- MGC -

MGC Course Program

Practical Linux 

Date4 September, 13:00 - 17:00, Location: LUMC, J1-82, Building 1 (route-555) - Organizer: Mihai Lefter.  After completing this short, half day, course attendees will be able to swiftly start using Linux both on a server as well as on their personal computer. Upcoming course dates: October (t.b.c.), 5 November, 3 December. When the first upcoming edition (4 September) is full, you will automatically be registered with the next edition and you will receive an email about this.  

There are no prerequisites, but the Linux course is mandatory for the courses: Shark, Code and data management with Git, Scripting for life science researcher, and Python programming.

For more information and registration or register directly via    (for September and upcoming editions)

Code and data management with Git

Date: 11 September, 9:00 - 15:00, location: LUMC, J1-84, Building 1 - Organizer: Mihai Lefter. (next edition 5 December; when the first upcoming edition is full, you will automatically be registered with the next edition and you will receive an email about this)

This course aims at everyone who works in the Bioinformatics field. We cover a version control system named Git. This system is widely used by software developers, but can also be used for project management. By keeping track of all versions, history, etc. collaboration with colleagues is easy and your analysis will be reproducible. Knowledge of Linux is required to follow this course.

For more information and registration  or register directly via

Using 'R' for data analysis

Date: 12, 13, 16 and 17 September, 4 days, Location: LUMC, Leiden - Organizer: Szymon Kielbasa

The MGC co-organizes this edition of the course 'R'. The course is part of the I/2 minor "Introduction to biomedical informatics". The course materials are available at the website course/ (We plan some changes to the order of the topics, but in general the contents will remain the same). Course is free of costs for MGC members.

For registration you can send an email to

Safely working in the Laboratory

Date: 9 October, 9:00 - 15:00. Location: LUMC, J-01-116, Building 1

This one day course provides guidelines for the objective assessment of risks in laboratory and, based on this knowledge, the application of the right measures according to the occupational hygiene strategy. On the one hand this is a refresher course, but on the other hand it will become clear to the participant which technical and organizational measures have been taken within the hospital and LUMC in specific to perform research responsibly

To register: PhD students from LUMC can register via 'Bedrijfsopleidingen LUMC', PhD students from Erasmus MC can send an email to

GITLab as a collaborative working environment

Date: 9 October, 9:00-12:00, Location: LUMC, J-01-128, Building 1 - Organizer: Mihai Lefter 

Aimed primarily at LUMC researchers, this short but concise course consists of an introduction to the LUMC GitLab. The course takes approximately three hours and provides participants an insight into how GitLab utilization enhances collaboration and greatly simplifies project management. 

For more information and registration or you can register directly via  

Next Generation Sequencing data analysis

Date: 26 - 28 August, 9:00 - 17:00, Location: LUMC, Building 1 - Organizer: Johan den Dunnen, Judith de Boer, Wilfred van IJken en Leon Mei

The aim of the course is to give a broad overview of the different applications of NGS with a focus on different ways to analyse the data. Presentations will discuss specifically the different choices available for data analysis, why a specific approach was selected and which alternatives are available. The course will, besides discussing and demonstrating some generally applicable tools, not include practical data analysis nor discuss in detail specific algorithms used. To get practical experience participants should, after this general introductory course, follow more specific courses (e.g. a course on RNAseq, de novo assembly, metagenomics, etc.). 

Participants are invited to bring a printed A3 summarising the aim of your project, experimental design, plan of investigation and possible problems/questions that you would like to address. The A3's can be shown on poster boards and discussed informally during lunch and coffee breaks.

The course is free of charge for all personnel of MGC associated institutes. Participants from the academic world but outside MGC pay € 350,00.Participants from outside the academic world pay € 700,00.

There is a minimum of 14 and a maximum of 50 places

In case of no show or cancellation after 21 August 2019, personnel of MGC associated institutes will be charged € 50,00, other participants have to pay the full price.

For more information and registration or you can register via this website

Single Cell analysis

Date: 14-18 October, Location Erasmus MC - Organizer: Chien, Kloet, Lelieveldt, Mahfouz, and Reinders 

This week-long course will cover the practicalities of single-cell sample prep and analysis with a particular focus on single-cell RNA-seq libraries. This course is aimed at both wet-lab researchers interested in learning how to analyze their own single-cell data sets, as well as bioinformaticians who are new to single-cell sequencing analysis. Basic knowledge of the programming language R is a prerequisite for participation in the course.

There is a minimum of 12 and a maximum of 20 places. Deadline for registration 1 October. The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 500 euro. In case of no show or cancellation after 7 October 2019, personnel of MGC associated institutes will be charged 100 euro, other participants have to pay the full price.

For more information and registration or you can register via the registration form

Protein aggregation disorders: from clinic to therapy

Date: 30-31 October, Location: LUMC, building 2 (Restaurant (registration) and room P5-34)

This course will discuss the main molecular mechanisms regulating protein homeostasis and protein folding with a focus a mechanistic foundation in protein aggregation disorders. We will focus on four selected diseases and will discuss genetic, clinic, and current knowledge of disease mechanisms and models for examples. The end point of this course will be development of novel therapeutic strategies to combat protein aggregation in pathological conditions. 

There is a minimum of 12 and a maximum of 30 places. Deadline for registration 14 October, 2019. The course is free of charge for all personnel of MGC associated institutes and for participants working in a research group of one of the course teachers. Participants from outside these organizations pay € 250 for this course. In case of no show without any notification you will be charged 100 euro. 

Click here for more information and program. To register: send an email to - including name, affiliation and email address

Stem cells, Organoids and Regenerative Medicine 

Date: 12-15 November, Location Erasmus MC (the date is changed: the course is one week earlier than originally planned)

Goal of this course is to provide post-graduate students (PhD students and post-docs)  a comprehensive overview of stem cells, organoids and regenerative medicine through lectures of experts in this field. You will learn about concepts, techniques and (future) medical applications (Knowledge and skills). Moreover there will be plenty opportunity  to get to know each other and to present/discuss your own research projects (Communication skills and Networking).

Registration via MolMed


14-18 October: Single-Cell Sequencing and Analysis course

4-8 November: OIC course Functional Imaging and Super Resolution