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

Bioinformatics Training and Education Program

Featured

Upcoming Classes & Events

October

Description

Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Significant advances in the field now allow high-parameter data collection (60+ targets); however, considerable expertise and capital are needed to validate antibodies, construct antibody panels, and acquire images. To overcome these challenges, we developed Iterative Bleaching Extends multi-pleXity (IBEX), an open-source, community supported method that can be completed at relatively low cost by biologists with basic laboratory skills. The IBEX Imaging Read More

Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Significant advances in the field now allow high-parameter data collection (60+ targets); however, considerable expertise and capital are needed to validate antibodies, construct antibody panels, and acquire images. To overcome these challenges, we developed Iterative Bleaching Extends multi-pleXity (IBEX), an open-source, community supported method that can be completed at relatively low cost by biologists with basic laboratory skills. The IBEX Imaging Community is an international group of scientists committed to sharing knowledge related to multiplexed imaging in a transparent and collaborative manner. Organ Mapping Antibody Panels (OMAPs) are community-validated resources that save time and money, increase reproducibility, and support the construction of a Human Reference Atlas. Open science empowers discovery across several domains including the construction of molecular and spatial atlases of normal and diseased tissues. To this end, we have employed advanced sequencing and imaging technologies to generate a multi-omic, multi-scale atlas of follicular lymphoma (FL) lymph nodes and the developing human thymus. In summary, a community approach to multiplexed imaging is needed to reduce financial costs, instill confidence in the resulting data, and accelerate translational research efforts.
 
Short Bio:
Dr. Andrea Radtke is an Associate Scientist at the National Institutes of Health. Dr. Radtke specializes in advanced microscopy techniques including IBEX, an open-source method that enables more than 65 protein biomarkers to be visualized in diverse tissues. She is passionate about team science and open science.
 
Zoom link: on demand
 
For more information, contact:
Gregoire.altan-bonnet@nih.gov
Sungm@nih.gov
Steven.cappell@nih.gov

Details
Organizer
Seminar - Systems Biology Interest Group
When
Tue, Oct 03, 2023 - 9:30 am - 10:30 am
Where
Building 4 – Room 433 (NIH Bethesda campus)
Description

Presented as part of the

Presented as part of the Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) Webinar Series

Dr. Kushal Dey is an Assistant Member and Josie Robertson Investigator in the Department of Computational and Systems Biology at the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center. He is also an Assistant Professor at the Gerstner Sloan Kettering Graduate School of Biomedical Sciences. In this webinar, Dr. Dey will discuss his work at the Kushal Dey Lab, which builds statistical and machine learning models that integrate genetic and genomic data to prioritize variants, genes, and cell types, and to decode the causal functional architecture underlying heritable complex diseases — including immune-related diseases, like Alzheimer’s and inflammatory bowel disease, and heritable cancers, like breast cancer.

Speaker:
Kushal Dey, PhD
Assistant Member and Josie Robertson Investigator, Department of Computational and Systems Biology
Assistant Professor, Gerstner Sloan Kettering Graduate School of Biomedical Sciences
Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center

Details
Organizer
NCI
When
Tue, Oct 03, 2023 - 3:00 pm - 4:00 pm
Where
Online Webinar
Description

Our series of talks continues this month with two 20-minute presentations.  There will be light refreshments and we encourage attendees to stay and chat with colleagues after the presentations.
 
 
Droplet-microfluidics-assisted transcriptome sequencing of HIV DNA+ cells reveals HIV silencing signatures of HIV-infected ‘latent reservoirs’
 
Eli Boritz, MD, PhD
Chief, Virus Persistence and Dynamics Section
National Institute of Allergy and Read More

Our series of talks continues this month with two 20-minute presentations.  There will be light refreshments and we encourage attendees to stay and chat with colleagues after the presentations.
 
 
Droplet-microfluidics-assisted transcriptome sequencing of HIV DNA+ cells reveals HIV silencing signatures of HIV-infected ‘latent reservoirs’
 
Eli Boritz, MD, PhD
Chief, Virus Persistence and Dynamics Section
National Institute of Allergy and Infectious Diseases (NIAID)
 
 
Single-nuclei RNA and ATAC Sequencing Uncovers Subtypes in Pancreatic Neuroendocrine Tumors
 
Shreya Rajhans 
CRTA Postbaccalaureate Fellow | Arda Lab
National Cancer Institute (NCI)
 

Single Cell and Spatial Genomics Users Group organizing committee:
Mala Ananth, Mark Cookson, Stefan Cordes, Jamie Diemer, and Mike Kelly

 

Information about attending the talks virtually is below:

Join by meeting number
Meeting number (access code): 2300 958 5424
 
Meeting password:    TbpjMsu*233

 

Details
When
Wed, Oct 04, 2023 - 10:00 am - 11:00 am
Where
Building 40 Room 1201/1203
Description

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 Read More

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.

Details
Organizer
NIH Library
When
Wed, Oct 04, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Distinguished Speakers Seminar Series

Description

There is an urgent need to take what we have learned in our new data-driven era of medicine, and use it to create a new system of precision medicine, delivering the best, safest, cost-effective preventative or therapeutic intervention at the right time, for the right patients.  Dr. Butte's teams at the University of California build and apply tools that convert trillions of points of molecular, clinical, and epidemiological data -- measured by researchers and Read More

There is an urgent need to take what we have learned in our new data-driven era of medicine, and use it to create a new system of precision medicine, delivering the best, safest, cost-effective preventative or therapeutic intervention at the right time, for the right patients.  Dr. Butte's teams at the University of California build and apply tools that convert trillions of points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade and now commonly termed “big data” -- into diagnostics, therapeutics, and new insights into disease.  Dr. Butte, a computer scientist and pediatrician, will highlight his center’s recent work on integrating electronic health records data from over 8 million patients across the entire University of California, and how analytics on this “real world data” can lead to new evidence for drug efficacy, new savings from better medication choices, and new methods to teach intelligence – real and artificial – to more precisely practice medicine.

   
Details
Organizer
BTEP
When
Thu, Oct 05, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

Dr. Hoifung Poon is the General Manager at Health Futures of Microsoft Research and an affiliated professor at University of Washington Medical School. He leads biomedical AI research and incubation, with the overarching goal of structuring medical data to accelerate discovery and improve delivery for precision health. His team and collaborators are among the first to explore large language models (LLMs) in health applications, from foundational research to incubations at large health systems and Read More

Dr. Hoifung Poon is the General Manager at Health Futures of Microsoft Research and an affiliated professor at University of Washington Medical School. He leads biomedical AI research and incubation, with the overarching goal of structuring medical data to accelerate discovery and improve delivery for precision health. His team and collaborators are among the first to explore large language models (LLMs) in health applications, from foundational research to incubations at large health systems and life science companies, and ultimately to commercialization. His prior work has been recognized with Best Paper Awards from premier venues, including as NAACL, EMNLP, and UAI.

Details
Organizer
NCI
When
Thu, Oct 05, 2023 - 3:00 pm - 4:00 pm
Where
Online Webinar
Description

This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over thirty plot functions along with the color selection, annotation, labeling, and zoom capabilities. User-guide, take-home video and sample plots from publications will be provided. No R Programming experience is required. By the end of this training,  students will be able Read More

This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over thirty plot functions along with the color selection, annotation, labeling, and zoom capabilities. User-guide, take-home video and sample plots from publications will be provided. No R Programming experience is required. By the end of this training,  students will be able to format data for omicCircos in R Shiny, use the point-and-click interface to set the parameters and generate circular plots, and export the plot for presentation and publication. 

This workshop will be taught by NCI staff and is open to NIH and HHS staff. This class is 2 hours and is a mix of lecture and demo. 

Details
Organizer
CBIIT
When
Fri, Oct 06, 2023 - 12:00 pm - 2:00 pm
Where
Online Webinar
Description

In this talk we will discuss what is a p-value and examples of p-value hacking. We will also review the basics of several statistical tests and when to use them. This session will be recorded, and materials will be shared with attendees a few days after the event. For details, please contact Natasha Pacheco (natasha.pacheco@nih.gov) from the Advanced Biomedical Computational Science group at FNLCR.

This will be a Read More

In this talk we will discuss what is a p-value and examples of p-value hacking. We will also review the basics of several statistical tests and when to use them. This session will be recorded, and materials will be shared with attendees a few days after the event. For details, please contact Natasha Pacheco (natasha.pacheco@nih.gov) from the Advanced Biomedical Computational Science group at FNLCR.

This will be a hybrid event.

Details
When
Tue, Oct 10, 2023 - 12:00 pm - 1:00 pm
Where
Building 549 Executive Board Room
Description

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. At NIH, Partek Flow is hosted on the Biowulf high performance computing cluster (HPC). Researchers interact Read More

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. At NIH, Partek Flow is hosted on the Biowulf high performance computing cluster (HPC). Researchers interact with the software through a web browser using a URL supplied by Biowulf once a Biowulf and Partek Flow account has been set up. This setup allows users to take advantage of the compute power offered by HPC while using a graphical user interface to construct a sequencing data analysis workflow. Partek Flow enables the creation of publication quality visualizations.

This online class is not hands-on. Biowulf and Partek Flow accounts are not required to attend. Participants will be presented with instructions for obtaining access to Partek Flow at the beginning of class.

This training session will address bulk RNA and ATAC sequencing analysis using Partek Flow. Participants will learn how to integrate these two assays to gain insights on the epigenetic regulation of gene expression. Topics covered include:

  • Import of fastq files
  • Alignment of fastq files to reference genome
  • Detect peaks for ATAC sequencing data
  • Quantification for RNA sequencing data
  • Compare peak regions and gene expression
  • Integrate RNA sequencing and ATAC sequencing results

 

Meeting link:
https://cbiit.webex.com/cbiit/j.php?MTID=mc425f72619b46e5defe804bf67a43b70
 
Meeting number:
2304 390 4110
Password:
JeRmMFa*823

Join by video system
Dial 23043904110@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: 2304 390 4110
Host PIN: 2784

Register
When
Wed, Oct 11, 2023 - 11:00 am - 12:30 pm
Where
Online
Description

This session focuses on R data types and data structures. In R, more advanced libraries (code) may require data to be a particular data type or data structure to perform a function or analysis. Understanding the foundational concepts of data types and data structures will enable emerging coders to avoid programmatic pitfalls and correct coding errors effectively. This class will demonstrate how to determine data types, and build data structures, and convert data types Read More

This session focuses on R data types and data structures. In R, more advanced libraries (code) may require data to be a particular data type or data structure to perform a function or analysis. Understanding the foundational concepts of data types and data structures will enable emerging coders to avoid programmatic pitfalls and correct coding errors effectively. This class will demonstrate how to determine data types, and build data structures, and convert data types when needed for functions such as analysis and visualizations.

Details
Organizer
NIH Library
When
Wed, Oct 11, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

In this one-hour session we will describe various resources available to NIH researchers to learn bioinformatics skills. These include trainings by specific groups or institutes (NCI, NIH Library, ODSS), licenses available for online learning, mailing lists, training calendars, and resources available NIH-wide for Next Gen Sequencing Analysis (Biowulf, Cloud). If you are completely new to bioinformatics at NIH, or have been doing bioinformatics analyses for a while, you will find some useful information in Read More

In this one-hour session we will describe various resources available to NIH researchers to learn bioinformatics skills. These include trainings by specific groups or institutes (NCI, NIH Library, ODSS), licenses available for online learning, mailing lists, training calendars, and resources available NIH-wide for Next Gen Sequencing Analysis (Biowulf, Cloud). If you are completely new to bioinformatics at NIH, or have been doing bioinformatics analyses for a while, you will find some useful information in this presentation. 

Register
Organizer
BTEP
When
Thu, Oct 12, 2023 - 1:00 pm - 2:00 pm
Where
Online
Description

Zhiyong Lu, Ph.D. will present AI in Medicine: Improving Access to Literature Data for Knowledge Discovery at the monthly Data Sharing and Reuse Seminar. 


The explosion of biomedical big data and information in the past decade or so has created new opportunities for discoveries to improve the treatment and prevention of human diseases. But the large body of knowledge—mostly exists as free text in journal articles for Read More

Zhiyong Lu, Ph.D. will present AI in Medicine: Improving Access to Literature Data for Knowledge Discovery at the monthly Data Sharing and Reuse Seminar. 


The explosion of biomedical big data and information in the past decade or so has created new opportunities for discoveries to improve the treatment and prevention of human diseases. But the large body of knowledge—mostly exists as free text in journal articles for humans to read—presents a grand new challenge: individual scientists around the world are increasingly finding themselves overwhelmed by the sheer volume of research literature and are struggling to keep up to date and to make sense of this wealth of textual information. Our research aims to break down this barrier and to empower scientists towards accelerated knowledge discovery. This seminar will discuss the development of large-scale, AI-based solutions for better understanding scientific text in the biomedical literature. Moreover, I will demonstrate their uses in some real-world applications such as improving PubMed searches (Fiorini et al., Nature Biotechnology 2018), supporting precision medicine with LitVar (Allot et al., Nature Genetics 2023), and taming COVID-19 pandemic paper tsunami in LitCovid (Chen et al., Nature 2000).

About the Speaker

Dr. Zhiyong Lu is a (tenured) Senior Investigator at the National Library of Medicine Intramural Research Program, leading research in biomedical text and image processing, information retrieval, and AI/machine learning. In his role as Deputy Director for Literature Search at National Center of Biotechnology Information (NCBI), Dr. Lu oversees the overall R&D efforts to improve literature search and information access in resources like PubMed and LitCovid, which are used by millions worldwide each day. Dr. Lu also serves as an Associate Editor of Bioinformatics, and Organizer of the BioCreative NLP challenge. Over the last 15 years, Dr. Lu has mentored over 60 trainees, many of whom have gone on to become independent faculty members/researchers at academic institutions in the US, Europe, and Asia. With over 300 peer-reviewed publications, Dr. Lu is a highly cited author, and a Fellow of the American College of Medical Informatics (ACMI) and the International Academy of Health Sciences Informatics (IAHSI).

Details
Organizer
NIH Office of Data Science Strategy (ODSS)
When
Fri, Oct 13, 2023 - 12:00 pm - 1:00 pm
Where
Online Webinar
Description

This class introduces version control and how to use GitHub for project versioning. Participants will have a better understanding of version control, GitHub, and their advantages for managing projects.

Upon completion of this class participants should be able to recognize why version control is useful, discuss the difference between Git and GitHub, Read More

This class introduces version control and how to use GitHub for project versioning. Participants will have a better understanding of version control, GitHub, and their advantages for managing projects.

Upon completion of this class participants should be able to recognize why version control is useful, discuss the difference between Git and GitHub, list the options for authenticating to GitHub, and list the options for creating a personal access token (PAT).

Details
Organizer
NIH Library
When
Mon, Oct 16, 2023 - 2:00 pm - 3:00 pm
Where
Online Webinar
Description

Labeling signal data is a very important step in creating AI-based signal processing solutions.  However, this step can be very time consuming and manual. In this beginner/intermediate one-hour session, the attendees will be introduced to signal labeling for use in AI applications and discuss how MATLAB can be used to speed up and simplify the process, from preprocessing to extracting information from signals. The session will Read More

Labeling signal data is a very important step in creating AI-based signal processing solutions.  However, this step can be very time consuming and manual. In this beginner/intermediate one-hour session, the attendees will be introduced to signal labeling for use in AI applications and discuss how MATLAB can be used to speed up and simplify the process, from preprocessing to extracting information from signals. The session will cover different approaches for signal labeling, including using algorithms and automating with deep learning models. It will also discuss an iterative method of building deep learning models and reducing human effort in labeling. 

Details
Organizer
NIH Library
When
Tue, Oct 17, 2023 - 12:00 pm - 1:30 pm
Where
Online Webinar
Description

This October session of the BTEP Coding club will feature a tutorial on how to access data from GEO as well as how to submit data to GEO. 

 

 

This October session of the BTEP Coding club will feature a tutorial on how to access data from GEO as well as how to submit data to GEO. 

 

 

Register
Organizer
BTEP
When
Wed, Oct 18, 2023 - 11:00 am - 12:00 pm
Where
Online Webinar
Description

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 Read More

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.

Details
Organizer
NIH Library
When
Wed, Oct 18, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

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, Read More

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, and export. Learning these functions will enable users to have well formatted data frames for future clean and consistent analysis and visualizations.

Details
Organizer
NIH Library
When
Thu, Oct 19, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

Python is a programming language used for data science, specifically: data analysis, statistical analysis, and visualization of results. This class will demonstrate integrated development and learning (IDE) platforms for learning Python, the fundamentals of Python coding, and why it is advantageous to develop these skills.  The session will feature the following IDEs: Google Colaboratory: Jupyter Notebook; and Anaconda’s: Spyder, Jupyter Notebook, and JupyterLab.  It will also provide an overview of Read More

Python is a programming language used for data science, specifically: data analysis, statistical analysis, and visualization of results. This class will demonstrate integrated development and learning (IDE) platforms for learning Python, the fundamentals of Python coding, and why it is advantageous to develop these skills.  The session will feature the following IDEs: Google Colaboratory: Jupyter Notebook; and Anaconda’s: Spyder, Jupyter Notebook, and JupyterLab.  It will also provide an overview of programming constructs needed to learn Python. Finally, this class will demonstrate why these skills can boost productivity, rigor, and transparency in reporting research findings. 

Details
Organizer
NIH Library
When
Fri, Oct 20, 2023 - 10:00 am - 11:00 am
Where
Online Webinar
Description

In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical issues that can arise as well as recommendations to prevent them. At the end of the class, participants should have a good sense of what to do and not to do when writing the statistical sections of a manuscript. Most of Read More

In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical issues that can arise as well as recommendations to prevent them. At the end of the class, participants should have a good sense of what to do and not to do when writing the statistical sections of a manuscript. Most of the examples will be related to clinical research; however, anyone can benefit from the tips shared. Plenty of time will be devoted for questions, and references will be provided for more in-depth self-study.

This class complements, How to Write a Research Paper Parts 1 & 2, as it specifically covers key points in writing the statistical portion of a manuscript – particularly for clinical research. Attendance to How to Write a Research Paper is not required to benefit from this class.

Details
Organizer
NIH Library
When
Fri, Oct 20, 2023 - 1:00 pm - 2:00 pm
Where
Online Webinar
Description

This class focuses on using Git and GitHub, with RStudio. Using integrated RStudio tools, participants will have a chance to experiment with this integration and understand its advantages for collaboration and managing projects. You must have taken the Version Control and GitHub class to be successful in this class.

Upon Read More

This class focuses on using Git and GitHub, with RStudio. Using integrated RStudio tools, participants will have a chance to experiment with this integration and understand its advantages for collaboration and managing projects. You must have taken the Version Control and GitHub class to be successful in this class.

Upon completion of this class participants should be able to discuss the difference between Git and GitHub, list the options for authenticating to GitHub, create a new R project using a GitHub repository, and distinguish between pulling and pushing data from a repository.

Details
Organizer
NIH Library
When
Mon, Oct 23, 2023 - 10:00 am - 11:00 am
Where
Online Webinar
Description

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. At NIH, Partek Flow is hosted on the Biowulf high performance computing cluster (HPC). Researchers interact Read More

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. At NIH, Partek Flow is hosted on the Biowulf high performance computing cluster (HPC). Researchers interact with the software through a web browser using a URL supplied by Biowulf once a Biowulf and Partek Flow account has been set up. This setup allows users to take advantage of the compute power offered by HPC while using a graphical user interface to construct a sequencing data analysis workflow. Partek Flow enables the creation of publication quality visualizations.

This online class is not hands-on. Biowulf and Partek Flow accounts are not required to attend. Participants will be presented with instructions for obtaining access to Partek Flow at the beginning of class.

This training session will address RNA and ATAC sequencing analysis on the single cell level using Partek Flow. Participants will learn how to integrate these two assays to gain insights to the epigenetic regulation of gene expression at the single cell level. Topics covered include:

  • Import single cell ATAC sequencing Cellranger output
  • QA/QC
  • Visualization
  • Compare peak regions
  • Motif detection
  • Integration with single cell RNA-seq data

 

Meeting link:

https://cbiit.webex.com/cbiit/j.php?MTID=m53264dc1ee781615a0d289b1678feefc

Meeting number:
2300 641 2315
Password:
mcCG3P8kh@2

Join by video system
Dial 23006412315@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: 2300 641 2315
Host PIN: 2784

Register
When
Wed, Oct 25, 2023 - 11:00 am - 12:30 pm
Where
Online

November

Description

Analysis of medical images such as MRI, CT, X-ray and ultrasound requires a comprehensive environment for data access, visualization, processing, and algorithm development. MATLAB provides tools such as Medical Imaging Toolbox and Deep Learning Toolbox and algorithms for end-to-end medical image analysis and Artificial Intelligence (AI) workflow. This class will highlight the main challenges of extracting clinically meaningful information based on advanced techniques such as AI. Participants will learn how to clean, segment, register, Read More

Analysis of medical images such as MRI, CT, X-ray and ultrasound requires a comprehensive environment for data access, visualization, processing, and algorithm development. MATLAB provides tools such as Medical Imaging Toolbox and Deep Learning Toolbox and algorithms for end-to-end medical image analysis and Artificial Intelligence (AI) workflow. This class will highlight the main challenges of extracting clinically meaningful information based on advanced techniques such as AI. Participants will learn how to clean, segment, register, and label a large collection of images. 

This is an introductory level class. No installation of MATLAB is necessary.

Details
Organizer
NIH Library
When
Wed, Nov 01, 2023 - 12:00 pm - 1:30 pm
Where
Online Webinar
Description

Dr. Ting Wang is a Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine at the McDonnell Genome Institute, Washington University School of Medicine in St. Louis. Dr. Wang’s lab investigates epigenetic determinants of cell fates in normal development and regeneration, in cancer, and in evolution, by integrating cutting-edge experimental and computational technologies. His lab developed widely used DNA methylomics technologies, algorithms to identify regulatory motifs and modules, and analytical and Read More

Dr. Ting Wang is a Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine at the McDonnell Genome Institute, Washington University School of Medicine in St. Louis. Dr. Wang’s lab investigates epigenetic determinants of cell fates in normal development and regeneration, in cancer, and in evolution, by integrating cutting-edge experimental and computational technologies. His lab developed widely used DNA methylomics technologies, algorithms to identify regulatory motifs and modules, and analytical and visualization tools to integrate large genomic and epigenomic data.

Dr. Karen Miga is an Assistant Professor in the Biomolecular Engineering Department at the University of California, Santa Cruz (UCSC). She is also the Associate Director of the UCSC Genomics Institute. In addition, she co-leads the Telomere-to-Telomere (T2T) Consortium and is the Project Director of the Human Pangenome Reference Consortium (HPRC) Production Center at UCSC. Her lab aims to uncover a new source of genetic and epigenetic variation in the human population, which is useful to investigate novel associations between genotype and phenotype of inherited traits and disease.

Details
When
Tue, Nov 14, 2023 - 3:00 pm - 4:00 pm
Where
Online Webinar
Description

This session introduces two versions of  R/ Bioconductor package OmicCircos to generate high-quality circular plots for visualizing multi-dimensional omics daa:

  1. coding in the R environment for programmers;
  2. point and click OmicCircos R Shiny app on the Cancer Genoomics Cloud (CGC) for non-programmers. 

 

Meeting number:2310 050 3184

Password:3sfNDMBq*66

Join by phone

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

Access Read More

This session introduces two versions of  R/ Bioconductor package OmicCircos to generate high-quality circular plots for visualizing multi-dimensional omics daa:

  • coding in the R environment for programmers;
  • point and click OmicCircos R Shiny app on the Cancer Genoomics Cloud (CGC) for non-programmers. 
  •  

    Meeting number:2310 050 3184

    Password:3sfNDMBq*66

    Join by phone

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

    Access code: 2310 050 3184
    Register
    Organizer
    BTEP
    When
    Wed, Nov 15, 2023 - 11:00 am - 12:00 pm
    Where
    Online Webinar

    December

    No scheduled events