- MGC -

MGC Course Program

 Python Programming

 Date: 12 - 15 October, 2020, Note: this course will be given on-line and not in the LUMC!!- Organizer: Mihai Lefter

 The course is targeted at PhD students, postdocs, or anyone willing to learn how to program in Python. Participants are assumed to have some experience with programming, but not necessarily in Python, and the UNIX shell. Knowledge of Git is required to attend this course.

 There will be a focus on bioinformatics and programming to support scientific research in general. The program consists of four mornings with lessons and some assignments to be done in your own time (i.e., during the afternoons).

The course is free of charge for all personnel from MGC institutes. Participants from outside these institutes pay €200. There is a maximum of 25 places. Should the course be oversubscribed then places will be allocated based on a first-come first-serve basis.

 Single Cell analysis (course is now fully booked! - pre-registration for next edition is possible)

 Date: 19-23 October, 2020 in an online version - Organizer: Susan Kloet, Miao-Ping Chien, and Ahmed Mahfouz 

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.

The course features a mix of lectures and practicals, and you will have the opportunity to perform hands-on analysis of scRNA-seq data in R. Topics to be covered in the course include (but not limited to): an overview of different single cell platforms, experimental design, preprocessing of scRNA-seq data, normalization, dimensionality reduction, clustering, batch correction, differential expression, trajectory inference. The fifth day of the course will be a mini-symposium featuring guest lectures from scientists using various single-cell techniques in their research.

All potential participants are asked to write a motivation letter that will be use to make a selection out of the registered people. The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 200 euro. 

You can pre-register via the registration form Please, include your motivation. Your name will be placed on a reserve list. When a person cancels their participation, the first person on this list will be asked to participate (and so on).  Pre-registration gives you priority to participate in next edition of this course.

Multiomics Data Analysis using R (course is fully booked, additional registrations will be put on a reserve list)

Date: 2 - 6 November, 2020

Course is on-line

By following this course, you will gain an understanding of the nature of different omics data types. You will learn how to find and access data from public repositories, join data of different types, from different sources and in different formats. You will also learn how to integrate multiomics data in different ways using R with powerful packages such as mixOmics and SEA, the latter developed here at the LUMC. We will introduce the network analysis and visualization software Cytoscape and use the RCy3 package to integrate it in R. As part of this course you will gain a basic familiarity with the statistical and graph theoretical concepts on which the software builds.

The course is free of charge for all personnel from MGC institutes. Participants from outside these institutes pay €200. Should the course be oversubscribed then places will be allocated based on motivation and further by a first-come first-serve basis.

Follow the links for more information and registration

 SCORE PhD course: Stem Cells, Organoids and Regenerative Medicine 

 Date: 10 - 13 November, 2020 - Location Erasmus MC (course is fully booked; upon registration your name is put on a reserve list)

 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 

Practical Linux 

Date7 May - cancelled , new dates will be posted a.s.a.p.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.   

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 pre-register directly via  

Code and data management with Git

Date: to be decided

For more information and pre-registration  or pre-register directly via

Next Generation Sequencing data analysis

Date: Postponed to next year, august 2021 - Organizers: Johan den Dunnen, Susan Kloet, Judith de Boer, Wilfred van IJken en Leon Mei

 For pre-registration follow this link

Epigenetic Regulation in Health and Disease

Date: Lucia Clemens-Daxinger, Raymond Poot en Haico van Attikum hope to organize a physical meeting in spring 2021

For pre-registration follow this link

Functional Imaging and Super resolution

Date: Postponed to next year - probably November 2021 - Contact person: Gert van Capellen (OIC, Erasmus MC)


List of MGC PhD courses including links to general information (for a quick look at (expected) course dates and ECTS/course check here)

Technology Facilities

Genome Maintenance and Cancer 

Introduction to Cytoscape

Epigenetic regulation in health and disease 

The ins and outs of CRISPR-Cas

Scripting for Life Science Researchers

Genetic engineering in model organisms: technology and applications
 in basic and medical research

Next Generation Sequencing data analysis

Python programming

Functional Imaging and Super resolution

Stem Cells, Organoids and Regenerative Medicine (new in   2018) 

Protein aggregation disordes: from clinic to therapy (new in 2019)

Practical Linux 

GITLab as a collaborative working environment (new in 2017)

Version control with Git / code and data management with Git

 Safely working in Laboratory

Incollaboration with MolMed ErasmusMC

Basic and translational oncology