Commit History
-
Rebuild content: remove obsolete flowcharts, add research arc, live-fetch counts
Gary Welz +1: Claude Sonnet 5Targeted content changes, approved by Gary, not a ground-up rebuild: - Removed "Browse and explore" (E. coli/Yeast batch circuits, Foundation Document) entirely -- 63 files deleted outright, not archived. Inbound-link check first: zero external references anywhere (GitHub repo, Zenodo markdown + deposited PDF, collaborations/), confirmed before deleting. - Added "The research arc" section: the five current papers (paper-I/II/III, synthesis-biorxiv, methods-mermaid-perturbation-design) as a linked sequence with one-line descriptions. Methods entry notes the separate, frozen, DOI-cited Zenodo version (10.5281/zenodo.20831780, v1.6) alongside the actively-revised GitHub draft -- they're different files, not a duplicate link. - Added a neutral-text link to the shared circuit-diagrams doc (no longer named after the reviewer in the link text). - Added the 217-process catalog link with an explicit caveat: the Circuit Class (I-V) stratification is known to be partly wrong …85e2a0e
-
Upload 2 files
Verified signaturee1561b1 -
Rename processes/yeast/yeast_index_updated.html to processes/yeast/yeast_index.html
Verified signaturef4dc5f9 -
Delete processes/yeast/yeast_index.html
Verified signature8a75673 -
Upload yeast_index_updated.html
Verified signature4f6007c -
Upload 2 files
Verified signaturec553b1f -
Upload yeast_batch06_chromatin_transcription.html
Verified signaturec03863c -
Delete processes/yeast/yeast_batch03_protein_synthesis.html
Verified signature87a8359 -
Delete processes/yeast/yeast_batch04_metabolic_pathways.html
Verified signature91d1f8b -
Upload yeast_batch34_metabolic_pathways.html
Verified signature0fae9cf -
Upload yeast_batch05_cell_division.html
Verified signature9b09966
-
Upload yeast_batch04_metabolic_pathways.html
Verified signature2931108 -
Upload 2 files
Verified signature0b07b1b -
Upload 2 files
Verified signature99a8d60 -
Upload 3 files
Verified signature3f321f0 -
Upload 3 files
Verified signature161e821
-
Delete processes/yeast/yeast_batch23_synthetic_biology.html
Verified signature58d408c -
Delete processes/yeast/yeast_batch22_metabolic_engineering.html
Verified signature5db29bd -
Delete processes/yeast/yeast_batch21_epigenetic_regulation.html
Verified signature76ab02d -
Delete processes/yeast/yeast_batch20_aging_senescence.html
Verified signature08c612f -
Delete processes/yeast/yeast_batch19_stress_response.html
Verified signature6c8df1a -
Delete processes/yeast/yeast_batch18_developmental_biology.html
Verified signature372a7d4 -
Delete processes/yeast/yeast_batch17_cell_communication.html
Verified signature444b5fb -
Delete processes/yeast/index.html
Verified signaturea47ecb5 -
Delete processes/yeast/yeast_batch15_quality_control_systems.html
Verified signature404cde0 -
Delete processes/yeast/yeast_batch14_developmental_processes.html
Verified signaturead87ab6 -
Delete processes/yeast/yeast_batch13_environmental_adaptation.html
Verified signature8408d93 -
Delete processes/yeast/yeast_batch12_advanced_regulatory_networks.html
Verified signature4c06273 -
Delete processes/yeast/yeast_batch10_stress_response_adaptation.html
Verified signature9cf0ab4 -
Delete processes/yeast/yeast_batch09_rna_processing_transport.html
Verified signature22f63d3 -
Delete processes/yeast/yeast_batch08_chromatin_transcription.html
Verified signature48fac79 -
Delete processes/yeast/yeast_batch07_cell_wall_extracellular.html
Verified signature419e0e8 -
Delete processes/yeast/yeast_batch06_lipid_membrane_biology.html
Verified signatureba2c30e -
Delete processes/yeast/yeast_batch05_energy_metabolism.html
Verified signature84c3e89 -
Delete processes/yeast/yeast_batch01_dna_replication_repair_UPDATE.html
Verified signature174761c -
Upload 34 files
Verified signatureb603015 -
Delete processes/ecoli/ecoli_batch21_iron_homeostasis.html
Verified signature455b0a8 -
Delete processes/ecoli/index.html
Verified signature3270490 -
Delete processes/ecoli/ecoli_simple_index.html
Verified signature11cf6de -
Delete processes/ecoli/ecoli_batch20_motility_chemotaxis.html
Verified signature6dbc3ef -
Delete processes/ecoli/ecoli_batch19_transport_membrane.html
Verified signature4f15e5e -
Delete processes/ecoli/ecoli_batch18_stress_response.html
Verified signature3b3784f -
Delete processes/ecoli/ecoli_batch17_central_metabolism.html
Verified signature1512b33 -
Delete processes/ecoli/ecoli_batch16_protein_synthesis_quality.html
Verified signature37187d4 -
Delete processes/ecoli/ecoli_batch15_translation_protein_synthesis.html
Verified signature3123cd5 -
Delete processes/ecoli/ecoli_batch14_transcription_regulation.html
Verified signaturec54868b -
Delete processes/ecoli/ecoli_batch13_specialized_metabolism.html
Verified signaturec9a9251 -
Delete processes/ecoli/ecoli_batch12_environmental_adaptation.html
Verified signature8d7222e -
Delete processes/ecoli/ecoli_batch11_phage_defense.html
Verified signature73d5eb5 -
Delete processes/ecoli/ecoli_batch15_quorum_sensing.html
Verified signature5220a44