Vladimir Benes
EMBL Heidelberg
Germany
EMBL Course
Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.
Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues and organisms operate in their biological context. Among the key technologies driving this forward are next-generation sequencing and proteomics, as they provide powerful means to determine global expression levels of genes and proteins. Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology.
During this course, participants will gain theoretical insight in the structure of sequencing and proteomic data, and they will receive training in data analysis for the annotation, quantification, and statistical analysis of gene and protein expression using various computational tools. In addition, training will be provided in the use of Cytoscape to derive biological insights from the integration of both data types.
This course is targeted at biologists and biochemists who are (starting to be) involved in both next-generation sequencing and mass spectrometry-based proteomics, but who are not experts in these fields.
The aim of this practical course is to provide insight in techniques that are frequently used for transcriptome and proteome analysis, and to provide hands-on experience turning primary data into information that can be used for further biological interpretation. To achieve these goals, participants will gain insight in the basic principles of gene expression analysis (RNAseq data quantification and differential expression analysis), protein identification and quantification, and they will be trained in the use of software tools to analyse sequencing and proteomic data (SearchGUI, PeptideShaker, MaxQuant). In addition, the course will provide insight in the complementarity of transcriptome and proteome data by their integrative analysis via Cytoscape.
“This course organised by EMBL is an excellent opportunity for wet lab biologists to gain skills and understand the necessary bioinformatic background for both designing experiments and performing data analysis.” – Katarzyna Tutak, Institute of Human Genetics, Polish Academy of Science
EMBL Heidelberg
Germany
National University of Singapore
Singapore
Ghent University
Belgium
German Cancer Research Centre (DKFZ)
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
VIB University of Ghent
Belgium
University of Ghent
Belgium
University of California, San Francisco
USA
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
University of Turin
Italy
German Cancer Research Centre (DKFZ)
Germany
Course and Conference Manager
EMBL Heidelberg
Germany
Training Lab Technician
EMBL Heidelberg
Germany
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The preliminary programme below is a draft and is subject to change.
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00 – 09:15 | Arrival, welcome and safety introductions | Courtyard room |
09:15 – 11:00 | RNA-seq: cool but is it that simple? Vladimir Benes – EMBL Heidelberg, Germany | Courtyard room |
11:00 – 11:30 | Coffee break | ATC Foyer |
11:30 – 12:30 | RNAseq: Reads to genes Jonathan Landry – EMBL Heidelberg, Germany Jan Provaznik – EMBL Hiedleberg, Germany Kristina Roucova – Univerzita Karlova, Czech Republic | Courtyard room |
12:30 – 13:30 | Lunch | EMBL Canteen |
13:30 – 16:00 | Practical: From Reads to Genes (Bulk and single cell) Jonathan Landry – EMBL Heidelberg, Germany Jan Provaznik – EMBL Hiedleberg, Germany Kristina Roucova – Univerzita Karlova, Czech Republic | Computer Training Lab |
16:00 – 16:30 | Coffee break | Computer Training Lab |
16:30 – 18:00 | Q&A on RNAseq and scRNAseq | Computer Training Lab |
18:00 | Departure to ISG Hotel | ATC entrance |
18:30 | Dinner | ISG Hotel |
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00 – 10:00 | Flash talk presentations | Computer Training Lab |
10:00 – 12:30 | Practical & theory: Differential expression analysis. Jonathan Landry – EMBL Heidelberg, Germany Jan Provaznik – EMBL Hiedleberg, Germany Kristina Roucova – Univerzita Karlova, Czech Republic with flexible coffee break | Computer Training Lab |
12:30 – 13:30 | Lunch | EMBL Canteen |
13:30 – 16:00 | Practical session: Ribosome profiling Gerben Menschaert – University of Ghent, Belgium | Computer Training Lab |
16:00 – 16:30 | Coffee break | Computer Training Lab |
16:30 – 18:30 | Lecture/practicals: Ribosome profiling Gerben Menschaert – University of Ghent, Belgium | Computer Training Lab |
18:30 – 19:40 | Dinner | EMBL Canteen |
19:40 | Departure to ISG Hotel | ATC entrance |
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00- 11:00 | Introduction to Proteomics Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany | Computer Training Lab |
11:00 – 11:30 | Coffee break | Computer Training Lab |
11:30 – 12:30 | Lecture: Quantitative proteomics: TMT Mikhail Savitski – EMBL Heidelberg, Germany | Computer Training Lab |
12:30 – 13:30 | Lunch | EMBL Canteen |
13:30 – 15:00 | Lecture: Bioinformatics for proteomics Lennart Martens – University of Ghent, Belgium | Computer Training Lab |
15:00 – 16:00 | Practical Session: Turning data into information-peptide and protein identification, database searching Lennart Martens – University of Ghent, Belgium | Computer Training Lab |
16:00 – 16:30 | Coffee Break | Computer Training Lab |
16:30 – 18:00 | Q&A to Bioinformatics for proteomics Lennart Martens – University of Ghent, Belgium | Computer Training Lab |
18:00 – 19:00 | Dinner | EMBL Canteen |
19:00 | Departure to ISG Hotel | ATC entrance |
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00 – 10:00 | Lecture: Quantitative proteomics: SILAC and other MS1-based approaches Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany | Computer Training Lab |
10:00 – 10:30 | Coffee break | |
10:30 – 12:00 | Lecture: Introduction to MaxQuant; analysis of MS data Daria Fijalkowska – University of Ghent, Belgium | Computer Training Lab |
12:00 – 13:00 | Lunch | EMBL Canteen |
13:00 – 14:30 | Practical Session: Proteomics data interpretation Daria Fijalkowska – University of Ghent, Belgium | Computer Training Lab |
14:30 – 16:15 | Lecture: P-values and multiple testing correction Hyungwon Choi – National University of Singapore, Singapore | Computer Training Lab |
16:15 | Free afternoon | |
16:15 | Departure to ISG Hotel and downtown |
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00 – 10:00 | Q&A to Bioinformatic tools for data comparison and integration John “Scooter” Morris – University of California, San Francisco, USA | Computer Training Lab |
10:00 – 10:30 | Coffee break | |
10:30 – 12:30 | Practical: Introduction to Cytoscape John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany Santhust – EMBL Heidelberg, Germany | Computer Training Lab |
12:30 – 13:30 | Lunch | EMBL Canteen |
13:30 – 16:00 | Practical: Introduction to Cytoscape John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany Santhust – EMBL Heidelberg, Germany | Computer Training Lab |
16:00 – 16:30 | Coffee break | Computer Training Lab |
16:30 – 17:45 | Lecture and Practical: Enrichment analysis John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany Santhust – EMBL Heidelberg, Germany | Computer Training Lab |
17:45 | Departure to ISG Hotel and downtown | ATC entrance |
18:30 | Downtown Dinner |
Time (Europe/Berlin) | Speaker | Location |
---|---|---|
08:40 – 09:00 | Bus from ISG Hotel to EMBL ATC entrance | ISG Hotel bus stop |
09:00 – 10:00 | Application talk: Network-oriented integrative multi-omics analysis of tissues and fluids – case studies in cancer and cardiovascular diseases Hyungwon Choi – National University of Singapore, Singapore | Computer Training Lab |
10:00 – 10:30 | Coffee break | |
10:00 – 12:30 | Practical Session: Data integration John “Scooter” Morris – University of California, San Francisco, USA | Computer Training Lab |
12:30 – 13:30 | Lunch | EMBL Canteen |
13:30 – 16:00 | Practical Session: Data integration John “Scooter” Morris – University of California, San Francisco, USA Manjeet Kumar – EMBL Heidelberg, Germany Santhust – EMBL Heidelberg, Germany with flexible coffee break | Computer Training Lab |
16:00 – 16:30 | Course wrap-up and farewell | Computer Training Lab |
16:30 | Departure to Train Station and Downtown | 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 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 |
NO visa support letters will be issued until payment of the registration fee is confirmed.
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 detailed instructions, please watch 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 (25 Feb – 3 March 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code PRO23-01). 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.
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 on-site 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 events, 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.
EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.
Please also note that:
Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.
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Date: 26 Feb - 3 Mar 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
Contact: Maria Bacadare