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 are closed
€400 (inclusive of full board accommodation)
A bird view of the Hotel Montanyà, venue of the PerMedCoE Summer School 2023.
Audience:
This course is primarily aimed at PhD students and 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:
- Check the information in the PerMedCoE grants document.
- Complete the application form for the course.
- Email Daniel Thomas López after the submission of your application explaining why you should 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.
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 16 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 31 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 |
| 18:00 – 20:00 | Travel from Barcelona airport to hotel and registration | |
| 20:30 | 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) | Henrik Nortamo |
| 11:00 – 11:30 | Coffee break | |
| 11:30 – 13:00 | Lecture: Logical modelling of cell signalling | Pablo Rodríguez Mier and Denes Turei |
| 13:00 – 14:00 | Lunch break | |
| 14:00 – 16:00 | Hands-on: Logical modelling of cell signalling with CellNOpt and CARNIVAL | Pablo Rodríguez Mier and Denes Turei |
| 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: Constraint-Based Reconstruction and Analysis for metabolic modelling | Miguel Ponce de León |
| 10:30 – 11:00 | Coffee break | |
| 11:00 – 13:00 | Hands-on: Analysis of metabolic models with COBREXA.jl | Miguel Ponce de León and Pablo Rodríguez Mier |
| 13:00 – 14:00 | Lunch break | |
| 14:00 – 15:30 | Lecture and Demo: Qualitative modelling of biological systems with MaBoSS | Vincent Noël |
| 15:30 – 16:00 | Coffee break | |
| 16:00 – 16:30 | Introductions and flash talks from participants II | |
| 16:30 – 17:30 | Career session | Núria Castell, Paula Petrone, Daniel Thomas López and Mariano Vázquez |
| 17:30 – 18:00 | Drinks and nibbles | |
| 18:00 | End of day | |
| 20:00 | Dinner | |
| Day three – Wednesday 28 June 2023 | ||
| Time | Topic | Trainer |
| 09:00 – 10:30 | Lecture: Simulation of multicellular systems | Arnau Montagud, Miguel Ponce de León and Thalia Diniaco |
| 10:30 – 11:00 | Coffee break | |
| 11:00 – 13:00 | Hands-on: Multiscale modelling of cell systems with PhysiCell and PhysiBoSS | Arnau Montagud, Miguel Ponce de León and Thalia Diniaco |
| 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 – 20:00 | Excursion | |
| 20:00 – 22:00 | Dinner in Viladrau | |
| 22:00 – 22:45 | Return to hotel | |
| 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 | Åsmund 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 and speakers:
- Núria Castell, Universitat Politecnica de Catalunya
- Davide Cirillo, Barcelona Supercomputing Center
- Javier Conejero, Barcelona Supercomputing Center
- Thalia Diniaco, Barcelona Supercomputing Center
- Åsmund Flobak, Norwegian University of Science and Technology
- Arnau Montagud, Barcelona Supercomputing Center
- Vincent Noël, Institut Curie
- Henrik Nortamo, CSC – IT Center for Science Ltd
- Paula Petrone, ISGlobal
- Miguel Ponce de León, Barcelona Supercomputing Center
- Pablo Rodríguez Mier, University of Heidelberg
- Marco Ruscone, Institut Curie
- Denes Turei, University of Heidelberg
- Mariano Vázquez, ELEM-BIO and Barcelona Supercomputing Center
Organisers:
- Laurence Calzone, Institut Curie
- Jose Carbonell Caballero, Barcelona Supercomputing Center
- Jesse Harrison, CSC – IT Center for Science Ltd
- Marta Lloret Llinares, EMBL-EBI
- Daniel V. Thomas López, EMBL-EBI
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.