiting nano and returning to the prompt? {{Sdet}}{{Ssum}}Solution{{Esum}} Hit control x If you made edits, nano will ask if you like Read More...

Upon signing onto Biowulf, users will land in the log-in node. Later on in this series, compute nodes will be introduced but essentially, the log-in nodes should not be used to perform compute intensive tasks. Read More...

We land on the log in node once we connect to Biowulf. "The log in node is your point of access to the Biowulf cluster" -- Biowulf accounts and log in node The Read More...

The Unix command syntax is composed of The command Option(s) that will alter how a command functions Argument(s), what you want the command to operate on command options argument For instance, to make Read More...

The Unix command syntax is composed of The command Option(s) that will alter how a command functions Argument(s), what you want the command to operate on command options argument For instance, to make Read More...

The Lasergene Molecular Biology package includes the following applications: SeqBuilder Pro, SeqMan Ultra, MegAlign Pro, GeneQuest, GenVision, SeqNinja, and DNASTAR Navigator. These applications provide tools to perform in silico gel electrophoresis and cloning, plasmid vector Read More...

Caution "As with other keys, when you hit Enter or ↵ or on Macs, Return on your keyboard, your computer encodes this input as a character. Different operating systems use different character(s) to represent Read More...

You can go back to your original folder at any time by clicking on a link in the upper left corner. You can also create multiple branches of the same workbook (default is called “master”) Read More...

Users will be greeted by the dashboard upon signing into GitHub. The following items are presented in the dashboard. Top repositories A green button labeled "New" allows for the creation of a new 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...

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...

We use a command line interface and a Secure shell protocol (SSH) to establish a remote connection to the login node / head node. Most of us are likely used to a graphical user interface (GUI), Read More...

We use a command line interface and a Secure shell protocol (SSH) to establish a remote connection to the login node / head node. Most of us are likely used to a graphical user interface (GUI), Read More...

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program. SnapGene is a point and click proprietary software program used for designing Read More...

06/06/2024 - The Brooks Lab developed a computational tool called FLAIR (Full-Length Alternative Isoform Analysis of RNA) to produce confident transcript isoforms from long-read RNA-seq data with the aim of alternative isoform detection and quantification. With Read More...

Excel is a great program for visualizing and manipulating small data sets. However, it isn't great for working with "big data", and resulting plots are generally not publishable. Learning R and associated Read More...

11/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

06/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

02/07/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/01/2021 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

04/14/2021 - Register Session Description Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited Read More...

11/05/2020 - Register Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens Read More...

05/28/2020 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

11/09/2015 - A Short Course in R for Biologists "A Short Course in R for Biologists" is a two-day course given in four three-hour sessions entitled: Introduction to R, Introduction to Bioconductor, Introduction to Read More...

10/13/2015 - Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and chemical systems foundational to human health and disease. Quickly identify biological relationships, mechanisms, pathways, functions and diseases most Read More...

12/17/2014 - Day 1 - AM (9:30 AM – 12:30 PM)  Ingenuity IPA -   Basic Training  ( Kate Wendelsdorf, Ph.D. -  Ingenuity Pathway Analysis)   Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and Read More...

ssh (connect to remote computer such as a high performance computing cluster) pwd (print working directory) cd (change directory) ls (list directory content) mkdir (make a directory) touch (creates an empty file) nano (basic editor Read More...

Learning R and associated plotting packages is a great way to generate publishable figures in a reproducible fashion. With R you can: 1. Create simple or complex figures. 2. Create high resolution figures. 3. Generate scripts that can Read More...

Learning R and associated plotting packages is a great way to generate publishable figures in a reproducible fashion. With R you can: 1. Create simple or complex figures. 2. Create high resolution figures. 3. Generate scripts that can Read More...

Recall that we are not supposed to use the login nodes to perform any computation intensive tasks on Biowulf. Instead, we should either submit a job (if staying in the log in node) with sufficient Read More...

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program used for, but not limited to, the following: DNA sequence alignment, annotation, Read More...

To get started, as always, we will need to log in to Biowulf. Make sure you are on VPN. Open your Terminal if you are using a mac or the Command prompt if you are Read More...

Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{Esum}} Classic Computational Molecular Read More...

{{Sdet}}{{Ssum}}Sequence comparison{{Esum}} CLC Genomics Workbench What file types can I start my analysis with? FASTA Genbank Geneious Prime What file types can I start my analysis with? FASTA Genbank Lasergene What file Read More...

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Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...

Course Wrap-up This lesson concludes the Bioinformatics for Beginners course series. Please email us any time at ncibtep@nih.gov for help with your bioinformatics questions or concerns. Lesson Objectives Short course overview. Review BTEP 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 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...

Introduction to ggplot2 Objectives Learn how to import spreadsheet data. Learn the ggplot2 syntax. Build a ggplot2 general template. By the end of the course, students should be able to create simple, pretty, and effective Read More...

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...

12/20/2016 - ABOUT THE COURSE R is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series Read More...

11/22/2016 - ABOUT THE COURSE R is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series Read More...

10/22/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...

01/29/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...

Nano is a built-in Unix text editor. We can use nano to create SRR1553606_fastqc.sh. The syntax here is nano file_to_edit so in this example do the following. nano SRR1553606_fastqc.sh Read More...

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...

For this portion of the class, change back to the /data/username folder cd /data/username Then make a new directory called SRP045416 and change into it. mkdir SRP045416 cd SRP045416 In Biowulf, a swarm Read More...

For this portion of the class, change back to the /data/username folder cd /data/username Then make a new directory called SRP045416 and change into it. mkdir SRP045416 cd SRP045416 In Biowulf, a swarm Read More...

Upon connecting to Biowulf, the user lands in the login node. Warning Do not use the login node to perform any computation intensive tasks on Biowulf. Instead, we should either submit a job (if staying Read More...