BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools
Abstract Motivation The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top of common biomolecular simulation and bioinformatics tools. The possibility to access the library remotely and programmatically increases its usability, allowing individual and sporadic exec...
| Authors: | , , , , |
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| Format: | article |
| Publication Date: | 2022 |
| Country: | España |
| Institution: | Universitat Politècnica de Catalunya (UPC) |
| Repository: | UPCommons. Portal del coneixement obert de la UPC |
| Language: | English |
| OAI Identifier: | oai:upcommons.upc.edu:2117/367414 |
| Online Access: | https://hdl.handle.net/2117/367414 https://dx.doi.org/10.1093/bioinformatics/btac316 |
| Access Level: | Open access |
| Keyword: | Application program interfaces (Computer software) Bioinformatics Data sharing Biomolecular simulation Simulació per ordinador Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
| Summary: | Abstract Motivation The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top of common biomolecular simulation and bioinformatics tools. The possibility to access the library remotely and programmatically increases its usability, allowing individual and sporadic executions and enabling remote workflows. Results BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations, and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, voiding the need for tool installation. Availability All the information related to the BioBB REST API endpoints is accessible from https://mmb.irbbarcelona.org/biobb-api/. Links to extended documentation, including OpenAPI endpoints specification and examples, Read-The-Docs documentation and a complete workflow tutorial can be found in the Suppl. Table 1. |
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