MGC Course Program
Date: 7 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.
Code and data management with Git
Date: to be decided
Safely working in the Laboratory
Date: 19 May, Location Building 3, LUMC room V4-52 - Canceled
Date: - to be decided, hopefully we are able to organize the course second part 2020
- The aim of the course is to familiarize participants with the mechanisms that are involved in maintaining genome stability. The course will provide an up to date insight in the chain of reactions from exposure to ultimate consequences. Lectures will deal with the basic principles of several cell biological aspects such as DNA damage formation, signaling pathways, DNA repair and mutation formation. A few lectures will deal with more applied research. There is a minimum of 14 and a maximum of 30 places. The course is free of charge for all personnel of MGC associated institutes and OOA (VUMC, AMC, NKI departments), CTO (UMC Utrecht), and RIMLS/RIHS (Radboud UMC) associated departments. 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.
Multiomics Data Integration Using R
Date: 11 - 15 May, 2020, due to the coronavirus the organizer will give this course remotely - Organizer: Magnus Palmblad
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.
The registration is closed.
For more information see the Google doc.
The course is free of charge for all personnel of MGC associated institutes and PhD students of OOA (Onderzoekschool Oncologie Amsterdam). Participants from outside these organizations pay € 200 (academic world)
Scripting for life science researchers
Date: 29 - 30 June, 2020, the organizers are busy converting this course to an online version - 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 100 euro.
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
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 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
For pre-registration follow this link
Epigenetic Regulation in Health and Disease
Date: 1-2 October, 2020, Location LUMC, lecture room 2 (first day) and room V4-36/40 (second day), 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 DNA damage response, X-inactivation and stem cells.
There is a minimum of 14 and a maximum of 50 places. The course is free of charge for all personnel of 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
Date: 12 - 15 October, 2020, Location LUMC room J1-83 - 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. 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 including lunch. 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
Date: September (to be decided) - the organizers are busy converting this course to an online version - Organizer: Chien, Kloet, Lelieveldt, Mahfouz, and Reinders
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.
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 register via the registration form Please, include your motivation.
Stem cells, Organoids and Regenerative Medicine
Date: autumn, 2020 - Location Erasmus MC
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).
You can pre-register. Pre-Registration via MolMed
List of MGC PhD courses including links to general information (for a quick look at (expected) course dates and ECTS/course check here)
Introduction to Cytoscape
Stem Cells, Organoids and Regenerative Medicine (new in 2018)
GITLab as a collaborative working environment (new in 2017)
Incollaboration with MolMed ErasmusMC