Merging latest from JimHokanson's repo#1
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slarson merged 4 commits intoopenworm:masterfrom Sep 26, 2013
JimHokanson:master
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Merging latest from JimHokanson's repo#1slarson merged 4 commits intoopenworm:masterfrom JimHokanson:master
slarson merged 4 commits intoopenworm:masterfrom
JimHokanson:master
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slarson
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Merging latest from JimHokanson's repo
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Update mkdocs.yml - use github.repository_owner
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DD017's foundation model → ODE parameter pipeline (Component 3) had no infrastructure dependencies and derisks DD005's uncertain expression→ conductance mapping. BioEmu-1's 100,000x MD speedup invalidated the original "computationally expensive" rejection. Extracted into standalone DD025 (Protein Foundation Model Pipeline) scheduled as Phase A parallel track with Phase 1 integration into DD005 calibration. Files changed: - NEW: DD025_Protein_Foundation_Model_Pipeline.md - DD017: Component 3 section replaced with redirect to DD025 - DD005: Alternative #1 promoted, roadmap/issues updated with DD025 refs - DD001: Cross-reference updated from DD017 Component 3 to DD025 - DD_PHASE_ROADMAP: DD025 added to Phase A scope/deliverables/datasets, Phase 1 scope, FAQ, dependency summary, timeline (+7 DDs) - index.md: DD025 added, count updated to 26 - references.md: BioEmu-1 and Boltz-2 entries added, DD025 cross-refs - mkdocs.yml: DD025 nav entry under Infrastructure Bootstrap Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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