PerMedCoE summer school: from pathway modelling tools to cell-level simulations

PerMedCoE summer school

From pathway modelling tools to cell-level simulations

The PerMedCoE summer school will take place on the 25 – 30 June 2023 at the Hotel Montanyà in Seva, less than an hour away from Barcelona.

The course will combine lectures and hands-on exercises to:

  • Introduce attendees to key practicalities of working with high-performance computing (HPC) clusters
  • Build first-hand experience in using PerMedCoE modelling tools (CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell and PhysiBoSS)
  • Develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows

Join us and expand your skills on cell-level simulations

Applications close 6 March 2023

€400 (inclusive of full board accommodation)

Hotel Montanya view

A bird view of the Hotel Montanyà, venue of the PerMedCoE Summer School 2023.

Audience:

This course is aimed primarily at PhD students and early postdoctoral researchers from Computational Biology, Systems Biology, or Life Sciences with an interest in the area of cell-level simulations, gaining first-hand experience in using diverse biomedical modelling tools, and how such tools could be used as part of workflows on HPC environments.

At the end of the sessions, the participants will be able to:

  • Use a range of biological modelling and cell-level simulation software: CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell, and PhysiBoSS
  • Describe and execute basic workflows using PerMedCoE modelling tools on a high-performance computing (HPC) cluster
  • Discuss current trends and challenges in cell-level simulations

Prerequisites:

  • Basic use of command line and access to Unix shell terminal
  • Basic use of Python or R programming languages
  • Experience using containers and workflow managers is considered a benefit

Participants will need to bring their own laptop to the course. Further instructions will be provided after registration.

We highly encourage applications from women and underrepresented groups.

Registration fee and grants:

The cost of the course is €400 (to be paid after the selection process). It includes five nights of accommodation in a double room shared with another participant (single occupancy is available at an additional fee), all meals shown in the programme and transportation between the airport and course venue.

A limited number of grants will be available for this event. If you would like to be considered for a grant:

 Posters

All participants will be expected to present a poster that will be displayed during the course in the poster room.

We expect the posters to act as a talking point between you, other participants, and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

 

Do you have any questions? Contact our colleague Juanita Riveros.

Montseny Park

The Hotel Montanyà is on the outskirts of the Montseny Natural Park, a UNESCO Biosphere Reserve.

Selection process
Participation will be based on an open application with a selection. 30 applicants will be selected for the course.

To apply you will need to complete the application form and attach the following information:

  • Support letter from your supervisor or a senior co-worker explaining why you should be selected for this course (in word or pdf format)
  • Research Abstract (limit: 300 words – you will be able to present and discuss your research during the course)

We highly encourage applications from women and underrepresented groups.

Please complete the application process by 23:59 (CET) on Monday 6 March 2023. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 24 March. If you have any questions regarding the application process, please contact Juanita Riveros.

Tips for a good application

1) During the selection process we focus on:

  • Do you have the pre-requisite knowledge?
  • Will your research and research group benefit from what you learn in this course?

So, please pay special attention to the following 3 questions on the application form:

  • Describe your current work
  • Describe how this course will benefit your own work
  • Describe how this course will benefit the work of your group

2) You are asked to add an abstract about your research to be presented during the PerMedCoE Summer School. If you do not have any results yet, you can write your abstract as a short introduction to the topic and a working plan.

 

 

Programme

Note: Please note that the programme is still subject to changes.
All times in the programme are listed in CEST.

Arrival day – Sunday 25 June 2023
Time Topic Trainer
16:00 – 18:00 Travel from Barcelona airport to hotel and registration
20:00 Dinner
Day one – Monday 26 June 2023
Time Topic Trainer
09:00 – 09:30 Welcome and Introduction Daniel Thomas López
09:30 – 11:00 Lecture and Hands-on: Introduction to High Performance Computing (HPC) TBC
11:00 – 11:30 Coffee break
11:30 – 13:00 Lecture: CellNOpt – CARNIVAL Pablo Rodríguez Mier
13:00 – 14:00 Lunch break
14:00 – 16:00 Hands-on: CellNOpt – CARNIVAL Pablo Rodríguez Mier
16:00 – 16:30 Coffee break
16:30 – 17:00 Introductions and flash talks from trainers Trainers
17:00 – 18:00 Introductions and flash talks from participants I
18:00 End of day
20:00 Dinner
Day two – Tuesday 27 June 2023
Time Topic Trainer
09:00 – 10:30 Lecture: COBREXA Miroslav Kratochvil
10:30 – 11:00 Coffee break
11:00 – 13:00 Hands-on: COBREXA Miroslav Kratochvil
13:00 – 14:00 Lunch break
14:00 – 15:30 Lecture and Demo: MaBoSS Vincent Noël
15:30 – 16:30 Career session TBC
16:30 – 17:00 Coffee break
17:00 – 17:30 Introductions and flash talks from participants II
17:30 End of day
20:00 Dinner
Day three – Wednesday 28 June 2023
Time Topic Trainer
09:00 – 10:30 Lecture: PhysiCell and PhysiBoSS Arnau Montagud and Miguel Ponce de León
10:30 – 11:00 Coffee break
11:00 – 13:00 Hands-on: PhysiCell and PhysiBoSS Arnau Montagud and Miguel Ponce de León
13:00 – 14:00 Lunch break
14:00 – 15:00 Project work in groups I All
15:00 – 16:30 Poster session I
16:30 – 21:00 Excursion and dinner
Day four – Thursday 29 June 2023
Time Topic Trainer
09:00 – 10:30 Lecture: Containers, Building blocks and workflows Javier Conejero and Henrik Nortamo
10:30 – 11:00 Coffee break
11:00 – 13:00 Hands-on: Containers, BB and workflows Javier Conejero and Henrik Nortamo
13:00 – 14:00 Lunch break
14:00 – 16:00 Project work in groups II All
16:00 – 16:30 Coffee break
16:30 – 18:00 Poster session II
18:00 End of day
20:00 Dinner
Day five – Friday 30 June 2023
Time Topic Trainer
09:00 – 10:00 Keynote lecture I Asmund Flobak
10:00 – 11:00 Keynote lecture II: Sex and gender bias in research Davide Cirillo
11:00 – 11:30 Coffee break
11:30 – 12:30 Project work in groups III All
12:30 – 13:30 Project work in groups IV All
13:30 – 14:00 Final questions, course wrap up and feedback Daniel Thomas López
14:15 Take away lunch
14:30 Bus to Barcelona airport

 

Organisers and trainers

Trainers:

  • Davide Cirillo, Barcelona Supercomputing Center
  • Javier Conejero, Barcelona Supercomputing Center
  • Åsmund Flobak, Norwegian University of Science and Technology
  • Miroslav Kratochvil, University of Luxembourg
  • Arnau Montagud, Barcelona Supercomputing Center
  • Vincent Noël, Institut Curie
  • Henrik Nortamo, CSC – IT Center for Science Ltd
  • Pablo Rodríguez Mier, University of Heidelberg
  • Miguel Ponce de León, Barcelona Supercomputing Center

Organisers:

COVID-19 safety policy

At PerMedCoE we are committed to the safety of our participants and trainers. Both PerMedCoE and our community of participants need to take new precautions when planning how we come together again in person for learning and scientific exchange. PerMedCoE continuously monitors local and international guidelines and regulations relating to the COVID-19 pandemic. Due to the changing nature of the pandemic and in order to be compliant with relevant national and international regulations, it may be necessary for PerMedCoE to update, from time to time, these COVID-19 specific safety rules. We will inform registered participants about substantial changes to this document.

For more information, please see the Spanish Government website.