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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

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

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 data management and analysis. 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
  • 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:

“EMBL is doing an extraordinary job of reaching scientists from different backgrounds toward inter-disciplinary learning. The present era on multi-omics requires knowledge of programming, hence this data carpentry workshop was really useful for beginners. And the last-minute registration fee waiver award for persons in the waitlist was quite useful for me, as I have to attend this workshop without funding. It was a great experience learning R program and I am planning to adopt this in my current work. I am looking forward to an advanced data carpentry workshop focusing on genomic data analysis. EMBL courses are always on my wish list, as they are well organised and informative.” – Dinesh Kumar Kandaswamy, Cardiff University, United Kingdom

“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 and Trainers

Renato Alves

EMBL Heidelberg

Germany

Gaurav Diwan

DKFZ Heidelberg

Germany

Supriya Khedkar

EMBL Heidelberg

Germany

Lisanna Paladin

EMBL Heidelberg

Germany

Fotis Psomopoulos

Center for Research and Technology Hellas (CERTH)

Greece

Christian Schudoma

EMBL Heidelberg

Germany

Hugo Tavares

Sainsbury Laboratory

UK

Scientific Organisers

Renato Alves

EMBL Heidelberg

Germany

Lisanna Paladin

EMBL Heidelberg

Germany

Fotis Psomopoulos

Center for Research and Technology Hellas (CERTH)

Greece

Christian Schudoma

EMBL Heidelberg

Germany

Course Organisers

Maryann Heck

Deputy Head of Course and Conference Office

EMBL Heidelberg

Germany

Irena Provaznikova

Training Lab Technician

EMBL Heidelberg

Germany

Programme

Got something to say? Tweet it with #EMBLdatacarpentry 

  • The virtual course will start on Monday 24 January 2022 with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on Monday 31 January 2022 with the regular programme.
  • During the five-day course duration, full-time attendance is required.  

All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and date along with your city into the Time Zone Converter.

Day 0 – (Onboarding) Monday 24 January 2022
TimeSpeaker
TBCTestrun
TBCTesting cloud /VM
TBCIntroduction to Material

Day 1 – Monday 31 January 2022
TimeSpeaker
08:45-09:00check-in
09:00-10:00Welcome and house notes and course overview and interactive onboarding
10:00-10:30Lightning talks (instructors)
10:30-10:45Break
10:45-12:30Practical:
Data organization and cleaning
12:30-13:30Lunch break
13:30-14:50Practical:
Data organization and cleaning (cont.)
14:50-15:00Coffee break
15:00-15:40Interactive:
Lightning talks (participants)
15:40-15:50Coffee break
15:50-17:00Virtual Social Programme:
Speed networking: 1-1

Day 2 – Tuesday 1 February 2022
09:45-10:00check-in of the day
10:00-11:00Practical:
Introduction to R
11:00-11:10Coffee break
11:10-12:30Practical:
Introduction to R (cont.)
12:30-13:30Lunch break
13:30-14:50Practical:
Introduction to R (cont.)
14:50-15:00Coffee break
15:00-15:40Interactive:
Lightning talks (participants)
Day 3 – Wednesday 2 February 2022
TimeSpeaker
09:45-10:00check-in of the day
10:00-11:00Data analysis and visualization in R
Data manipulation with dplyr
11:00-11:10Coffee break
11:10-12:30Practical:
Data analysis and visualization in R (cont.)
Data manipulation with dplyr
12:30-13:30Lunch break
13:30-14:50Practical:
Data analysis and visualization in R (cont.)
Data visualisation with ggplot2
14:50-15:00Coffee break
15:00-16:00Practical:
Data visualisation with ggplot2 (cont.)
16:00-16:10Coffee break
16:10-17:10Virtual Social Programme
: TBC
Day 4 – Thursday 3 February 2022
TimeSpeaker
09:45-10:00check-in of the day
10:00-11:00Practical:
Data visualisation with ggplot2 (cont.)
11:00-11:10Coffee break
11:10-12:30Practical:
Data visualisation with ggplot2 (cont.)
12:30-13:30Lunch break
13:30-14:50Practical:
Data analysis with applications to genomics
14:50-15:00Coffee break
15:00-16:00Practical:
Data analysis with applications to genomics (cont.)
Day 5 – Friday 4 February 2022
TimeSpeaker
09:45-10:00check-in of the day
10:00-11:00Practical:
Data analysis with applications to genomics (cont.)
11:00-11:10Coffee break
11:10-12:30Practical:
Data analysis with applications to genomics (cont.)
12:30-13:30Group photo & Lunch break
13:30-14:50Practical:
Data analysis with applications to genomics (cont.)
14:50-15:00Coffee break
15:00-16:00Q&A
16:00-16:30Interactive:
Discussion & Wrap-Up
16:30End of course

Practical information

Registration Fees and Motivation Letter

The course is limited to 26 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration Fees (include admission and all course materials):

Academia180 Euro
PhD Student180 Euro
Industry320 Euro

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:

Motivation letter length: 
The maximum limit of 2000 characters (ca. 200 words) refers to manually typed text (spaces included).

Free field text length: The maximum characters for your answers in the free field text boxes is 255 (spaces included).Text only: If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.

Symbols: If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

Further Details

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

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to 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

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal. Read the instructions on how to apply for financial assistance.

Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons 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 some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

Check out this list of external funding opportunities or get more information on attending the conference as an event reporter.

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

Technical Requirements

Technical Requirements

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

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

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.

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 conferences, 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.

Date: 31 Jan - 4 Feb 2022

Location: Virtual


Deadline(s):

Registration: 8 Nov 2021


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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