CWL version of the md_list.cwl workflow for HPC. This performs a system setup and runs a molecular dynamics simulation on the structure passed to this workflow. This workflow uses the md_gather.cwl sub-workflow to gather the outputs together to return these. To work with more than one structure this workflow can be called from either the md_launch.cwl workflow, or the md_launch_mutate.cwl workflow. These use scatter for parallelising the workflow. md_launch.cwl operates on a list of individual ...
Type: Common Workflow Language
Submitter: Douglas Lowe
This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is 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 STI, DrugBank Ligand Code DB00619), a small molecule kinase inhibitor used to treat certain types of cancer.
Workflow engine is a jupyter notebook. It ...
A workflow and associated files for use in SEEK's tests
Creator: Finn Bacall
Submitter: Finn Bacall
- Name of the application: Adapter removal hello world
- Name of the application: Mapping and bam sorting goodbye world
1. Name of the application: Adapter removal hello world 2. Name of the application: Mapping and bam sorting goodbye world
Preprocessing of raw SARS-CoV-2 reads
The raw reads available so far are generated from bronchoalveolar lavage fluid (BALF) and are metagenomic in nature: they contain human reads, reads from potential bacterial co-infections as well as true COVID-19 reads.
Jupyter Notebook containing a tutorial 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 minimize the structure, and generate parameters for the GROMACS package. With Generalized ...