How ebbrg/genome-wide-workbench works
GWW is an offline-first graphical bioinformatics workbench. Researchers provide sequence or genome inputs through the desktop application, run individual analyses or combine stages from sequence discovery and alignment through phylogenetic and evolutionary interpretation, and inspect visualizations or classification results. The README documents the broader integrated workflows; sampled modules confirm several UI-to-worker/tool patterns, but do not establish all module wiring or a single central orchestrator, so uncertain call relationships are omitted.
Main entry points: main_app.py Workbench interface · primer_designing_adv.py Primer design · app_vigna.py Protein classification · fasta_formatter.py FASTA filtering
Components 19
Desktop interface
- Workbench interface
src/main_app.py
Sequence analysis
- FASTA filtering
src/fasta_formatter.py - BLAST search
src/blast.py - HMM search
src/hmm_search.py - Homology search
src/homologus_pair.py - Sequence alignment
src/align.py - Alignment trimming
src/align_triming.py - Primer design
src/primer_designing_adv.py - Basic primer design
src/primer_designing_basic.py
Evolution and comparison
- Phylogenetic analysis
src/phylogenetic_analysis.py - Ka/Ks analysis
src/kaks.py - Comparative genomics
src/intersect.R
Visualization and classification
- Gene-density mapping
src/loci_map.py - Expression heatmaps
src/heatmap.py - Genomic ideograms
src/generate_ideogram.R - Protein classification
src/app_vigna.py
Other components
- Researcher
- Primer3
- ESM-2 model
Connections 33
- Researcher → Workbench interface: uses
- Workbench interface → FASTA filtering: opens tool
- Workbench interface → BLAST search: opens tool
- Workbench interface → HMM search: opens tool
- Workbench interface → Homology search: opens tool
- Workbench interface → Sequence alignment: opens tool
- Workbench interface → Alignment trimming: opens tool
- Workbench interface → Phylogenetic analysis: opens tool
- Workbench interface → Ka/Ks analysis: opens tool
- Workbench interface → Primer design: opens tool
- Workbench interface → Basic primer design: opens tool
- Workbench interface → Gene-density mapping: opens tool
- Workbench interface → Expression heatmaps: opens tool
- Workbench interface → Genomic ideograms: opens tool
- Workbench interface → Comparative genomics: opens tool
- Workbench interface → Protein classification: opens tool
- BLAST search → Researcher: shows results
- HMM search → Researcher: shows results
- Homology search → Researcher: shows results
- Sequence alignment → Researcher: shows output
- Phylogenetic analysis → Researcher: shows tree
- Ka/Ks analysis → Researcher: shows results
- Primer design → Primer3: calls
- Primer design → Researcher: shows candidates
- Basic primer design → Primer3: uses
- Gene-density mapping → Researcher: shows map
- Expression heatmaps → Researcher: shows heatmap
- Genomic ideograms → Researcher: shows output
- Comparative genomics → Researcher: shows comparison
- Protein classification → ESM-2 model: embeds sequences
- Protein classification → Researcher: returns labels
- FASTA filtering → Researcher: writes filtered FASTA
- Alignment trimming → Researcher: writes trimmed alignment