Analysis of huge metabolic models with COBREXA.jl

COBREXA.jlis a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base building block.We will talk about the problems that motivated the development of COBREXA.jl and show several of its main applications. We will show the COBREXA.jlinterface that allows biologists and bioinformaticians to easily specify large amounts of analyses and execute it on super computers. Later, we will use COBREXA.jl for creating a model of a small microorganism community, and demonstrate how the software helps to answer questions about the viability and chemical activity of microbe ecosystems.

About the speaker

Miroslav Kratochvíl has recently finished his PhD in computer science at Charles University in Prague; currently he is a researcher focusing on bioinformatics-oriented topics at Luxembourg Centre for Systems Biomedicine. His research concerns mainly the high-performance algorithms for processing large datasets from life sciences.

Who is this course for?

This webinar is part of PerMedCoEwebinar series and is open for anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance.No prior knowledge is required.

Outcomes

By the end of this webinar, you will be able to:

• Describe some of COBREXA.jl main applications
• Navigate COBREXA.jl interface

Speakers

• Miroslav Kratochvil
  University of Luxembourg