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.claude
.claude
 
 
.github/workflows
.github/workflows
 
 
.vscode
.vscode
 
 
GAgent_backup_20260421_233939/figures
GAgent_backup_20260421_233939/figures
 
 
app
app
 
 
data/databases/temp
data/databases/temp
 
 
docker
docker
 
 
docs
docs
 
 
execute_memory
execute_memory
 
 
interaction_matrix_analysis
interaction_matrix_analysis
 
 
manuscript
manuscript
 
 
output
output
 
 
phagescope_analysis
phagescope_analysis
 
 
reference
reference
 
 
scripts
scripts
 
 
skills
skills
 
 
tool_box
tool_box
 
 
web-ui
web-ui
 
 
.dockerignore
.dockerignore
 
 
.gitignore
.gitignore
 
 
.pybiomart.sqlite
.pybiomart.sqlite
 
 
AGENTS.md
AGENTS.md
 
 
CLAUDE.md
CLAUDE.md
 
 
PHI_OT_Research_Plan.md
PHI_OT_Research_Plan.md
 
 
PHI_OT_Research_Plan_v2.md
PHI_OT_Research_Plan_v2.md
 
 
PHI_OT_Research_Plan_v3.md
PHI_OT_Research_Plan_v3.md
 
 
PHI_OT_Research_Plan_v3.md.analysis.md
PHI_OT_Research_Plan_v3.md.analysis.md
 
 
Research_Protocol_Patient_Experience.md
Research_Protocol_Patient_Experience.md
 
 
backend_startup.log
backend_startup.log
 
 
bio_tool_list.md
bio_tool_list.md
 
 
bio_tools_test_matrix.json
bio_tools_test_matrix.json
 
 
cell_communication_methods.txt
cell_communication_methods.txt
 
 
human_gut_phage_arms_race_research_project.md
human_gut_phage_arms_race_research_project.md
 
 
ovarian_cancer_scrna_qc_pipeline.py
ovarian_cancer_scrna_qc_pipeline.py
 
 
package-lock.json
package-lock.json
 
 
package.json
package.json
 
 
phage_bacteria_interaction_matrix_research_outline.md
phage_bacteria_interaction_matrix_research_outline.md
 
 
phage_bacteria_interaction_matrix_research_plan.md
phage_bacteria_interaction_matrix_research_plan.md
 
 
phage_diversity_research_outline.md
phage_diversity_research_outline.md
 
 
phage_genomic_diversity_research_protocol.md
phage_genomic_diversity_research_protocol.md
 
 
phage_host_interaction_literature_analysis.md
phage_host_interaction_literature_analysis.md
 
 
pytest.ini
pytest.ini
 
 
requirements.txt
requirements.txt
 
 
research_proposal_biology_driven.md
research_proposal_biology_driven.md
 
 
research_topic3_restructured_proposal.md
research_topic3_restructured_proposal.md
 
 
start_backend.sh
start_backend.sh
 
 
task
task
 
 
task10_data_suitability_assessment.md
task10_data_suitability_assessment.md
 
 
tasks.db
tasks.db
 
 
todo.md
todo.md
 
 
update_tools.sh
update_tools.sh
 
 

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