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829 Workflows visible to you, out of a total of 902
Lysozyme in water full version, using REMOTE dataset, two workers, data_persistence False

Lysozyme in water full COMPSs application run at MareNostrum IV, using full dataset with two workers

Type: COMPSs

Creator: Rosa M Badia

Submitter: Raül Sirvent

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Kos-Bodrum 2017 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Kos-Bodrum 2017 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.781.1

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Boumerdes-2003 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Boumerdes-2003 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.779.1

Jupyter Notebook Mutation Free Energy Calculations
Stable

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)

Based on the official pmx tutorial.

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital

Submitters: Douglas Lowe, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.55.6

Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital, Douglas Lowe

Submitters: Robin Long, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.54.6

Galaxy Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.778.1

Python Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.777.1

CWL Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.776.1

Jupyter Notebook Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Jupyter

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.775.1

Jupyter Notebook Amber Protein MD Setup tutorial
Stable

AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This 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) wrapping the Ambertools MD package.

Copyright & Licensing

This software has been developed in the MMB group ...

Type: Jupyter

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.130.5

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