Bioinformatics Training & Education Program

CellTypist was first developed as a platform for exploring tissue adaptation of cell types using scRNA-seq semi-automatic annotations. Now it's an open source tool for automated cell type annotations as well as a working group in charge of curating models and ontologies.

This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is a programming language and open source environment for statistical computing and graphics. The R class series is a comprehensive collection of training sessions offered by the NIH Library Data Services and Bioinformatics programs that is designed to teach non-programmers how to write modular code and to introduce best practices for using R for data analysis and data visualization. Each class uses both evidence-based best practices for programming and practical hands-on lessons.

By the end of this class, students should be able to: list reasons for using R; describe the purpose of the RStudio Script, Console, Environment, and Plots panes; describe the various methods for finding help on R and RStudio; organize files and directories for a set of analyses as an R Project; define the following terms as they relate to R: object, assign, comment, call, function, and arguments; and assign values to objects in R.

Students are encouraged to install R and RStudio before the class so that they can follow along with the instructor. Please bring your laptop with R and RStudio installed.

Welcome to Learning 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.

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)
• Learn how to run interactive, swarm and batch jobs as well as work with bioinformatics modules on Biowulf (lesson 4, June 6)

Meeting information:

Meeting link:
https://cbiit.webex.com/cbiit/j.php?MTID=m6c624a110f8fbdb607345593cf9c624f

Meeting number:
2318 574 8744
Password:
bmV565kRGp*


Join by video system
Dial 23185748744@cbiit.webex.com
You can also dial 173.243.2.68 and enter your meeting number.

Join by phone
1-650-479-3207 Call-in number (US/Canada)
Access code: 2318 574 8744

Global call-in numbers:
https://cbiit.webex.com/webappng/sites/cbiit/meeting/info/81852c4726654806992d399ac523771d#

Dr. Maximilian Haeussler is the co-PI for the UCSC Genome Browser, an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. Dr. Melissa Cline is program manager of the UCSC BRCA Exchange, a project which aims to advance the understanding of the genetic basis of breast, ovarian, pancreatic, and other cancers by pooling data on BRCA1/2 genetic variants and corresponding clinical data from around the world. In this webinar, Drs. Haeussler and Cline will discuss these programs and data resources for clinical variant interpretation.

In this webinar, participants will learn how to tell a story with their data using notebook-style live scripts and how to integrate MATLAB with Python code. Attendees will also learn how to share code and take advantage of MATLAB community tools such as File Exchange and GitHub. Finally, the participants will find out how they can host MATLAB offerings at their High-Performance Computing Centers or a Science Gateway. This session is for beginners; no software installation required.

Join us for the upcoming CCR Fellows & Young Investigators-Seminar Series (CCR FYI-SS 2022/2023) which is being held as a ‘virtual’ seminar that is open to everyone! 

Julianna King, Laboratory Animal Sciences Program (LASP)

“Genome-wide CRISPR Screening to Identify Factors Regulating ADAR-mediated RNA Editing”

If you wish to present your work via this series, please let me know as dates are still available – see below.  

This one-hour session builds on the Introduction to R & RStudio class. The session begins by introducing and identifying different categories of data. Participants will examine data types, create vectors, and assign values to vectors. They will also learn how to import data into RStudio, and examine those data frames for further cleaning, analysis and visualization. Participants will learn the differences between numeric, character, and logical data and how to change data types in R. They will also be able to create subsets and export project data for future use.

Dr. Nara Sobreira will present "PhenoDB, a phenotypic and genotypic data sharing tool" at the monthly Data Sharing and Reuse Seminar on June 9, 2023, at 12 p.m. EST.

This seminar will discuss the use of phenotypic and genotypic data sharing tools to facilitate the discovery of novel disease-causing genes and variants.

Dr. Sobreira, an associate professor at the McKusick-Nathans Department of Genetic Medicine at Johns Hopkins University, will present PhenoDB. Her research focuses on the identification of the genetic etiology of rare Mendelian diseases. To facilitate this work, she has development public genetic databases and genetic analytical tools that are highly valuable and widely used to promote data sharing, disease gene identification and facilitate collaborations. She participated in the development of PhenoDB and developed the PhenoDB analysis module that is in use around the world. Dr. Sobreira is one of the creators of GeneMatcher, the most widely used data sharing platform of rare Mendelian diseases. In addition, she has created VariantMatcher, for the sharing of gene variant information.

Dr. Sobreira received her medical degree from the Pernambuco University’s School of Medicine in 2003.  She completed a clinical genetics residency in Sao Paulo – Brazil (UNIFESP) before joining the Human Genetics graduate program at Johns Hopkins (2007 to 2012).  This was followed by a one-year postdoc and a two-year clinical genetics fellowship also at Johns Hopkins School of Medicine. 

Data Wrangling is another class in the NIH Library Introduction to R and RStudio Series. A basic understanding of using R and RStudio to manage data is expected. This one-hour class will introduce the R tidyverse package and how to use it to manipulate, analyze and export data. This class will explore options for using the tidyverse functions select, filter, pipes, mutate, head, is.na, and export. Learning these functions will enable users to have well formatted data frames for future clean and consistent analysis and visualizations.

This class focuses on using Git and GitHub, with RStudio.  Using integrated RStudio tools, learners will have a chance to experiment with this integration and understand its advantages for collaboration and version control. This intermediate-level class is designed to be relevant to participants from different disciplines. Some familiarity or experience in R and RStudio is recommended. Participants are encouraged to install R and RStudio before the class.  Participants will need to download the class data before the class.

Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing sequencing data through command line and/or code. In this training session, you will learn to analyze bulk RNA sequencing data using Partek Flow. This class is not hands-on.

Meeting link: https://cbiit.webex.com/cbiit/j.php?MTID=m6da28111eefd3ab12d0d59477796d6bb

Meeting number: 2309 032 9788

Password: pxJpAyn7*49

Host key: 652701

Join by video system:
Dial 23090329788@cbiit.webex.com
You can also dial 173.243.2.68 and enter your meeting number.

Join by phone:
1-650-479-3207 Call-in number (US/Canada)br>Access code: 2309 032 9788
Access code: 2309 032 9788

Global call-in numbers

Generative modeling is an artificial intelligence (AI) technique that creates unique content (such as text, graphics, audio, and video) by first analyzing training examples. Generative AI includes ChatGPT, which generates text in a dialogue format, and DALL·E 2, which can create images based on natural language description. Generative AI is a rapidly expanding field that offers many possible applications for biomedical researchers and support staff. Join this roundtable discussion to learn about Generative AI and discuss possible applications and potential ethical concerns and issues with the use of Generative AI within scientific research and publishing.

This class is designed for those who want to learn the basic of R Markdown and apply those skills in Quarto. Quarto is an open-source scientific and technical publishing system that offers multilingual programming language support to create dynamic and static documents, books, presentations, blogs, and other online resources.  In this intermediate-level class participants will learn the basics of creating markdown documents. Some familiarity or experience in R and RStudio is recommended. Participants are encouraged to install R and RStudio before the class.

Webex meeting information:

https://cbiit.webex.com/cbiit/j.php?MTID=meadc52474c7d3816f0ae22444b9f05d1

Thursday, June 15, 2023 1:00 PM | 2 hours | (UTC-04:00) Eastern Time (US & Canada)

Meeting number: 2310 553 2989

Password: nXDjj9kX@69

Join by video system

Dial 23105532989@cbiit.webex.com

You can also dial 173.243.2.68 and enter your meeting number.

Join by phone

1-650-479-3207 Call-in toll number (US/Canada)

Access code: 231 055 32989

Data Wrangling is another class in the NIH Library Introduction to R and RStudio Series. A basic understanding of using R and RStudio to manage data is expected. This one-hour class will build on the introduction provided in Data Wrangling Part 1 to further explore the R tidyverse package and how to use it to manipulate, analyze and export data. This class will explore options for using the tidyverse functions group_by, summarize, count, arrange, pivot_wider, pivot_longer, and export. Learning these functions will enable users to have well formatted data frames for future clean and consistent analysis and visualizations.

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 four-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.

Part 1 will address fundamental statistical concepts including hypothesis testing, p-values and confidence intervals, types of data and their distributional importance, and bias and confounding. During the class, time will be devoted to questions from attendees and references will be provided for in-depth self-study.

Although you may attend any part of this series by itself, attending all four parts will provide a more comprehensive review of important statistical and epidemiological considerations that build on each other. You must register separately for each part of this class series.

This class is designed for those who want to extend the basics of R Markdown and apply those skills in Quarto. Quarto is an open-source scientific and technical publishing system that offers multilingual programming language support to create dynamic and static documents, books, presentations, blogs, and other online resources. In this intermediate-level class, participants will learn how to render documents in multiple format, and format citations and bibliographies using Zotero. Zotero is a free, easy-to-use tool to help collect, organize, annotate, cite, and share research. Some familiarity or experience in R and RStudio is recommended. Participants are encouraged to install R and RStudio before the class.

Biowulf is the high-performance computing cluster (HPC) at NIH. In addition to its vast compute power, Biowulf has hundreds of bioinformatics tools and databases for analyzing Next Generation Sequencing (NGS) data. This coding club will provide participants the foundations for harnessing Biowulf’s computing power to analyze NGS data. Participants will learn to request computing resources on and to submit scripts to the Biowulf system. This class is not hands-on so no need to obtain a Biowulf account prior to attending.

Meeting link:
https://cbiit.webex.com/cbiit/j.php?MTID=m39e6aa973e1500fbac8d3516e23cfaf8

Meeting number:
2317 419 7733
Password:
yKZJuSQ*983
Host key:
520526

Join by video system
Dial 23174197733@cbiit.webex.com
You can also dial 173.243.2.68 and enter your meeting number.

Join by phone
1-650-479-3207 Call-in number (US/Canada)
Access code: 2317 419 7733
Host PIN: 2784

Global call-in numbers:
https://cbiit.webex.com/webappng/sites/cbiit/meeting/info/431acd8d9e5f4ad79e425d4832178a31#

Scientists and educators from many different fields need to find and understand chemical data to perform their work. As such, understanding PubChem, the world’s largest collection of freely accessible chemical information, is a powerful skill for researchers, clinicians, and more. For educators, using PubChem in the classroom can facilitate active learning and exploration related to chemistry principles. In this workshop, participants will have access to NCBI experts and be introduced to the functionality of the PubChem Database.

In this online, interactive workshop, we will learn:

• Best practices of searching in PubChem
• Where to find molecular and chemical safety information
• How to use the PubChem Sketcher to find information about your chemical structure
• How to find a possible inhibitor for your gene

Note: This workshop is designed for life scientists, including educators and students, without exhaustive training in chemistry. Additionally, materials used for this workshop will remain available after the course for your use in research projects and curriculum development. More advanced PubChem workshops will be available in the future.

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status approximately 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This training will introduce ChIP sequencing data analysis followed by a tutorial showing ChIP-seq analysis workflow.  This workshop will be taught by NCI staff and is open to NIH and HHS staff.

This class is a mixture of lecture and hands-on exercises. By the end of this class, students will be able to: independently run basic ChIP-seq analysis for peak calling, run quality control on ChIP-seq data, map raw reads to a reference genome, generate alignment statistics and check mapping quality, call peaks using MACS, annotate peaks, and visualize the enriched regions.

All biology research projects involve finding relevant literature and identifying related biological information. Often high school or new undergraduate students need guidance on how to effectively search for helpful information. For almost 35 years, the NCBI has provided free access to high-quality biological databases for the research community. In addition, we’ve created tools to help organize selected literature and biological data records for quick and easy access.

In this online, interactive workshop we will take you step-by-step through how to:

• Use the web interface to effectively search NCBI databases
• Create and use your NCBI account to:
  • Save a search and set up weekly or monthly emails to notify you of new records
  • Store selected records in an online folder to access and share them
• Find information related to a proposed research project topic across linked NCBI databases, from publications and associated genome sequences down to protein structures
• Begin to interpret the information you’ve found in the context of the project

Note:  This workshop was designed for both student researchers, and the educators and mentors who want to help students use these resources.

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status approximately 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .

MATLAB provides two-way integration with many programming languages such as Python, which allows for greater collaboration between investigators. This webinar will cover how to call MATLAB from Python and how to call Python libraries from MATLAB. Attendees will learn how to use MATLAB’s Python integration to improve the compatibility and usability of their code. This webinar will be helpful for participants who have collaborators using Python with MATLAB, or for attendees who want to integrate MATLAB’s capabilities in a Python program. This session is for beginners; no software installation required.

The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species comparisons. You can view chromosome-scale rearrangements, search for genes, and display aligned regions at the sequence level.

In this workshop, you will have the opportunity to:

• Compare the human T2T CHM3 assembly to the current reference assembly, GRCh38.14
• Explore the extent of gene order conservation (synteny) between two organisms
• Transfer a viewed region to the Genome Data Viewer where you can expand your analysis
• View pairwise alignment at the sequence level
• Download a FASTA alignment file for a region, or download complete whole genome alignment data
• Generate a scalable vector graphics image (SVG) of your current view

This online, interactive workshop is designed for any life scientist, including research students and educators, who want to visually compare genomes to gain biological insight and share these insights with others.  Some familiarity with genomics vocabulary and concepts is recommended for attendees.

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status approximately 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will cover exome sequencing data analysis, followed by tutorials showing the use of exome analysis workflow. The hands-on exercise will run on a Galaxy platform using Illumina paired-end exome sequencing data. This workshop will be taught by NCI staff and is open to NIH and HHS staff. 

Participants will have a chance to: independently run basic exome analysis for variant detection, run quality control check on sequencing data, align the sequencing reads to a reference genome, generate alignment statistics and check mapping quality, identify variants, and visualize the exome sequencing data and variants. 

This class is 3 hours and is a mix of lecture and hand-on exercise. 

When it comes to data analysis and visualization, technical professionals who use Excel often encounter functional limitations. MATLAB supplements the capabilities of Excel by providing access to pre-built mathematical and analysis functions, visualization tools, and the ability to automate analysis workflows. Attendees will learn the main steps required for performing data analysis with MATLAB, including data access and pre-processing, modeling, and deployment. Attendees will gain an understanding of how to efficiently apply data analysis techniques using the MATLAB platform. This session is for beginners; no software installation required.

This workshop is for life scientists, including educators and research students, who would like to learn to use the command line for searching and fetching NCBI data. In this workshop, we will begin with an introduction to working in a command line environment and then show you how to use the EDirect suite to access biological data from several NCBI databases. You do not need to have had prior experience with the command line, but we do recommend that you have some familiarity with NCBI databases get the most of this workshop.

In this workshop you will learn how to:

• Write Bash commands with parameters
• Construct search queries using NCBI’s EDirect to search in a specific database
• Download selected data in chosen file formats
• Link to related data in another database
• Combine commands into reproducible workflows

Note:  This workshop is appropriate for both student researchers themselves as well as educators and mentors who want to help their students learn to use these resources.

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .

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 four-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. 

Part 4 will provide a brief review of the principles of epidemiology, outbreak investigations, implications in public health, key concepts and terms, and commonly used statistics in epidemiology (e.g., morbidity and mortality rates; incidence and prevalence; relative risk; odds ratio; sensitivity and specificity). The instructor will present a set of exercises to work through during the lesson (a calculator will be needed). 

Although you may attend any part of this series by itself, attending all four parts will provide a more comprehensive review of important statistical and epidemiological considerations that build on each other.

You must register separately for each part of this class series.

For 35 years, NCBI has collected a vast amount of sequence information including from a diverse array of organisms, including viruses, bacteria and fungi. With all of the databases and tools available at NCBI, it is sometimes daunting to know where to start looking to find helpful data for a research project. This workshop is designed to provide guided, hands-on experience with the NCBI website to find biosequence-based information to support viral, bacterial or fungal pathogen research.

In this workshop you will learn how to:

• • Identify pathogens based on isolate sequences.
  • Discover available NCBI information for a particular or closely-related organism.
  • View and download genomic sequences and annotation data.
  • Access specialty resources including the Pathogen Detection Project and NCBI Virus.

Note:  This workshop was designed for both student researchers and their supportive educators and mentors. We expect that participants in this workshop will already have familiarity with basic molecular biology concepts. 

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status approximately 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .

This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. By the end of this course, participants will have an understanding of data management best practices, data management tools, and resources that enable data sharing.

This is an introductory two-part course for those who want to learn about research data management and sharing, or for those who are interested in a refresher. Part 1 of this training will cover understanding research data, how to manage research data, and how to work with data. Audience: Researchers, fellows, post-docs, and trainees. You must register separately for Part 2 of this class.

This course provides detailed information on managing and sharing data from the first data planning stage, through the data life cycle, to data archiving, and finally to selecting an appropriate repository for data preservation. By the end of this course, participants will have an understanding of data management best practices, data management tools, and resources that enable data sharing.

This is an introductory two-part course for those who want to learn about research data management and sharing, or for those who are interested in a refresher. During Part 2 of this training, participants will learn about sharing and archiving data. Audience: Researchers, fellows, post-docs, and trainees. You must register separately for Part 1 of this class.

Identification of evolutionarily related DNA or protein sequences (homologs) is a crucial step in many biology workflows. For example, homologous sequences are used to infer relationships between organisms, understand how sequence changes affect observable traits, and identify potential animal models for genetic disorders.  

NCBI’s BLAST program is a standard tool for identifying homologs, and this virtual workshop will teach you best practices for using it for your analysis goals. You will learn when and how to use important but often misunderstood aspects of the BLAST programs and databases, such as when it’s helpful to change the BLAST program by using filters and adjusting parameters such as word size, e-value cutoff, and maximum target sequences.

In this workshop, you will use web-based NCBI resources to: 

• Select the correct NCBI alignment tool and BLAST database for your search goal 
• Use other NCBI sequence analysis services including COBALT, a multiple protein sequence alignment tool 
• Make use of the new organism-based nucleotide and ClusteredNR protein databases to easily assess the taxonomic diversity of your BLAST results 
• Visually examine results using auxiliary tools such as TreeViewer, Multiple Sequence Alignment, Graphical Sequence, and the Genome Data viewers.  

Note: This online, interactive workshop is designed for any life scientist, including research students and educators, who wants to use BLAST in their project or workflow.  Familiarity with genetics and evolutionary biology vocabulary and concepts is recommended for attendees. 

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status approximately 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .