15 November 2022, 9-13 h CET, online

Overview

Constraint-based reconstruction and analysis (COBRA) refers to a vast collection of methods that build and scrutinise large metabolic networks, traditionally using the methodology of linear optimization. Many current analysis methods work with models that are personalised or customised to reflect genomic, proteomic and other measurements. At the same time, there is a natural need to simulate more complex phenomena that emerge from combinations of many individual models, such as multi-organ and multi-organism networks. The complexity of the computations that need to be organised to run such simulations naturally grows, up to a point where the analysis may become infeasible. 

In this course we will introduce COBREXA.jl, a toolkit for working with large constraint-based metabolic models and running very large parallel analysis tasks on these models. Its main purpose is to make the COBRA methods scale to problem sizes that require the use of large computer clusters and high performance computing (HPC). Visit COBREXA.jl website to find more information and guides.

The course will combine lectures and hands-on exercises using several new design patterns implemented in COBREXA.jl to organise many different model combinations, constraints, modifications and personalizations in a systematic way, allowing short and concise implementations of extremely complex, huge-scale analyses.

Learning outcomes

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

• Use COBREXA.jl for solving common problems in metabolic modelling
• Port analyses from other COBRA implementations to benefit from COBREXA.jl performance.
• Explain the challenges and possibilities in combining the functionalities of common analyses in constraint-based modelling, using the semantic of model wrappers and variants implemented in COBREXA.jl.
• Simulate complex metabolic phenomena using the infrastructure of COBREXA.jl, and add customizations to the models using the wrapper mechanisms. In particular, we will
  • Build small community models of gut microbiota and simulate their survival and growth
  • Build models that carry personalizations based on both genomics data that increase the precision of the simulations
  • Explore and visualise how the variability in gene expression affects metabolic phenotype
• Modify the wrappers present in COBREXA.jl and implement new ones, possibly adding novel functionality to the simulations.

Audience

This course is aimed at researchers from Computational Biology, Life Sciences, Computer Sciences, and general Bioinformatics who have some experience with constraint-based modelling of biological systems.

Pre-requisites:

• Basic knowledge of the COBRA methodology (common representations of the constraint-based metabolic models and common analysis tasks, such as flux balance and variability analysis, and flux sampling)
• Basic knowledge of programming in a managed language (Python/R/Julia) and experience with structured programming (variables, loops and basic array processing should be sufficient)
• Some experience in using UNIX-like systems and interacting with REPL-based analysis environments in a terminal is a benefit.

Registration

Registration is closed.
Applications are open until the 2nd of November and are first-come first-served based. We will review applications on a rolling basis to select suitable candidates until the 25 places available are filled. A waiting list will be established if needed.

How the course will run

The course will combine lectures and hands-on exercises using new design patterns implemented in COBREXA.jl.

The training will take place virtually in Zoom on the 15th of November 2022, 9-13 h CET, including breaks. Participants are expected to attend all sessions. 

Please note that the course might be recorded.

Trainers

• Miroslav Kratochvìl (University of Luxembourg, PerMedCoE)

If you have any questions or comments, you can contact Daniel Thomas López (dthlopez@ebi.ac.uk).