Whole transcriptome data analysis

Time (Berlin/Europe)	Speaker	Location
14:00-14:30	Welcome and course overview Vladimir Benes – EMBL Heidelberg, Germany Inna Bösselmann – EMBL Heidelberg, Germany	ISG Hotel meeting room Weimar/Dessau
14:30-15:00	Participants flash talks	ISG Hotel meeting room Weimar/Dessau
15:00-16:00	RNA-seq, cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany	ISG Hotel meeting room Weimar/Dessau
16:00-16:30	Coffee Break	ISG Hotel meeting room Weimar/Dessau
16:30-18:00	RNA-seq, cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany	ISG Hotel meeting room Weimar/Dessau
18:00-19:00	Dinner	ISG Hotel beer garden

Time (Berlin/Europe)	Speaker	Location
08:40	Bus from ISG to EMBL	ISG Hotel entrance
09:00-10:00	Docker container and reproducibility Marco Beccuti – University of Turin, Italy	Computer Training Lab
10:00-10:30	Coffee Break	ATC Foyer
10:30-11:00	Experimental design bulk RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
11:00-12:00	QC bulk RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
12:00-13:00	Lunch	EMBL Canteen
13:00-14:30	Counting reads bulk RNAseq Raffaele Calogero & Marco Beccuti – University of Turin, Italy	Computer Training Lab
14:30-15:00	Coffee Break	ATC Foyer
15:00-17:30	Counting reads miRNA Francesca Cordero – University of Turin, Italy	Computer Training Lab
17:30 – 18:30	Social programme: Facility tour
18:30-19:30	Dinner	EMBL Canteen
19:45	Bus to ISG Hotel	ATC Entrance

Time (Berlin/Europe)	Speaker	Location
08:40	Bus from ISG to EMBL	ISG Hotel entrance
09:00-10:30	PCA a linear dimensionality reduction method Raffaele Calogero – University of Turin, Italy	Computer Training Lab
10:30-11:00	Coffee Break	ATC Foyer
11:00-12:30	Differential expression analysis for bulk RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
12:30-13:30	Lunch	EMBL Canteen
13:30-14:30	Differential expression analysis for multiple groups: ANOVA-like Raffaele Calogero – University of Turin	Computer Training Lab
14:30-16:00	Visualising differentially expressed data (Heat maps) Raffaele Calogero & Marco Beccuti– University of Turin, Italy	Computer Training Lab
16:00-16:30	Coffee Break	ATC Foyer
16:30-18:00	Mining differential expression results for bulk RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
18:00-19:00	Pizza dinner in the Rooftop Lounge	Rooftop lounge
19:00	Bus to ISG Hotel	ATC Entrance

Time (Berlin/Europe)	Speaker	Location
08:40	Bus from ISG to EMBL	ISG Hotel entrance
09:00-10:00	Exercises on Mining differential expression results for bulk RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
10:00-11:00	Experimental design scRNAseq Counting reads single cells RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
11:00-11:30	Coffee Break	ATC Foyer
11:30-12:30	QC single cells RNAseq Raffaele Calogero – University of Turin, Italy	Computer Training Lab
12:30-13:30	Lunch and group photo	EMBL Canteen
13:30-15:00	Non linear dimensionality reduction for single cell RNAseq Raffaele Calogero – University of Turin	Computer Training Lab
15:00-16:00	Sub-population discovery in single cell RNAseq: clustering Raffaele Calogero & Marco Beccuti – University of Turin, Italy	Computer Training Lab
16:00-16:30	Coffee Break	ATC Foyer
16:30-18:00	Annotating cell types after sub-population discovery Raffaele Calogero – University of Turin, Italy	Computer Training Lab
18:00	Bus to ISG from EMBL ATC (20 minutes at ISG hotel to drop things)	ATC Entrance
18:30	Bus from ISG to Neckarmünzplatz	ISG Hotel
19:00	Downtown dinner	Oskars

Time (Berlin/Europe)	Speaker	Location
08:40	Bus from ISG to EMBL	ISG Hotel entrance
09:00-10:00	scRNA data integration Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy	Computer Training Lab
10:00-11:00	Exercises	Computer Training Lab
11:00-11:30	Coffee Break	ATC Foyer
11:30-12:30	Individual exercises on bulk 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 RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy	Computer Training Lab
16:00-16:30	Coffee Break	ATC Foyer
16:30-17:30	Individual exercises on bulk RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy	Computer Training Lab
17:30-18:30	Individual exercises on bulk RNAseq Raffaele Calogero – University of Turin, Italy Marco Beccuti – University of Turin, Italy	Computer Training Lab
18:30-19:30	Dinner	EMBL Canteen
19:30	Bus to ISG Hotel	ATC Entrance

Time (Berlin/Europe)	Speaker	Location
08:40	Bus from ISG to EMBL	ISG Hotel entrance
09:00-11:00	Individual exercises on 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 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 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	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

Registration fees include admission, course materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

Academia	€750
PhD Student	€750
Industry	€1200

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

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.

Motivation letter submission

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

1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

• The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
• If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
• If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers, travel grants and childcare grants. 

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

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.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

Boehringer Ingelheim Fonds travel 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

Application

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.

Selection

The scientific organisers will select the recipients of registration fee waivers and travel grants during the motivation letter or abstract 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 meeting. Selection for registration fee waivers and travel grants 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.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that priority will be given to early-stage researchers.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

Hotel

Accommodation is not included in the registration fee. Participants are expected to book and pay for their own accommodation. A mix of single and twin rooms have been reserved for 6 nights from Saturday 31 May – Friday 6 June at the ISG Hotel. 

Single rooms are limited and will be available on a first come, first served basis. After the selection process, selected participants should contact the hotel directly to make a booking with a booking code (code of your course e.g. DAT25-01) by the deadline of Wednesday 30 April 2025. We recommend that all course participants stay in the dedicated hotel for the course.

Local transport

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.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For more information about accommodation and travel, please refer to the FAQ page.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

EMBL Merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order or get in contact with your Course Organiser.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

• The first aid room is located next to the ATC Registration Desk (room 10- 205).
• Dial the Emergency number 222 from any EMBL internal phone only.
• Where is the accident? What happened? How many injured?
• Emergency number 06221-387 7821 from mobile phones.
• Please report all accidents to the conference officer at the registration desk.

In case of fire …

• Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
• A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
• Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus. Log in using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

• Map to walk from ISG Hotel to EMBL

Additional information

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

• ATC orientation map

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

Technical requirements

Below you will find the software and technical requirements for this course.

• Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
• You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
• If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
• Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event software

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.