Training resource |
Associated competencies |
Introduction to HPC for life
scientists
|
- Operate effectively within a Linux environment
- Use a batch job system
- Monitor application execution
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem)
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Course on HPC-based
computational biomedicine
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- Apply expertise in medical or biomedical sciences – Operate effectively within a Linux environment – Use a batch job system
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem)
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Drug studies in signalling pathways models and their integration into multiscale models |
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice Use a batch job system
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Systematising complex and
combined metabolic analyses with COBREXA.jl
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- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
|
From transcriptomics to
mechanistic models of signalling
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- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
|
PerMedCoE summer school: from pathway modelling tools to
cell-level simulations
|
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
- Use a batch job system
- Use computational workflow systems, understanding their potential benefits and limitations
|
Training materials on MaBoSS Tutorials on COBREXA |
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem)
- Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
|
Tutorial on CellNOpt |
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem)
|
Tutorial on CellNOpt |
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem)
- Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
|
Tutorial on CARNIVAL |
- Follow the scientific method and proceed with all the steps in the process of solving a scientific problem
- Apply expertise in formal, natural and life sciences – Handle data from end to end following best practice
- Apply data science expertise to clinical and life sciences problems
- Evaluate the ability of a program running in a specific computing environment to perform a simulation (e.g. define algorithmic time and hardware resources required to solve a problem) – Write or adapt scripts and computer programs (software development) to perform simulations in compliance with good programming practice
|
Tutorial on how to develop Building blocks using the ‘permedcoe’ package
Working with computing clusters: information and resources
Tutorial on working with
computing clusters
|
- Package and distribute software
- Use computational workflow systems, understanding their potential benefits and limitations
- Use a batch job system
- Monitor application execution
- Use a batch job system
|
Introductory tutorial on using MPI with containers |
- Package and distribute software
- Write parallel programs
|