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Exploratory analysis of biological data: data carpentry – Course and Conference Office

EMBL Course

Exploratory analysis of biological data: data carpentry

Overview

Course overview

The missing step between data collection and research progress is a lack of training for researchers in crucial skills for effectively managing and analysing data, often in large amounts. This hands-on workshop teaches researchers the fundamental data skills they need to conduct their work and provides high-quality, domain-specific training covering the full lifecycle of data-driven research. The domain-specific approach allows participants to tailor the data, content, and tools to reflect the specific data and analysis needs of different areas.

Audience

The course is aimed at graduate students and other researchers in the life sciences who would like to learn good practices in project and data organisation and computational data analysis with R. The course is ideally suited to students without prior experience in computational research, but some familiarity with working with tabular data on a computer is welcome.

Modules

  • Data organisation and cleaning
  • Versioning with Git
  • Introduction to R
  • Data analysis and visualisation in R
  • Data analysis with applications to genomics

Learning outcomes

  • How to organise data and some practices for more effective data handling
  • To effectively clean and format data and automatically track any changes
  • To use R to handle, filter, and summarise tabular data
  • To use the split-apply-combine concept for data analysis
  • To visualise the results of these analyses in R using the ggplot2 library
  • To apply all of the concepts in an exploratory analysis of a typical biological dataset

What past participants say about the course

The best course to take first steps in data analysis! I learned a lot and wholeheartedly recommend it to everyone learning to program for science purposes.” – Magdalena Ziemianska, Maj Institute of Pharmacology Polish Academy of Sciences, Poland

“Excellent course to learn basics of R. A very friendly group of instructors who were easy to interact with and patient with all the queries we had. Also, the organisation team made it very easy for us: the pre- and post-course preparations and also during the stay.” – Balagopal Pai, University of Regensburg, Germany

Speakers

Speakers, trainers, and staff

Gaurav Diwan

University of Heidelberg

Germany

Ece Kartal

University of Heidelberg

Germany

Supriya Khedkar

EMBL Heidelberg

Germany

Eleonora Mastrorilli

EMBL Heidelberg

Germany

Francesco Tabaro

EMBL Rome

Italy

Scientific organisers

Course organisers

Iva Gavran

Course and conference officer

EMBL Heidelberg

Germany

Swetlana Krez

Training Lab Technician

EMBL Heidelberg

Germany

Programme

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  • Some pre-course work in the form of preinstalling software and attending a pre-course onboarding session will be required. Details will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
On-boarding session – Monday 15 January 2024
Time (Europe/Berlin)SpeakerLocation
tbaOn-boarding session and Q&A regarding software installationvirtual
Day 1 – Monday 22 January 2024
Time (Europe/Berlin)SpeakerLocation
10:45 – 11:00Bus from hotel to EMBL ATC EntranceISG Hotel
11:00 – 11:15Welcome and house notes and course overviewCourtyard Room A & B
11:15 – 12:30FlashtalksCourtyard Room A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 14:30Lecture: Data Organization in SpreadsheetsCourtyard Room A & B
14:30 – 14:50Coffee breakCourtyard foyer
14:50 – 16:20Lecture: OpenRefine for Data CleaningCourtyard Room A & B
16:20 – 16:40Coffee breakCourtyard foyer
16:40 – 18:10Lecture: OpenRefine for Data Cleaning (continued)Courtyard Room A & B
18:10 – 19:00Social networking / Q&ACourtyard Room A & B
19:00 – 20:00DinnerCourtyard Room A & B
20:00 – 20:15Shuttle bus to hotelATC Entrance
Day 2 – Tuesday 23 January 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus from hotel to EMBL ATC EntranceISG Hotel
09:00 – 11:00Practical session: Versioning with Git (using RStudio)Courtyard Room A & B
11:00 – 11:30Coffee breakCourtyard foyer
11:30 – 12:30Practical session: Versioning with Git (using RStudio)Courtyard Room A & B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00Practical session: Introduction to RCourtyard Room A & B
15:00 – 15:30Coffee breakCourtyard foyer
15:30 – 16:50Practical session: Introduction to RCourtyard Room A & B
16:50 – 17:10Coffee breakCourtyard foyer
17:10 – 18:30Practical session: Introduction to RCourtyard Room A & B
18:30 – 19:30DinnerEMBL Canteen
19:30 – 19:45Shuttle bus to ISG HotelATC Entrance
Day 3 – Wednesday 24 January 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus from hotel to EMBL ATC EntranceISG Hotel
09:00 – 11:00Practical session: Data manipulation with dplyrCourtyard Room A & B
11:00 – 11:30Coffee breakCourtyard foyer
11:30 – 12:30Practical session: Data manipulation with dplyrCourtyard Room A & B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00Practical session: Data visualisation with ggplot2Courtyard Room A & B
15:00 – 15:30Coffee breakCourtyard foyer
15:30 – 16:50Practical session: Data visualisation with ggplot2Courtyard Room A & B
16:50 – 17:10Coffee breakCourtyard foyer
17:10 – 18:30Practical session: Data visualisation with ggplot2Courtyard Room A & B
18:30 – 19:30DinnerEMBL Canteen
19:30 – 19:45Shuttle bus to ISG HotelATC Entrance
Day 4 – Thursday 25 January 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus from hotel to EMBL ATC EntranceISG Hotel
09:00 – 09:50Lecture: Data visualisation with ggplot2Courtyard Room A & B
09:50 – 10:00Short coffee breakCourtyard foyer
10:00 – 10:50Practical session: Data analysis with applications to genomicsCourtyard Room A & B
10:50 – 11:20Coffee breakCourtyard foyer
11:20 – 12:20Practical session: Data analysis with applications to genomicsCourtyard Room A & B
12:20 – 13:20Lunch breakEMBL Canteen
13:20 – 14:50Practical session: Data analysis with applications to genomicsCourtyard Room A & B
14:50 – 15:20Coffee breakCourtyard foyer
15:20 – 17:00Practical session: Data analysis with applications to genomicsCourtyard Room A & B
17:00 – 17:30Shuttle bus to downtownATC Entrance
17:30 – 19:00Free time
19:00 – 20:30Downtown dinnertbd
Day 5 – Friday 26 January 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus from hotel to EMBL ATC EntranceISG Hotel
09:00 – 10:30Practical session: Data analysis with applications to genomicsCourtyard Room A & B
10:30 – 11:00Coffee breakCourtyard foyer
11:00 – 12:00Practical session: Data analysis with applications to genomicsCourtyard Room A & B
12:00 – 13:00Lunch breakEMBL Canteen
13:00 – 14:00Debrief and wrap-upCourtyard Room A & B
14:00 – 14:30Shuttle bus to Heidelberg main train stationATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 15 on-site and 15 virtual participants. For selection purposes, please note that your application will not be considered without a letter of motivation and answering all additional questions.

Registration

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

Virtual registration fees include access to live-streamed course content (lectures, practical sessions, discussion rounds) as well as any learning activities in the virtual learning platform.

Onsite Academia€425
Onsite PhD Student€425
Onsite Industry€750
Virtual Academia€190
Virtual PhD Student€190
Virtual Industry€250

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

Financial assistance

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.

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

For 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 a childcare grant. 

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.

Selection

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.

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.

Accommodation and shuttles

Hotel

Accommodation is not included in the registration fee. On-site participants are expected to book and pay for their own accommodation. Single rooms have been reserved for 5 nights 21-26 January 2024 at ISG Hotel. 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. DTC24-01) by the deadline of 24 December 2023. We recommend that all course participants stay at 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 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.

On-site information

Catering

All meals and coffee breaks are included in the on-site 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 an EMBL souvenir (products presented in the glass display in the registration area), please ask at the registration desk for more information.

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.

Additional information

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

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

Technical requirements and event software

Technical requirements

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

  • On-site participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.All participants will be requested to install software before the course. Please make sure to bring the laptop with the installed software to the course.
  • 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. 

Additional information

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

Date: 22 - 26 Jan 2024

Location: EMBL Heidelberg and Virtual

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: 30 Oct 2023


Organisers:

  • Renato Alves
    EMBL Heidelberg, Germany
    • Lisanna Paladin
      EMBL Heidelberg, Germany
      • Fotis E. Psomopoulos
        The Centre for Research and Technology Hellas, Greece
        • Christian Schudoma
          EMBL Heidelberg, Germany

        Contact: Iva Gavran


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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