A project for miscellaneous testing of Workflow Hub.
Space: General
SEEK ID: https://dev.workflowhub.eu/projects/9
Public web page: Not specified
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 6th Apr 2020
Related items
Teams: MGnify, nf-core, Workflow Hub Administration, Galaxy COVID-19, Testing
Organizations: University of Manchester
Teams: Testing
Organizations: Swiss Institute of Bioinformatics

Teams: Demonstrator #7, Testing
Organizations: Barcelona Supercomputing Center

Teams: ELIXIR Cloud & AAI, Testing
Organizations: ELIXIR Switzerland

Teams: Testing, Finn's test team, PNDB, LifeMonitorDev
Web page: Not specified
Stable
KFDRC Alignment Workflow
Workflow for the alignment or realignment of input BAMs, PE FASTQ reads, and/or SE FASTQ reads; conditionally generate gVCF and metrics.
This workflow is a all-in-one workflow for handling any kind of reads inputs: BAM inputs, PE reads
and mates FASTQ inputs, SE reads FASTQ inputs, or any combination of these. The workflow will naively attempt
to process these
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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.
Live Resources
| usegalaxy.org | usegalaxy.eu | usegalaxy.org.au | usegalaxy.be |
|:--------:|:------------:|:------------:|:------------:|
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Stable
Summary
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
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Work-in-progress
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 2-propylphenol small molecule (3-letter Code JZ4).
Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels,
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