Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.
The workflows also appear on https://hub.ibisba.eu
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/1
Funding codes:- EU H2020 INRAIA-02 730976
Public web page: https://www.ibisba.eu
Organisms: Homo sapiens, Sars-cov-2
WorkflowHub PALs: No PALs for this Team
Team created: 6th Apr 2020
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Web page: Not specified
This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.
Workflow for tracking objects in Cell Profiler: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html
Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh
The workflow runs the RetroSynthesis algorithm to generate a collection of heterologous pathways in a host organism of choice, converts them to SBML files, performs analysis on the pathways to then rank the theoretical best performing ones.
Generate possible metabolic routes for the production of a target molecule in an organism of choice
This workflow converts the top-ranking predicted pathways from the "RetroSynthesis" and "Pathway Analysis" workflows to plasmids intended to be expressed in the specified organism
Given a set of pathways generated by RetroPath2.0, this workflow informs the user as to the theoretically best performing ones based on four criteria: FBA, thermodynamic feasibility, length of the pathway, and reaction rule score.