This implementation was done for the ELIXIR EXCELERATE Demonstrator to be run on WES-TES environment.

There is also task related to input file transfer (curl) and the output file transfer to a private FTP server. The needed URLs and FTP credential are given as input parameters.

The input files are assumed to come from a web server. Idea there is to make some configurations more modular and some tools like lftp or curl have easier to write script parameter files instead of command line parameters.

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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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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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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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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).

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, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.