ncibtep@nih.gov

Bioinformatics Training and Education Program

Qiagen IPA Pathway Analysis Online Webinars and Training in July

These trainings are offered by Qiagen, not BTEP, and are listed here for your convenience.
(Last updated July.9,2024)
  • July 9-11 @ 1 PM, QIAGEN Ingenuity Pathway Analysis (IPA) summer camp 

Register

Join us for three 60-minute training sessions for QIAGEN Ingenuity Pathway Analysis (IPA).
In this training, you’ll learn how to:
 
Tuesday July 9 – Session#1: 1pm ET/10am PT
• IPA general overview
• Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more)
• Set up core/pathway analysis in IPA
 
Wednesday July 10 – Session#2: 1pm ET/10am PT
• Understand the different result types produced (pathways, key regulators, and more)
• Customize chart outputs using filters and different chart types like a volcano plot like bubble chart
 
Thursday July 11 – Session#3: 1pm ET/10am PT
• Compare different experimental conditions (different ‘omics data, treatments, time points, single-cell clusters, disease types and more) and identify similarities and contrasts
• Generate a network even without a dataset or experimental design for hypothesis generation If you are able to attend, then we will have additional scientists on the call for Q&A. If you are unable to attend, registering will still allow you to view the recordings.
 
 
  • July 16 @ 1 PM, Discoveries through comparing user data (RNA-seq etc.) with high-quality genomics public data (derived from GEO,TCGA and other sources)

Register

Scientists across biopharma and academia, from early discovery and translational research, to toxicology and more, are highly interested in comparing and validating their ‘omics experiment results such as RNA-seq, microarray, and single cell RNA-seq against published datasets. With QIAGEN OmicSoft Lands collections of deeply curated omics datasets from biomarkers and drug target investigations, tissue and cell type profiling, drug response studies and more, it is quick and easy to discover, retrieve, and compare data from GEO, SRA, GTEx, TCGA, HCL, and other data sources against your own experiments.

In this webinar, you will learn how to compare your data with published datasets with clean metadata using two different approaches:

OmicSoft Studio Graphical User Interface: Many scientists interested in validating their omics datasets are comfortable with a no-code GUI. The trainer will teach you how to find interesting published datasets in the Land database, retrieve these data, then compare your data using OmicSoft Studio. OmicSoft Lands APIs: Data scientists and bioinformaticians, and others more comfortable working with command-line data exploration and visualization tools within R and Python, can use the OmicSoft Lands API. OmicSoft Lands API allows command-line users to efficiently search, explore, and analyze multi-omics data using consistent metadata and data models, then retrieve data of interest to compare directly with user datasets.

 

  • July 17, @ 1 PM, De novo assembly, BLAST and genome finishing with QIAGEN CLC Genomics Workbench

Register

This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.
 
Participants will learn the following:
 
o Download and install needed plugins.
o Import data required for the analysis.
o Run the de novo assembly workflow. o For long reads, improve a de novo assembly by polishing with short, high-quality reads.
o Map reads to a reference and visualize an assembly.
o For long reads, correct raw long reads for further analysis.
o Use BLAST to investigate the contigs. o Analyze and assemble contigs through Genome Finishing tools.
 
 
  • July 18 @ 1 PM, Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) with QIAGEN CLC Genomics Workbench

Register

You asked for it by popular demand, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).

In this training, we’ll cover:

• Introduction to AMR, MLST and relevant databases

• QIAGEN Microbial Insight – Antimicrobial Resistance database (QMI-AR)

• Importing data and downloading needed databases

• Finding resistance with nucleotide DB, PointFinder and ShortBRED

• Integrating AMR with MLST • Exporting high-resolution graphics and result tables.

 

  • July 23 @ 1 PM, Assessing drug safety with QIAGEN Biomedical KB-AI

Register

Are you a healthcare professional, clinical researcher or data scientist interested in drug safety research? If so, you know how vital understanding a drug’s adverse effects is to maximize its effect while minimizing its risks. This webinar will show how the QIAGEN Biomedical KB-AI knowledge graph can be used to explore scientific and pharmacovigilance data. Focusing on immune checkpoint inhibitors (ICIs), we will also demonstrate how Neo4j and Python can be combined to query, visualize and analyze this data effectively.

We’ll cover the following:

• Drug safety profiling in Biomedical KB-AI

• Pharmacovigilance case study of ICIs: Pembrolizumab

• Comparative analysis of ICIs for comprehensive safety monitoring.

 

  • July 24 @ 1 PM, Checkpoint inhibitor and immuno-oncology investigation through OmicSoft Lands APIs

Register

While there is great interest in the scientific community to investigate drug targets and biomarkers from public immune-oncology data, such investigation is hindered by the difficulty in finding and combining related datasets to perform large-scale meta-analyses. This webinar will focus on how high quality curated genomic repositories such as the QIAGEN OmicSoft Lands database immediately allows in-depth investigations across diverse data-sources (GEO, CPTAC, TCGA, GTEx and many more) to discover and validate candidate checkpoint inhibitor drug targets and biomarker investigation.

In this webinar you will learn how to

• Easily identify relevant samples using extensive manually curated clinical metadata

• Visualize and identify checkpoint inhibition biology related drug target and biomarkers expression patterns in bulk and single cell RNA-seq studies.

• Reveal how the expression of a group of biomarkers (or genes/proteins of interest) correlates in normal and disease tissue