Marco Beccuti
University of Turin
Italy
EMBL Course
This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq and rCASC packages use docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis.
Computers for hands-on exercises will be provided along with demo data sets.
This course was developed for biological researchers as the intended audience. Basic knowledge of massively parallel sequencing (MPS) is desirable, however R-coding skills and deep knowledge of statistics are not necessary.
“My research focus is on RNA sequencing, infectious diseases and next generation sequencing. Attending this course helped me understand the basics, got me career advice and extended my network. Overall, it made me a better researcher.” – Abhay Deep Pandey, Translational Health Science And Technology Institute, India
“Excellent course on the complete spectrum of RNA-Seq. I would highly recommend this course to all biologists.” – Issaac Rajan, King Abdullah University of Science and Technology, Saudi Arabia
University of Turin
Italy
EMBL Heidelberg
Germany
University of Turin
Italy
University of Turin
Italy
EMBL Heidelberg
Germany
University of Turin
Italy
Course and Conference Manager
EMBL Heidelberg
Germany
Training Lab Technician
EMBL Heidelberg
Germany
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Time (Berlin/Europe) | Speaker | Location |
---|---|---|
13:30 | EMBL shuttle bus from ISG to EMBL | ISG Hotel entrance |
14:00-14:30 | Arrival, welcome, course overview and safety briefing Vladimir Benes – EMBL Heidelberg, Germany Inna Bösselmann – EMBL Heidelberg, Germany Irena Provaznikova – EMBL Heidelberg, Germany | Courtyard Room A&B |
14:30-15:00 | Participants flash talks | Courtyard Room A&B |
15:00-16:00 | RNA-seq, cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany | Courtyard Room A&B |
16:00-16:30 | Coffee Break | Courtyard Foyer |
16:30-18:00 | RNA-seq, cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany | Courtyard Room A&B |
18:00-19:00 | Dinner | EMBL Canteen |
19:00 | EMBL shuttle bus to ISG Hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40 | Embl shuttle bus from ISG to EMBL | ISG Hotel entrance |
09:00-10:00 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
10:00-10:30 | Coffee Break | ATC Foyer |
10:30-11:00 | Experimental design Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
11:00-12:00 | Docker4seq/rCASC/4SeqGUI overview Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
12:00-13:00 | Lunch | EMBL Canteen |
13:00-13:30 | Docker container and reproducibility Marco Beccuti – University of Turin, Italy | Computer Training Lab |
13:30-14:30 | QC bulk Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
14:30-15:00 | Coffee Break | ATC Foyer |
15:00-16:00 | QC single cells Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
16:00-17:30 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
17:30 – 18:30 | Social programme: Facility tour | |
18:30-20:10 | Dinner | EMBL Canteen |
20:15 | EMBL shuttle bus to ISG Hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40 | EMBL shuttle bus from ISG to EMBL | ISG Hotel entrance |
09:00-10:30 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
10:30-11:00 | Coffee Break | ATC Foyer |
11:00-12:30 | Counting reads and data reduction Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
12:30-13:30 | Lunch | EMBL Canteen |
13:30-15:00 | Counting reads and data reduction Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
15:00-16:00 | Counting reads miRNA Francesca Cordero – University of Turin, Italy | Computer Training Lab |
16:00-16:30 | Coffee Break | ATC Foyer |
16:30-18:00 | Exercises | Computer Training Lab |
18:00-19:00 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
19:00-20:30 | Dinner | EMBL Canteen |
20:30 | EMBL shuttle bus to ISG Hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40 | Hoffmann Bus from ISG to EMBL | ISG Hotel entrance |
09:00-10:00 | Differential expression analysis for bulk RNAseq Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
10:00-11:00 | Sub-population discovery in single cell RNAseq: clustering Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
11:00-11:30 | Coffee Break | ATC Foyer |
11:30-12:30 | Differential expression analysis for multiple groups: ANOVA-like Raffaele Calogero – University of Turin | Computer Training Lab |
12:30-13:30 | Lunch and group photo | EMBL Canteen |
13:30-15:00 | Exercises Bulk RNAseq | Computer Training Lab |
15:00-16:00 | Exercises single cell RNAseq | Computer Training Lab |
16:00-16:30 | Coffee Break | ATC Foyer |
16:30-18:00 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
18:00 | EMBL shuttle bus to restaurant | ATC Entrance |
19:00 | Social Dinner at Oskar Restaurant |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40 | Hoffmann Bus from ISG to EMBL | ISG Hotel entrance |
09:00-10:00 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
10:00-11:00 | Mining differential expression results for bulk RNAseq Raffaele Calogero – University of Turin, Italy | Computer Training Lab |
11:00-11:30 | Coffee Break | ATC Foyer |
11:30-12:30 | Depicting clusters specific biomarkers in single cell RNAseq data Francesca Cordero – University of Turin, Italy | Computer Training Lab |
12:30-13:30 | Lunch | EMBL Canteen |
13:30-16:00 | Exercises | Computer Training Lab |
16:00-16:30 | Coffee Break | ATC Foyer |
16:30-17:30 | Exercises | Computer Training Lab |
17:30-18:30 | R pills theory and practice Marco Beccuti – University of Turin, Italy | Computer Training Lab |
18:30-20:00 | Dinner | EMBL Canteen |
20:00 | EMBL shuttle bus to ISG Hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40 | EMBL shuttle bus from ISG to EMBL | ISG Hotel entrance |
09:00-11:00 | Individual exercises on bulk or single cell RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy | Computer Training Lab |
11:00-11:30 | Coffee Break | ATC Foyer |
11:30-12:30 | Individual exercises on bulk or single cell RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy | Computer Training Lab |
12:30-13:30 | Lunch | EMBL Canteen |
13:30-16:00 | Individual exercises on bulk or single cell RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy | Computer Training Lab |
16:00-16:20 | Final remarks Vladimir Benes, Raffaele Calogero, Marco Beccuti | Computer Training Lab |
16:30 | Hoffmann shuttle bus to Heidelberg Train Station | ATC Entrance |
The course is limited to 28 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.
Registration Fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.
Participants are expected to book and pay their own accommodation and travel expenses.
Academia | €690 |
PhD Student | €690 |
Industry | €1200 |
The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.
After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.
Instructions
Please note:
For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.
For further information about registration and motivation letter submission please refer to the FAQ page.
Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.
Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.
The fee waiver will cover the registration sum that you have paid to attend the course.
The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:
– up to €400 for participants travelling to an EMBL Course within Europe.
– up to €1000 for participants travelling to an EMBL Course from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.
– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.
*Registration fees are only covered for EMBO Practical Courses
The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.
For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant.
Applies to selected courses only. Availability will be indicated during the motivation letter submission process.
This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):
– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course
You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.
For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.
The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
Single rooms have been reserved for 6 nights (20 – 26 May 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code DAT23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.
Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.
Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
For further information on getting to EMBL Heidelberg visit our Travel Information page.
For enquiries about accommodation and local transportation please refer to the FAQ page.
Below you will find the software and technical requirements for this course.
The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus.
Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.
COVID-19 information for onsite events at EMBL Heidelberg can be found in our COVID-19 FAQs.
Sponsorship opportunities
We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.
If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.
Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.
Date: 21 - 26 May 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
Contact: Inna Boesselmann