UCSC Genome Browser -- display engine for NGS sequencing data

Course date: 07 May 2018 - 08 May 2018
Location: Erasmus MC, C00-3/Ee

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The Erasmus Postgraduate School Molecular Medicine organizes a series of courses and workshops on Bioinformatics.

We organize two one-day workshops on the use of the UCSC genome browser: one basic course and one advance course. This is the basic course. Participants here will have the possibility of gaining lots of hands-on experience in the use of the UCSC genome browser and also be provided with the necessary background information.

This workshop will be given by Dr. Robert Kuhn of the UC Santa Cruz, California, U.S.A.


Monday 7 and Tuesday 8 May, 2018
Each course will take up one day and will include practical sessions.

The course starts at 9.30 and ends at 17.00.

Coffee break 10.45 - 11.00

Lunch break 12.30 - 13.30

Coffee break 14.45 - 15.00 

It will be held in computer room C00-3/Ee-15.28 at the Medical Faculty of Erasmus MC. See here for convenient maps: www.molmed.nl/maps/maps.asp

Course summary

The UCSC Genome Browser is a display engine for visualizing genomic data covering a large number of data types and experimental protocols.  Ranging from gene predictions and mRNA mapping to human variation at large (CNV) and small (SNP) scales to transcription-factor binding sites and histone modification locations to conservation across 100 species, these data are available across the entire genome and may be viewed together in unlimited combination at all scales from single-nucleotide to whole chromosome. 

Personal data such as those from whole-genome and whole-exome sequencing experiments may uploaded to the Browser and viewed alongside resident data sets.  The Browser supports many data types, including BAM, VCF, BED, wiggle and more.  The Table Browser may be used to perform intersections between datasets.  The Variant Annotation Integrator may be used to make biochemical predictions for variant data from sequencing experiments, exporting information such as type of change (missense, nonsense, splice junction, etc) and SIFT and PolyPhen scores.

Attendees are encouraged to come with questions/problems.

The only prerequisite for this workshop is general knowledge of molecular biology/ genomics and a familiarity with web browsers.

Attendees are encouraged to come with questions. 

Participation in this course equals 0,6 ECTS.

Registration fee

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

If you also participate in the advanced course, the total fee is € 350.

Discounts are handled as follows: 

All participants from the postgraduate school MolMed receive a discount of 100% and pay €0.

All PhD students get a discount of 50% and pay €100/€175.

Other Erasmus MC participants, like MGC, NIHES members, and master students from elsewhere get a discount of 50% and pay €100/€175.

Master students from elsewhere who pay the fee from their personal budget get a discount of 75% and pay €50/€87,50.

MGC-Erasmus MC members receive 100% discount if they follow both the basic and the advanced course.

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. 

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