Including HAL in a community-based benchmarking activity

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Arnau Montagud

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Jan 14, 2022, 1:41:10 PM1/14/22

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We are reaching out to HAL developers about a community-based benchmarking activity that the H2020 PerMedCoE project (https://permedcoe.eu/) is organising.

Briefly, the aim of PerMedCoE, a recently created European Center of Excellence (CoE) in Personalised Medicine, is to provide an efficient and sustainable roadmap to scale up various computational biology tools to leverage the next generation of HPC exascale platforms.

PerMedCoE aims to organise a set of community-driven benchmarks of tools aimed at cell-level simulations: signalling pathways, metabolism and population of cells. These benchmarks will allow to vertebrate the community of the tools users and developers, simplify benchmarking of new tools by tool developers, provide good scenarios and metrics for tool comparison, and, in result, offer the end users a comprehensive view of the state of the field and a useful reference for choosing best tools for specific use cases.

PerMedCoE is calling out to developers of simulation tools to participate and help in this effort, and decide on scope, metrics and reference datasets that could be used to compare our cell-level simulation tools.

The outcomes of these efforts will become a public website at ELIXIR’s OpenEBench platform, mapping the organization of the tool landscape, and improving the visibility and discoverability of your tool for users. The site will host both the open methodology and results of the benchmarks, serving as a base point for many other tool authors and users to add their observations and benchmarks. We aim to publish a community paper from the initial benchmark participants to help define and maintain the computational biology simulation community.

More information is available at the dedicated benchmark website: https://permedcoe.eu/observatory-2/.

If you are interested to be involved in this effort, please contact me (arnau.m...@bsc.es) and we will contact you about our future meetings to discuss these benchmark efforts.

Yours sincerely,

Arnau Montagud, Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center (BSC)