Bioinformatics Training & Education Program

This hour-and-a-half online training will examine how humans process and encode visual information and how visual attributes can be utilized to create effective visualizations. This will focus on enhancing graphic literacy, exploring methods for making better visualizations, and using stakeholder needs to guide your design choices.

By the end of this training, attendees will be able to:

• Discuss the value of data visualization and key visualization goals
• Provide an introduction to human perception and its role in visualization
• Describe the principles of visual encoding.
• Provide an overview of core visualization techniques
• Outline the steps for effectively presenting your visualizations to different audiences.

Dr. Theodore Alexandrov leads a multidisciplinary team of scientists and software engineers dedicated to developing cutting-edge technologies for spatial and single-cell metabolomics (https://ateam.ucsd.edu). They have developed METASPACE, a cloud software platform for spatial metabolomics used by thousands of scientists worldwide, and SpaceM, a method for single-cell metabolomics which can probe metabolism with the single-cell resolution.

Join Drs. Eytan Ruppin (presenter) and Timothy Shaw (moderator) as they present on four approaches for predicting how patients respond to checkpoint immunotherapy.

• Approach #1: Predicting patient response to the tumor bulk transcriptome
• Approach #2: Predicting response directly from the blood via simple routine lab tests and the tumor mutational burden
• Approach #3: Predicting patient immunotherapy response from the tumor histopathological images
• Approach #4: Building predictors of the tumor microenvironment and developing spatially grounded biomarkers of treatment response

This presentation describes the basic mechanics of constructing a decision tree and interpreting the results. Decision trees will be used to determine factors associated with 2-year survival for individuals with Stage IV lung cancer and whether Kyphosis (a type of deformation) occurs in children after spinal cord surgery. A relative hazard can also be used within a decision tree to construct a survival tree. Finally, random forest, which constructs a large number of sub-optimal decision trees, will be discussed. This presentation will be very light on mathematics, and no prior knowledge is required.

This lesson will introduce the "split-apply-combine" approach to data analysis and the key players in the dplyr package used to implement this type of workflow.  

This session of the BTEP Coding Club will demonstrate the use of R programming to perform decision tree analysis, survival tree analysis, and random forest. This event complements a Statistics for Lunch event, "Decision Trees, Survival Trees, and Random Forest", organized by the Advanced Biomedical Computational Science group at the Frederick National Laboratory for Cancer Research. The Statistics for Lunch event will provide a theoretical introduction to these topics, while this coding club session will focus on practical implementation using R.
The session will cover the following: 1. Decision Tree Analysis
The decision tree analysis will use the “kyphosis” dataset to predict the absence or presence of kyphosis (a type of deformation) following corrective spinal surgery.
2. Survival Tree Analysis
The survival tree analysis uses the recurrence-free survival time from a prospective randomized clinical trial conducted by the German Breast Cancer Study Group.
3. Random Forest
Random forest will be applied to the German Credit Data set, which contains 20 variables for 1000 individuals, to determine whether they should or should not receive a loan of a given amount.   This class requires knowledge and experience with R programming.  

From image analysis to federated learning and multimodal modeling, generative AI can be used to study observational succession across scales and data types. At DCEG's Data Science and Engineering Research Group (DSERG), we are developing user-facing, FAIR, privacy-preserving infrastructure for cancer research based on numerical embedding shared across, and between data types. This presentation is configured as a show-and-tell activity with live applications ranging from digital pathology to real-time epidemiology trackers. Particular focus will be placed on showing where and how does genAI modeling expose a numeric representation of the underlying latent space.

 CDr. Jonas Almeida leads a multidisciplinary program of data science and engineering research that combines systems biology, computational statistics, and software engineering for biomedical applications. The primary focus of his research is to accelerate the investigation of epidemiologic and genetic causes of cancer by developing innovative digital methods that advance the computational research infrastructure for precision prevention.

Diagnostic errors remain a leading cause of preventable harm in healthcare, particularly in high-stakes, time-pressured environments like the emergency department. Large Language Models (LLMs) offer promising new capabilities for transforming diagnostic safety surveillance and clinical decision support. In this talk, Dr. Taylor will explore emerging applications of LLMs to improve diagnostic performance, with a focus on real-time chart review, trigger-based systems, and the augmentation of quality improvement processes. He will share recent research evaluating the feasibility, accuracy, and implementation challenges of these models, as well as lessons learned from deploying them in clinical and operational workflows. We’ll also discuss the broader implications for trust, oversight, and future regulatory frameworks as we bring these tools closer to the bedside.

This is the final lesson in the course Introductory R for Novices: Introduction to Data Wrangling. This lesson will show attendees how to join multiple data frames and transform and create new variables using dplyr.

NIDDK Biostats Seminar Series: From Research Study Design to Collecting, Managing, and Analyzing Data.

Learning Objectives

1. The learner should know the difference between observational studies, clinical trials (drug and non-drug studies), and secondary data (new data from stored samples, existing data) as defined for the NIH Clinical Center and how study development differs for each.

2. The learner should understand the development process, know the timeline, and know the resources available for successful protocol development.

3. The learner should understand the purpose and scope of ClinicalTrials.gov.

4. The learner should be able to identify and understand key data elements and each step of trial registration and reporting.

5. The learner should be able to understand the differences between a scientific hypothesis and a statistical hypothesis.

6. The learner should be able to translate scientific hypotheses into statistical design elements: study design, primary outcomes, statistical hypotheses, sample size calculation, and statistical analysis plan.

 

Tentative Webinar Outline:

2:30-3:00pm – Dr. Paige Studlack(Clinical Protocol Coordinator, NIDDK)

Research study types, timelines, and process for successful protocol development, IRB approval, and study initiation at the NIH, with particular emphasis on NIDDK resources and processes.

3:00– 3:30pm – Dr. Elizabeth Wright (Mathematical Statistician, Biostatistics Program Office, NIDDK)

Understanding ClinicalTrial.gov elements and how they are used in trial registration and reporting for studies at the NIH.

3:30-4:00pm – Dr. Sungyoung Auh (Mathematical Statistician, Biostatistics Program Office, NIDDK)

Translating scientific questions to needed statistical design elements for research study planning, documentation, completion, and reporting.

Considerations for protecting private data when training AI models is a topic of increasing concern. During this event, participants will discuss the use of synthetic data for privacy-preserving AI.

This one and a half-hour online training covers the basic principles of FAIR (Findable, Accessible, Interoperable, Reusable) data and why it is important to make your data FAIR.  This is an introductory level training.

•  By the end of this training, attendees will be able to:  
• Define FAIR data   
• Explain what purpose FAIR data serves 
• Apply FAIR data principles to make data findable, accessible, interoperable, and reusable 

Harnessing the Power of Transcriptomics for Scientific Discovery

The "Data Visualization in R" series focuses on using ggplot and the broader tidyverse ecosystem to create insightful and customizable visualizations. It covers key principles of data visualization, from basic plots to advanced techniques, emphasizing the flexibility and power of ggplot within a tidy data workflow. By the end of the series, participants will be proficient in building plots using the tidyverse ecosystem. 

This hour and half online training will explore the topics of perception and cognition, and how these apply to data visualization. This training will also teach you how to visualize your data using ggplot2. We will start by creating a simple scatterplot and use that to introduce aesthetic mappings and geometric objects, the fundamental building blocks of ggplot2. You must have taken Introduction to R and RStudio training to be successful in this training. 

You can register for the other training in this series via the link below.

• Data Visualization in R: Customizations Part 2 of 2

By the end of this training, participants should be able to: 

• Describe how perception and cognition inform visualizations.
• Distinguish between aesthetic mappings and geometric objects, the fundamental building blocks of ggplot.
• Create a simple scatterplot.
• Create a plot and save it in a high-resolution format.
• Attendees are expected to have a basic understanding of R and RStudio. To proceed, attendees should have done the following:
• Installed R and RStudio.
• Have a basic understanding of R and RStudio.
• Reviewed our R basics training on the NIH Data Services: On Demand Content YouTube Playlist, if you are new to R.

NIDDK Biostats Seminar Series: From Research Study Design to Collecting, Managing, and Analyzing Data.

Learning Objectives:

1.         To delineate features of REDCap to support project management for research studies.

2.         To outline steps to create detailed data collection plans which fulfill regulatory requirements. 

3.         To identify principled approaches to data collection and management. 

4.         To explain the connections between research rigor and reproducibility.

 

Outline:

2:30-3:00pm – Matthew Breymaier (Informatics Specialist, Office of the Clinical Director, NIDDK), Sai Theja (Senior Data Analyst, Office of the Clinical Director, NIDDK)

RedCap – functionality and basics of setup and how different types of studies can be designed in RedCap (longitudinal vs cross-sectional etc), with emphasis on NIDDK RedCap.  

 

3:00– 4:00pm – Dr. Kenneth Wilkins (Mathematical Statistician, Biostatistics Program Office, NIDDK)

Document organization and access as part of study planning: regulatory, clinical, and case report forms 

Data Management and Sharing Plans

Data Management for Reproducibility

The "Data Visualization in R" series focuses on using ggplot and the broader tidyverse ecosystem to create insightful and customizable visualizations. It covers key principles of data visualization, from basic plots to advanced techniques, emphasizing the flexibility and power of ggplot within a tidy data workflow. By the end of the series, participants will be proficient in building plots using the tidyverse ecosystem. 

This one hour and half online training builds on the topics covered in the Data Visualization in ggplot training. This training emphasizes advanced customization techniques in ggplot, to create effective and clear visualizations. Participants will build on the foundational skills learned in Part 1 of the series and apply various customization options, such as faceting, labeling, themes, and color scales.  You must have taken Data Visualization in R: Introduction to ggplot: Part 1 of 2 training to be successful in this training.  

By the end of this training, attendees should be able to:  

• Create a scatterplot in ggplot 
• Learn how to facet a plot 
• Demonstrate options for customizing the title and axis 
• Apply different ggplot themes Attendees are expected to have a basic understanding of R and RStudio. To proceed, attendees should have done the following:
• Installed R and RStudio.
• Have a basic understanding of R and RStudio.
• Reviewed our R basics training on the NIH Data Services: On Demand Content YouTube Playlist, if you are new to R.
• You can register for the training in this series via the link below:  
• Data Visualization in R:  introduction to ggplot Part 1 of 2 

Globus is a GUI-based software suitable for efficiently transferring large datasets such as those generated from Next Generation Sequencing (NGS) to and from high performance computing systems such as NIH’s Biowulf. This demonstration only class will show participants how to access and setup Globus for transferring data from local computer as well as sequencing facility data management environment (DME) to Biowulf. This class is open only to NIH staff. Meeting link will be provided upon approval of registration.

Registeration link: https://cbiit.webex.com/weblink/register/re8dc373ea594662a5e3b0e92a71582fb

The role of computational science in biomedical research has typically been downstream of experiments, where it plays important roles in signal processing, data integration, pattern detection, and hypothesis testing. But this is changing, and predictive models are now being used to generate and test hypotheses in silico. In this talk, Dr. Pollard will share examples from human genetics, where they have built deep learning models of 3D chromatin interactions that take only sequence as input and then used them to interpret disease variants. This strategy leads to causal hypotheses and enables them to prioritize variants with predicted functional effects. Experiments designed using model outputs are accelerating the rate of discoveries, shedding light on genetic mechanisms in cancer and developmental disorders. This prediction-first strategy exemplifies Dr. Pollard's vision for a more proactive, rather than reactive, role for computational science in biomedical research.

NIDDK Biostats Seminar Series: From Research Study Design to Collecting, Managing, and Analyzing Data.

Learning Objectives:

Be able to identify, load, and use R resources/packages based upon needs and experience level with R.  

1. For beginners, know how to load R Commander, import data, and navigate the GUI.  

2. For those interested in learning more about coding/functions, how to use R Swirl to learn foundations for functions and coding higher level operations (loops, combining functions, and building new functions).  

3. For regular users of R, how to use tidyverse for data manipulation, organization, and preparation for analysis.  

4. For those using R for research work, how to utilize R Markdown for appropriate and thorough project documentation and management.  

 

Outline:

2:30-3:00pm –Beginner level (Dr. Wilkins, Mathematical Statistician, Biostatistics Program Office, NIDDK)

How to get the basics accomplished: load data, navigate RCommander GUI, and export data.

3:00– 3:30pm – Intermediate level (Dr. Leary, Chief, Biostatistics Program Office, NIDDK)

Data manipulation and organization for analysis with focus on tools for more complex coding and functionality.

3:30-4:00pm – Advanced topics (Dr. Leary)

Leveraging R Markdown and other resources for project management, documentation, and archiving.

This one-hour online training will provide a high-level overview of Python coding concepts, as well as some of the integrative development environments (IDEs, such as Jupyter notebooks) used for Python coding. Python is a programming language used for data science, specifically: data analysis, statistical analysis, and visualization of results. The training will feature the following IDEs: Google Colaboratory: Jupyter Notebook; and Anaconda’s: Spyder, Jupyter Notebook, and JupyterLab. This overview training will demonstrate how these skills can boost productivity, rigor, and transparency in reporting research findings.  

By the end of the training, attendees will be able to: 

• Recognize four freely available IDEs for python coding 

• Identify fundamental components of python code 

• Understand how and why notebooks support rigor and transparency in analysis 

Attendees are not expected to have any prior knowledge of python coding or the IDEs to be successful in this training.  

If you choose to follow along with Google Colab or Jupyter Notebooks, these IDEs should be installed and ready to go. Code will be provided during the training for this option. 

Join the National Heart, Lung, and Blood Institute (NHLBI) for a hybrid workshop to explore how medicine will be transformed by the current artificial intelligence (AI) revolution. Participants will engage with leading experts to learn the current state and visionary outlook of the field and to identify research gaps and opportunities in AI, focusing on clinical decision support.

The primary aim of this workshop is to explore how AI can be utilized to aid in diagnosing and treating heart, lung, blood, and sleep disorders (HLBS). AI is a computer science field focused on creating systems that perform tasks requiring human intelligence. These tasks include learning, reasoning, problem-solving, perception, language understanding, and interaction. AI includes subfields like machine learning, natural language processing, robotics, and computer vision. In biomedical research and health care, AI analyzes complex datasets, enhances diagnostic accuracy, personalizes treatment plans, and improves healthcare delivery. 

Additionally, the workshop aligns with the broader mission of NHLBI to promote the prevention and treatment of heart, lung, and blood diseases, and enhance the health of all individuals so that they can live longer and more fulfilling lives.

Please use this link to access overview, registration, and other information:

https://events.cancer.gov/nci/ods-data-jamboree

Childhood cancer is a rare disease with ~15,000 cases diagnosed annually in the United States in individuals younger than 20 years. Despite extensive efforts made over the last two decade by programs such as National Institutes of Health (NIH)'s Gabriela Miller Kids First Programand NCI's Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Childhood Cancer Data Initiative (CCDI) to generate, collect and share the data, pediatric and AYA cancer datasets remain underutilized. Finding and accessing datasets, building specific pediatric cancer cohorts, and aggregating or linking datasets from various data systems still present tremendous challenges for the wider community. To overcome these barriers and raise awareness of existing childhood cancer data resources to inform better diagnosis and treatment options for children, this data jamboree is to bring together researchers and citizen scientists with diverse expertise and experience to collaborate and explore scientific or other questions using childhood cancer data. The goals of the jamboree include:

• Promoting access and reuse of pediatric cancer data and raising awareness about the availability of these datasets.
• Promoting interdisciplinary collaborations to expand the size, technical, and scientific diversity of the pediatric cancer research community.
• Promoting development of new methods and tools for data analysis.
• Identifying gaps and limitations of existing data and resources including barriers to real time access to the data.