Research school MEDICAL GENETICS CENTER SOUTH-WEST NETHERLANDS

- MGC -

Practical Linux 

Date:  10 April, 2024, 10:00 - 14:00, LUMC, room J-01-082 (route 555) Fully booked !!

Next edition is on June 5th 

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

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 for the edition on June 5th via https://forms.lumc.nl/lumc2/LINUX 

The course is free of charge. See cancellation rules at the bottom of this page

Code management with Git
Date: 17 April, 2024, 10:00 - 16:00, LUMC , room J1-82 Fully booked!!

Next edition is on 7 June 

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

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 reproduciblehttps://strato-editor.com/.cm4all/widgetres.php/com.cm4all.wdn.Separatingline/images/thumbnail.svg. Knowledge of Linux is required to follow this course.

For more information and registration or register directly for the edition on 7 June via the link

The course is free of charge. See cancellation rules at the bottom of this page

Technology Facilities: "Genomics and Transcriptomics" 

The course is directed primarily at PhD candidates who just started their research or are not familiar with the different topics but other participants are welcome too. One can also subscribe for individual days.

- Course day Genomics and Transcriptomics - 15 March, LUMC J1-117 

Organizers: Susan Kloet (LUMC), and Wilfred van IJcken (Erasmus MC)

Provisional Program (edition 2023). Registration via https://forms.lumc.nl/lumc2/GenomicsTranscr

There is a minimum of 14 and a maximum of 40 places per course day. Deadline for registration is 21 days before the specific course day.
The course is free of charge for all personnel from MGC institutes. Participants from outside these institutes pay for a single day €100. See also cancellation rules at the bottom of this page.

Note: planned course day "Imaging" on March 1, LUMC, J1-116 is cancelled

Python Programming

Date: 7, 8, 11 and 12 March, 2024. Location: LUMC, J01- 83  (fully booked)

Next edition: 20, 21, 24 and 25 June, 2024. LUMC, building 1, room J-01-83

To participate in the course knowledge of Linux and Git is required! 

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

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. See cancellation rules at the bottom of this page.

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

Interactive workshop: From “PhD ‘struggles & stress’ to Phd ‘achievements & freedom’"
Date: March 8 (9:00-17:00) and March 22 (9:00-13:00), LUMC, room J1-117 

Last call!!!

Organizer: Wouter Leonhard
Doing a PhD is demanding. In a short amount of time you are expected to perform at a high level at almost everything. Chronic stress, anxiety, overwhelm, work/life disbalance, perfectionism, imposter syndrome are very common and maybe you are experiencing some or much of that too. It is this interplay between YOU and your PhD environment that can either lead you into a vicious cycle where burnout is always lurking, or into a virtuous cycle that allows you to grow stronger, more resilient and happier. In this workshop you will learn how to break out of this vicious cycle and to step into that virtuous cycle.
More information about the content and trainer can be found in the
pdf document.
The workshop is meant especially for second and third year PhD candidates  but first years PhD candidates or PhD candidates at the end of their project are welcome too.
The maximum number of participants is 25. If the workshop is oversubscribed selection will be made mainly based of the content of the motivation field included in the registration form.

Registration form : https://forms.lumc.nl/lumc2/MentalHealth
Deadline for registration is February 26, 2024. You will be informed shortly thereafter if you are selected for the workshop. Workshop is free of charge for PhD students of the MGC associated departments.

Metagenomics Data Analysis with QIIME2 - 1 day workshop

Date: March 29, 2024, 9:00 - 17:00, lecture room V3-18/22, LUMC building 3

Organizer: Magnus Palmblad

Shotgun metagenomics analysis is a major new feature of QIIME 2, and this will be the first workshop the team teaches on this topic. This is a great opportunity to learn cutting edge analytic techniques to simplify your shotgun metagenomics analysis with QIIME 2. And as usual, QIIME 2 doesn't try to reinvent the wheel: through new QIIME 2 plugins, you'll learn to apply top-performing tools from the CAMI benchmarks, including Kracken2, Bracken, and Megahit for processing your data without worrying about shuffling data between tools.
A unique feature of QIIME 2 is its data provenance tracking system, which ensures reproducibility of your bioinformatics results. To learn more about how this can improve your workflows, see the team's most recent article, “Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay” (PLOS Computational Biology, November 2023).Software is free, not commercial. 

For more information and registration via  https://forms.lumc.nl/lumc2/QIIME2

The maximum number of participants is 25. Places will be allocated on a first-come, first-served basis.
The workshop is free of charge

Genome Browser - 1 day workshop

Date: April 29, 2024, 9:00 - 17:00, lecture room 5, LUMC building 1
Organizer: Bob Kuhn (more than 19 year experience as part of the Browser staff)

The UCSC Genome Browser is a widely used platform for accessing genomic data of many kinds. Both research scientists and clinical geneticists use it extensively in their work. A coordinate-based system that allows viewing data at all scales, from a single nucleotide to an entire chromosome, the Browser presents data on variants large and small (CNVs and SNVs) both pathogenic and benign, collected from all of the major databases (OMIM, dbSNP, LOVD, ClinVar, gnomAD, DGV, DECIPHER, and more) in one place, viewed simultaneously. Epigenetic data from many labs around the world are viewable on the Browser, as is expression data from the GTEx project. Move easily between genome assemblies (hg19 <-> hg38) using the convert feature and liftOver. Comparative genomics data gives insight into evolutionary relationships among hundreds of vertebrates.
A workshop from an expert is the best way to learn all of the ways to put the Browser to work for you. Features such as loading your own data, saving sessions for sharing, downloading high-resolution images for your publications and much more will be presented. Do you wish you were not constrained to viewing contiguous regions and would like to see several of your favorite genes at once? Dr. Kuhn will show how to use Multi-Region Mode.... and Exon-only Mode as well.

Registration: https://forms.lumc.nl/lumc2/GenomeBrowser
The maximum number of participants is 100. Places will be allocated on a first-come, first-served basis.
The workshop is free of charge for participants of one of the MGC departments. For people from outside these departments the course fee is 100 euro. (See cancellation rules at the bottom of this page)

Scripting for life science researchers
Date: 29 - 30 May, 2024

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 per course day, other participants have to pay the full price.
There is a minimum of 12 and a maximum of 20 participants. 

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

MGC courses: general cancellation rules for MGC members 

The courses are free of charge but please note that we have set up strict cancellation rules:
•            Free cancellation up to 2 weeks before the start of the course
•            Cancellations after the mentioned time interval until one day before the start of the course: €50 per course day unless you have a replacement. In that case name and email address plus confirmation from the replacement is included in the cancellation email to the MGC secretariat nivard@lumc.nl 
•            In case of no-show up: €100 per course day

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

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