Supported by CCR Office of Science and Technology Resources (OSTR)
ncibtep@nih.gov

Bioinformatics Training and Education Program

Featured

Upcoming Classes & Events

March

Description

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 followed by ddPCR application areas.  Presentation will include  30 minutes of QX Manager software training (software introduction + data analysis)  followed by Q&A

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 followed by ddPCR application areas.  Presentation will include  30 minutes of QX Manager software training (software introduction + data analysis)  followed by Q&A

Details
Organizer
CCR Genomics Core
When
Thu, Mar 23, 2023 - 12:00 pm - 2:00 pm
Where
Bldg. 37, Room 2041/2107
Description
The upcoming presentations will showcase research from different Cancer Moonshot initiatives that support the 10 recommendations of the Blue Ribbon Panel report. They will inform the community about the progress of Cancer Moonshot-funded projects, provide outreach related to Cancer Moonshot projects, enhance discussions and collaborations related to Cancer Moonshot research, and promote the sharing of data from Cancer Moonshot Read More
The upcoming presentations will showcase research from different Cancer Moonshot initiatives that support the 10 recommendations of the Blue Ribbon Panel report. They will inform the community about the progress of Cancer Moonshot-funded projects, provide outreach related to Cancer Moonshot projects, enhance discussions and collaborations related to Cancer Moonshot research, and promote the sharing of data from Cancer Moonshot initiatives. Speaker: Sandro Santagata, M.D., Ph.D., Brigham and Women’s Hospital
Details
Organizer
Cancer Moonshot
When
Thu, Mar 23, 2023 - 12:00 pm - 1:00 pm
Where
Online
Description

This afternoon workshop will give attendees an understanding of how single cell technologies are used to study cancer.

To start us off, Mike Kelly, head of the Single Cell Analysis Facility (SCAF), will give an overview of the current and emerging high-value single cell sequencing and closely associated spatial transcriptional profiling methods along with some example applications in cancer research. He will discuss some of the Read More

This afternoon workshop will give attendees an understanding of how single cell technologies are used to study cancer.

To start us off, Mike Kelly, head of the Single Cell Analysis Facility (SCAF), will give an overview of the current and emerging high-value single cell sequencing and closely associated spatial transcriptional profiling methods along with some example applications in cancer research. He will discuss some of the strengths and limitations of these existing technologies, and preview some of the most promising upcoming assays that may be of interest to the community.

Following this we will have Kimia Dadkhah, bioinformatics analyst (SCAF), who will talk about the essential quality control metrics in single cell data analysis and important factors to keep in mind in interpretation of the data.

Next up is Abdalla Abdelmaksound (CCBR), [topic to be announced], and Stefan Cordes (NHLBI) – who will review trajectory inference – with and without the incorporation of RNA velocity – as a tool to reconstruct cell state dynamics from single cell genomics data.  He will show that the inclusion of single cell lineage-tracing indices to follow heritable barcodes can improve reconstruction.

Register
Organizer
BTEP
When
Thu, Mar 23, 2023 - 1:00 pm - 5:00 pm
Where
Online Webinar
Distinguished Speakers Seminar Series

Description

Building a Mind for Cancer

Cancer neurodegenerative disorders and other diseases have multiple subtypes, each with their different causes, effective treatments, and clinical outcomes. Tumor genome sequences provide a rich new source of data for uncovering these subtypes, but they have proven difficult to compare, as two tumors rarely share the same somatic or germline mutations.

The Ideker Lab previously introduced the concept and method of Read More

Building a Mind for Cancer

Cancer neurodegenerative disorders and other diseases have multiple subtypes, each with their different causes, effective treatments, and clinical outcomes. Tumor genome sequences provide a rich new source of data for uncovering these subtypes, but they have proven difficult to compare, as two tumors rarely share the same somatic or germline mutations.

The Ideker Lab previously introduced the concept and method of network-based stratification (NBS), which integrates tumor genomes with knowledge of hallmark cancer pathways encoded in gene networks [Chuang et al. Mol Sys Biol 2007 and Hofree et al. Nature Methods 2013; first translated to the clinic in Chuang et al. Blood 2012]. This approach allows for stratification of cancer neurodegenerative disorders and other diseases into informative subtypes by clustering together patients with molecular alteration in similar network regions (e.g. distinct mutations in the same hallmark pathway). These network-defined subtypes have turned out to be predictive of clinical outcomes such as patient survival, response to therapy or tumor histology. Thus far the evidence suggests that network biomarkers, which aggregate together mutations in multiple genes, will not just be useful in clinical interpretation of cancer genomes, in many cases they may be necessary. – Ideker Lab, https://idekerlab.ucsd.edu/research/cancer/

Register
Organizer
BTEP
When
Thu, Mar 30, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar

April

Description

Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream Read More

Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis. - Satija Lab

The development of Azimuth is led by the New York Genome Center Mapping Component as part of the NIH Human Biomolecular Atlas Project (HuBMAP).

Register
Organizer
BTEP
When
Thu, Apr 06, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

Wondering why you should use R for data visualization? Lesson 1 of the Data Visualization with R course series will address this question and introduce the various plot types that will be generated throughout the course. Lesson 1 will also showcase related plots that you will be able to create in the future using the foundational skills gained over the next 5 lessons.

This will not be a hands-on lesson so no coding just yet. Read More

Wondering why you should use R for data visualization? Lesson 1 of the Data Visualization with R course series will address this question and introduce the various plot types that will be generated throughout the course. Lesson 1 will also showcase related plots that you will be able to create in the future using the foundational skills gained over the next 5 lessons.

This will not be a hands-on lesson so no coding just yet. The hands-on portion of this series will start with lesson 2, Getting Started with ggplot2. 

This lesson is the first lesson of a multi-lesson course series. Registering here will register you for the entire course series.

IMPORTANT: 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.

Register
Organizer
BTEP
When
Tue, Apr 11, 2023 - 1:00 pm - 2:15 pm
Where
Online Webinar
Description

Lesson 2 of the Data Visualization with R course series 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.

Registering for lesson 1 of this course series will enroll you in the entire course series.

Lesson 2 of the Data Visualization with R course series 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.

Registering for lesson 1 of this course series will enroll you in the entire course series.

Register
Organizer
BTEP
When
Thu, Apr 13, 2023 - 1:00 pm - 2:15 pm
Where
Online Webinar
Description

Lesson 3 of the Data Visualization with R course series 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 RNA-seq data.

Read More

Register
Organizer
BTEP
When
Tue, Apr 18, 2023 - 1:00 pm - 2:15 pm
Where
Online Webinar
Description

It is common to obtain summary statistics for a dataset to understand parameters like mean, standard deviation, and distribution. In Lesson 4 of the Data Visualization with R course series, we will learn to generate plots that will help with visualization of summary statistics including bar plots with error bars, histograms, and box and whiskers plots.

Registering for lesson 1 of this course series will enroll you Read More

It is common to obtain summary statistics for a dataset to understand parameters like mean, standard deviation, and distribution. In Lesson 4 of the Data Visualization with R course series, we will learn to generate plots that will help with visualization of summary statistics including bar plots with error bars, histograms, and box and whiskers plots.

Registering for lesson 1 of this course series will enroll you in the entire course series.

Register
Organizer
BTEP
When
Thu, Apr 20, 2023 - 1:00 pm - 2:15 pm
Where
Online
Description

Lesson 5 of the Data Visualization with R course series will introduce the heatmap and dendrogram as tools for visualizing clusters in data. This lesson will primarily use the R package pheatmap. 

Registering for lesson 1 of this course series will enroll you in the entire course series.

Lesson 5 of the Data Visualization with R course series will introduce the heatmap and dendrogram as tools for visualizing clusters in data. This lesson will primarily use the R package pheatmap. 

Registering for lesson 1 of this course series will enroll you in the entire course series.

Register
Organizer
BTEP
When
Tue, Apr 25, 2023 - 1:00 pm - 2:15 pm
Where
Online Webinar
Description

Scientific journals almost always have limits on the number of figures that can be included in a publication. Don't fret, in the 6th and final lesson of the Data Visualization with R course series, we will focus on generating sub-plots and multi-plot figure panels using ggplot2 associated packages.

Registering for lesson 1 of this course series will enroll you in the entire course series.

Scientific journals almost always have limits on the number of figures that can be included in a publication. Don't fret, in the 6th and final lesson of the Data Visualization with R course series, we will focus on generating sub-plots and multi-plot figure panels using ggplot2 associated packages.

Registering for lesson 1 of this course series will enroll you in the entire course series.

Register
Organizer
BTEP
When
Thu, Apr 27, 2023 - 1:00 pm - 2:15 pm
Where
Online Webinar

May

Description

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 introduce RNA-seq data analysis followed by tutorials showing the use of popular RNA-seq analysis packages and preparing participants to independently run basic RNA-Seq analysis for expression profiling. The hands-on exercises will run on the Galaxy platform using Illumina paired-end RNA-seq data. The workshop will Read More

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 introduce RNA-seq data analysis followed by tutorials showing the use of popular RNA-seq analysis packages and preparing participants to independently run basic RNA-Seq analysis for expression profiling. The hands-on exercises will run on the Galaxy platform using Illumina paired-end RNA-seq data. The workshop will be taught by NCI staff and is open to NIH and HHS staff.

Register
Organizer
NIH Library
When
Fri, May 12, 2023 - 12:00 pm - 3:00 pm
Where
Online Webinar