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Fix API response handling: extract molecules/proteins arrays from wrapped response
yassinekolsi550eaf1 -
Fix Next.js 16 build: disable cacheComponents, add force-dynamic to all API routes and pages with server fetches
yassinekolsia3ea1a9 -
Add NEXT_PUBLIC_API_URL env pointing to HF Space backend
yassinekolsi54470b5 -
Fix all TypeScript errors: remove unused imports, delete orphan reactflow components
yassinekolsi532554f -
Fix explorer service argument mismatch and hardcoded URL, duplicate param type fixes
yassinekolsi9a9542b -
Fix Next.js 15 breaking change: await params in API routes
yassinekolsi804dcb2 -
Add vercel.json for Next.js deployment
yassinekolsie84bd01
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fix: PR review fixes - dockerfile, encoders, orchestrator, paths
yassinekolsi- dockerfile: use conda run for pip installs, remove hardcoded proxy, add COPY, fix ENV PATH syntax - orchestrator: remove duplicate Optional import, fix retriever API (modality param), safe getattr - encoders: batch_encode honors pooling setting in protein/text encoders - qdrant_retriever: safe modality mapping for legacy values - plugins/__init__: replace print with logging - run_summary.json: convert absolute paths to relative (5 files) - BIOFLOW_README: fix license badge (Apache->MIT) - USE_POLICY: fix spelling (sperate->separate) - model_customization.ipynb: fix config path - enhanced_search: sort by score after MMR, qdrant API fallback - UI: database filter state management, result display improvements5770d80
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Merge Rami into main-merge-rami (manual conflict resolution)
3c27eba -
Fix explorer/ingestion UI and 3D endpoints
673a52e -
feat: enhance visualization with mock data fallback and update readme
yassinekolsicd3cb84 -
fix: remove /dashboard prefix, fix theme toggle position, fix 3D viewer, remove langflow
yassinekolsif2bd2d1 -
feat: merge Rami's bioflow architecture with core-progress fixes
yassinekolsiMerged from origin/Rami: - Full bioflow/ package with agents, orchestrator, plugins - open_biomed/ integration for advanced models - Professional UI dashboard architecture - Docker support and batch scripts - Examples and workflow configs Kept from core-progress (our fixes): - Simplified theme toggle (single click, not dropdown) - 3Dmol viewer backgroundColor crash fix - Original server/api.py, config.py, ingest_qdrant.py - TECHNICAL_REPORT.md documentation - Original data/ and runs/ with prediction results - README.md Combined: Both DeepPurpose and OpenBioMed implementations2b2f173 -
feat: Complete Phase 4 UI/UX Polish with 3D visualization and workflow builder
ca41776
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fix: resolve 3Dmol viewer background color crash
yassinekolsia85e132 -
fix: restructure dashboard pages and fix 404 errors
yassinekolsidedd15b -
fix: move theme toggle to status section and reduce visualization spacing
yassinekolsi- Move theme toggle next to Status label in sidebar - Make theme toggle a simple click toggle (light/dark) - Add ThemeProvider wrapper for proper dark mode support - Reduce gap and padding in visualization pages (gap-4 p-4)10283cc -
feat: add complete visualization system from feat/raed-ui
RaedAddala +1: RaedAddala- Add dashboard layout with sidebar navigation - Add molecules 2D page with SMILES visualization (smiles-drawer) - Add molecules 3D page with 3Dmol.js viewer - Add proteins 3D page with PDB structure viewer - Add API routes for molecules and proteins (mock data) - Add scroll-area and alert UI components - Add theme toggle component - Update sidebar with visualization menu items - Update routes to use /dashboard prefix Co-authored-by: RaedAddala <raed.addala@example.com>af68ace -
Phase 1: FastAPI integration with DeepPurpose DTI predictor
- Added bioflow/api/ with FastAPI server (port 8000) - Integrated DeepPurposePredictor from deeppurpose002.py logic - Updated Next.js API routes to call FastAPI backend - Created launch_bioflow_full.bat for dual-server startup - Merged OpenBioMed core + lacoste001 Next.js UIadecc9b -
feat: add protein 2D/3D visualization components
- Add Smiles2DViewer for 2D molecule visualization using smiles-drawer - Add ProteinViewer for 3D protein visualization using 3Dmol.js - Add visualization-api.ts for fetching molecule/protein data - Add visualization-types.ts for type definitions - Install smiles-drawer and 3dmol dependencies Co-authored-by: RaedAddala <addala.raed@gmail.com>3a0ae3e -
fix: Replace batch runner with Python script and ensure Lucide icons usage
yassinekolsif5a9683 -
chore: restructure app into dashboard architecture; move routes, add dashboard layout, theme toggle, providers, and error handling
0f68a94 -
feat: add molecular and protein visualization dashboard
- Added 2D SMILES visualization using smiles-drawer - Added 3D Molecule visualization using 3Dmol.js - Added 3D Protein visualization using 3Dmol.js - Implemented mock API routes for molecules and proteins - Integrated visualization pages into the sidebar navigation - Added shadcn/ui ScrollArea and Alert components - Integrated PubChem and RCSB PDB data fetching20883f8 -
feat: Complete BioFlow Orchestrator hackathon implementation
yassinekolsiMajor Features: - Langflow visual workflow builder integration (embedded iframe) - Drug discovery search with real Qdrant vector search (23,531 vectors) - 3D embedding explorer with real PCA projections - FastAPI backend with DeepPurpose Morgan + CNN encoding Bug Fixes: - Fixed division by zero error (bypass data_process, direct Morgan encoding) - Fixed CUDA/CPU device mismatch (auto-detect from model parameters) - Fixed encoding dimension alignment for vector search UI Improvements: - Clean white design (removed dark gradients) - Real API calls only (no fake/mock data) - Simplified workflow page (removed hover effects, indicators) - Working search with Similarity/Binding Affinity/Properties modes Cleanup: - Removed INSTRUCTIONS.md, setup_venv.txt - Updated .gitignore for langflow_venv, data files - Added Langflow pipeline template Services: - Qdrant: 6333 - FastAPI: 8001 - Next.js: 3000 - Langflow: 7860a712e78 -
docs: Updated README
yassinekolside77cc2 -
improve sidebar (cherry-picked from feat/raed-ui)
680788a -
feat: Complete Qdrant pipeline with real PCA + cleanup
yassinekolsi- Ingestion pipeline: TDC KIBA dataset -> DeepPurpose embeddings -> Qdrant - API server on port 8001 with /health, /api/points, /api/search - Real sklearn PCA (not fake first-3-dims) - Fixed shuffle bug (preserve data ordering) - Fixed result_folder override for saved config.pkl - Cleaned up: deleted old/, .github/, added proper .gitignore - 23,531 drug-target pairs indexed with 3D projections7fb740b -
improve sidebar
85ba650 -
chore: integrate UI snapshot from raed-ui branch
yassinekolsic5474d5 -
Improve sidebar
eaf815d -
refactor
56d7f80 -
Improve UI and unify api, types and schemas
64e5c41 -
add loading and metadata to layout
1008099 -
Dashboard
cf1ba50 -
ui init
a9bbc87
