Research school MEDICAL GENETICS CENTER SOUTH-WEST NETHERLANDS

- MGC -

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MGC Course Program

 Practical Linux 

Next edition: 7 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 pre-registration or pre-register directly via https://forms.lumc.nl/lumc2/LINUX  

Code management with Git

Next edition: 19 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.

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

 Next edition: data to be decided and will depend on the number of pre-registrations

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 or pre-register directly via https://forms.lumc.nl/lumc2/Scripting

Single-cell Analysis

Date: scheduled for 10-14 October, Location Erasmus MC
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.

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 maximum number of 40 participants for this course. All potential participants are asked to write a motivation letter that will be used to make a selection out of the registered people.
Deadline for registration September 2nd. We will make selections the week after so you will be informed before 9 September. The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 500 euro.

Registration is closed

Protein aggregation disorders: from clinic to therapy

24-25 November, Location LUMC

Organizers: Ronald Buijsen, Wim Mandemakers, Vered Raz, and Willeke van Roon-Mom

Provisional Program 2022

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 registration follow this link.

 Python Programming

Next edition: data to be decided and will depend on the number of pre-registrations

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 €400. 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.

For more information or pre-register directly

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

 

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