S2M2 - Summer School in Metabolic Modelling 2023, Portugal, June / July

[Johan Gustafsson]

Hi all

Sharing information about an upcoming training course in Portugal.

It will be possible to participate remotely.

Please see below.

Best

Johan

Dear colleagues,

We are pleased to announce the 4th edition of the Summer School in Metabolic Modelling that will be held from the 28th of June to the 5th of July 2023. This year's event will take place on-site (preferential), although remote online participation will be possible.

This summer school will focus on computational tools for metabolic model reconstruction and its use for phenotype simulation and strain optimization, as well as omics data integration with metabolic models and community modelling.

The course is directed to everyone interested in learning how to use metabolic modelling in their research, spanning diverse applications in microbial metabolic engineering, microbial communities, use of human models in health-related themes (e.g. cancer metabolism, metabolic-related diseases, host-pathogen interactions), and plant sciences.

The course will focus on the use of both user-friendly software tools and python-based tools (using Jupyter Notebooks). Hence, whilst no programming skills are required, an optional online session is included before the course, covering a simple introduction to python. This session may be needed for the ones less familiar with python-based tools.

The course will last 7 days (with a free day in the middle). Each day will be divided into a theoretical morning session and practical afternoon sessions, also featuring a social program. The morning lectures will be guided by an expert in the field that will present background information, key concepts, algorithms, and computational tools. Afternoon sessions will be dedicated to extensive in silico practical work. Most days will close with an invited talk reflecting on the different applications of metabolic modeling, both in the academy and industry. Participants will have some time to prepare their own projects, to be presented in the final session.

Course attendants will participate in activities covering the following topics:

- Basic concepts in metabolic modelling

- Genome annotation and metabolic model reconstruction with merlin

- Flux analysis, phenotype simulation, and strain optimization using OptFlux, COBRApy, and MEWpy

- Analysis and integration of omics data into genome-scale metabolic models, using Troppo and other tools.

- Novel modeling paradigms including protein allocation constraints, transcription/ translation, regulatory interactions, and community models using MEWpy

- (Optional) An online hands-on introduction to Python and Jupyter Notebooks covering the main skills needed for the remaining of the course.

Scientific coordination

Miguel Rocha and Oscar Dias

Important dates:

Early registration Deadline: May 14th

Regular registration Deadline: June 14th

Late registration: June 23rd

Summer School: June 28-July 5

Please register by filling out this form: Registration form.

For further information, including fees, please check the website: http://s2m2.bio.di.uminho.pt/

Feel free to contact us for help regarding your travel arrangements.

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Best regards,

The S2M2 Course Office

e-mail:s2m2....@gmail.com
Website:http://s2m2.bio.di.uminho.pt/