Practical Linux 

New dates:  16 September (date is changed!!!; original date was 20 September) and 4 November, 2024, 10:00 - 14:00, LUMC, room J-01-082 (route 555) 

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition. 

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 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 

The course is free of charge. See cancellation rules at the bottom of this page

Code management with Git
New dates: 25 September and 15 November, 2024, 10:00 - 16:00, LUMC , room J1-82

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition.

Organizer: Mihai Lefter

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 the link

The course is free of charge. See cancellation rules at the bottom of this page

Python Programming

Date: 20, 21, 24 and 25 June, 2024. LUMC, building 1, room J-01-83 (fully booked)

Next edition: 28 November - 3 December

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition.

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. For this reason it is mandatory to follow the Practical Linux and Code management with git courses before.

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  and Erasmus MC institutes. Participants from outside these institutes pay €400. There is a maximum of 20 places. See cancellation rules at the bottom of this page.

Registration: via the link  (https://forms.lumc.nl/lumc2/Pythonprog) 

Next Generation Sequencing data analysis

Date: 28 -30 august, 2024 - Organizers: Susan Kloet, Judith Boer, Wilfred van IJcken en Leon Mei
Location: LUMC, building 1, lecture room 4

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.).

The course is free of charge for all personnel of ErasmusMC and 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

Program edition 2023 . Registration via the link

Scripting for life science researchers

Date: 14-15 October, 2024, Location LUMC room J1-82 9:30-16:00

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. 
There is a minimum of 12 and a maximum of 20 participants.
You can register via the registration form https://forms.lumc.nl/lumc2/scripting

Single Cell analysis

Date: 29 October - 1 November, 2024, Room CQ-1Da, GK building, Erasmus MC, Rotterdam

Course coordinators: Dr. Susan Kloet (LUMC), Dr. Miao-Ping Chien (Erasmus MC), Dr. Ahmed Mahfouz (LUMC)

Organizer: MGC & BioSB research school

This 4 days-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 used to make a selection out of the registered people. You can register via the registration form: follow the link: https://forms.lumc.nl/lumc2/SingleCell

Deadline for registration 31 August and you will be informed soon thereafter if you are selected for the course or not. There is a max of 40 participants.

The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 400 euro.

Course Credits: the study load of this course is 2 ECTS credits. You can send an email to nivard@lumc.nl to receive a certificate after successfully completing this course.

Protein aggregation disorders: from clinic to therapy 
Date: 28 - 29 November, 2024, location: Erasmus MC

Course coordinators: Willeke Roon-Mom , Ronald Buijsen,  Vered Raz (LUMC) and Wim Mandemakers (Erasmus MC)

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.

MGC courses: general cancellation rules for MGC members 

The courses are free of charge but please note that we have set up strict cancellation rules:
•            Free cancellation up to 2 weeks before the start of the course
•            Cancellations after the mentioned time interval until one day before the start of the course: €50 per course day unless you have a replacement. In that case name and email address plus confirmation from the replacement is included in the cancellation email to the MGC secretariat nivard@lumc.nl 
•            In case of no-show up: €100 per course day

In collaboration with the Erasmus MC graduate school - see course program

Safely working in the Laboratory

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