ncibtep@nih.gov

Bioinformatics Training and Education Program

BTEP Video Archive of Past Classes


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 Recent BTEP Classes

Online Classes 2024

Distinguished Speakers Seminar Series

Apr 11th- Engineering Serendipity: Computational Methods for Large-Scale Data Extraction (Casey Greene)
Recording link: https://cbiit.webex.com/recordingservice/sites/cbiit/recording/playback/c1ec198c551c4cc9885e0449fedcf204

Getting Started with scRNA-Seq Seminar Series

Apr 3rd – The CCR Single Cell Analysis Facility (SCAF): An Overview (Mike Kelly)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=18785288d22f105303a3d215300fd805
Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/2024-04-03-BTEP-Intro-to-SCAF-Mike-Kelly-v2.pdf

Apr 10th – Introduction to single cell RNA-Seq (Charlie Seibert, Saeed Aghdam)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ee12bfaf912d5104b3fc3a837f99f096

Apr 17th – SCAF: Overview of Cell Ranger output files and single cell data analysis quality control(Kimia Dadkhah)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=875af03d230855d7615079bd195002c7
Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/BTEP_2024-04-17_Kimia_Dadkhah.pdf

Introduction to Geneious Prime (Mar 20)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b949d5b7abc34b5cc2de10a32b9f7124

AI in Biomedical Research at NIH Seminar Series

Feb 29 Artificial Intelligence in Biomedical Sciences (Brian Ondov)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5fc0f655a5f6feecce259f7d560af94d
Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/Ondov.pdf

Mar 21 How Large Language Models (LLMs) Accelerate Data Discovery and Harmonization (Mike Nalls)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=dd89edda484ef6ae282e0ee5c4ae92bf
Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/mike_nalls_seminar_20240321.pdf

Apr 4 Explainable Artificial Intelligence (XAI) and Single Cell Genomics to Understand the Cellular Complexity of the Human Brain (Richard Scheuermann)
Recording link: https://cbiit.webex.com/recordingservice/sites/cbiit/recording/playback/43c3002dd4d3103cbdff00505681965e
Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/NCI-CCR-BTEP_2024_04_04_v2.pdf

Introduction to Bioinformatics Resources for CCR Scientists (Feb 22)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4d0f25f4fd5187c42ac688b3a3028c34

Topics in Bioinformatics

Introduction to Pathway Analysis using the Reactome Pathway Knowledgebase (Feb 14) Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=8dca0e487e0f738ea20df664e1735703

Streamlining microbial shotgun analysis with JAMS – from fastqs to pdfs (Mar 28)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3c90c9d8f035e3872e73ef543670b272

BTEP Coding Club

Course documentation: https://bioinformatics.ccr.cancer.gov/docs/btep-coding-club/


R Introductory Series 2024 (January 23 – February 15)

Course documentation: https://bioinformatics.ccr.cancer.gov/docs/rintro/index.html

Introduction to Unix on Biowulf (January 22 – February 7)

Course documentation: https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-2024/

Online Classes 2023

Capabilities of the NIDAP platform for Transcriptomic Analysis (Dec 14, 2023)

Slides: https://bioinformatics.ccr.cancer.gov/btep/wp-content/uploads/sites/2/NIDAP_Overview_20231214.pdf
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=14ad1204eaf2612ee650e4d6fdf8bc53

Variant Analysis: Experimental Design, Best Practices, and Workflows (Dec 7, 2023)

Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=9da35c476972e99969d37a2c613916c6

Data Wrangling with R (November 27 – December 20)

Course documentation: https://bioinformatics.ccr.cancer.gov/docs/data-wrangle-with-r/

Introduction to Unix on Biowulf (September 7 – September 28)

Course documentation: https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-september-2023/index.html
  • Lesson 2, September 14, 2023: Navigating the Biowulf directory structure, downloading files from the web, and viewing file content
    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ea7ee90b07049e93d1659b2c453d1742
  • Lesson 3, September 21, 2023: Working with files and directories, interactive sessions, and exploring Next Generation Sequencing data
    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2b02b4f8acd2dfb7654d839042ea04af
  • Lesson 4, September 28, 2023: Working with bioinformatics applications on Biowulf and submitting shell as well as swarm scripts to the Biowulf batch system
    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=15e40b308b36b0d84f47186bcc68ce42


    Python Introductory Series (August 15 – August 29)

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/pies-2023/

    Toward Reproducibility with R on Biowulf (July 6 – July 27)

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/reproducible-r-on-biowulf/index.html

    Analyzing your data WITHOUT coding experience: CCR Bioinformatics Licensed Software (June 15)

    Introduction to Bioinformatics Summer Series (June 13 – July 27)

    Course documents: https://bioinformatics.ccr.cancer.gov/docs/intro-to-bioinformatics-ss2023/

    Introduction to Biowulf (May 16 – June 6)

    This course series introduces the basics of working on the Biowulf high performance computing cluster.

    Course documents: https://bioinformatics.ccr.cancer.gov/docs/biowulf-introduction-summer-2023/

    Data visualization with R (Apr 11 – Apr 27)

    In this course series, the audience will learn how to visualize data using the ggplot2 package from R.

    BTEP Distinguished Speakers Seminar Series

    Single Cell Annotation Seminar Series

    BTEP Single Cell Half Day (March 23rd)

    BTEP Coding Club

    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.

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/btep-coding-club/

    Partek Flow Training

    Introduction to Unix on Biowulf (Jan – Feb)

    This course series introduces scientists to working on Biowulf, the Unix-based and high-performance compute system at NIH. Biowulf staff installs and maintains hundreds of tools for working with large datasets such as those generated from high-throughput sequencing.

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-2023/

    R Introductory Series (Jan – Feb)

    This course will include a series of lessons for individuals new to R or with limited R experience. The purpose of this course is to introduce the foundational skills necessary to begin to analyze and visualize data in R. This course is not designed for those with intermediate R experience and is not tailored to any one specific type of analysis.

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/rintro_2023/index.html

    Qlucore



    Introduction to Bioinformatics Resources for NCI CCR Scientists

    Learn about the: (1) NIH Bioinformatics Calendar, (2) Training Opportunities, (3) Upcoming Events, (4) New BTEP Website Resources, (5) Biowulf, (6) Next-Gen Seq Analysis Tools (Partek Flow, Qlucore, Qiagen IPA), (7) Workflows, (8) Cloud Resources, (9) NCI Sequencing Cores, (10) NIH Training Resources.
    •  
    Online Classes 2022

    Microbiome Analysis with QIIME 2

    Course materials: https://bioinformatics.ccr.cancer.gov/docs/qiime2/ Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4d90e55b0adaebe54bff0ed5030783f3

    Greg Caporaso: Toward Fully Reproducible Microbiome Multi-omics Bioinformatics with QIIME 2 (Oct 19th)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c44af836ce9dd1631b58ccc285880a56
     

    Bioinformatics for Beginners: RNA-Seq Data Analysis (Sept 27th – Dec 13th)

    Course materials: https://bioinformatics.ccr.cancer.gov/docs/b4b/
     

    Qiagen Pathway Analysis for Beginners: Generating a Gene Network from Experimental Data (August 31)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e141aefc6a798f6510fbae29ad98ea41 Qiagen IPA upcoming webinars and trainings Previously recorded webinars and trainings for IPA For questions, email Qiagen technical support: ts-bioinformatics@qiagen.com
     

    Creating Publication Ready RNA-Seq Graphs in Partek Flow (Aug 24)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3d5ea2c9c65a811972d0ff1f884e2dda
     

    Bioinformatics Resources for CCR Scientists (July 26)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=9d83c3a41b5c017de966f39178ea6b03 Presentation slides: Presentation Intro to Bioinformatics Resources FINAL VERSION
     

    Variant Analysis – Experimental Design, Best Practices, and Workflows (June 30)

    Recording link: https://cbiit.webex.com/recordingservice/sites/cbiit/recording/8cd6adf4dacc103a83be00505681c451
    Presentation slides:

    Qlucore: Bulk RNA-Seq Data Analysis (June 29)

    Recording link: https://cbiit.webex.com/webappng/sites/cbiit/recording/c788382fd9e1103ab7f6005056818fce
     

    Data Wrangling with R (June 7 – July 7)

    Course Materials: https://bioinformatics.ccr.cancer.gov/docs/data-wrangle-with-r/
     

    Partek Flow: Bulk and Single Cell Gene Expression Visualization (May 18)

    Recording link:  https://cbiit.webex.com/cbiit/ldr.php?RCID=b5b1948aab3093124275d06fa55b08ae
     

    Qlucore: Import and analyze public data from SRA, GEO and TCGA (May 11)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c8e8e8ff837caeb2d4d3839bc180b9bb

    Training: Access GEO, SRA, ArrayExpress, TCGA, GTEx and more with Qiagen IPA Land Explorer (April 20)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=d081980970fce4cb50dd20d3f4f3e172
     

    Single Cell RNA-Seq Analysis with Partek Flow (April 13)

    Recording Link: https://cbiit.webex.com/cbiit/ldr.php%3FRCID%3D02b734d9f2b8466bf996ccc5d52d0c02
     

    Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA) (April 6)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=8cfdd939b601f0402b312ba2f8e85262
      Recommended Resources:
    1. GSEA hands-on webinar_Qlucore.pdf
    2. GSEA in Qlucore.pdf
    3. GSEA_MSigDB Collections.pdf
    4. How to do Pathway Analysis A.pdf
    5. MSigDB Hallmark human gene sets UCSD.pdf
    6. PNAS-2005-Subramanian-GSEA.pdf

     

    Data Visualization with R (April 5 – May 10)

    Course Materials: https://bioinformatics.ccr.cancer.gov/docs/data-visualization-with-r/
    • Lesson 1, April 5: Introduction to plot types Why R for data visualization? We will introduce the various plot types that will be generated throughout the course and will showcase related plots that you will be able to create in the future using the foundational skills gained. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5bfc45c875be766b41f8a9948487a822
    • Lesson 2, April 12: Basics of ggplot2 In lesson 2 of the Data Visualization with R series we will focus on the basics of ggplot2, including the grammar of graphics philosophy and its application. This lesson will provide a hands on introduction to the ggplot2 syntax, geom functions, mapping and aesthetics, and plot layering. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c2bacdc4f78ef005f1356fb2d8b798c4
    • Lesson 3, April 19:  Scatter plots and ggplot2 customization In lesson 3 of the Data Visualization with R series we will continue the discussion on the grammar of graphics, with a focus on ggplot2 plot customization including axes labels, coordinate systems, axes scales, and themes. This hands on lesson will showcase these features of plot building through the generation of increasingly complex scatter plots using data included with a base R installation as well as RNASeq data. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ee0789d3b2cb5cc40c77f0d9e8bb3790
    • Lesson 4, April 26: Visualizing summary statistics with histograms, bar plots, and box plots In lesson 4 of the Data Visualization with R series we will learn to generate plots that will help with visualization of summary statistics including a bar plot with error bars, histogram, as well as the box and whiskers plot. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=83a227f93612bdc27637783e586d7025
    • Lesson 5, May 3: Visualizing clusters with heatmaps In lesson 5 of the Data Visualization with R series we will introduce the heatmap and dendrogram as tools for visualizing clusters in data. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4183dc8595b722b9eed9aa32a0e016ef
    • Lesson 6, May 10: Combining multiple plots to create a figure panel In lesson 6 of the Data Visualization with R series we will focus on generating sub plots and multi plot figure panels using ggplot2 associated packages. This will allow us to meet any figure limitations that scientific journals may have. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=890e966d5e6520052426214db0345d96

     

    Introducing QIIME2, a Powerful Platform for Microbiome Analysis (March 24)

    QIIME2 is a powerful microbiome analysis platform with a wide array of tools that can be used throughout all stages of your microbiome workflow, from raw data to statistical evaluation and visualization. This course will provide an overview of QIIME2, which will include an introduction to the core plugins and methods available with a base QIIME2 installation, tools for reproducibility and visualization, features available for community support and help, and additional learning opportunities. Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2ad95564340a539395ff3c62e1126ae3 Link to Slides: qiime2_overview

    Qlucore: Single Cell Data, from 10x Output to Clustering, Cluster ID and Statistical Analysis in a Visual Qlucore Platform (February 23)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e5cdeb4d9a3720b6807ab767d78c4e40
     

    R Introductory Series (Jan – Feb)

    This course will include a series of lessons for individuals new to R or with limited R experience. The purpose of this course is to introduce the foundational skills necessary to begin to analyze and visualize data in R. This course is not designed for those with intermediate R experience and is not tailored to any one specific type of analysis.

    Course documentation: https://bioinformatics.ccr.cancer.gov/docs/rintro/
     

    Partek Flow: Variant DNA-Seq Data Analysis (January 19)

    Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=95300876cd21dcdf724b34450edf02b7

    Recorded Videos of Other BTEP Events

    Distinguished Speaker Series  
    NGS Analysis
    Programming
    Single Cell
    Commercial Software