Datasets:

garywelz
/

glmp-biological-processes

process_id int64 1 732	process_name stringlengths 6 60	kingdom float64	or_gates bool 1 class	and_gates bool 1 class	not_gates bool 1 class	feedback_loops bool 1 class	state_machines bool 1 class	decision_trees bool 1 class	flowchart_link stringlengths 103 190 ⌀
1	Nutrient Gradient Sensing	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-6-2-nutrient-gradient-sensing
2	Stress Response Decision	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-7-3-stress-response-decision
3	Quorum Sensing Threshold	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-8-4-quorum-sensing-threshold
4	Antibiotic Resistance Decision	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-9-5-antibiotic-resistance-decision
5	Biofilm Formation Decision	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-10-6-biofilm-formation-decision
6	Sporulation Timing Decision	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-11-7-sporulation-timing-decision
7	Horizontal Gene Transfer Decision	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_chemotaxis.html#process-12-8-horizontal-gene-transfer-decision
8	AHL Autoinducer Synthesis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_quorum_sensing.html#process-1-ahl-autoinducer-synthesis
9	AHL Signal Detection	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_quorum_sensing.html#process-2-ahl-signal-detection
10	Population Density Assessment	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_quorum_sensing.html#process-3-population-density-assessment
11	Biofilm Formation Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/bacterial_decision_systems_batch01_quorum_sensing.html#process-10-4-biofilm-formation-response
12	Bacterial Implementation of Viral Decision Logic	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/synthetic_circuit_construction.html#process-4-1-bacterial-implementation-of-viral-decision-logic
13	Bacterial Transcription Factor Circuit	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/synthetic_circuit_construction.html#process-2-bacterial-transcription-factor-circuit
14	Experimental Validation Protocol	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/synthetic_circuit_construction.html#process-3-experimental-validation-protocol
15	Framework Validation Metrics	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/synthetic_circuit_construction.html#process-4-framework-validation-metrics
16	Iron Homeostasis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
17	Siderophore Synthesis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
18	Iron Uptake Systems	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
19	Heme Acquisition	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
20	Iron Storage	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
21	Iron-Sulfur Cluster Assembly	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
22	Oxidative Iron Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
23	Iron Export and Detoxification	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
24	Iron Homeostasis (Fur Regulation)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
25	Siderophore Synthesis (Enterobactin)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
26	Iron Storage (Ferritin)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch10_iron_homeostasis.html
27	Chromosome Replication	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
28	Chromosome Segregation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
29	Cell Elongation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
30	Septum Formation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
31	Cell Constriction	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
32	Cell Separation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
33	Daughter Cell Formation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
34	Division Completion	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_cell_division.html
35	Drug Detection	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
36	Efflux Pumps	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
37	Target Modification	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
38	Drug Inactivation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
39	Membrane Alteration	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
40	Biofilm Protection	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
41	Persister Formation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
42	Resistance Evolution	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_antibiotic_resistance.html
43	Beta-Galactosidase	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
44	Chemotaxis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch08_motility_chemotaxis.html
45	SOS Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_stress_response.html
46	Tryptophan Biosynthesis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
47	Iron Homeostasis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
48	Heat Shock Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch10_stress_response_adaptation.html
49	Nitrogen Metabolism	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
50	Cell Division	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
51	Biofilm Formation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/s_aureus_batch01_pathogenicity_biofilm.html
52	CRISPR-Cas	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
53	Beta-Galactosidase (Lac Operon)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes.html
54	Phage Defense (CRISPR-Cas)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes.html
55	Glycolysis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch05_energy_metabolism.html
56	TCA Cycle	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch05_central_metabolism.html
57	Pentose Phosphate Pathway	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch05_energy_metabolism.html
58	Fatty Acid Metabolism	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch05_energy_metabolism.html
59	Amino Acid Metabolism	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch04_metabolic_pathways.html
60	Nucleotide Metabolism	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch14_specialized_metabolism.html
61	Anaerobic Respiration	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch06_respiration_energy.html
62	Metabolic Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch04_metabolic_pathways.html
63	Beta-Galactosidase (reuse from ecoli_10_processes.html)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
64	Tryptophan Biosynthesis (reuse from ecoli_10_processes.html)	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
65	Arabinose Operon	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
66	CAP-cAMP Global Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
67	Sigma Factor Competition	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
68	RNA Polymerase Recycling	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch03_gene_regulation_transcription.html
69	Transcription Termination	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch08_chromatin_transcription.html
70	Attenuation Control	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
71	Transcription Initiation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch08_chromatin_transcription.html
72	Sigma Factor Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
73	Operon Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
74	Transcription Termination	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch08_chromatin_transcription.html
75	Attenuation Control	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
76	Antisense Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
77	Riboswitch Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
78	Global Regulation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_transcription_regulation.html
79	Beta-Galactosidase	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
80	Chemotaxis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch08_motility_chemotaxis.html
81	SOS Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch09_stress_response.html
82	Tryptophan Biosynthesis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
83	Iron Homeostasis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
84	Heat Shock Response	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch10_stress_response_adaptation.html
85	Nitrogen Metabolism	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
86	Cell Division	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
87	Biofilm Formation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/s_aureus_batch01_pathogenicity_biofilm.html
88	CRISPR-Cas	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_10_processes_html_only.html
89	Active Transport	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
90	Passive Transport	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
91	Membrane Biogenesis	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch06_lipid_membrane_biology.html
92	Protein Secretion	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/yeast_batch16_membrane_transport.html
93	Membrane Proteins	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
94	Lipid Transport	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
95	Membrane Dynamics	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
96	Cellular Organization	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch07_transport_membrane.html
97	Cell Division	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
98	Chromosome Segregation	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
99	Min System	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html
100	Nucleoid Occlusion	null	false	false	false	false	false	false	https://huggingface.co/datasets/garywelz/glmp-biological-processes/resolve/main/ecoli_batch02_cell_division_segregation.html

End of preview. Expand in Data Studio

GLMP Biological Processes Dataset

Overview

This dataset contains 732 biological processes with computational pattern analysis for the GLMP (Gene Logic Modeling Project).

⚠️ Important: This dataset uses the pattern audit table as the baseline to avoid double-counting processes that appear in both batch files and articles.

Dataset Information

Version: 1
Last Updated: 2025-09-04
Total Processes: 732
License: CC BY 4.0
Paper: Process Visualization in Biology: A Programming Framework for Systematic Analysis of Complex Systems

Files

Core Data Files

process_inventory.csv - Clean inventory of 732 biological processes (no duplicates)
pattern_audit_table.csv - Interactive audit table with all 732 processes (use Dataset Viewer)
simple_process_list.html - Simplified process list organized by kingdom
process_summary.txt - Text summary of all processes

Metadata

dataset_info.json - Structured metadata about the dataset
README.md - This file

Computational Patterns Analyzed

OR Gates: Alternative pathway activation mechanisms
AND Gates: Multiple signal requirement systems
NOT Gates: Inhibitory regulatory mechanisms
Feedback Loops: Positive and negative feedback systems
State Machines: Developmental and cell cycle processes
Decision Trees: Immune response and adaptation systems

Data Quality

Baseline: Pattern audit table (avoids double-counting)
Scope: Only processes in batch files (not articles/index pages)
Deduplication: Removes duplicates from Hugging Face articles
Anchors: Direct links to specific processes within HTML files

Quick Access to Audit Table

For Reviewers and Researchers

📊 Dataset Viewer - Interactive, sortable table with all 732 processes
Direct CSV Access: pattern_audit_table.csv

How to Use the Dataset Viewer

Click the "Dataset Viewer" link above
The interactive table will load automatically (if not, click the "Dataset" tab)
Use the built-in sorting and filtering to navigate the data
Click on flowchart_link column to view Mermaid flowcharts
Examine flowcharts for computational patterns (OR Gates, AND Gates, NOT Gates, Feedback Loops, State Machines, Decision Trees)
Use the boolean columns (or_gates, and_gates, etc.) to track pattern analysis

Alternative Access

Direct CSV Download: Click the CSV link above to download and open in Excel/Google Sheets
Individual Process Links: All 732 processes have direct links to their flowcharts

Usage

This dataset is designed for:

Computational biology research
Pattern analysis in biological systems
Educational purposes
Reproducible research verification

Citation

If you use this dataset, please cite:Welz, G. (2025). Process Visualization in Biology: A Programming Framework for Systematic Analysis of Complex Systems. [Journal TBD]

Contact

For questions about this dataset, contact: [email protected]

Related Resources

Interactive Space: https://huggingface.co/spaces/garywelz/glmp
Source Code: https://github.com/garywelz/glmp
Paper: Process Visualization in Biology: A Programming Framework for Systematic Analysis of Complex Systems

Downloads last month: 223

Size of downloaded dataset files:

142 kB

Size of the auto-converted Parquet files:

25.3 kB

Number of rows:

732