diff --git a/benchmarks/frontierchallenge/site/DEPLOYMENT.md b/benchmarks/frontierchallenge/site/DEPLOYMENT.md new file mode 100644 index 0000000..205b20a --- /dev/null +++ b/benchmarks/frontierchallenge/site/DEPLOYMENT.md @@ -0,0 +1,8 @@ +# FrontierChallenge website deployment + +- Canonical URL: https://apodexai.github.io/FrontierAgent/benchmarks/FrontierChallenge/ +- Published source: `benchmarks/frontierchallenge/site/` in `ApodexAI/FrontierAgent` +- GitHub Pages workflow: `.github/workflows/frontierchallenge-pages.yml` +- Deployment branch: `main` + +The former standalone `ApodexAI/FrontierChallenge-site` repository is not the deployment target. diff --git a/benchmarks/frontierchallenge/site/case-calorimetry.html b/benchmarks/frontierchallenge/site/case-calorimetry.html index c3c23c1..b39edf0 100644 --- a/benchmarks/frontierchallenge/site/case-calorimetry.html +++ b/benchmarks/frontierchallenge/site/case-calorimetry.html @@ -1 +1 @@ -Reaction calorimetry safety — FrontierChallenge
← All selected cases

Process chemistry · Hard

Reaction-calorimetry safety assessment

Convert calibration pulses, blank dosing experiments, and reaction heat-flow traces into auditable run metrics, replicate summaries, and protocol-level scale-up decisions.

From raw traces to an auditable decision

Every screening outcome must remain traceable to calibration, corrections, and protocol-level evidence.

Input 01Electrical pulsesheat-flow sensitivity
Input 02Blank dosingnon-reaction heat
Input 03Reaction runstime + feed + events
01Calibratepulse-derived sensitivity
→
02Correctbaseline + blank
→
03Summarizeruns + replicates
→
04Screendeclared criteria
ΔTadMTSRaccumulationpost-feed heatheat recovery

Derived metrics remain linked to the corrected trace and source protocol.

3 stagescalibration, correction, assessment
6 CSVstraceable tabular outputs
3 plotsheat flow and safety summaries
1 reportmethods and screening rationale

Workflow

  1. Establish calibration

    Derive heat-flow sensitivity from electrical pulses and quantify blank dosing heat.

  2. Correct the time series

    Apply baseline and blank corrections while retaining run, protocol, time, feed, and event provenance.

  3. Derive thermal metrics

    Integrate released heat and calculate reaction enthalpy, adiabatic rise, accumulation, MTSR, post-feed heat, and recovery.

  4. Screen by protocol

    Summarize replicates and map each decision and reason back to declared configuration criteria.

Artifact contract

analysis.pycalibration + blank CSVsprocessed time seriesrun thermal metricsprotocol safety summaryscale-up decision table3 diagnostic plotsreaction_calorimetry_report.md
+Reaction calorimetry safety — FrontierChallenge
← All selected cases

Process chemistry · Hard

Reaction-calorimetry safety assessment

Convert calibration pulses, blank dosing experiments, and reaction heat-flow traces into auditable run metrics, replicate summaries, and protocol-level scale-up decisions.

From raw traces to an auditable decision

Every screening outcome must remain traceable to calibration, corrections, and protocol-level evidence.

Input 01Electrical pulsesheat-flow sensitivity
Input 02Blank dosingnon-reaction heat
Input 03Reaction runstime + feed + events
01Calibratepulse-derived sensitivity
→
02Correctbaseline + blank
→
03Summarizeruns + replicates
→
04Screendeclared criteria
ΔTadMTSRaccumulationpost-feed heatheat recovery

Derived metrics remain linked to the corrected trace and source protocol.

3 stagescalibration, correction, assessment
6 CSVstraceable tabular outputs
3 plotsheat flow and safety summaries
1 reportmethods and screening rationale

Workflow

  1. Establish calibration

    Derive heat-flow sensitivity from electrical pulses and quantify blank dosing heat.

  2. Correct the time series

    Apply baseline and blank corrections while retaining run, protocol, time, feed, and event provenance.

  3. Derive thermal metrics

    Integrate released heat and calculate reaction enthalpy, adiabatic rise, accumulation, MTSR, post-feed heat, and recovery.

  4. Screen by protocol

    Summarize replicates and map each decision and reason back to declared configuration criteria.

Artifact contract

analysis.pycalibration + blank CSVsprocessed time seriesrun thermal metricsprotocol safety summaryscale-up decision table3 diagnostic plotsreaction_calorimetry_report.md
diff --git a/benchmarks/frontierchallenge/site/case-cell-migration.html b/benchmarks/frontierchallenge/site/case-cell-migration.html index 068df34..e42f0f5 100644 --- a/benchmarks/frontierchallenge/site/case-cell-migration.html +++ b/benchmarks/frontierchallenge/site/case-cell-migration.html @@ -1,4 +1,4 @@ -Cell migration imaging — FrontierChallenge +Cell migration imaging — FrontierChallenge
← All selected cases

Life science · Medium

Cell migration from time-lapse microscopy

Turn a structured image experiment into reviewed segmentations, correctly paired migration rates, statistical comparisons, plots, and a reproducible report.

Bright-field inputs at zero, twelve and twenty-four hours
One control replicate across time. White closed contours were drawn by the experimenter and are part of the agent-visible input.
diff --git a/benchmarks/frontierchallenge/site/case-eis.html b/benchmarks/frontierchallenge/site/case-eis.html index e56cf5c..0f2e3c4 100644 --- a/benchmarks/frontierchallenge/site/case-eis.html +++ b/benchmarks/frontierchallenge/site/case-eis.html @@ -1,4 +1,4 @@ -EIS equivalent-circuit analysis — FrontierChallenge +EIS equivalent-circuit analysis — FrontierChallenge
← All selected cases

Electrochemistry · Hard

Equivalent-circuit analysis of impedance spectra

Fit prescribed circuit families, compare them with traceable metrics and residuals, and connect the frequency response to electrochemical processes without hiding uncertainty.

Raw Nyquist spectra
Two raw input traces before preprocessing, candidate-circuit fitting, or model selection.
diff --git a/benchmarks/frontierchallenge/site/case-gitt.html b/benchmarks/frontierchallenge/site/case-gitt.html index ba3bfa8..39da037 100644 --- a/benchmarks/frontierchallenge/site/case-gitt.html +++ b/benchmarks/frontierchallenge/site/case-gitt.html @@ -1,4 +1,4 @@ -GITT diffusion analysis — FrontierChallenge +GITT diffusion analysis — FrontierChallenge
← All selected cases

Electrochemistry · Hard

Sodium-ion diffusion from GITT sequences

Resolve pulse, rest, and relaxation segments across hard-carbon cells, assess pulse quality from measured stability, and preserve SOC-dependent transport calculations in a checkable bundle.

Raw GITT voltage sequence from one hard-carbon cell
A complete raw cell record showing the repeated voltage steps and relaxations before pulse segmentation, QC, or diffusion calculations.
diff --git a/benchmarks/frontierchallenge/site/case-lfa.html b/benchmarks/frontierchallenge/site/case-lfa.html index ab546f0..a2ac8c4 100644 --- a/benchmarks/frontierchallenge/site/case-lfa.html +++ b/benchmarks/frontierchallenge/site/case-lfa.html @@ -1,4 +1,4 @@ -Laser-flash thermal analysis — FrontierChallenge +Laser-flash thermal analysis — FrontierChallenge
← All selected cases

Materials characterization · Hard

Thermal transport from laser-flash curves

Reassemble shuffled temperature-rise traces, judge curve quality from their shapes, and carry accepted runs through thermal diffusivity, conductivity, and sample-level statistics.

Raw laser-flash temperature-rise curves
One raw detector trace from each BN loading before ordering, baseline treatment, curve QC, or thermal-property calculations.
diff --git a/benchmarks/frontierchallenge/site/case-photoredox.html b/benchmarks/frontierchallenge/site/case-photoredox.html index 638ddf5..4f6e9ef 100644 --- a/benchmarks/frontierchallenge/site/case-photoredox.html +++ b/benchmarks/frontierchallenge/site/case-photoredox.html @@ -1,4 +1,4 @@ -Photoredox photon balance — FrontierChallenge +Photoredox photon balance — FrontierChallenge
← All selected cases

Photochemistry · Hard

Photoredox photon balance and quantum yield

Connect ferrioxalate actinometry, LED emission, reaction absorbance, quantitative assays, dark controls, and an independent condition without mixing calibration, training, or validation roles.

Raw blue LED spectra from three experimental conditions
Three raw pre-reaction LED spectra before dark correction, detector-response correction, spectral weighting, or photon-balance calculations.
diff --git a/benchmarks/frontierchallenge/site/case-qnmr.html b/benchmarks/frontierchallenge/site/case-qnmr.html index 144676d..640a94d 100644 --- a/benchmarks/frontierchallenge/site/case-qnmr.html +++ b/benchmarks/frontierchallenge/site/case-qnmr.html @@ -1,4 +1,4 @@ -qNMR purity and spectral QC — FrontierChallenge +qNMR purity and spectral QC — FrontierChallenge
← All selected cases

Analytical chemistry · Hard

Quantitative NMR purity with spectrum-level QC

Reference, process, and integrate replicate ¹H NMR spectra while keeping quality-control decisions, batch summaries, and every reported purity value mutually consistent.

Four raw quantitative proton NMR spectra
Four agent-visible replicate spectra before reference correction, baseline processing, integration, or anomaly decisions.
diff --git a/benchmarks/frontierchallenge/site/case-qpcr.html b/benchmarks/frontierchallenge/site/case-qpcr.html index f09f684..4c33b23 100644 --- a/benchmarks/frontierchallenge/site/case-qpcr.html +++ b/benchmarks/frontierchallenge/site/case-qpcr.html @@ -1 +1 @@ -RT-qPCR primer design — FrontierChallenge
← All selected cases

Molecular biology · Hard

RT-qPCR primer design with recomputable QC

Design one to three primer pairs while keeping junction logic, thermodynamics, offline paired specificity, coordinates, and the final recommendation mutually consistent.

Agent-visible input contract

The task supplies a synthetic target, explicit coordinate rules, locked thermodynamic conditions, and a fixed offline background panel.

Target structure

GeneXSynthetic cDNA / mRNAtarget.fasta · 350 bp
Exon 11–150J1150 | 151Exon 2151–350

Hard constraintForward primer spans J1 with at least 5 nt inside each exon; the reverse binding region remains entirely in exon 2.

Input groups

Sequencestarget.fastaofftargets.fasta · 33 sequences
Coordinate + panel metadataexon_junctions.jsonbackground_panel_metadata.json
Locked method + specificationtm_params.json · primer3-py 2.3.0requirements.md

Independent verification

01Geometrycoordinates · amplicon · junction
02ThermodynamicsTm · hairpins · homo/heterodimers
03Paired specificityboth strands · F–R / F–F / R–R
04Handoff integrityfour files · consistent declarations
33synthetic background sequences
1–3qualified primer pairs
J1required forward-primer junction
4 filesrequired deliverables

Workflow

  1. Generate constrained candidates

    Respect the declared junction, exon placement, amplicon range, and coordinate semantics.

  2. Recompute thermodynamic QC

    Use the pinned Primer3 engine for melting temperature, hairpins, homodimers, and heterodimers.

  3. Check paired specificity

    Search both strands of all 33 backgrounds under the deterministic mismatch and product-size rules.

  4. Defend the recommendation

    Compare the recommended pair with a specific downgraded alternative and state offline validation limits.

Artifact contract

primers.csvqc_summary.jsonreport.mdREADME.md
+RT-qPCR primer design — FrontierChallenge
← All selected cases

Molecular biology · Hard

RT-qPCR primer design with recomputable QC

Design one to three primer pairs while keeping junction logic, thermodynamics, offline paired specificity, coordinates, and the final recommendation mutually consistent.

Agent-visible input contract

The task supplies a synthetic target, explicit coordinate rules, locked thermodynamic conditions, and a fixed offline background panel.

Target structure

GeneXSynthetic cDNA / mRNAtarget.fasta · 350 bp
Exon 11–150J1150 | 151Exon 2151–350

Hard constraintForward primer spans J1 with at least 5 nt inside each exon; the reverse binding region remains entirely in exon 2.

Input groups

Sequencestarget.fastaofftargets.fasta · 33 sequences
Coordinate + panel metadataexon_junctions.jsonbackground_panel_metadata.json
Locked method + specificationtm_params.json · primer3-py 2.3.0requirements.md

Independent verification

01Geometrycoordinates · amplicon · junction
02ThermodynamicsTm · hairpins · homo/heterodimers
03Paired specificityboth strands · F–R / F–F / R–R
04Handoff integrityfour files · consistent declarations
33synthetic background sequences
1–3qualified primer pairs
J1required forward-primer junction
4 filesrequired deliverables

Workflow

  1. Generate constrained candidates

    Respect the declared junction, exon placement, amplicon range, and coordinate semantics.

  2. Recompute thermodynamic QC

    Use the pinned Primer3 engine for melting temperature, hairpins, homodimers, and heterodimers.

  3. Check paired specificity

    Search both strands of all 33 backgrounds under the deterministic mismatch and product-size rules.

  4. Defend the recommendation

    Compare the recommended pair with a specific downgraded alternative and state offline validation limits.

Artifact contract

primers.csvqc_summary.jsonreport.mdREADME.md
diff --git a/benchmarks/frontierchallenge/site/case-ti.html b/benchmarks/frontierchallenge/site/case-ti.html index 7a0dd00..3299507 100644 --- a/benchmarks/frontierchallenge/site/case-ti.html +++ b/benchmarks/frontierchallenge/site/case-ti.html @@ -1 +1 @@ -Hydration free energy by TI — FrontierChallenge
← All selected cases

Molecular simulation · Hard

Hydration free energy by thermodynamic integration

Execute a fixed alchemical protocol across aqueous and gas phases, preserve every AMBER-native artifact, and reconcile per-window evidence with the reported free energy.

Fixed TI contract

Two phases × two interaction legs, each resolved through the same nine declared windows.

Electrostaticvan der WaalsGas phase
9λ windows
9nonlinear windows
Water phase
9λ windows
9nonlinear windows

Per-path window schedule

λ start9 fixed pointsλ end
ABCG2 chargesno soft-core potentials
01Prepare systemscharges + topologies
→
02Run all windows4 paths × 9 logs
→
03Integratecomponent evidence
→
04Reconcile handoffJSON + plot + report
9Gaussian-quadrature windows
4phase × interaction paths
2electrostatic and vdW legs
AMBERnative evidence required

Workflow

  1. Prepare the molecule

    Apply ABCG2 atomic charges and construct charged-ligand and missing-parameter files.

  2. Build both phases

    Create water and gas endpoint topologies, then minimize and equilibrate each system.

  3. Run all windows

    Execute electrostatic and nonlinear van der Waals legs at every declared λ value.

  4. Integrate and reconcile

    Trace the component and total values back to the per-step DV/DL series in unedited output logs.

Artifact contract

results.jsondvdl_vs_lambda.pngreport.mdcharged ligand + frcmodwater/gas topologiesminimization + equilibration logsall per-window TI outputs
+Hydration free energy by TI — FrontierChallenge
← All selected cases

Molecular simulation · Hard

Hydration free energy by thermodynamic integration

Execute a fixed alchemical protocol across aqueous and gas phases, preserve every AMBER-native artifact, and reconcile per-window evidence with the reported free energy.

Fixed TI contract

Two phases × two interaction legs, each resolved through the same nine declared windows.

Electrostaticvan der WaalsGas phase
9λ windows
9nonlinear windows
Water phase
9λ windows
9nonlinear windows

Per-path window schedule

λ start9 fixed pointsλ end
ABCG2 chargesno soft-core potentials
01Prepare systemscharges + topologies
→
02Run all windows4 paths × 9 logs
→
03Integratecomponent evidence
→
04Reconcile handoffJSON + plot + report
9Gaussian-quadrature windows
4phase × interaction paths
2electrostatic and vdW legs
AMBERnative evidence required

Workflow

  1. Prepare the molecule

    Apply ABCG2 atomic charges and construct charged-ligand and missing-parameter files.

  2. Build both phases

    Create water and gas endpoint topologies, then minimize and equilibrate each system.

  3. Run all windows

    Execute electrostatic and nonlinear van der Waals legs at every declared λ value.

  4. Integrate and reconcile

    Trace the component and total values back to the per-step DV/DL series in unedited output logs.

Artifact contract

results.jsondvdl_vs_lambda.pngreport.mdcharged ligand + frcmodwater/gas topologiesminimization + equilibration logsall per-window TI outputs
diff --git a/benchmarks/frontierchallenge/site/case-xrd.html b/benchmarks/frontierchallenge/site/case-xrd.html index aab5023..fb3a565 100644 --- a/benchmarks/frontierchallenge/site/case-xrd.html +++ b/benchmarks/frontierchallenge/site/case-xrd.html @@ -1,4 +1,4 @@ -XRD phase quantification — FrontierChallenge +XRD phase quantification — FrontierChallenge
← All selected cases

Materials characterization · Hard

Duplex phase quantification from X-ray diffraction

Correct instrumental zero shift, quantify ferrite and austenite, and carry the calculation from nine raw scans to a reproducible sample-level handoff.

Three raw diffraction patterns
One unprocessed scan from each processing condition. The curves are visual context only; quantitative work uses the supplied deconvolved peak table.
diff --git a/benchmarks/frontierchallenge/site/cases.html b/benchmarks/frontierchallenge/site/cases.html index a1f6bae..55617bc 100644 --- a/benchmarks/frontierchallenge/site/cases.html +++ b/benchmarks/frontierchallenge/site/cases.html @@ -9,7 +9,7 @@ - +