Bioinformatics Training & Education Program

Qlucore Omics Explorer is a desktop-based point-and-click software with built-in machine learning capabilities. It also enables single cell RNA sequencing and metabolomics analysis. This software is available to NCI CCR scientists upon submitting a ticket at https://service.cancer.gov/ncisp. In this demonstration-only class, participants will learn to use regression approaches to identify correlations between gene expression and methylation data. Experience using or installation of this software is not required for attendance.

Qiagen’s CLC Genomics Workbench is a point-and-click software that enables analysis of multi-omics sequencing data and is available to NCI researchers only. Submit a ticket with service.cancer.gov to request installation on local computer. Long reads aid structural variant and transcript isoform discovery. This class covers 1) de novo assembly and mapping high-quality long reads to reference and 2) polishing de novo assembly of poor-quality long reads using high-quality short reads. No prior experience or installation is needed to attend.

This one-hour online training introduces participants to predictive modeling techniques for evaluating the toxicity of small molecules using MATLAB. Participants will explore the principles of cheminformatics, learn how to preprocess molecular data, and build predictive models using machine learning. The training highlights MATLAB's specialized tools for feature extraction, model development, and performance evaluation tailored to small-molecule datasets. Designed for researchers and data scientists in fields such as drug discovery and toxicology, this session equips attendees with practical skills for leveraging AI in molecular analysis.

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

• Understand the role of data science and AI in predicting toxicity of small molecules
• Import and preprocess molecular data, including handling chemical descriptors and cleaning datasets
• Extract relevant features from molecular datasets to enhance model accuracy
• Develop and evaluate machine learning models, such as classification algorithms, for toxicity prediction
• Visualize model results and interpret performance metrics to assess predictive accuracy
• Utilize MATLAB’s built-in resources and toolboxes to further explore cheminformatics and predictive modeling

Basic familiarity with MATLAB and machine learning concepts is helpful but not required.

The director of the Bridge2AI Cell Maps for AI (CM4AI) Data Generation Project, will discuss the virtual cell models and associated data being generated by the CM4AI project. CM4AI seeks to map the spatiotemporal architecture of human cells and use these maps to interpret cell structure and function in health and disease. 

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. 

At this time, this workshop is only for NIH-affiliated staff & scientists only. Please use your NIH email when registering. 

Join Allen Institute scientists for a one-day, hands-on workshop at NIH focused on helping researchers explore and use cell type taxonomy data and tools from the Brain Knowledge Platform. The workshop will begin with an accessible overview of what cell types are and how they are defined, followed by guided tutorials and interactive exercises using resources for exploring open datasets such as the Allen Brain Cell Atlas. Designed to be highly interactive and applicable across experience levels, the workshop will combine short presentations with individual and guided hands-on time to help participants build practical skills and confidence in applying these tools to their own research and teaching. 

Breakfast, coffee/tea, and lunch will be provided. Registration is free, but required. There is a hybrid option for lectures only, please still register if you need the remote option.

Agenda:
9:00-9:30 Check-in / breakfast

9:30-9:40 Welcome, logistics, overview of the Allen Institute 9:40-10:05 Cell typing at the Allen Institute: taxonomies, data sets, and use cases 10:05-10:30 Deep-dive into the human and mammalian brain atlas 10:30-10:40 Break 10:40-11:05 Localizing cell types with spatial transcriptomics 11:05-11:30 Cell-type targeted enhancer development 11:30-11:55 Deep-dive into the Seattle Alzheimer's disease brain cell atlas 11:55-12:10 Overview of Brain Knowledge Platform tools and resources 12:10-12:15 Preview of afternoon tracks 12:15-1:15 Lunch --- Breakout session 1: Connecting multimodal data to brain cell types 1:15-1:35 Defining and using common coordinate frameworks  1:35-1:55 Patch-seq overview and tools for analysis  1:55-2:30 Additional multimodal datasets from Allen  --- Breakout session 2: Analysis of your own sequencing data using Allen Institute resources 1:15-1:45 Cell type analysis, taxonomy creation, and mapping  1:45-2:10 Cross-species alignment and comparative analyses  2:10-2:30 Other interactive tools for -omics data exploration   --- 2:30-2:40 Break 2:40-3:00 ABC Atlas demo & external use case examples 3:00-3:30 User exploration of Allen Institute tools  3:30-3:45 Tool feedback and Discussion 3:45-4:00 Workshop Survey / closing of formal program 4:00-5:00 Additional time for user exploration

AI-ready science is constrained less by model sophistication than by the shortage of high-quality, well-described data and by infrastructure that cannot keep pace with evolving methods. Drawing on experiences with FaceBase and the Deriva platform across craniofacial, hearing, and ophthalmology research, we argue that FAIR data largely subsumes "AI-ready" data, and that sustainable repositories follow SCALE principles: Self-service curation, domain-Agnostic platforms, Lightweight models, and Evolvable systems.

As large language model agents become the layer through which researchers interact with data, a further question arises: what makes a repository agent-ready? We propose three architectural requirements—documented service interfaces with full coverage, FAIR metadata annotated with community ontologies, and an introspectable data model with an LLM-aligned query interface—and show how an agent built on them can mediate the full research lifecycle, from discovery through citable dataset assembly to curation of results back into the repository, capturing experimental context that artifact-level reproducibility alone cannot.

Partek Flow is a point-and-click platform for building analysis workflows for Next Generation Sequences (NGS), including DNA, bulk and single-cell RNA, spatial transcriptomics, ATAC, and ChIP, helping scientists avoid the steep learning curve of code-based NGS analysis. In this demonstration-only class, an Illumina scientist will show steps for spatial transcriptomics analysis including QC, exploratory analysis, batch effect removal, integration of spatial and gene expression information, as well as differential expression and pathway analysis.  No prior experience or access to Partek Flow is required. Attendance is limited to NIH staff.