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ro-crate-preview.html
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"description": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.",
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<body>
<h1>Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs</h1>
<a href="https://github.com/bioexcel/biobb_hpc_workflows" target="_blank">https://github.com/bioexcel/biobb_hpc_workflows</a>
<p>
This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.
</p>
<dl>
<dt>Author</dt>
<dd>[<#ROCrate::Person https://orcid.org/0000-0002-8291-8071 @properties={"@id"=>"https://orcid.org/0000-0002-8291-8071", "@type"=>"Person", "name"=>"Adam Hospital"}>, <#ROCrate::Person https://orcid.org/0000-0003-2116-3880 @properties={"@id"=>"https://orcid.org/0000-0003-2116-3880", "@type"=>"Person", "name"=>"Pau Andrio"}>]</dd>
<dt>Contact</dt>
<dd>#<ROCrate::ContactPoint:0x00007fd427817538></dd>
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<h2>Contents</h2>
<ul>
<li id="__data_entity_workflows/MD/md_list.py">
<strong>md_list.py</strong>
</li>
<li id="__data_entity_workflows/">
<strong>workflows</strong>
</li>
<li id="__data_entity_launchers/">
<strong>launchers</strong>
</li>
</ul>
</body>
</html>
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