Analysis of huge metabolic models with COBREXA.jl

PerMedCoE webinars are open to everyone interested in PerMedCoE tools and activities. The webinars will include a 30-40 minutes presentation and a Q&A section of around 15 minutes. The recording of this webinar will be publicly available on this web page and the PerMedCoE YouTube channel.

Analysis of huge metabolic models with COBREXA.jl

SpeakerMiroslav Kratochvíl (Luxembourg Centre for Systems Biomedicine)
Date and timeThursday 21 October 2021, 15.00-16.00 CEST
Target group:Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Learning outcomes:Describe some of COBREXA.jl main applications
Navigate COBREXA.jl interface
Watch the recording
Access the slides

COBREXA.jl is 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.jl interface that allows biologists and bioinformaticians to easily specify large amounts of analyses and execute it on supercomputers.  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. 

Miroslav Kratochvíl, Luxembourg Centre for Systems Biomedicine

Speaker bio:

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.