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Computing skills for reproducible research: data carpentry – Course and Conference Office

EMBL Course

Computing skills for reproducible research: data carpentry

Overview

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

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 large amounts of data. 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/resources

  • 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 programming for scientific purposes.” – Magdalena Ziemianska, Maj Institute of Pharmacology Polish Academy of Sciences, Poland

“I have to thank all the instructors and organisers that made this course a success. Very intuitive and everyone was very helpful, leaving no doubts unanswered. I highly recommend this course to anyone who wants to start learning R.” – Soraia Vieira, University of Évora, Portugal

Speakers

Speakers, trainers, and staff

Scientific organisers

Course organisers

Programme

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  • On Monday 16 January participants will be required to attend a virtual onboarding and software installation check via eCampus. The course will continue on site on Tuesday 24 January and finish on Friday 27 January, following the regular programme.
  • Participants need to bring their own laptops. They will be requested to install software at a later stage.
  • The preliminary programme below is a draft and is subject to change
Day 1 – Tuesday 24 January 2023
Time (Europe/Belin)SpeakerLocation
08:40Shuttle bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:30Arrival, welcome, course overview and safety briefingCourtyard room A&B
09:30 – 10:30Lighting talks and setup checkCourtyard room A&B
10:30 – 11:00Coffee BreakCourtyard foyer
11:00-12:30Data Organization in SpreadsheetsCourtyard room A&B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00OpenRefine for Data Cleaning, Social NetworkingCourtyard room A&B
15:00-15:30 Coffee Break Courtyard foyer
15:30-17:30OpenRefine for Data Cleaning, Social Networking Courtyard room A&B
17:30 – 18:30DinnerEMBL Canteen
18:40Shuttle bus to ISG HotelATC entrance

Day 2 – Wednesday 25 January 2023
Time (Europe/Belin)SpeakerLocation
08:40 Shuttle bus from ISG Hotel to EMBL ISG Hotel entrance
09:00 – 11:00Versioning with Git Courtyard Room A&B
11:00 – 11:30Coffee Break Courtyard foyer
11:30 – 12:30Versioning with GitCourtyard Room A&B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00Introduction to R Courtyard Room A&B
15:00 – 15:30Coffee Break Courtyard foyer
15:30-18:00Introduction to RCourtyard Room A&B
18:00DinnerEMBL Canteen
18:30 Shuttle bus to ISG Hotel ATC entrance
Day 3 – Thursday 26 January 2023
Time (Europe/Belin)SpeakerLocation
08:40Shuttle bus from ISG Hotel to EMBL ISG Hotel entrance
09:00 – 10:30Data manipulation with dplyr Courtyard room A&B
10:30 – 11:00Coffee Break Courtyard Foyer
11:00 – 12:30Data manipulation with dplyr Courtyard room A&B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 17:00Data visualisation with ggplot2 Courtyard room A&B
15:00 – 15:30Coffee Break Courtyard foyer
15:30 – 17:30Data visualisation with ggplot2 Courtyard room A&B
17:40Shuttle bus to downtownATC entrance
18:00Social Course Dinner Downtown
Day 4 – Friday 27 January 2023
Time (Europe/Belin)SpeakerLocation
08:40 Shuttle bus from ISG Hotel to EMBL ISG Hotel entrance
09:00 – 10:30Data analysis with applications to genomicsCourtyard room A&B
10:30 – 11:00Coffee BreakCourtyard foyer
11:00 – 12:30Data analysis with applications to genomicsCourtyard room A&B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00Data analysis with applications to genomicsCourtyard room A&B
15:00-15:30Coffee Break Courtyard foyer
15:30 – 17:00Data analysis with applications to genomics Courtyard room A&B
17:00 – 17:30Debrief and wrap-up Courtyard room A&B
17:30Shuttle bus to Heidelberg main train station ATC entrance

Practical information

Registration fees and motivation letter

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, COVID-19 safety measures, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

Academia€320
PhD Student€320
Industry€530

NO visa support letters will be issued until payment of the registration fee is confirmed.

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 (EMBO Practical Courses only)

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. 

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 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
Hotel rooms have been reserved for 4 nights (23-27 January 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code DTC23-01). We recommend that all course participants stay at the ISG Hotel which is 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.

Technical requirements and event software

Technical requirements

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

  • Participants need to bring their own laptops. They will be requested to install software at a later stage, for which they will need admin rights on their laptops.
  • 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.
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, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

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.

Warning

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:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

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.

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Date: 24 - 27 Jan 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • Renato Alves
    EMBL Heidelberg, Germany
    • Lisanna Paladin
      EMBL Heidelberg, Germany

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

Founder partners

Corporate partners

Associate partners

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