| Course Details | Start Date | |
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R Introductory Series 2024 Archived
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01/23/2024 | This course, designed for novices and beginners, will introduce the foundational skills necessary to begin to analyze and visualize data with R. Why learn R? R is a great resource for statistical analysis, data visualization, and report generation. R also provides packages and functions specific to the analysis of -omics data through efforts like Bioconductor. Topics covered in this course include getting started with R and RStudio, working with data structures with an emphasis on data frames, an introduction to data wrangling and data visualization with the tidyverse, and an introduction to Bioconductor. This course includes eight 1-hour lessons over four weeks (T, Th, 1:00 - 2:00 PM). Each 1-hour lesson will be immediately followed by an optional 1-hour help session. You will not need to install R on your computer for this class. Instead, we will be using R through DNAnexus, a cloud platform for bioinformatics analysis. Details will follow upon registration. |
Introduction to Unix on Biowulf: January 2024 Archived
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01/22/2024 | Biowulf is the high-performance compute cluster (HPC) at NIH and runs Linux, a Unix-like operating system. It offers more compute power than a personal computer and has over 900 software applications installed, including those for bioinformatics. Using Biowulf requires working knowledge of a command line interface. While many people are accustomed to working with graphical driven operating systems such as Windows or Mac, a completely text and command driven environment can be challenging to learn. The ability to work on Biowulf however is central to using bioinformatics applications at NIH. This course series will teach the basic Unix commands needed for working on Biowulf. Participants will be able to immediately apply skills learned in their own data analysis. This course is composed of six lessons, occurring on Mondays and Wednesdays from January 22 through February 7, 2024. Each lesson runs from 1 – 2 PM and will be followed by an optional 1-hour help session. Course learning objectives: After this series, participants will Know how to obtain a Biowulf account if they do not have one already. Know how to sign onto Biowulf. Be proficient with navigating the Biowulf directory structure. Become proficient with copying, moving, and renaming files as well as folders on Biowulf. Be able to view and edit with text files as well as scripts. Perform basic wrangling tasks on tabular data. Know how to work with software installed on the cluster. Be able to submit shell and swarm scripts to the Biowulf batch system. Be aware of tools used for transferring data between local computer and the Biowulf cluster. |
Data Wrangling with R Archived
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11/27/2023 | Welcome to the Data Wrangling with R course series! The purpose of this course is to introduce you to essential R packages and functions that will make your life easier when it comes time to explore, clean, transform, and summarize your data. Around 50-80 % of a data scientists time is often said to be devoted to data wrangling, or the act of getting data into a specific format. We can reduce some of this time simply by becoming more familiar with the packages and tools dedicated to tidying, transforming, and summarizing data. In R, one such collection of packages is known as the tidyverse, which will be the focus of this course. Each lesson will immediately be followed by a one-hour help session. Help sessions will be structured around a set of practice problems for you to test your new skills. Though, we welcome all questions! No experience with R is necessary to attend this course. The first few lessons will be focused on getting acquainted with R and RStudio. You will not need to install R on your computer for this class. Instead, we will be using R through DNAnexus, a cloud platform for bioinformatics analysis. Details will follow upon registration. |
Fall 2023 Introduction to Unix on Biowulf Archived
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09/07/2023 | Welcome to the fall 2023 edition of Introduction to Unix on Biowulf. Biowulf is the Unix/Linux-based high-performance computing (HPC) cluster at NIH. Unix is an operating system like Windows and Mac OS. However, in Unix, users interact with the computer by issuing commands rather than using a graphical user interface (GUI). Reasons to consider using Biowulf include: Access to much more compute power than a personal computer. Availability of more than 900 scientific softwares including those used for Next Generation Sequencing analysis. Mastery of Unix commands is needed to take advantage of the resources provided on Biowulf. This course is aimed at the beginners who have no experience using Unix or high-performance computing systems such as Biowulf. Participants will learn the essentials of Biowulf and basic Unix commands that will enable them to start using the cluster. There will be four one-hour lessons that run weekly on Thursdays from 11 AM - 12 PM starting on September 7th, 2023. Subsequent lessons will be held on September 14th, September 21st, and September 28th. Registering for the any of the lessons in this series will enroll you for all lessons, you do not need to register for each lesson separately. Everyone will use a Biowulf student account for this course. A personal Biowulf account is not required for participation. Within 24 to 48 hours after each lesson, the recording will be made available on the BTEP website (https://bioinformatics.ccr.cancer.gov/btep/btep-video-archive-of-past-classes/). Please only sign up for the course if you can attend all 4 scheduled lessons, as class size is limited. This course will repeat in the future. The topical outline for this course is shown below. Lesson 1 (September 7th, 2023): Overview of Unix and Biowulf Logging into Biowulf Lesson 2 (September 14th, 2023): Navigating around the Biowulf directory structure Lesson 3 (September 21st, 2023): Working with files and directories Interactive sessions Exploring Next Generation Sequencing data Lesson 4 (September 28th, 2023): Bioinformatics applications on Biowulf Submitting swarm and shell scripts to the Biowulf batch system |
Python Introductory Education Series (PIES) Archived
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08/15/2023 | The Python Introductory Education Series (PIES) is composed of four lessons and aims to help participants get started using Python for data analysis. A Biowulf account and knowledge of working on Biowulf is required for this course series. |
Toward Reproducibility with R on Biowulf Archived
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07/06/2023 | This course includes a series of four lessons designed for beginner to intermediate R users interested in working with R on Biowulf. The purpose of this course is to introduce the various ways to use R on Biowulf, while emphasizing reproducible practices such as project organization and R package dependency management. This course is not designed for advanced R users. Course participants must have a Biowulf account to follow along with course material. In addition, attendees should have beginner level knowledge of working on the Unix command line, Biowulf, and R. Course documentation: https://bioinformatics.ccr.cancer.gov/docs/reproducible-r-on-biowulf/ |
Introduction to Bioinformatics Summer Series Archived
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06/13/2023 | A series of 6 stand-alone classes to learn about bioinformatics. Will be held on Tuesdays at 1 PM in June and July. You can attend any class, just one class, or all classes. Introduction to Bioinformatics Resources at NCI Central Dogma of Molecular Biology: Analyzing DNA, RNA, and Proteins Keeping your Data FAIR: Organizing, Managing, and Sharing your Data Introduction to High Performance Computing at NIH: Biowulf Introduction to R and Python Programming Languages Managing Bioinformatics Projects with Jupyter Notebook Classes will be recorded and made available within 48 hours of the event on the BTEP Video Archive https://bioinformatics.ccr.cancer.gov/btep/btep-video-archive-of-past-classes/ Course materials: https://bioinformatics.ccr.cancer.gov/docs/intro-to-bioinformatics-ss2023/ |
Course: Introduction to Unix on Biowulf Archived
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05/10/2023 | Welcome to "Introduction to Unix on Biowulf". This course consists of four one-hour lessons that will run weekly on Tuesdays from 1 -2 PM starting May 16. Subsequent lessons will be held on May 23, May 30, and June 6. Registering for the first lesson will enroll you for all lessons, you do not need to register for each lesson separately. An optional help session will follow each lesson from 2 – 3 PM. Everyone will use a Biowulf Student Account for this course, you do not need to have your own Biowulf account. All lessons will be recorded and made available on the BTEP website. Please only sign up for the course if you can attend all 4 scheduled lessons, as class size is limited. This course will repeat in the near future. In this course, participants will Learn to log onto Biowulf (lesson 1, May 16) Learn to navigate the folder and file (directory) structure on Biowulf (lesson 2, May 23) Learn to work with very large Next Generation Sequencing (NGS) files on a Unix system (lesson 3, May 30) Understand how to run interactive, swarm and batch jobs as well as work with bioinformatics modules on Biowulf (lesson 4, June 6) |
Data Visualization with R Archived
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04/11/2023 | Welcome to the Data Visualization with R course series! Here, we hope to help you establish the foundations for generating publication quality plots in R. We will mostly be using ggplot2 (https://ggplot2.tidyverse.org/), a powerful yet easy to learn R package that will enable users to visually explore their data and / or generate publication quality figures. This series will include 6 lessons over 3 weeks. Each lesson will be held online on Tuesdays / Thursdays at 1 pm via Webex. The lessons will be 1 - 1.25 hours in duration followed immediately by a 45 minute help session. Topics include an introduction to plot types and plotting with R, getting started with ggplot2, scatter plots and non-data elements of ggplot2 customization, visualizing summary statistics, visualizing clusters with heatmaps, and creating a multi-plot figure. You do not need to download or install any software to participate in the course. This course will be taught on the DNAnexus platform. Every learner will need to create a free DNAnexus account at https://dnanexus.com. After you have created your DNAnexus account, please complete this form. If you fail to complete the form, we will not be able to give you access to the course on DNAnexus. Class materials will be accessible online at https://bioinformatics.ccr.cancer.gov/docs/data-visualization-with-r/. Registering for the first lesson in the series will register you for all lessons. |
BTEP Coding Club Archived
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03/14/2023 | The BTEP Coding club is a new initiative to provide more tailored bioinformatics training to the NCI community. Each month we will feature a 1-hour demo / tutorial of a bioinformatics tool, software, skill, or platform. We welcome suggestions from the NCI community. Email us at ncibtep@nih.gov if there is a specific topic you would like to see featured. View course materials here! |
Statistics and Epidemiology with BCES and the NIH library Archived
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03/07/2023 | In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This five-part lecture series will help participants better understand statistical and epidemiological features in biomedical research, interpret results and findings, design and prepare studies, and understand/critically review the results in published literature. |
NIH Data Sharing and Reuse Seminar Series Archived
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01/01/2023 | The National Institutes of Health (NIH) Office of Data Science Strategy hosts a seminar series to highlight exemplars of data sharing and reuse on the second Friday of each month at noon ET. The monthly series highlights researchers who have taken existing data and found clever ways to reuse the data or generate new findings. A different NIH institute or center (IC) will also share its data science activities each month. The seminar is open to the public and registration is required each month. Individuals who need interpreting services and/or other reasonable accommodations to participate in this event should contact Rachel Pisarski(link sends e-mail) at 301-670-4990. Requests should be made at least three days in advance of the event. A recording will be available on this page after each event. |
ncibtep@nih.gov