MGC Course Program
Date: 7 May - cancelled - 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
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.
Safely working in the Laboratory
Date: 19 May, Location Building 3, LUMC room V4-52
This one day course provides guidelines for the objective assessment of risks in laboratory and, based on this knowledge, the application of the right measures according to the occupational hygiene strategy. On the one hand this is a refresher course, but on the other hand it will become clear to the participant which technical and organizational measures have been taken within the hospital and LUMC in specific to perform research responsibly
Date: - will be postponed due to coronavirus. People who registered will be informed
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 dataof different types, from different sources and in different formats.
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 € 400 (academic world) or € 800 (commercial companies) 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.
Scripting for life science researchers
Date: 29 - 30 June, 2020, Location LUMC room J1-82 (29/6) and J1-84 (30/6) - 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 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 16 participants.
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: October, 2020 Location Erasmus MC - 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.
There is a minimum of 12 and a maximum of 20 places. 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.
The second edition of this course will be organized in 2020. If you are interested you can pre-register which will give you priority for the 2020 edition. 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
Autumn: Epigenetic regulation in health and disease
August/September: Next generation sequencing data analysis
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