MGC Course Program

Practical Linux 

Date:  4 March, 9:00 - 13:00, Location: LUMC, J1-82, Building 1 (route-555) - 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. (Next editions: 7 May)   

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 registration or register directly via https://forms.lumc.nl/lumc2/LINUX    (for December and upcoming editions)

Code and data management with Git

Date: 25 March, 9:00 - 15:00, location: LUMC, J1-82, Building 1 - Organizer: Mihai Lefter. (Next edition: 25 March)

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 https://forms.lumc.nl/lumc2/GITcourse

Safely working in the Laboratory

Date: to be announced

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

To register: PhD students from LUMC can register via 'Bedrijfsopleidingen LUMC', PhD students from Erasmus MC can send an email to nivard@lumc.nl

GITLab as a collaborative working environment

Date: 12 February, 2020, 9:00 - 12:00, location: LUMC, J1-0128, building 1 - Organizer: Mihai Lefter

Aimed primarily at LUMC researchers, this short but concise course consists of an introduction to the LUMC GitLab. The course takes approximately three hours and provides participants an insight into how GitLab utilization enhances collaboration and greatly simplifies project management. 

For more information and registration or you can register directly via https://forms.lumc.nl/lumc2/GITLABcourse  

Technology Facilities 

Date: 17 - 20 February, 2020, Location LUMC

The course will deal with four topics: day 1 Genomics & Transcriptomics, day 2 Proteomics, day 3 Metabolomics, and day 4 Imaging

The course is meant for PhD students, technicians, postdocs and other interested people who just started their research or are not familiar with the different topics. One can subscribe also for individual days. 

For more information and registration  There is a minimum of 14 and a maximum of 35 places. Deadline for registration 3 February, 2020.

If you want to attend one or more course days please contact nivard@lumc.nl

The course is free of charge for all personnel of MGC institutes. Participants from outside these institutes pay €400. Registration costs for a single day is €100. In case of no show participants from the MGC institutes will be charged 50 euro, other participants have to pay the full price.

The ins and outs of CRISPR-Cas

Date: 2, 3 and 10, 11 March, 2020, Location Erasmus MC - Organizer: Joyce Lebbink

For PhD students with an active interest in genome engineering using this technique AND an interest in understanding the molecular mechanism of its function. The course runs for 4 full days within a period of 2 weeks and has assignments that require preparation (2 ECTS)

Course is free of costs for MGC members, for non-MGC members the course fee is 500 euro. When registering for this course, please provide a short motivation of max 100 words. In case of no show participants from the MGC institutes will be charged 50 euro, other participants have to pay the full price.

For more information and registration or register directly The course is fully booked. If you register your name will be placed on a waiting list.

Genome Maintenance & Cancer

Date: 26 - 27 March, 2020, Location LUMC room P5-34

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.  

For more information and registration or register directly  There are a few places left. If the course is fully booked, you can still register, but will be placed on a waiting list. 

Multiomics Data Integration Using R

Date: 11 - 15 May, 2020, Location LUMC - 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.

For more information see the Google doc. You can register via this link

There is a minimum of 12 and a maximum of 25 places. The course is fully booked. You can still register, but will be placed on a waiting list.

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.

For more information and registration or register directly via https://forms.lumc.nl/lumc2/SCRIPTINGcourse

 Python Programming

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.

For more information and registration or register direct via this form.

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.

For more information and preregistration or you can preregister via the registration form

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 

Announcements 

Autumn: Epigenetic regulation in health and disease

August/September: Next generation sequencing data analysis