cDNA Sequencing Observations
coverage
42.7×
42.7×
reads
2.4M
2.4M
quality
Q38.2
Q38.2
samples
48
48
Gene Expression Matrix
← genes (n=2,847) →
samples ↓
CONDITION 4
TIMEPOINT 6
REPLICATE 2
CELL TYPE 3
Data Validation · semantics.py
10 VALIDATOR RULES
version
■ PASS
discriminant
■ PASS
value/missing
■ PASS
raw count
■ PASS
decimal
■ PASS
reference
■ WARN
quantity kind
■ PASS
exclusion
■ PASS
source bytes
■ PASS
synthetic origin
■ PASS
Semantic Quantity Classification
Observed
measurement
Inferred
posterior estimation
Derived
deterministic transform
Predicted
model output
Constrained
MiniZinc
Encoded
representation
Executed
run evidence
DNA
cDNA READS
EXPRESSION
SEMANTICS
BINARY
PTM STATES
POSTERIOR
CONSTRAINTS
MODEL
Biological Observations
cDNA Expression Data
Data Validation
Gene Expression
Stan Model
Posterior State
MiniZinc Model
Computational Result
Visualizer
Human-Readable Model
Bayesian Inference · Stan
Prior
→
Likelihood
→
Posterior
| Parameter | Mean | Median | σ | R̂ | ESS |
|---|---|---|---|---|---|
| α | 2.347 | 2.341 | 0.128 | 1.001 | 4200 |
| β₁ | -0.892 | -0.887 | 0.064 | 1.002 | 3800 |
| β₂ | 1.156 | 1.149 | 0.091 | 1.001 | 4100 |
| σ | 0.423 | 0.419 | 0.032 | 1.000 | 4500 |
| φ | 0.067 | 0.065 | 0.018 | 1.003 | 3600 |
RUN ID BSM-2026-0908-001
Constraint Solver · MiniZinc
minimize f(x) subject to C1 ∧ C2 ∧ … ∧ Ck
Variables 12
Domains 3
Constraints 8
Objective 1
Quantum Circuit · Quipper
semantic transformation → quantum circuit → quipper
5
Qubits
14
Gate Count
7
Circuit Depth
PTM-BIT-PARITY/1
qeven
qodd
qaccept
| State | Read | Write | Move | Next |
|---|---|---|---|---|
| qeven | 0 | 0 | R | qeven |
| qeven | 1 | 1 | R | qodd |
| qodd | 0 | 0 | R | qodd |
| qodd | 1 | 1 | R | qeven |
| qeven | □ | □ | — | qaccept |
8 input symbols · 9 transitions · O(1) auxiliary storage
Binary Semantics
semantic value → encoding → bits → state → transition
| State ID | Tape Pos | Symbol | Transition | Next |
|---|---|---|---|---|
| S₀ | 0x0000 | 0 | δ(S₀,0) | S₀ |
| S₀ | 0x0001 | 1 | δ(S₀,1) | S₁ |
| S₁ | 0x0002 | 0 | δ(S₁,0) | S₁ |
| S₁ | 0x0003 | 1 | δ(S₁,1) | S₀ |
Immutable Artifact Provenance
RPG/JCL · Legacy Integration
//* BIO-SEMANTICS VAULT CONTROL
//BSEM001 JOB BIOSEM,CLASS=A
//STEP01 EXEC PGM=BSEMVLT
//VAULT DD DSN=BSEM.PROV.VAULT,DISP=SHR
//ARCHIVE DD DSN=BSEM.ARCH.V001,DISP=NEW
//SYSPRINT DD SYSOUT=*
JOB0001BSEM Vault SealCOMPLETE
JOB0002Provenance ArchiveCOMPLETE
JOB0003Artifact VerifyRUNNING
JOB0004Batch ExportQUEUED
Repository Structure
bio-semantics/
src/
semantics.py
test_semantics.py
dashboard.html
spec/
types.ts
contract.md
system_prompt.md
templates/
workflow.rpgle
vault.jcl
src/
semantics.py
test_semantics.py
dashboard.html
spec/
types.ts
contract.md
system_prompt.md
templates/
workflow.rpgle
vault.jcl
Biological Observations are not the same thing as Model Inference
Model Inference is not the same thing as Semantic Transformation
Semantic Transformation is not the same thing as Binary Representation
Binary Representation can be represented as Formal Machine State
Formal Machine State can be verified through PTM Transitions
Selected Transformations can be represented through Quipper
RPG and JCL provide Integration Infrastructure
Immutable Provenance connects Every Artifact