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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
  • Interacting with databases from 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

Christian Schudoma

EMBL Heidelberg

Germany

Hugo Tavares

Sainsbury Laboratory, University of Cambridge

UK

Scientific Organisers

Christian Schudoma

EMBL Heidelberg

Germany

Course Organiser

Raili Pall

EMBL Heidelberg

Germany

Programme

Got something to say? Tweet it with #EMBLDataCarpentry

The following times are used in the programme below:

  • Central European Time (CET): eg. Berlin, Amsterdam Paris
  • Eastern Standard Time (EDT): eg. New York, Quebec

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

Day 0 – Friday 22 January 2021
09:00-10:00 (CET)
04:00-05:00 (EDT)
Technical troubleshooting (optional)
Instructors
10:00-10:30 (CET)
05:00-05:30 (EDT)
Technical troubleshooting (optional)
Inna Bösselmann, Raili Pall, Irena Provaznikova – EMBL Heidelberg, Germany
Day 1 – Monday 25 January 2021
09:00-10:00 (CET)
04:00-05:00 (EDT)
Interactive:
Onboarding & Ice-Breaker
Inna Bösselmann, Raili Pall, Irena Provaznikova and Elisabeth Zielonka – EMBL Heidelberg, Germany
10:00-10:30 (CET)
05:00-05:30 (EDT)
Interactive:
Lightning talks (instructors)
10:30-10:45 (CET)
05:30-05:45 (EDT)
Coffee break
10:45-12:30 (CET)
05:45-07:30 (EDT)
Practical:
Data organization and cleaning
Fotis E. Psomopoulos – Institute of Applied Biosciences, CERTH, Greece
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Practical:
Data organization and cleaning (cont.)
Fotis E. Psomopoulos – Institute of Applied Biosciences, CERTH, Greece
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-15:40 (CET)
10:00-10:40 (EDT)
Interactive:
Lightning talks (candidates)
15:40-15:50 (CET)
10:40-10:50 (EDT)
Coffee break
15:50-17:00 (CET)
10:50-12:00 (EDT)
Virtual Social Programme:
Speed networking: 1-1
Day 2 – Tuesday 26 January 2021
10:00-11:00 (CET)
05:00-06:00 (EDT)
Practical:
Introduction to R
Thea Van Rossum – EMBL Heidelberg, Germany
Ece Cevirgen – EMBL Heidelberg, Germany

11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Practical:
Introduction to R (cont.)
Thea Van Rossum – EMBL Heidelberg, Germany
Ece Kartal – EMBL Heidelberg, Germany
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Practical:
Introduction to R (cont.)
Thea Van Rossum – EMBL Heidelberg, Germany
Ece Kartal – 
EMBL Heidelberg, Germany
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-15:40 (CET)
10:00-10:40 (EDT)
Interactive:
Lightning talks (candidates)
15:40-15:50 (CET)
10:40-10:50 (EDT)
Coffee break
15:50-17:00 (CET)
10:50-12:00 (EDT)
Virtual Social Programme:
Speed networking: 1-1
Day 3 – Wednesday 27 January 2021
10:00-11:00 (CET)
05:00-06:00 (EDT)
Practical:
Data analysis and visualization in R
Data manipulation with dplyr
Gaurav Diwan – Heidelberg University, Germany
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Practical:
Data analysis and visualization in R (cont.)
Gaurav Diwan – Heidelberg University, Germany
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Practical:
Data analysis and visualization in R (cont.)
Data visualisation with ggplot2
Florian Huber – EMBL Heidelberg, Germany
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Practical:
Interacting with databases from R (cont.)
Florian Huber – EMBL Heidelberg, Germany
16:00-16:10 (CET)
11:00-11:10 (EDT)
Coffee break
16:10-16:40 (CET)
11:10-11:40 (EDT)
Virtual Social Programme:
Bar Mixer

 

Day 4 – Thursday 28 January 2021
10:00-11:00 (CET)
05:00-06:00 (EDT)
Practical:
Interacting with databases from R
Florian Huber – EMBL Heidelberg, Germany
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Practical:
Interacting with databases from R (cont.)
Florian Huber – EMBL Heidelberg, Germany
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Practical:
Data analysis with applications to genomics
Hugo Tavares – Sainsbury Laboratory, University of Cambridge, United Kingdom
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Practical:
Data analysis with applications to genomics (cont.)
Hugo Tavares – Sainsbury Laboratory, University of Cambridge, United Kingdom
16:00-16:10 (CET)
11:00-11:10 (EDT)
Coffee break
16:10-17:00 (CET)
11:10-12:00 (EDT)
Virtual Social Programme:
Pub Quiz

 

Day 5 – Friday 29 January 2021
10:00-11:00 (CET)
05:00-06:00 (EDT)
Practical:
Data analysis with applications to genomics (cont.)
Hugo Tavares – Sainsbury Laboratory, University of Cambridge, United Kingdom
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Practical:
Data analysis with applications to genomics (cont.)
Hugo Tavares – Sainsbury Laboratory, University of Cambridge, United Kingdom
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Practical:
Data analysis with applications to genomics (cont.)
Hugo Tavares – Sainsbury Laboratory, University of Cambridge, United Kingdom
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Q&A
16:00-16:30 (CET)
11:00-11:30 (EDT)
Interactive:
Discussion & Wrap-Up
16:30 (CET)
11:30 (EDT)
End of course

Additional information

Registration Fees and Motivation Letter

Application is no longer possible. The course was limited to 26 participants.

For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration Fees (included admission, course materials):

Academia170 Euro
PhD Student170 Euro
Industry300 Euro

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Follow us on Twitter @EMBLEvents or visit our Facebook page to stay up to date with all of our events!

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. 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 course to the fee waiver recipients.

Childcare Grants
For participants with children, there is the possibility to apply for a childcare grant provided by the EMBL Advanced Training Centre Corporate Partnership Programme, to offset childcare costs incurred by participants or speakers 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. A maximum amount of 500 EUR can be awarded per participant selected for the virtual childcare grant. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. In order to apply for this grant, you must be registered by the abstract submission deadline.

Application

Registration Fee Waivers

You may apply for financial assistance when submitting your abstract for this conference. In your application you will be asked to answer questions regarding your motivation for applying, 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.

Childcare Grants

Participants registered by the abstract deadline will be emailed information about the childcare grants. You should apply for the grant by the deadline specified in the email.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process. 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

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

Technical Requirements

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

Participants are asked to use a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) and to install a few specific software packages. 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

A classroom application like 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.

Virtual Participation Guidelines

Guidelines

Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Share Slack, live stream or poster session links with others
  • Broadcast the conference to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the events Slack workspace for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use Slack to ask your questions in the dedicated session channels or via direct message.

Time zone

The programme is planned based on Central European Time (CET), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accomodate as many timezones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

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: 25 - 29 Jan 2021

Location: Virtual


Deadline(s):


Contact: Inna Boesselmann


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

Founder partners

Corporate partners

Associate partners

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