celltype-cli 0.1.0__py3-none-any.whl

ct/tools/experiment.py

@@ -0,0 +1,604 @@
+"""
+Experimental assay design tools: protocol templates, timeline estimation, and assay listing.
+
+Provides structured experimental protocols for TPD/molecular glue validation workflows,
+covering degradation, binding, viability, expression, structural, and screening assays.
+"""
+
+import math
+from ct.tools import registry
+
+
+# ---------------------------------------------------------------------------
+# Assay protocol templates (TPD / molecular-glue relevant)
+# ---------------------------------------------------------------------------
+
+ASSAY_TEMPLATES: dict[str, dict] = {
+    "hibit": {
+        "name": "HiBiT Degradation Assay",
+        "description": "Promega HiBiT lytic/kinetic assay measuring target protein degradation via split-NanoLuc luminescence",
+        "category": "degradation",
+        "protocol_steps": [
+            "Plate HiBiT-tagged cells in 384-well white plates (2000 cells/well)",
+            "Allow cells to adhere overnight (16-20 h)",
+            "Prepare compound serial dilutions in DMSO (typically 10-point, 3-fold)",
+            "Add compounds to plates using acoustic dispenser or pin tool",
+            "Incubate at 37C / 5% CO2 for desired timepoints (2h, 6h, 24h)",
+            "Add Nano-Glo HiBiT Lytic Reagent (1:1 v/v)",
+            "Incubate 10 min at room temperature on orbital shaker",
+            "Read luminescence on plate reader (integration time 0.5s)",
+            "Normalize to DMSO controls and calculate DC50/Dmax",
+        ],
+        "reagents": [
+            "HiBiT-tagged cell line (endogenous CRISPR knock-in preferred)",
+            "Nano-Glo HiBiT Lytic Detection System (Promega N3030)",
+            "384-well white plates (Corning 3570)",
+            "DMSO (cell-culture grade)",
+            "Complete growth medium",
+        ],
+        "controls": {
+            "positive": "Known degrader of target (or proteasome inhibitor MG132 as rescue)",
+            "negative": "DMSO vehicle control",
+        },
+        "readout": "Luminescence (RLU) proportional to target protein level",
+        "hands_on_hours": 3.0,
+        "calendar_days": 3,
+        "cost_per_plate": 800,
+    },
+    "nanobret": {
+        "name": "NanoBRET Ternary Complex Assay",
+        "description": "Measures proximity between E3 ligase and target protein via BRET energy transfer in live cells",
+        "category": "binding",
+        "protocol_steps": [
+            "Co-transfect HEK293 cells with NanoLuc-E3 and HaloTag-target constructs",
+            "Plate transfected cells into 384-well plates (8000 cells/well)",
+            "Allow 24 h for expression",
+            "Add HaloTag NanoBRET 618 Ligand (200 nM final)",
+            "Add test compounds in dose-response",
+            "Incubate 2-4 h at 37C",
+            "Add NanoBRET Nano-Glo Substrate",
+            "Read donor (460 nm) and acceptor (618 nm) emissions",
+            "Calculate milliBRET ratio: (618/460) x 1000",
+        ],
+        "reagents": [
+            "NanoLuc-E3 ligase fusion construct",
+            "HaloTag-target fusion construct",
+            "HaloTag NanoBRET 618 Ligand (Promega G9801)",
+            "NanoBRET Nano-Glo Substrate (Promega N1571)",
+            "Transfection reagent (FuGENE HD or Lipofectamine 3000)",
+        ],
+        "controls": {
+            "positive": "Known molecular glue or PROTAC forming ternary complex",
+            "negative": "DMSO + no-acceptor control (donor-only)",
+        },
+        "readout": "milliBRET ratio (higher = stronger ternary complex)",
+        "hands_on_hours": 5.0,
+        "calendar_days": 4,
+        "cost_per_plate": 1200,
+    },
+    "western_blot": {
+        "name": "Western Blot Degradation Confirmation",
+        "description": "Orthogonal confirmation of target protein degradation by immunoblotting",
+        "category": "degradation",
+        "protocol_steps": [
+            "Seed cells in 6-well plates (500K cells/well)",
+            "Treat with compound at multiple doses and timepoints",
+            "Include MG132 co-treatment to confirm proteasome dependence",
+            "Lyse cells in RIPA buffer with protease/phosphatase inhibitors",
+            "Quantify protein by BCA assay and normalize loading (20-30 ug)",
+            "Run SDS-PAGE (4-12% Bis-Tris gel)",
+            "Transfer to PVDF membrane (wet transfer, 100V 1h or semi-dry)",
+            "Block in 5% BSA/TBST 1h at RT",
+            "Probe with primary antibody overnight at 4C",
+            "Wash, secondary HRP antibody 1h at RT",
+            "Develop with ECL substrate and image",
+            "Quantify band intensity and normalize to loading control (vinculin/GAPDH)",
+        ],
+        "reagents": [
+            "Primary antibody against target protein",
+            "Anti-vinculin or anti-GAPDH loading control antibody",
+            "HRP-conjugated secondary antibodies",
+            "RIPA lysis buffer",
+            "Protease inhibitor cocktail",
+            "4-12% Bis-Tris SDS-PAGE gels (NuPAGE)",
+            "PVDF membrane",
+            "ECL substrate (SuperSignal West Pico/Femto)",
+        ],
+        "controls": {
+            "positive": "MG132 rescue (5 uM, 2h pre-treatment) to confirm UPS dependence",
+            "negative": "DMSO vehicle and untreated cells",
+        },
+        "readout": "Band intensity (densitometry) normalized to loading control",
+        "hands_on_hours": 8.0,
+        "calendar_days": 3,
+        "cost_per_plate": 200,
+    },
+    "qpcr": {
+        "name": "qPCR Transcript-Level Analysis",
+        "description": "RT-qPCR to confirm degradation is post-transcriptional (mRNA unchanged) or detect transcriptional effects",
+        "category": "expression",
+        "protocol_steps": [
+            "Treat cells with compound (same conditions as degradation assay)",
+            "Extract total RNA using RNeasy or TRIzol",
+            "Quantify RNA (NanoDrop) and check quality (A260/280 > 1.8)",
+            "Reverse-transcribe 1 ug RNA with oligo-dT primers",
+            "Design qPCR primers spanning exon-exon junctions",
+            "Set up qPCR reactions in 384-well plates (10 uL volume)",
+            "Run qPCR: 95C 10min, 40x(95C 15s, 60C 1min), melt curve",
+            "Analyze by delta-delta-Ct method normalized to housekeeping genes",
+        ],
+        "reagents": [
+            "RNA extraction kit (Qiagen RNeasy or TRIzol)",
+            "Reverse transcription kit (SuperScript IV or High-Capacity cDNA)",
+            "SYBR Green or TaqMan master mix",
+            "Target-specific primers (2 sets for redundancy)",
+            "Housekeeping gene primers (GAPDH, ACTB, HPRT1)",
+            "384-well qPCR plates",
+        ],
+        "controls": {
+            "positive": "Known transcriptional modulator (e.g., actinomycin D for mRNA stability)",
+            "negative": "DMSO vehicle; no-RT control for genomic DNA contamination",
+        },
+        "readout": "Relative mRNA expression (fold change vs DMSO)",
+        "hands_on_hours": 6.0,
+        "calendar_days": 2,
+        "cost_per_plate": 300,
+    },
+    "ctg_viability": {
+        "name": "CellTiter-Glo Cell Viability",
+        "description": "ATP-based luminescent cell viability assay for dose-response curves and IC50 determination",
+        "category": "viability",
+        "protocol_steps": [
+            "Plate cells in 384-well white plates (500-2000 cells/well depending on growth rate)",
+            "Allow overnight adherence",
+            "Add compounds in dose-response (10-point, 3-fold dilution, 10 uM top dose)",
+            "Incubate 72 h at 37C / 5% CO2",
+            "Equilibrate plates to room temperature (30 min)",
+            "Add CellTiter-Glo reagent (1:1 v/v)",
+            "Shake 2 min, incubate 10 min at RT",
+            "Read luminescence",
+            "Fit 4-parameter logistic curve to calculate IC50",
+        ],
+        "reagents": [
+            "CellTiter-Glo 2.0 (Promega G9241)",
+            "384-well white plates",
+            "Complete growth medium",
+            "DMSO (cell-culture grade)",
+        ],
+        "controls": {
+            "positive": "Staurosporine (1 uM) or bortezomib as cytotoxic control",
+            "negative": "DMSO vehicle control",
+        },
+        "readout": "Luminescence (RLU) proportional to ATP/viable cells; IC50 from curve fit",
+        "hands_on_hours": 2.0,
+        "calendar_days": 4,
+        "cost_per_plate": 500,
+    },
+    "flow_cytometry": {
+        "name": "Flow Cytometry",
+        "description": "Multi-parameter flow cytometry for surface marker expression, cell death (Annexin V/PI), and cell cycle analysis",
+        "category": "viability",
+        "protocol_steps": [
+            "Treat cells with compound at chosen doses/timepoints",
+            "Harvest cells (trypsinize adherent or collect suspension)",
+            "Wash 2x with cold PBS",
+            "For surface markers: stain with fluorochrome-conjugated antibodies (30 min, 4C, dark)",
+            "For apoptosis: stain with Annexin V-FITC and PI per kit protocol",
+            "For cell cycle: fix in 70% ethanol, stain with PI/RNase A",
+            "Acquire on flow cytometer (minimum 10,000 events/sample)",
+            "Analyze with FlowJo or similar software",
+            "Gate on singlets, then live cells, then markers of interest",
+        ],
+        "reagents": [
+            "Fluorochrome-conjugated antibodies for markers of interest",
+            "Annexin V-FITC/PI Apoptosis Kit",
+            "Propidium iodide + RNase A (for cell cycle)",
+            "FACS buffer (PBS + 2% FBS + 0.1% NaN3)",
+            "70% ethanol (cell-cycle fixation)",
+            "CompBeads for compensation",
+        ],
+        "controls": {
+            "positive": "Staurosporine (apoptosis) or nocodazole (G2/M arrest)",
+            "negative": "DMSO vehicle; unstained and single-stain compensation controls",
+        },
+        "readout": "Percentage of cells in each population (live, apoptotic, necrotic; cell cycle phase)",
+        "hands_on_hours": 6.0,
+        "calendar_days": 2,
+        "cost_per_plate": 400,
+    },
+    "tr_fret": {
+        "name": "TR-FRET Binding Assay",
+        "description": "Time-resolved FRET assay for measuring binary binding (compound-protein) or ternary complex formation",
+        "category": "binding",
+        "protocol_steps": [
+            "Prepare assay buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 0.01% Tween-20, 0.1% BSA)",
+            "Dispense DMSO/compound into 384-well low-volume plates",
+            "Add Eu-labeled donor protein (e.g., Eu-anti-His for His-tagged E3)",
+            "Add AF647-labeled acceptor protein (e.g., AF647-target)",
+            "For ternary complex: add both proteins + compound simultaneously",
+            "Incubate 1-2 h at room temperature",
+            "Read TR-FRET: excite 320 nm, read 665/620 nm ratio",
+            "Calculate FRET ratio and fit dose-response",
+        ],
+        "reagents": [
+            "Europium-labeled donor (anti-tag antibody or direct protein label)",
+            "AlexaFluor647-labeled acceptor protein",
+            "Purified recombinant proteins (E3 ligase, target)",
+            "384-well low-volume black plates (Corning 4514)",
+            "Assay buffer components",
+        ],
+        "controls": {
+            "positive": "Known binder at saturating concentration",
+            "negative": "DMSO vehicle; protein-only (no compound) for baseline FRET",
+        },
+        "readout": "FRET ratio (665 nm / 620 nm); EC50 from dose-response",
+        "hands_on_hours": 4.0,
+        "calendar_days": 1,
+        "cost_per_plate": 600,
+    },
+    "alphalisa": {
+        "name": "AlphaLISA Protein-Protein Interaction",
+        "description": "Bead-based proximity assay for detecting protein-protein interactions and ternary complex formation",
+        "category": "binding",
+        "protocol_steps": [
+            "Prepare assay buffer (25 mM HEPES pH 7.4, 100 mM NaCl, 0.1% BSA, 0.01% Tween-20)",
+            "Dispense compounds into 384-well AlphaPlates",
+            "Add biotinylated protein 1 and His-tagged protein 2",
+            "Incubate 1 h at room temperature",
+            "Add Anti-His AlphaLISA Acceptor beads (10 ug/mL final)",
+            "Incubate 1 h at room temperature",
+            "Add Streptavidin Donor beads (40 ug/mL final) in subdued light",
+            "Incubate 1 h at room temperature in dark",
+            "Read on Alpha-compatible reader (EnVision or CLARIOstar)",
+        ],
+        "reagents": [
+            "Biotinylated protein 1",
+            "His-tagged protein 2",
+            "Anti-His AlphaLISA Acceptor beads (PerkinElmer AL128)",
+            "Streptavidin Alpha Donor beads (PerkinElmer 6760002)",
+            "384-well AlphaPlates (PerkinElmer 6005350)",
+            "Assay buffer components",
+        ],
+        "controls": {
+            "positive": "Known PPI stabilizer or molecular glue at saturating concentration",
+            "negative": "DMSO vehicle; beads-only (no protein) for background",
+        },
+        "readout": "Alpha signal (counts); EC50 from dose-response curve",
+        "hands_on_hours": 4.0,
+        "calendar_days": 1,
+        "cost_per_plate": 900,
+    },
+    "dsf": {
+        "name": "Differential Scanning Fluorimetry (Thermal Shift)",
+        "description": "Measures compound-induced thermal stabilization of target protein as evidence of direct binding",
+        "category": "structural",
+        "protocol_steps": [
+            "Prepare protein at 2-5 uM in assay buffer (PBS or HEPES-based, low detergent)",
+            "Add SYPRO Orange dye (5x final concentration)",
+            "Dispense 18 uL protein/dye mix into 384-well PCR plates",
+            "Add 2 uL compound (10x stock) or DMSO control",
+            "Seal plates with optical adhesive film",
+            "Run thermal ramp on qPCR instrument: 25C to 95C at 1C/min",
+            "Monitor SYPRO Orange fluorescence (Ex 470, Em 570)",
+            "Determine Tm by fitting Boltzmann sigmoid to melt curves",
+            "Calculate delta-Tm = Tm(compound) - Tm(DMSO)",
+        ],
+        "reagents": [
+            "Purified recombinant target protein (>90% purity)",
+            "SYPRO Orange Protein Gel Stain (Invitrogen S6650)",
+            "384-well PCR plates (optically clear)",
+            "Optical adhesive film",
+            "Assay buffer (PBS or 50 mM HEPES, 150 mM NaCl, pH 7.5)",
+        ],
+        "controls": {
+            "positive": "Known ligand that shifts Tm by >2C",
+            "negative": "DMSO vehicle (matched % DMSO); protein-only for intrinsic Tm",
+        },
+        "readout": "Melting temperature (Tm) shift in degrees C; delta-Tm > 2C suggests binding",
+        "hands_on_hours": 3.0,
+        "calendar_days": 1,
+        "cost_per_plate": 150,
+    },
+    "spr": {
+        "name": "Surface Plasmon Resonance (SPR)",
+        "description": "Label-free real-time binding kinetics: measures ka, kd, and KD for compound-protein interactions",
+        "category": "structural",
+        "protocol_steps": [
+            "Immobilize target protein on CM5 sensor chip via amine coupling",
+            "Inject EDC/NHS to activate surface, then protein (10-50 ug/mL in acetate pH 4.0-5.5)",
+            "Block remaining sites with ethanolamine",
+            "Prepare compound dilution series in running buffer (+ matched DMSO%)",
+            "Inject compound at multiple concentrations (single-cycle or multi-cycle kinetics)",
+            "Monitor association (120-180 s) and dissociation (300-600 s)",
+            "Regenerate surface between cycles if needed (10 mM glycine pH 2.0)",
+            "Fit sensorgrams to 1:1 Langmuir model to extract ka, kd, KD",
+            "Perform solvent correction for DMSO bulk effects",
+        ],
+        "reagents": [
+            "CM5 sensor chip (Cytiva BR100530)",
+            "Amine Coupling Kit (Cytiva BR100050)",
+            "Purified target protein (>95% purity, activity confirmed)",
+            "Running buffer (HBS-EP+: 10 mM HEPES, 150 mM NaCl, 3 mM EDTA, 0.05% P20)",
+            "Regeneration buffer (10 mM glycine-HCl pH 2.0)",
+        ],
+        "controls": {
+            "positive": "Known binder with published KD for assay validation",
+            "negative": "Reference channel (no protein) for bulk refractive index subtraction",
+        },
+        "readout": "Binding kinetics: ka (1/Ms), kd (1/s), KD (M); steady-state affinity if kinetics too fast",
+        "hands_on_hours": 8.0,
+        "calendar_days": 2,
+        "cost_per_plate": 2000,
+    },
+    "tmt_proteomics": {
+        "name": "TMT Multiplexed Proteomics",
+        "description": "Global proteomics by TMT labeling and LC-MS/MS to profile degradation selectivity across the proteome",
+        "category": "screening",
+        "protocol_steps": [
+            "Treat cells (1-5 million per condition) with compound vs DMSO (3+ replicates)",
+            "Lyse in 8M urea / 50 mM TEAB buffer",
+            "Reduce (TCEP 10 mM, 30 min 37C) and alkylate (IAA 20 mM, 30 min RT dark)",
+            "Digest with trypsin (1:50 enzyme:protein, overnight 37C)",
+            "Desalt on C18 Sep-Pak cartridges",
+            "Label peptides with TMT reagents (TMT-16plex or TMT-18plex)",
+            "Combine labeled samples, desalt, and fractionate by high-pH reversed-phase (8-12 fractions)",
+            "Analyze each fraction by nanoLC-MS/MS (2h gradient, Orbitrap or timsTOF)",
+            "Search with MaxQuant or Proteome Discoverer",
+            "Filter: 1% FDR at peptide and protein level",
+            "Statistical analysis: limma or MSstats for differential abundance",
+        ],
+        "reagents": [
+            "TMT-16plex or TMT-18plex reagent kit (Thermo A44520 / A52045)",
+            "Trypsin (sequencing grade, Promega V5111)",
+            "TCEP and iodoacetamide",
+            "C18 Sep-Pak cartridges (Waters WAT054955)",
+            "High-pH reversed-phase fractionation kit",
+            "nanoLC-MS/MS instrument access (Orbitrap Exploris/Eclipse or timsTOF)",
+        ],
+        "controls": {
+            "positive": "Include known degrader condition as positive control channel",
+            "negative": "DMSO vehicle (3+ replicates for statistical power)",
+        },
+        "readout": "Log2 fold-change per protein (compound vs DMSO); volcano plot of selectivity",
+        "hands_on_hours": 20.0,
+        "calendar_days": 14,
+        "cost_per_plate": 5000,
+    },
+    "crispr_screen": {
+        "name": "Genome-Wide CRISPR Screen",
+        "description": "Pooled CRISPR knockout screen to identify genetic dependencies and resistance/sensitization mechanisms",
+        "category": "screening",
+        "protocol_steps": [
+            "Expand cells to sufficient scale (500-1000x library coverage, e.g., 100M cells for 100K library)",
+            "Transduce with lentiviral sgRNA library at MOI 0.3",
+            "Select with puromycin (2-4 ug/mL) for 48-72 h",
+            "Confirm >30% transduction by flow cytometry (if GFP reporter)",
+            "Split into treatment arms: compound vs DMSO (maintain 500x coverage)",
+            "Treat for 14-21 days (passage every 3 days, re-dose compound)",
+            "Harvest cells, extract genomic DNA",
+            "PCR-amplify sgRNA cassettes with indexed primers",
+            "Sequence on NextSeq/NovaSeq (aim for 500 reads per sgRNA)",
+            "Analyze with MAGeCK or CRISPR-CASA to identify depleted/enriched genes",
+        ],
+        "reagents": [
+            "Lentiviral sgRNA library (Brunello, TKOv3, or custom focused library)",
+            "Puromycin selection antibiotic",
+            "Genomic DNA extraction kit (Qiagen Blood & Cell Culture DNA Midi)",
+            "PCR primers for sgRNA amplification (library-specific)",
+            "NextSeq/NovaSeq sequencing access",
+            "MAGeCK software for analysis",
+        ],
+        "controls": {
+            "positive": "Essential gene sgRNAs should deplete (e.g., core essential gene list from Hart et al.)",
+            "negative": "Non-targeting sgRNAs and DMSO-treated arm for baseline",
+        },
+        "readout": "Gene-level enrichment/depletion scores; beta scores from MAGeCK-MLE",
+        "hands_on_hours": 40.0,
+        "calendar_days": 35,
+        "cost_per_plate": 15000,
+    },
+}
+
+
+# ---------------------------------------------------------------------------
+# Tools
+# ---------------------------------------------------------------------------
+
+
+@registry.register(
+    name="experiment.list_assays",
+    description="List all available experimental assay templates with name, description, and category",
+    category="experiment",
+    parameters={},
+    usage_guide="You want to see all available experimental assay types before designing a specific protocol.",
+)
+def list_assays(**kwargs) -> dict:
+    """Return a catalogue of all available assay templates."""
+    assays = []
+    for key, tmpl in ASSAY_TEMPLATES.items():
+        assays.append({
+            "assay_type": key,
+            "name": tmpl["name"],
+            "description": tmpl["description"],
+            "category": tmpl["category"],
+        })
+
+    by_category: dict[str, list[str]] = {}
+    for a in assays:
+        by_category.setdefault(a["category"], []).append(a["assay_type"])
+
+    cat_summary = "; ".join(f"{cat}: {', '.join(types)}" for cat, types in sorted(by_category.items()))
+
+    return {
+        "summary": f"{len(assays)} assay templates available across {len(by_category)} categories. {cat_summary}",
+        "assays": assays,
+        "categories": by_category,
+    }
+
+
+@registry.register(
+    name="experiment.design_assay",
+    description="Design a detailed experimental protocol for a specific assay type, customized with target/compound/cell line information",
+    category="experiment",
+    parameters={
+        "assay_type": "Assay template key (e.g. 'hibit', 'nanobret', 'tmt_proteomics')",
+        "target": "Target protein or gene name",
+        "compound": "Compound name or identifier",
+        "cell_line": "Cell line to use",
+        "goal": "Specific experimental goal or question",
+    },
+    usage_guide="You need to design an experimental protocol for validating a computational finding. Use before experiment.estimate_timeline and cro.match_experiment.",
+)
+def design_assay(
+    assay_type: str,
+    target: str = None,
+    compound: str = None,
+    cell_line: str = None,
+    goal: str = None,
+    **kwargs,
+) -> dict:
+    """Design a customized experimental protocol from a template."""
+    if assay_type not in ASSAY_TEMPLATES:
+        available = ", ".join(sorted(ASSAY_TEMPLATES.keys()))
+        return {"error": f"Unknown assay type '{assay_type}'. Available: {available}", "summary": f"Unknown assay type '{assay_type}'. Available: {available}"}
+    tmpl = ASSAY_TEMPLATES[assay_type]
+
+    # Customize protocol steps with target/compound/cell_line info
+    customized_steps = []
+    for step in tmpl["protocol_steps"]:
+        s = step
+        if target:
+            s = s.replace("target protein", f"{target} protein")
+            s = s.replace("target gene", f"{target} gene")
+        if compound:
+            s = s.replace("compound", compound).replace("test compounds", compound)
+        if cell_line:
+            s = s.replace("cells", f"{cell_line} cells").replace("Plate cells", f"Plate {cell_line} cells")
+        customized_steps.append(s)
+
+    # Build customized controls
+    controls = dict(tmpl["controls"])
+    if target:
+        controls["positive"] = controls["positive"].replace("target", target)
+    if compound:
+        controls["negative"] = controls["negative"].replace("compound", compound)
+
+    # Build context string
+    context_parts = []
+    if target:
+        context_parts.append(f"target={target}")
+    if compound:
+        context_parts.append(f"compound={compound}")
+    if cell_line:
+        context_parts.append(f"cell_line={cell_line}")
+    if goal:
+        context_parts.append(f"goal={goal}")
+    context_str = ", ".join(context_parts) if context_parts else "generic protocol"
+
+    # Assemble protocol
+    protocol = {
+        "assay_type": assay_type,
+        "name": tmpl["name"],
+        "description": tmpl["description"],
+        "category": tmpl["category"],
+        "context": context_str,
+        "protocol_steps": customized_steps,
+        "reagents": list(tmpl["reagents"]),
+        "controls": controls,
+        "readout": tmpl["readout"],
+        "estimated_hands_on_hours": tmpl["hands_on_hours"],
+        "estimated_calendar_days": tmpl["calendar_days"],
+        "estimated_cost_per_plate": tmpl["cost_per_plate"],
+    }
+
+    if goal:
+        protocol["experimental_goal"] = goal
+
+    summary_parts = [f"Designed {tmpl['name']} protocol"]
+    if target:
+        summary_parts.append(f"for {target}")
+    if compound:
+        summary_parts.append(f"with {compound}")
+    if cell_line:
+        summary_parts.append(f"in {cell_line}")
+    summary_parts.append(
+        f"({len(customized_steps)} steps, ~{tmpl['hands_on_hours']}h hands-on, "
+        f"{tmpl['calendar_days']} calendar days, ~${tmpl['cost_per_plate']}/plate)"
+    )
+
+    return {
+        "summary": ". ".join(summary_parts),
+        "protocol": protocol,
+    }
+
+
+@registry.register(
+    name="experiment.estimate_timeline",
+    description="Estimate hands-on time, calendar time, and cost for an experiment scaled by number of compounds, replicates, and doses",
+    category="experiment",
+    parameters={
+        "assay_type": "Assay template key (e.g. 'hibit', 'ctg_viability')",
+        "n_compounds": "Number of compounds to test",
+        "n_replicates": "Number of biological replicates",
+        "n_doses": "Number of dose points per compound",
+    },
+    usage_guide="You need to estimate how long an experiment will take and how much it will cost. Use after experiment.design_assay.",
+)
+def estimate_timeline(
+    assay_type: str,
+    n_compounds: int = 1,
+    n_replicates: int = 3,
+    n_doses: int = 8,
+    **kwargs,
+) -> dict:
+    """Estimate timeline and cost scaled by experimental parameters."""
+    if assay_type not in ASSAY_TEMPLATES:
+        available = ", ".join(sorted(ASSAY_TEMPLATES.keys()))
+        return {"error": f"Unknown assay type '{assay_type}'. Available: {available}", "summary": f"Unknown assay type '{assay_type}'. Available: {available}"}
+    tmpl = ASSAY_TEMPLATES[assay_type]
+
+    # Calculate number of wells needed
+    # Each compound x dose x replicate = 1 well, plus controls (~10% overhead)
+    wells_per_compound = n_doses * n_replicates
+    total_wells = n_compounds * wells_per_compound
+    control_wells = max(16, int(total_wells * 0.1))  # at least 16 control wells
+    total_wells_with_controls = total_wells + control_wells
+
+    # Number of 384-well plates needed
+    wells_per_plate = 384
+    n_plates = math.ceil(total_wells_with_controls / wells_per_plate)
+
+    # Scale hands-on time: base time per plate, with efficiency gains for batching
+    base_hours = tmpl["hands_on_hours"]
+    # First plate takes full time, each additional plate adds ~60% of base
+    hands_on_hours = base_hours + max(0, n_plates - 1) * base_hours * 0.6
+    hands_on_days = round(hands_on_hours / 8.0, 1)
+
+    # Calendar days: base + extra days for additional plates (batching helps)
+    base_cal_days = tmpl["calendar_days"]
+    extra_plate_days = max(0, math.ceil((n_plates - 1) / 4))  # ~4 plates per batch
+    calendar_days = base_cal_days + extra_plate_days
+
+    # Cost
+    total_cost = n_plates * tmpl["cost_per_plate"]
+
+    return {
+        "summary": (
+            f"{tmpl['name']}: {n_compounds} compounds x {n_doses} doses x {n_replicates} replicates = "
+            f"{total_wells_with_controls} wells ({n_plates} plates). "
+            f"Estimated {hands_on_hours:.1f}h hands-on ({hands_on_days} days), "
+            f"{calendar_days} calendar days, ~${total_cost:,}"
+        ),
+        "assay_type": assay_type,
+        "assay_name": tmpl["name"],
+        "n_compounds": n_compounds,
+        "n_doses": n_doses,
+        "n_replicates": n_replicates,
+        "total_wells": total_wells_with_controls,
+        "n_plates": n_plates,
+        "hands_on_hours": round(hands_on_hours, 1),
+        "hands_on_days": hands_on_days,
+        "calendar_days": calendar_days,
+        "estimated_cost": total_cost,
+        "cost_per_plate": tmpl["cost_per_plate"],
+    }