Analysis and integration of transcriptome and proteome data

Time (Europe/Berlin)	Session	Location
2 h (exact time TBC)	Onboarding session Raffaele Calogero – University of Turin, Italy	Zoom

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 09:15	Arrival, welcome and safety introductions	Courtyard Room
09:15 – 11:00	Lecture: RNA-seq: cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany	Courtyard Room
11:00 – 11:30	Coffee break	Computer Training Lab
11:30 – 12:30	Practical session: RNAseq: Reads to genes Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 16:00	Practical session_ RNAseq: Reads to genes Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
16:00 – 16:30	Coffee break	Computer Training Lab
16:30 – 18:30	Q&A on RNAseq Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
18:30 – 19:30	Canteen dinner	Canteen
19:30	Departure to hotel	EMBL bus stop

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 10:30	Practical & theory: Differential expression analysis Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
10:30 – 11:00	Coffee break	Computer Training Lab
11:00 – 12:30	Practical & theory: Batch correction Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 15:00	Practical & theory: Batch correction Raffaele Calogero – University of Torino, Italy Luca Alessandri – University of Torino, Italy Mathias Boulanger – EMBL Heidelberg, Germany	Computer Training Lab
15:00 – 15:30	Coffee break	Computer Training Lab
15:30 – 17:30	Lecture: Ribosome profiling Gerben Menschaert – University of Ghent, Belgium	Courtyard Room
17:30 – 18:30	Flash talk presentations	Courtyard Room
18:30 – 20:00	BBQ dinner	Operon Foyer
20:00	Departure to hotel	ATC entrance

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 10:00	Introduction to Proteomics Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany	Courtyard Room
10:00 – 11:00	Practical: peptide and protein identification Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany	Computer Training Lab
11:00 – 11:30	Coffee break	Computer Training Lab
11:30 – 12:00	Practical: peptide and protein identification Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany	Computer Training Lab
12:00 – 13:00	Lunch and group photo (12:00-12:15)	EMBL Canteen
13:00 – 13:30	Lecture: Bioinformatics for proteomics Lennart Martens – University of Ghent, Belgium	Computer Training Lab
13:30 – 14:30	Q&A to Bioinformatics for proteomics Lennart Martens – University of Ghent, Belgium	Courtyard Room
14:30 – 15:00	Coffee Break	Computer Training Lab
15:00 – 18:30	Practical Session: Turning data into information-peptide and protein identification, database searching Lennart Martens – University of Ghent, Belgium	Computer Training Lab
18:30 – 19:00	Pizza dinner	Rooftop lounge
19:00 – 20:00	Pub quiz with drinks	Rooftop lounge
20:15	Departure to hotel	ATC entrance

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 10:00	Lecture: Introduction to DIA proteomics data analysis Daria Fijalkowska – University of Ghent, Belgium	Courtyard Room
10:00 – 10:30	Coffee break	Computer Training Lab
10:30 – 12:00	Practical Session: DIA proteomics data analysis Daria Fijalkowska – University of Ghent, Belgium	Computer Training Lab
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 14:30	Practical Session: DIA proteomics data analysis Daria Fijalkowska – University of Ghent, Belgium	Computer Training Lab
14:30 – 15:00	Coffee break	Computer Training Lab
15:00 – 16:00	Q&A to Bioinformatic tools for data comparison and integration Scooter Morris – University of California, San Francisco, USA	Courtyard Room
16:00 – 17:00	Practical session: Introduction to Cytoscape Manjeet Kumar – EMBL Heidelberg, Germany John “Scooter” Morris – University of California, San Francisco, USA	Computer Training Lab
17:15	Departure to Hotel: Free evening	EMBL bus stop

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 10:00	Lecture: MOFA data integration talk Oliver Stegle – EMBL Heidelberg, Germany	Courtyard Room
10:00 – 10:30	Coffee break	Courtyard Room
10:30 – 12:00	Practical session: MOFA data integration Oliver Stegle – EMBL Heidelberg, Germany	Computer Training Lab
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 14:30	Practical session: Introduction to Cytoscape Manjeet Kumar – EMBL Heidelberg, Germany John “Scooter” Morris – University of California, San Francisco, USA	Computer Training Lab and Courtyard Room
14:30 – 15:00	Coffee break	Courtyard room
15:00 – 16:15	Practical seesion: Introduction to Cytoscape Manjeet Kumar – EMBL Heidelberg, Germany John “Scooter” Morris – University of California, San Francisco, USA	Computer Training Lab and Courtyard Room
16:15 – 18:00	GeneCore and Proteomics Core facilities tours	GeneCore and Proteomics Core facilities
18:00 – 18:45	Departure to downtown with a short stop at the hotel	EMBL bus stop
18:45 – 22:00	Downtown Dinner	TBC

Time (Europe/Berlin)	Session	Location
08:40 – 09:00	Bus from hotel to EMBL ATC entrance	ISG hotel
09:00 – 12:00	Practical Session: Data integration John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany with flexible coffee break	Computer Training Lab and Courtyard room
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 15:00	Practical Session: Data integration John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany with flexible coffee break	Computer Training Lab and Courtyard room
15:00 – 15:30	Course wrap-up and farewell	Courtyard room
15:40	Departure to Train Station	ATC entrance

The course is limited to 24 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration fees

Your registration for this course includes:

• Admission to the event
• Possibility to submit an abstract (if applicable)
• Meals and coffee breaks
• Course materials
• Access to the e-learning platform
• A letter to support your visa application (for more information, check the ‘Travel and accommodation’ tab)

Accommodation and travel are not included in the fees — participants are expected to book and pay their own expenses.

Academia	€750
PhD Student	€750
Industry	€1200

Confirmation and payment

The registration fee should be paid only after acceptance to the course. We aim to announce the results 3 weeks (21 days) after the abstract submission deadline but delays may occur.

Cancellation policy

If you are no longer able to take part in the course, please inform your course contact responsible for this event. Your registration and the submitted motivation letter will be deleted.

Please also check our Terms and Conditions for the cancellation policy.

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 2,000 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.

Please note it is not possible to apply after the motivation letter deadline!

Selection

The selection process will take place with the results announced by email to all applicants / submitters. We aim to announce 3 weeks (21 days) after the motivation letter submission deadline but delays may occur.

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 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 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

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. Receipts must be provided via email with your signature for all costs incurred within two months of completion of travel.

Childcare grants

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.

Application

You may apply for financial assistance when submitting your motivation letter. In the application system, you will be asked which type of grant you want to apply for.

Applications for financial support will not influence the outcome of the selection results.

Results

Grant allocations are announced by email to all applicants after the selections results.

Selection for financial assistance 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.

Please note that for childcare grants, priority will be given to early-stage researchers.

Further details

Check out this list of external funding opportunities. 

For further information about financial assistance please refer to the FAQ page.

Visa

We can send you a registration confirmation to support your visa procedure (not an official invitation letter). Please contact the Conference Officer responsible for your event. Read our FAQ for more information.

Travel

If you are travelling to Heidelberg via aeroplane, train, car, or long-distance bus, you can find useful information on our travel information page.

Accommodation

Accommodation is not included in the registration fee.

A mix of single and twin rooms have been reserved for 6 nights from 24 to 30 April 2027 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. PRO27-01 by the deadline of 27 March 2027.

We recommend that all course participants stay at the dedicated hotel for the course.

Please note: Heidelberg City Council has in place an overnight stay tax for tourists visiting Heidelberg (including work related trips). The cost is 3.50 EUR per night for the first five nights of a consecutive stay and is added to the hotel’s nightly rate. Please contact the individual hotel directly if you have any questions.

Local transportation

Course shuttle buses

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.

Other local transportation

In addition to the shuttle busses, there is also the public bus 28 that serves the EMBL campus and taxis can be easily booked at any time. For more information,  please refer to the local transportation (RNV) website.

You may also walk from the ISG Hotel to EMBL (takes up to 30 minutes)

Map to walk from ISG Hotel to EMBL

Further details

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

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

Here you will find useful information for when you are onsite at the event.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a 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 computer training lab or wet labs.

Internet

Wi-Fi is available on campus 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.

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.

Charging stations

There are lockers available next to the stairs leading down into the Auditorium. You will find some of those equipped with sockets to charge your smartphone/tablet etc.

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.

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.

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 course.

Lost and found

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

Nursing room

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

Room for prayers, meditation, and yoga

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

EMBL campus map

Health and safety notes

Please take a moment to read our health and safety policy.

• Do not smoke in any EMBL building.
• Eating and drinking is prohibited in the Auditorium and 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.
• Be prepared to answer the following questions: 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

The Heidelberg University Hospital or ‘Universitätsklinikum‘ has a 24 hour accident and emergency facility and is at ‘Im Neuenheimer Feld 672’. It is a 8km or a 20 minute taxi ride away from EMBL. In a medical emergency, the ambulance service generally transports patients to this hospital.

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.

The EMBL course and conference office team are able to advise you on where to turn for emergency or non-emergency medical treatment in Heidelberg and can assist you in making appointments and / or arranging transport to get to the pharmacy or a doctor of your choice if necessary. Please note, we are not however permitted to personally accompany you off campus.

Sightseeing

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

Technical requirements

Participants are required to bring their own laptops to the course or inform us ahead otherwise. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Additional 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. 

Other information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Please find additional information including FAQs and terms and conditions on our Information for Participants page.