feat: Cytiva Biacore T200 Evaluation -- Update parser to extract kinetics data (kd, ka, RMax, chi-squared, errors)#1183
Merged
Conversation
Allow measurements to have multiple processed data documents when both kinetics and affinity models are present. This enables proper representation of files where both 1:1 binding kinetics and steady state affinity analyses are performed on the same data. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Updated Cytiva Biacore T200 Control and T200 Evaluation parsers to work with the new binding_affinity_analyzer schema that uses list[ProcessedData] instead of individual processed data fields on Measurement. Changes to T200 Control: - Added ProcessedData import - Wrap report points in a ProcessedData object (required by new schema where report points are nested inside processed data documents) - Create empty ProcessedData with model_name="N/A" when report points exist Changes to T200 Evaluation: - Added ProcessedData import - Extract kinetic parameters (kon, koff, kd, rmax) into variables - Create ProcessedData object with kinetic parameters and custom info - Pass processed_data=[ProcessedData(...)] instead of individual fields This maintains backward compatibility while supporting the enhanced schema that allows multiple analysis models per measurement (e.g., both kinetics and affinity models in Cytiva Biacore Insight). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Updated EvaluationKinetics.get_data() to return list[KineticsData] instead of a single KineticsData object. This aligns with the internal storage (_data) which already stores lists of KineticsData (to support multiple analysis models like both kinetics and affinity in the same measurement). This fixes a type mismatch where get_data was returning the wrong type, and enables proper support for measurements with multiple analysis models. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…ture Updated test expected outputs to reflect the new schema structure where kinetic analysis data is wrapped in ProcessedData objects within processed data aggregate documents. Changes: - Added processed data aggregate document containing ProcessedData with: - model_name extracted from kinetic data - Kinetic parameters (kon, koff, kd, rmax) - Custom info (kinetics chi squared, ka/kd/Rmax errors) All T200 Evaluation tests passing (1/1). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…calculated concentration Updated test expected outputs to include changes from main branch: - Dynamic extraction of Analyte 1-N columns (from PR #1171) - Calculated concentration support (from PR #1172) - Support for multiple ProcessedData documents (kinetics + affinity models) Changes include: - Multiple Analyte fields (Analyte 2, Analyte 3) in device control and sample custom info - Multiple Regeneration fields (Regeneration 2, Regeneration 3) - Two processed data documents per measurement when both models exist: 1. 1:1 binding kinetics model with kon, koff, KD, Rmax 2. Steady state affinity model with KD, Rmax, offset - Test data masking updates (sensor chip ID, lot number, solution names) All Insight tests passing (4/4). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…ht-kinetics-affinity
… kinetics extraction Extends kinetic analysis extraction to handle the newer "Fits/Fit0" structure in addition to the legacy "modelFits" format. Also extracts actual flow cell IDs from CurveSet CurveName fields to ensure accurate data mapping. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Apply code formatting fixes to kinetics extraction logic and update test file identifiers to match actual filenames. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…luation files - Add support for extracting KD (equilibrium dissociation constant) and Rmax (maximum binding capacity) from steady-state affinity analysis - Add error fields for KD and Rmax to custom information document - Enhance CalculatedValue class to support error values - Update decoder to handle affinity analysis parameter format (0:KD|value|error) - Add new test file: biacore_evaluation_module_example4.bme (affinity analysis) - Update existing test outputs to include newly extracted KD error and Rmax error fields Data now captured for affinity analysis: - KD (equilibrium dissociation constant) in M - KD error in M - Rmax (maximum binding capacity) in RU - Rmax error in RU - Chi-squared (fit quality) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
james-leinas
changed the title
Resolve conflicts from the schema model refactor (MeasurementDocument → MeasurementDocumentItem, field casing changes). Fix missing TQuantityValueSquareResponseUnit by using TQuantityValue directly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
kinetic_data is always a KineticResult dataclass, never a dict, so the isinstance check was always False and model_name was always "N/A". Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
nathan-stender
approved these changes
Apr 21, 2026
stephenworlow
approved these changes
Apr 22, 2026
This was referenced Apr 22, 2026
nathan-stender
added a commit
that referenced
this pull request
Apr 22, 2026
### Added - Cytiva Biacore T200 Evaluation -- Update parser to extract kinetics data (kd, ka, RMax, chi-squared, errors) (#1183)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Update parser to extract kinetics data (kd, ka, RMax, chi-squared, errors)
Co-Authored-By: Claude Sonnet 4.5 noreply@anthropic.com