This workflow provides a calculaiton of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) ...

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

1. Bionano data [cmap]
2. Estimated genome size [txt]
3. Phased assembly generated by Hifiasm [gfa1]

Outputs

1. Scaffolds
2. Non-scaffolded contigs
3. QC: Assembly statistics
4. QC: Nx plot
5. QC: Size plot

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Inputs

1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
3. Assembly to purge (e.g. hap1) ...

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

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 ...

Protein Ligand Complex MD Setup tutorial 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 in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the ...

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. ...

Protein MD Setup tutorial 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). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

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

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 ...

Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...