Research school MEDICAL GENETICS CENTER SOUTH-WEST NETHERLANDS

- MGC -

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MGC Course Program

 Practical Linux 

Edition 16 May, 10:15  - 14:15, LUMC, J1-82  (half day course) Course is fully booked

Next edition: data to be decided (either end of June or first week September)

Organizer: Mihai Lefter

 In the coming months, several editions of the course are organized in the LUMC.  If one of these editions at registration is fully booked, your name is placed on a reserve list and you will receive an email as soon as new date(s) are known for coming editions of the course.

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 register directly via https://forms.lumc.nl/lumc2/LINUX  

Code management with Git

Edition 2 June 10 AM - 4 PM, LUMC, J1-82 Course is fully booked

Organizer: Mihai Lefter

In the coming months, several editions of the course are organized in the LUMC.  If one of these editions at registration is fully booked, your name is placed on a reserve list and you will receive an email as soon as new date(s) are known for coming editions of the course.

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 (pre)registration 

Scripting for life science researchers

 Date: 19 -20 May, 2022, Location LUMC, room J1-82  - Organizer: Mihai Lefter

 This course is designed for researchers, who frequently handle large datasets or large numbers of files (images, sequence reads, mass spectra etc.) and who need a more efficient way of working with such data. The goal of the course is to empower students and researchers with backgrounds in biology or biomedicine to navigate, manage and perform operations on files and data and metadata in tabular text formats. The data may be microscopy images, FASTA sequences, gene ontology files, chromatograms, mass spectra or tables with data on genes or proteins. The course is not a general introduction to programming and will not deal with XML data, Web services or more advanced topics. For the Scripting course it is required to have followed the Linux course first.

 Course is free of costs for MGC members, for non-MGC members the course fee is 200 euro. In case of no show participants from the MGC associated institutes will be charged 50 euro, other participants have to pay the full price.

 There is a minimum of 12 and a maximum of 20 participants.

 For more information and registration or register directly via https://forms.lumc.nl/lumc2/Scripting

The Ins and Outs of CRISPR-Cas

Date: May 23, 24, 30 and 31, 2022 (the course runs for 4 full days and requires preparation), Location: Erasmus MC 

Organizers: Joyce Lebbink, Niels Galjart and Sreya Basu (Erasmus MC)

For PhD students with an active interest in genome engineering using this technique AND an interest in understanding the molecular mechanism of Cas9 function 
The CRISPR-Cas9 system is revolutionizing the field of biomedical science by allowing efficient mammalian genome editing. This course will offer students the latest advances in this technique and allows them interactions with leading scientists in the field. Students will study the underlying biochemical and biophysical principles of Cas9 structure-function relations, through literature study and protein structure visualization and analysis. Furthermore students will design a genome modification strategy based on their own research project or available case studies. Focus will be on assimilation and application of background and new knowledge in an interactive setting including computer assignments, discussion sessions and student presentations.
There is a minimum of 16 and a maximum of 20 places.
When registering for this course, please provide a short motivation of max. 100 words (this will be used for selection in case the course is oversubscribed).
The course is free for all members of the MGC institutes. Course fee for participants from outside these institutes is € 500

Deadline for registration May 12th

For registration: follow the link

Announcements (open for pre-registration that gives you priority for participating in the course)

Next Generation Sequencing data analysis
Date: end of August  beginning of September - 3 days course (t.b.d.)
Organizers: Susan Kloet, Judith de Boer, Wilfred van IJcken
, Leon Mei and Saskia Hiltermann
The aim of the course is to give a broad overview of the different applications of NGS with a focus on different ways to analyze 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.).
The course is free of charge for all personnel of MGC associated institutes.
Participants from the academic world but outside MGC pay € 300. Participants from outside the academic world pay € 600,00.
For (pre-)registration: follow this link


Single-cell Analysis
Date: scheduled for 10-14 October, Location to be decided
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 500 euro.
You can (pre-)register via the registration form.

Protein aggregation disorders: from clinic to therapy

24-25 November, Location t.b.d.

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.

The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 250 euro.
For (pre-)registration follow this link.


Safely working in the Laboratory

This course is temporarily not offered face to face. You can request login details of the video recordings of the lectures of the course from 2020 at nivard@lumc.nl

See the page 'MEETINGS' to register for the MGC symposium on May 19



List of MGC PhD courses including links to general information and for a quick overview of all course click 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