Workflows
What is a Workflow?Filters
gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread
Overview
gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...
COMPSs Matrix Multiplication resourceUsage profiling example.
MN5 MSIZE=20 BSIZE=768 7 Nodes (6 workers) (--num_nodes=7 --worker_in_master_cpus=0).
- Total number of tasks: 20^3 = 8000
- Maximum code parallelism: 20^2 = 400
- Total cores: 112*6 = 672
- Maximum utilisation: 400 / 112 = 3,57 Nodes
Overall stats from "pycompss inspect":
│ └── overall
│ ├── matmul_tasks
│ │ └── multiply
│ │ ├── maxTime = 91,111 ms
│ │ ├── executions = 8,000
│ │ ├── avgTime = 84,839 ms
│ │ └── minTime = 79,278 ms
...
Application that perform the multiplication between matrices. In this experiment, a new profiling visualization is available, showing the resource usage such as CPU, memory, data read and written to disk, and data sent and received over the network.
Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...
Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 1 (WF7501) uses new data to create a multi-scale model of the Earth, which is used to update the REVEAL/CSEMv3 velocity model. The WF7501 workflow models an inversion-based update process for CSEMv3 (Computational Seismic Earth Model). Below is a simple explanation of the STEPs:
- ST750101 - Data Catalog Update: Collects external data sources and updates the database for further processing.
- ST750102 - Inversion Setup: Configures ...
Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 2 (WF7502) generates synthetic shaking simulations (shakemaps) for seismic sources at different time scales, and automatically incorporates new data as it becomes available.
The workflow consists of multiple steps (ST), datasets (DT), and software services (SS). Below is a simplified breakdown:
Data Ingestion & Preprocessing
- ST750201: Assimilates real-time earthquake data from external sources.
- ST750202: Extracts earthquake ...
Type: Common Workflow Language
Creators: Johannes Kemper, Cedric Bhihe, Georgina Díez
Submitter: Johannes Kemper
AnnoAudit - Annotation Auditor
AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.
Overview of the workflow
The workflow assess the annotation quality based on different criteria:
- Protein evidence support
- RNASeq evidence support
- Statistics of the predictions (i.e., gene length, exon number, etc.)
- Ortholog analysis (BUSCO, OMArk)
Input data
- Reference genome
genome.[.fna, .fa, .fasta]
- Annotation ...