Research school MEDICAL GENETICS CENTER SOUTH-WEST NETHERLANDS

Practical Linux

Date: 31 May LUMC, Leiden, room J1-82

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. 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: 14 June from 10:00 - 16:00, LUMC , Leiden, room J1-82

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

Genome Maintenance & Cancer

Date: 25-26 April, 2023

Location: LUMC, room V4:36/40 (building 3)

Organizers: Marcel Tijsterman and Haico van Attikum

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, Erasmus MC 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. Program will be posted here in due time. Provisional program: follow link

Registration via the link https://forms.lumc.nl/lumc2/GMandC

Deadline registration: Thursday 13 April in connection with ordering the catering.

Python Programming

Date: 9 - 12 May, 2023

Location: LUMC building 3: room V4:36/40 (only on May 9, for the other days see the program), Time: 9:00-16:00

Organizer: Mihai Lefter

Course is fully booked. When registering, your name will be placed on the reserve list, which will give you priority for participation in the next edition (autumn 2023)

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

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

Next Generation Sequencing data analysis
Date: 28-30 August, 2023

Location: LUMC, building 1, lecture room 4 and others

Organizers: Susan Kloet, Judith de Boer, Wilfred van IJcken, Saskia Hiltermann 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 including the Erasmus MC. Participants from the academic world but outside these mentioned 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 go to https://forms.lumc.nl/lumc2/NGS

Scripting for life science researchers
Date: date to be decided (autumn 2023)

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 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 pre-registration go to https://forms.lumc.nl/lumc2/scripting

Single cell data analysis

Date: October, 2023 (the exact date has yet to be determined and depends on the availability of suitable rooms)
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.
The course is free of charge for all personnel of MGC associated institutes. Participants from outside these organizations pay 400 euro.
You can pre-register via the registration form.