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

It will also include poster sessions where participants can present their work and plenty of time for interaction between participants and between participants and trainers.

This course will take place at the Hotel Montanyà in Seva, less than an hour away from Barcelona.

Visit the PerMedCoE summer school website for more information.

Who is this course for?

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.

Previous experience of using Python and command-line interfaces are considered a benefit. Experience of using workflow managers is also beneficial, but not mandatory for attending the course.

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

What will I learn?

Learning outcomes

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

• Use a range of biological modeling 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

Trainers

Visit the PerMedCoE summer school website for more information.

Accommodation 

Hotel rooms (including breakfast) will be provided at Hotel Montanyà. The accommodation will be in double room shared with another participant (single occupancy is available at an additional fee). Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are 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.