COBREXA

Section outline

• Izberi poglavje COBREXA.jl

  COBREXA.jl

  Skrči vse Razširi vse

  • Izberi aktivnost Welcome to COBREXA course! Here you can find many ...

    

    Welcome to COBREXA course! Here you can find many useful links that will help you master the use of COBREXA.

    
    
  • Izberi aktivnost A metabolic modeling at scale.COBREXA.jl is a pack...

    A metabolic modeling at scale.
    

    
    COBREXA.jl is a package for COnstraint Based Reconstruction and EXascale Analysis, designed for researchers interested in metabolic modeling. Using constrained models, COBREXA includes algorithms such as finding optimal balanced fluxes involved in metabolism, and discovering the limits of known metabolic networks. As a distinctive feature, COBREXA.jl is highly parallelizable, allowing users to employ high-performance computing resources to speed up their analysis. The design allows it to scale to exascale supercomputer systems, which can perform as many as 10^18 floating point operations per second.
    
    
• Izberi poglavje Tool repositories

  Tool repositories

  A link to tool repository / repositories

  • Izberi aktivnost COBREXA repositories

    

    COBREXA repositories URL
  • Izberi aktivnost COBREXA on bio.tools

    

    COBREXA on bio.tools URL
• Izberi poglavje Tools platforms/specifics

  Tools platforms/specifics

  • Izberi aktivnost see https://github.com/LCSB-BioCore/COBREXA.jlAny ...

    • see https://github.com/LCSB-BioCore/COBREXA.jl
    • Any OS supported by Julia, see https://julialang.org/downloads/
    • https://github.com/LCSB-BioCore/COBREXA.jl
      
• Izberi poglavje Prior Knowledge needed for this tool:

  Prior Knowledge needed for this tool:

  • Izberi aktivnost Running COBREXA.jl requires basic knowledge of wri...

    Running COBREXA.jl requires basic knowledge of writing scripts. Algorithms model metabolic pathways, requiring some understanding of the underlying biological processes and terminology. A rich source of examples is available to get you started.
    
    To learn the terminology about metabolic models: https://www.nature.com/articles/nbt.1614
    
    Accelerating the analysis:
    For accelerating the analysis using high-performance computing, users should have basic familiarity with working in the command line, and have access to a supercomputing environment.
    
    You can learn about the command line with the following tutorials:
    https://ubuntu.com/tutorials/command-line-for-beginners#1-overview
    https://tutorial.djangogirls.org/en/intro_to_command_line/
    
    To learn about Slurm (job scheduler): https://researchit.las.iastate.edu/slurm-basics

  • Izberi aktivnost Command line (mac, linux, windows) 1

    

    Command line (mac, linux, windows) 1 URL
  • Izberi aktivnost Command line (mac, linux, windows) 2

    

    Command line (mac, linux, windows) 2 URL
  • Izberi aktivnost julia programing language

    

    julia programing language URL
  • Izberi aktivnost Recommended: basics of Slurm or some other job submission system

    

    Recommended: basics of Slurm or some other job submission system URL
  • Izberi aktivnost A brief overview of the "most basic" analysis

    

    A brief overview of the "most basic" analysis URL
• Izberi poglavje Work with COBREXA

  Work with COBREXA

  • Izberi aktivnost To start using COBREXA.jl, follow the simple examp...

    To start using COBREXA.jl, follow the simple examples on the COBREXA.jl page

    
    
• Izberi poglavje Tutorials & resources:

  Tutorials & resources:

  Here you can find our recommended tutorials and resources for COBREXA.

  • Izberi aktivnost Documentation and tutorials

    

    Documentation and tutorials URL

    includes: reference, 4 basic tutorials (a good training material), 2 advanced tutorials, many notebooks (good as a copypaste resource)
  • Izberi aktivnost Training material

    

    Training material URL
  • Izberi aktivnost Distributed processing tutorial

    

    Distributed processing tutorial URL
  • Izberi aktivnost COBREXA.jl: Metabolic Modeling on HPC

    COBREXA.jl: Metabolic Modeling on HPC

    
    
  • Izberi aktivnost Analysis of huge metabolic models with COBREXA.jl ...

    Analysis of huge metabolic models with COBREXA.jl

    
    
  • Izberi aktivnost Oznaka