Workshop Ingenuity Pathway Analysis (IPA) + CLC Workbench / Ingenuity Variant Analysis

Course date: 07 November 2017 - 07 November 2017
Location: Erasmus MC, Ee-15.28

Click here for details of programme
Click here to register for this course
Click here for abstracts/reviews in preparation of the course


Attached is an old program to give you an impression

This workshop will take place on Tuesday 7th, 2017 at 09:30 hours.
 
One day training workshop by the team from Ingenuity about Ingenuity Pathway Analysis (IPA).

IPA Training  
This hands-on training workshop will introduce new users to Ingenuity Pathway Analysis (http://www.ingenuity.com/products/ipa) for the biological interpretation of ‘omic data, and provide additional information for inexperienced users of the system. The training will use an RNA-Seq data set as a case study. For example, the temporal transcriptional changes observed during the differentiation of mouse embryonic stem cells to cardiomyocytes. The course will also highlight the considerations when analysing and integrating other data types such as proteomics or metabolomics data, and will touch on the analysis of miRNA.

Course Topics:

  • Introduction to QIAGEN Sample to Insight and Ingenuity Pathway Analysis (IPA)
  • Uploading data and running a Core Analysis
  • Interpreting a Core Analysis
    o Canonical Pathways Analysis
    o Upstream Regulator Analysis
    o Functional Analysis
    o Molecular Network Analysis
  • Search & Pathway Building; Search & Explore case study
  • Comparison Analysis
  • Sharing & Collaboration
  • Best Practice Tips & Tricks
  • Overview of other IPA analysis tools

 CLC Workbench and Ingenuity Variant Analysis Training

This topic will introduce users to the CLC Cancer Research Workbench (http://clccancer.com/software/) for the fast and efficient processing and visualisation of Human NGS data, and to Ingenuity Variant Analysis (http://www.ingenuity.com/products/variant-analysis) for the identification, prioritisation and biological interpretation of DNA Variants. The case study will cover the basics of data visualisation, QC, the creation of user-constructed workflows, and the identification of variants from targeted human DNA resequencing using the Workbench. The biological significance of the variants will then be interpreted using Ingenuity Variant Analysis which will allow users to additionally annotate, filter and prioritise variants based on their biological relevance.

Course Topics:

  • Introduction to QIAGEN Sample to Insight, CLC Cancer Research Workbench and Ingenuity Variant Analysis
  • Getting Started with the Cancer Research Workbench
  • Loading human fastq data and performing QC
  • Alignment of reads to a Reference genome, coverage and QC
  • Variant Calling and variant-level annotation
  • Workflows for different data types
  • Integrating the Workbench with Ingenuity Variant Analysis
  • Creating an Analysis of multiple samples in Variant Analysis
  • Biological interpretation of variants
  • Refining filters, refining the analysis
  • Advanced Analysis Tips and Tricks 

Course location

Computer room Ee-1528, Bioinformatics dept., Medical Faculty, Erasmus MC

ECTS
For this course you will receive a certificate of attendance with 0,3 ECTS for full participation.

Registration fee
The subscription fee of non-commercial participants for this course is € 200.

Discounts are handled as follows:

  • All PhD students get a discount of 50% and pay €100.
  • All participants from the postgraduate school MolMed receive a discount of 100% and pay €0.
  • Master students from elsewhere who will need to pay the fee themselves, receive a discount of 75% and pay €50,00.

General information

Financial regulation of the Postgraduate School MolMed

From January 1st, 2017 the following financial rules apply, but they may differ per course still. Look at the course fee of each course to be sure which discounts are really applied:

Non-commercial course, symposium or workshop fee: €200/day, €750/week

• Participants of the postgraduate school MolMed: discount of 100%

• However, the Research Management course and the workshops Photoshop/Illustrator/Indesign have to be paid from the ‘personal budget’ of employees, MolMed members and PhD students included. So they will receive an invoice from us which you have to pay and which will be reimbursed by your Department. When you will pay from your personal budget you need to provide us your home address details for the invoice

• PhD students and Master’s students, regardless of institution: discount of 50%.

  • The course fees of research master’s students will be paid by their master program at rate of €100/ECTS. For not I&I master students: please inform your master program in advance whether they agree to pay.
  • Master’s students who are paying the fee from their private budget: discount of 75%. When you will pay from your personal budget you need to provide us your home address details for the invoice.
  • However, 2 courses in statistics are paid centrally by the Dept. of Research policy for all PhD students from Erasmus MC! These are R and the SPSS course. So for Erasmus MC PhD students, these courses are always free, provided you are officially registered as a PhD student.

There is one fee for the entire course. There is no reduction for partial participation.

Some courses have less course days: SPSS 3 days, Survival Analysis 2 days, Management 2 days, Presenting 1,5 days and also other may be shorter as indicated on the website.

Commercial participants, companies & sponsors are invited to inquire about commercial tuition fees and about sponsoring.

All invoices will be sent by email to the mail address that you filled in upon registration. If this address is not correct we use your Erasmus MC address.

Those who register for a course, symposium or workshop agree with these financial conditions.



Click here for details of programme
Click here for Abstracts/reviews in preparation of the course (available soon!)
Click here to register for this course


Click here for the other items