ncibtep@nih.gov

Bioinformatics Training and Education Program

Qiagen IPA Pathway Analysis Online Webinars and Training in May

These trainings are offered by Qiagen, not BTEP, and are listed here for your convenience.
(Last updated May 6,2024)
  • May 7 @ 1 PM, New user training: Large dataset analysis and knowledge base queries using QIAGEN Ingenuity Pathway Analysis (IPA)

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Join us for a 120-minute training session for new users of QIAGEN IPA.
In this training, you’ll learn how to:
• Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA
• Understand the different result types produced (pathways, key regulators, impact on biological functions/diseases and more)
• Compare different experimental conditions (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
 
For those with an IPA license: to install IPA before or after this training, please use the link below. https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI
 
To learn more about IPA or request for a trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/?cmpid= CM_QDI_DISC_052024webinars-NUT
 
  • May 14 @ 1 PM, QIAGEN Biomedical KB-HD: data- and analytics-driven drug discovery

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Ingenuity Pathway Analysis (IPA), currently cited in tens of thousands of publications and used by a large number of biopharmaceutical companies, is backed by QIAGEN Biomedical KB-HD. Accordingly, biomedical relationships knowledge has practically become required for innovative data- and analytics-driven drug discovery. It powers biomedical knowledge graph analysis, artificial intelligence (AI)-driven target identification and many more applications.

In this webinar, we will introduce Biomedical KB-HD and how it allows its users to tackle applications that are not feasible with the Ingenuity Pathway Analysis graphical user interface or can be done faster and with more flexibility programmatically. We will demonstrate queries such as

• Quickly find the shortest connections between genes/proteins/metabolites of interest in the context of specific disease through queries

• Systematically build a network given a short list of genes/proteins/metabolites/chemicals

• Recreate a drug mechanism of action Please note that the above agenda may be altered per attendee feedback, as we wish to cover what is most relevant to you.

To learn more about Biomedical KB-HD: https://digitalinsights.qiagen.com/biomedical-knowledge-base/#kb-hd

 

  • May 16, @ 11 AM,  Leveraging the power of API-based omics (RNA-seq, proteomics and more) queries for discovery

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There is a strong interest in the scientific community to use public (GEO, SRA, TCGA, LINCS, etc.) omics (RNA-seq, scRNA-seq, microarray, proteomics, etc.) data for a variety of discoveries. This webinar, aimed at data scientists, bioinformaticians and similar roles in biopharma and academia, explores a comprehensive way of accessing and analyzing high-quality, expertly curated omics data via the QIAGEN OmicSoft APIs. These OmicSoft APIs provide a powerful and flexible platform for discovering, retrieving, filtering, analyzing and visualizing multi-omic data. You can learn how to access the OmicSoft APIs and programmatically leverage extensive metadata to perform custom analyses and identify targets of interest.

Topics to be covered in this webinar:

• Leveraging curated metadata to structure queries (metadata refers to cell type, tissue, disease, drug treatment etc., associated with public data)

• Finding multiple samples with the same metadata and creating cohorts

• Identifying expression and correlation

• Performing gene set enrichment analysis

• Testing cell specificity with custom aggregation Please note that the above agenda may be altered per attendee feedback, as we wish to cover what is most relevant to you.

To learn more about OmicSoft data: https://digitalinsights.qiagen.com/news/blog/discovery/boost-your-agility-and-speed-in-drug-development/?cmpid=CM_QDI_DISC_052024webinars-OPI

 

  • May 21, @ 1 PM, Isolate typing, strain identification and anti-microbial resistance analyses using CLC Genomics Workbench

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QIAGEN CLC Genomics Workbench provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization through SNP and K-mer trees using NGS data and antimicrobial resistance characterization. CLC Genomics Workbench is widely used to analyze bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

Topics covered in this webinar include:

I. Overview of the different tools within MGM application and research areas supported

II. Focused review of isolate typing and characterization

     a. Importing data

     b. Utilization of metadata

     c. Downloading and managing references

         i. Database of Isolates/ Resistances/ MLST

d. Walkthrough of Type a Known Species workflow

          i. Review details for each isolate

e. Creating SNP profiles to a specific reference

f. Generate a SNP tree for isolate comparison

g. Export tabular and high-quality graphical outputs in wide range of file formats

To learn more or request a trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-workbench-premium/?cmpid=CM_QDI_DISC_052024webinarsAMR

 

  • May 22, @ 1 PM,   Scale up NGS bioinformatics analysis throughput with CLC Genomics Server and Cloud solutions

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More and more biopharma and academic groups are looking to process a large number of samples simultaneously or for a quicker turnaround time. This webinar will introduce a flexible and powerful setup for running your NGS sequence analyses through servers or Amazon Web Services (AWS), depending on user preference. We will demonstrate how CLC Genomics Workbench can be used to customize workflows and send analyses for batch execution. We will also highlight analysis automation solutions, use of third-party dockers, audit trails and user management – all of which are available with the CLC Genomics Server software.

You will learn to:

• Customize template workflows to meet your NGS analysis requirements

• Set up a CLC Genomics Cloud environment on AWS

• Submit workflows to run on internal servers or AWS and retrieve results from these analyses

• Use third-party dockers and automate workflow execution

To learn more: CLC Genomics Server: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/enterprise-ngs-solutions/qiagen-clc-genomics-server/?cmpid=CM_QDI_DISC_052024webinars

CLC Genomics Cloud Module: https://digitalinsights.qiagen.com/plugins/clc-cloud-module/?cmpid=CM_QDI_DISC_052024webinars

 

  • May 28, @ 1 PM,  Discovery from public data (GEO, SRA and more) using Ingenuity Pathway Analysis

Register

Per public demand, we are hosting a comprehensive training on how to effectively use sample-level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources through Ingenuity Pathway Analysis (IPA) and IPA Analysis Match Explorer feature. The trainer will walk through use cases in biomarker discovery, drug–target investigation, studying survival in custom patient cohorts, multi-gene correlation and more.

Note: The word “condition” below refers to different diseases, disease subtypes, treatments, cell types, cell lines and more.

This training will cover topics like

• How is a gene of interest expressed across different conditions?

• Is there a correlation in the expression of two genes or biomarkers of interest for a given condition?

• Can we derive a list of genes (for example, genes specific to a disease, treatment or cell type) for a given condition of interest?

• Can we generate custom cohorts of patients (for example, TP53 wt vs. mutant or PDCD1 high vs. low expression) and then generate survival curves representing those cohorts? Can we generate p-values to see if there is a significant difference?

• Can we detect the expression of a gene in different cell types from single-cell data?

To learn more about IPA or request for a trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/?cmpid=CM_QDI_DISC_052024webinars-pubdata