OLISSIPO Workshops | EMBL Trainings in Computational Biology

OLISSIPO Workshops | EMBL Trainings in Computational Biology

The EMBL team, one of the partner institutions of the OLISSIPO project, will visit INESC-ID to give a series of workshops in the area of Computational Biology. You are free to choose the workshops you want to attend (only Workshop 2 requires the attendance of Workshop 1).

Location: INESC-ID (Lisboa, Portugal), Room 9, Floor -1 (ask at the reception)


Workshop 1 (WS1) (May 9, 09:00-16:00)

Title: Introduction to R

Lecturer: Mike Smith

This one day course provides an introduction to data handling with the R language and will cover some useful tools for data wrangling, exploration and plotting using the tidyverse.  The course material is suitable for beginners, although basic familiarity with R will be advantageous.

Prerequisites: A working installation of R and RStudio.  Installation instructions for both can be found under “Setup Instruction” on https://grp-bio-it-workshops.embl-community.io/introduction-to-R/index.html


Workshop 2 (WS2) (May 10-11, 09:00-13:00)
To attend this course it is necessary to attend Workshop 1

Title: Biostatistical Basics in R

Lecturer: Sarah Kaspar

This course will equip you with basic statistical concepts that will immediately help you to better understand your biological data, and which are also the foundation for many advanced biostatistical topics.

We will cover:

  • statistical distributions
  • hypothesis testing
  • multiple testing
  • contingency tables

Prerequisites: You need to have R and RStudio installed, and basic knowledge of R and data visualisation using the tidyverse. If you don’t have this pre-knowledge you can complete one of the following:


Workshop 3 (WS3) (May 10, 14:00-18:00)

Title: Drug Synergy

Lecturer: Petr Smirnov

This workshop introduces the fundamental concepts behind analysing drug combination experiments on immortalised cancer cell lines; discusses common models for assessing drug synergy, and introduces R/Bioconductor tools implementing these methods. A hands on analysing public drug combination data is included.

The learning goals behind this workshop are:

  • Describe pharmacogenomic mono and combination datasets and usefulness in cancer research
  • Understand how experimental designs and research questions map onto data structures
  • Learn how to extract information from these datasets
  • Learn how to visualise experimental results from these datasets
  • Learn how to model dose-response for both monotherapy and combination small compound datasets
  • Learn measures to quantify response and synergy in cell line sensitivity screens

Prerequisites: You need working knowledge of R and a basic familiarity with Bioconductor. Experience with the data.table R package is helpful, but not required.


Workshop 4 (WS4) (May 11, 14:00-18:00; May 12, 09:00-13:00)

Title: Single-Cell

Lecturers: Donnacha Fitzgerald, Hosna Baniadam, Harald Vöhringer, Petr Smirnov

The aim of this workshop is to introduce single-cell (including multi-omic and spatial) methods, what can be achieved with them and principles for their analysis. It will include the following topics:

  • Overview of single-cell methods
  • Single-cell transcriptomics analysis
  • Single-cell data integration (horizontal and vertical)
  • Spatial analysis + probabilistic factor models for the analysis of single cell data

Each topic includes a 30 minutes talk followed by a 45 minutes practical component.

We will also add a consultation hour (60 minutes) at the end of the program for people to ask questions related to their own projects or to bring data for help with their analysis.


Registration is free but mandatory. Please register here (https://docs.google.com/forms/d/e/1FAIpQLSf_y78l3tCNyxm7cdWOTFWmyH4fSiHktzj-YUH7NkdPBjmVXQ/viewform?usp=sf_link) until April 28, 2023. We have 30 seats for each workshop. We might have to close the registrations before the registration deadline.

The event is finished.


INESC-ID, “Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento em Lisboa” is a Research and Development and Innovation Organization (R&D+i) in the fields of Computer Science and Electrical and Computer Engineering. INESC-ID mission is to produce added value to people and society, supporting the response of public policies to scientific, health, environmental, cultural, social, economic and political challenges. INESC-ID promotes cooperation between academia and industry by addressing research on daily life issues, such as healthcare, space, mobility, agri-food, industry 4.0, and smart grids. This high level of knowledge transfer is achieved through both competitive research projects and direct contracted research. Public and private entities have therefore access to a pool of knowledge, resources and services provided through the unique competencies available at the institution.


INESC-ID is supported by:

Join our newsletter

* indicates required

Subscriber consent

The data submitted through this form will be used exclusively for the sending of INESC-ID Newsletter, NEWS-ID, and will not, under any circumstances, be shared with third parties. If you choose to, you can easily unsubscribe from the newsletter by following the link presented in the footer. In that case, your data will be automatically deleted from our information system. If you need to update your contact information or clarify any questions related to the newsletter, please contact info@inesc-id.pt. By submitting this form, you give permission to the use of your personal data according to the conditions above.

We use Mailchimp as our marketing platform. By clicking below to subscribe, you acknowledge that your information will be transferred to Mailchimp for processing. Learn more about Mailchimp's privacy practices here.