Practical Linux

Date: provisional date 24 January, 2024

The date has been provisionally set for January 24. When registering your name is placed on the pre-registration list and you will be informed as soon as the date is final.

Organizer: Mihai Lefter

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

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. Places are allocated on a first come first serve basis. If the course is fully booked your name will be put on a reserve list that gives you priority for next edition.

Code management with Git
Date: 4 October, 10:00 - 16:00, LUMC , room J1-82

Fully booked! When registering your name is placed on the pre-registration list for next edition that also gives you priority for that edition. The date of next edition has been provisionally set for February 14

Organizer: Mihai Lefter

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

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

Python Programming

Date:  23, 24, 27 and 28 November,  4 days course

Couse is fully booked. If you fill in the registration form your name will be put on a reserve list which give you priority for next edition.

Location: LUMC, J01-83 

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. Should the course be oversubscribed then places will be allocated based on a first-come first-serve basis.

Deadline for registration: 1 November

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

Scripting for life science researchers
Date: 12 - 13 October, LUMC, J1-82

Couse is fully booked. If you fill in the registration form your name will be put on a reserve list which give you priority for next edition

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, and participants from the Erasmus MC. For people outside these institutes the course fee is 250 euro. In case of no show participants from the 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. Deadline for registration: 20 September
For registration go to https://forms.lumc.nl/lumc2/scripting

Single-cell analysis

Date: 23 - 26 October, 2023, Erasmus MC
Organizers: 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 used to make a selection out of the registered people. Maximum number of participants is 40. 

Deadline for registration: 31 August (Registration is closed)
The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 400 euro.
You can Register via the registration form.

Epigenetic regulation in health and disease

Date: 31 October - 1 November, 2023

 Location: Erasmus MC, room COO-3 

Organizers: Lucia Clemens-Daxinger, Raymond Poot, Haico van Attikum

The course aims to introduce students to epigenetic technologies by providing an overview of the state-of-the-art chromatin and gene regulation studies in the Netherlands. The course consists of lecture sessions in the morning and the afternoon.
Some of the topics induced are: genome wide methylation profiling, genetic and epigenetic pathways in health and disease, transcription factors, chromatin remodeling, chromatin and the
There is a minimum of 14 and a maximum of 50 places. The course is free of charge for all personnel of Erasmus MC and MGC associated institutes. Participants from outside these organizations pay € 200 for this course. In case of no show participants from the associated institutes will be charged 50 euro, other participants have to pay the full price.
For registration follow this link

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

- Basic and Translational Oncology,  9 - 13 October, Erasmus MC

- SCORE: Stem cells, Organoids and Regenerative Medicine, 13 - 16 November, Erasmus MC, and Delft

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