Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs

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Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs

@id ./
name [?] Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs
@type Dataset
description [?] 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.
datePublished [?] 2021-09-28T17:27:00+0100
author [?]
citation [?] BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
contactPoint [?] biobb forum at ask.bioexcel.eu
hasPart [?]
identifier [?] https://doi.org/10.48546/workflowhub.workflow.200.1
license [?] Apache License 2.0
mainEntity [?] md_list.py
publisher [?] Molecular Modeling and Bioinformatics unit
url [?] https://github.com/bioexcel/biobb_hpc_workflows
Items that reference this one
about [?] ro-crate-metadata.json


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Go to: BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

@id https://doi.org/10.1038/s41597-019-0177-4
name [?] BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
@type ScholarlyArticle
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.
datePublished [?] 2019-09-10T00:00:00.000Z
author [?]
copyrightYear [?] 2019-09-10T00:00:00.000Z
license [?] Creative Commons Attribution 4.0 International
Items that reference this one
citation [?] Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs


Go to: biobb forum at ask.bioexcel.eu



workflows

@id workflows/
name [?] workflows
@type Dataset
description [?] HPC workflows using PyCOMPSs
dateModified [?] 2021-09-28T10:02:17.833Z
hasPart [?] MD
Items that reference this one
hasPart [?] Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs


launchers

@id launchers/
name [?] launchers
@type Dataset
description [?] HPC launchers for PyCOMPSs workflows
dateModified [?] 2021-09-28T10:02:17.833Z
hasPart [?]
Items that reference this one
hasPart [?] Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs


Go to: Apache License 2.0

@id https://spdx.org/licenses/Apache-2.0
name [?] Apache License 2.0
@type CreativeWork
description [?] Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
identifier [?] https://www.apache.org/licenses/LICENSE-2.0
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license [?]


⬇️ Download: md_list.py

@id workflows/MD/md_list.py
name [?] md_list.py
@type
  • File
  • SoftwareSourceCode
  • ComputationalWorkflow
description [?] Performs a system setup and runs a molecular dynamics simulation on each one of the structures listed in the YAML properties file.
author [?]
dateModified [?] 2021-09-03T00:00:00.000Z
hasPart [?]
isBasedOn [?] Research Object Crate for Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
programmingLanguage [?] PyCOMPSs
runtimePlatform [?] Python 3.8.0
Items that reference this one
mainEntity [?] Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs
hasPart [?] MD
isBasedOn [?]


Go to: Molecular Modeling and Bioinformatics unit