LAB / BUILDING MY DIGITAL SELF

Building my digital self through real work.

My long-term goal is to build my own digital self, starting with peptide research and gradually connecting knowledge, reasoning and action. These are records of real work, reusable capabilities, validation and open questions.

LAB / BUILD LOG

Building, day by day

Research capabilities and knowledge, built day by day.

2026-09-29 → 2026-10-28 · UTC

agentic_ai_platform

Research capabilities · methods & execution

30 days · Commits
Commits
2786
PRs created
290
PRs merged
267
Each track uses its own peak; color intensity is not comparable across tracks.

knowledge_wiki

Knowledge & experience · sources & memory

30 days · Commits
Commits
11
PRs created
3
PRs merged
2
Each track uses its own peak; color intensity is not comparable across tracks.

UTC Partial day

agentic_ai_platform94commits

knowledge_wiki0commits

Updated: · UTC · — unavailable

A TREE IN THE MAKING

Rooted in curiosity. Room to grow.

Each maple leaf is a method. New capabilities take root through evidenced work.

Follow a leaf. See where it leads.

63 methods · counted once across stages

Leaves name methods, not experimentally validated results. Hit validation, hit-to-lead and lead optimization have distinct boundaries; experimental feedback can return to any round.

01Target & site1

Target & epitope triage

target or complex structure and explicit chain mapping → contact, SASA and epitope hotspot assessments.

Biological advice, contact hotspots, geometric feasibility and trajectory evidence remain distinct; no causal target validation.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

02Genomic evidence4

Regulatory tracks

model-specific DNA arrays or variants, track identities and selected assets → model-bound track predictions or variant effects.

Enformer, Borzoi and Flashzoi are distinct native operations; genomic signal is not protein binding or causal validation.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ChromBPNet

registered reference FASTA, chromosome sizes, peaks and selected assets → native profile and track predictions.

Reference and peak identity must match; predicted accessibility is not a causal or protein-binding result.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Evo2

DNA sequences, layer or generation controls and explicit assets → DNA generations, likelihoods or layer embeddings.

This worker does not score proteins; generation and embeddings are not phenotype or binding measurements.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

GPN Star

registered primary hg38 reference, variants and selected model assets → native gpn star vep variant effects.

The caller retains only the declared primary hg38 surface; other models or embeddings are not qualified here.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

03Retrieval & selection2

Display count analysis

pre/post count tables, selection paths and controls → enrichment tables, QC and candidate evidence.

Enrichment needs background and orthogonal binding validation.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

04Molecular generation15

RFD4–Proteina

Registry-resolved compiled case and hash-bound checker contract, explicit monomer/binder/motif task, count, seed and batch size → Durable asynchronous compute JobHandle, native operation manifest, generated complex CIFs and candidate identity mappings.

Canonical L-proteins only; native qualification pending; cyclic and noncanonical chemistry refused.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

BoltzGen

target structures and explicit generation constraints → generated structures, sequences and provenance.

Software source and controls do not establish native cyclic support or experimental affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

BindCraft2

target structure and explicit design and topology contract → designed sequences, structures and attempt provenance.

Source and extended request support do not qualify the native recipe; no silent v1 fallback.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Cyclic motif scaffolding

motif, scaffold and cyclic topology constraints → candidate scaffold structures and constraint evidence.

Closure geometry is not synthesis or binding proof.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

RFdiffusion3

RFD3 specifications or RF3 named molecular records and selected assets → generated RFD3 designs or RF3 predicted structures with sample provenance.

RFD3 generation and RoseTTAFold3 RF3 prediction are distinct operations; cyclic chemistry requires specific admission.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ComplexA

target and sequence conditions with explicit cyclic flow recipe → generated structures and source-bound evidence.

The software candidate remains natively unqualified; cyclic generation is not a binding measurement.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

ESMFold2 gradient design

target structure, sequence logits and gradient objective → designed sequences and predicted structures.

Design feedback is not independent refolding or experimental affinity; topology and restart conditions remain explicit.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ColabDesign

target PDB, chain roles, binder length and explicit gradient schedule → designed sequence and final predicted structure.

This is a bounded gradient operation, not the BindCraft campaign driver; confidence is not experimental affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

RFdiffusion

target or motif coordinates, contigs and explicit diffusion controls → generated protein backbones and sample provenance.

Backbone generation needs downstream sequence design and independent evaluation; native constraint support is conditional.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Genie3

selected source config, conditioning inputs, seeds and model assets → native generated candidates and source-bound outputs.

Native search, sampler and conditioning stay upstream; software readiness is not native or scientific qualification.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Mosaic

target and sequence design inputs, seed and explicit recipe → designed sequences, structures and completion evidence.

Scientific qualification pending; completed-unit reuse is not mid-job recovery.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

PXDesign

native design input, selected assets and dtype controls → generated structures and native output provenance.

The selected design dependency is required; software transfer does not establish affinity or native qualification.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

HalluDesign

explicit receptor and peptide chains, topology, cycles and predictor settings → authenticated per-cycle sequence, prediction and selection evidence.

MPNN packing plus AF3 or ESMFold2 forward feedback supplies no sequence gradient; parent workflow owns authorization.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

BoltzDesign1

validated design inputs and explicit cyclic overlay conditions → design invocation and environment contract.

Research stage; production generator not admitted; licence and native-output bindings remain unresolved.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

PepMLM

target protein sequence, peptide length, count and explicit assets → generated peptide sequences and selected-source provenance.

Selected-source licence and native qualification remain unresolved; generated sequences are not confirmed binders.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

05Sequence & representation8

MPNN + FastRelax

backbone, fixed positions and sampling protocol → sampled sequences and optional relaxed structures.

Backbone-conditioned sampling alone is not a complete binder generator.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Sequence compatibility

sequence and model-specific conditioning → scores with model and residue-index provenance.

Likelihood and embeddings do not measure affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ProteinMPNN

protein backbones, chain roles, fixed positions and sampling protocol → sampled or scored sequences with provenance.

Backbone-conditioned sampling alone is not a complete binder generator; scores are not affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ESMC

protein sequences, selected ESMC operation and explicit assets → sequence representations or operation-specific scores.

Offline representation does not submit work or alter resident 6B admission; likelihood and embeddings are not affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ProGen2

optional sequence prefix, model identity and sample protocol → generated sequences or bidirectional averaged likelihood.

Unconditional or prefix generation is not target-conditioned binder design; likelihood is not binding energy.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ESM-IF1

backbone coordinates, chain and sequence conditions → backbone-conditioned sequences or likelihood.

A supplied backbone is required; likelihood is not affinity. Native evidence is specific to the source, checkpoint, operation, device and fixture; it does not establish predictive accuracy.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Caliby

registered structures, selected model assets and design request → structure-conditioned protein sequences.

Structure-conditioned design does not establish binder activity or native qualification.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Profluent E1

protein sequence operations and host-bound selected assets → operation-specific scores, embeddings or predictions.

Built with Profluent-E1; software transport does not qualify accuracy or experimental affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

06Structure & evaluation12

Candidate evaluation

candidates, molecular identity and supplied evidence → normalized evidence and explicit qualification gaps.

Computational confidence cannot establish experimental binding.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Pose ensembles

molecular sequences or seed structures and explicit predictor or sampler mode → predicted poses, consistency or sampling evidence.

Consistency mode does not sample poses; confidence is not affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

AlphaFold 3

AF3 JSON entities and explicit seeds and sample census → native structure output census and protocol identity.

This is an input/output protocol boundary; native chemistry and model qualification remain separate.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Protenix

selected Protenix request entities, templates, seeds and assets → validated native request and complete structural output set.

Template hits and chemical atom validity require native featurisation evidence.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

OpenFold3 OpenBind

selected OpenBind entities, assets and explicit mode recipe → bound native request and complete output census.

OpenBind is distinct from preview2; chemistry, numerical mode and weights need qualification.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ESMFold2

protein sequences, selected assets and folding protocol → validated folding payload and model identity.

Forward folding is distinct from gradient design; confidence is not affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Boltz2

molecular entities, bonds and explicit sampling protocol → predicted structures with atom and sampling provenance.

Cyclic software overlays do not establish native chemistry or binding accuracy.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

AlphaFold2 / ColabFold

sequence, selected features, optional initial coordinates and folding protocol → AF2 forward structural prediction and provenance.

Coordinate-seeded forward prediction is distinct from ColabDesign gradient design; qualification is separate.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

AtlasFold

explicit folding task, inputs, seeds, samples and bound assets → complete native predicted output set.

Transport and output accounting do not qualify scientific accuracy, numerical equivalence or recovery.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Chai-1

molecular entities, explicit seeds, samples and selected assets → native structures with complete entity and sample accounting.

Source and transport checks do not establish chemistry accuracy, affinity or checkpoint recovery.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

OpenDDE

molecular input, seeds, samples and bound selected assets → native structures and complete unit accounting.

Migrated bf16 fast_layernorm differs from upstream fp32; scientific qualification and native long-job recovery remain separate.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Independent docking

Declared structures, sites and restraints → pose cross-checks with ADCP, HADDOCK3 or LightDock.

Docking provides pose evidence, not affinity ranking.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

07Physics & energy3

Free-energy protocols

molecular system, force field and declared physical protocol → protocol-bound energy estimates and diagnostics.

ddG_fold is not ddG_bind; distinct protocols cannot be fused implicitly.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Replica-exchange dynamics

Explicit topology, temperature ladder and protocol → replica-exchange simulation and analysis.

Job recovery and trajectory evidence require separate acceptance; submission is not a scientific conclusion.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Physical pose refinement

Explicit topology, structures and parameters → relaxed poses and protocol-bound interface quantities.

Crosslinks and noncanonical residues require retained parameters and closure identity; refinement scores are not affinity.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

08Leads & feedback6

Lead project rounds

registered assay evidence, goals and host-authored design cards → durable projects, rounds and design panels.

Project tools retain evidence and prepare method handoffs; they do not reason, predict, launch computation or order synthesis.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Interface optimization

parent complex, explicit operations and evaluation contract → candidate pools, provenance and evaluation evidence.

Parent optimization is distinct from de novo generation.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

ADMET recipe

SMILES, registered support data and fixed model recipe → endpoint predictions, refusal states and provenance.

Endpoint recipes have explicit provenance; peptide and noncanonical transfer are unvalidated; deployment is checked separately.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Pending qualification

Source checked ·

No public execution evidence attached.

Measured SAR

assay observations with source identity, units and censoring → SAR relationships with measured and inferred evidence separated.

Cross-assay values are not interchangeable; suggestions remain unmeasured.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Unified residue scanning

Explicit sites, context and scorers → a complete mutation matrix, coverage and rankings.

Binding and folding quantities remain distinct; fusion is explicit and native qualification is method-specific.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Rational design

Measured SAR, structure evidence and hypotheses → traceable proposals and molecular identities.

Proposals remain unevaluated; structural explanations need independent grounding.

Method & evidence

Research role · Composed tasks

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

09Chemistry & identity1

Cyclization sites

complex geometry and candidate bridge chemistry → ranked bridge pairs and feasibility observations.

Site choice is distinct from bond-closure validation, synthesis feasibility and binding evidence.

Method & evidence

Research role · Scientific operations

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

10Shared support11

Scientific delivery

verified claims, figures and evidence references → reports with claim-to-figure provenance.

Rendered output cannot close unfinished upstream scientific gates.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Scientific memory

source-bound hypothesis and finding cards → durable scientific context.

A recorded hypothesis is not a verified conclusion.

Method & evidence

Research role · Execution & learning support

The knowledge base retains sourced experience and methods for the next investigation.

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Workflow control

authorized contract, task state and evidence → durable execution and acceptance records.

Workflow completion does not independently qualify scientific outcomes.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Compute admission

owner-bound workload, measured capacity and budget → execution descriptors, results and recovery state.

Process exit success does not establish scientific validity.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Model identity

Registered logical model name → resolved model and weight identity.

Registration does not establish installed runtime or inference success.

Method & evidence

Research role · Shared contracts

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Service discovery

Authorized service discovery → declared service routes and runtime evidence.

A reachable endpoint is not a qualified scientific prediction.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Experience retrieval

question and maintained knowledge sources → ranked evidence references.

Retrieval, publication, adoption and measured effect are distinct states.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Registered data

logical dataset name and access context → registered data identity and access results.

Registration alone is not data QC or permission to access restricted data.

Method & evidence

Research role · Shared contracts

Registered data, benchmarks and provenance support comparable, reproducible research.

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Molecular identity

molecular graph, chains, residues and covalent declarations → identity mappings and validated topology records.

Graph validity does not prove chemical synthesis feasibility.

Method & evidence

Research role · Shared contracts

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Round lineage

explicit round identity, parent lineage, content-bound evidence and root control references → validated persistent round records and explicit historical migration exports.

Scientific rounds do not create root iterations or backtracks; records grant no compute or scientific authority.

Method & evidence

Research role · Execution & learning support

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Benchmark normalization

scalar values and explicit frozen or training-pool extrema → normalized or inverse-transformed protocol values.

Normalization is not a scientific model; extrema and affine-v2 clipping protocol must be explicit and historical v1 is read-only.

Method & evidence

Research role · Shared contracts

The source declaration or implementation was inspected; registration does not establish a native run.

Implementation
Contract recorded
Tests
Not independently checked
Deployment
Unknown
Scientific runs
Not independently checked
Scientific validation
Not independently checked

Source checked ·

No public execution evidence attached.

Rooted in sourced knowledge · traceable data · Methods & work records ↗Open the original record: Public method notebook ↗Open the original record: Method notebook ↗Open the original record: Work and validation records ↗Open the original record: Full work records ↗Open the original record: Retained historical snapshot ↗Open the original record: Protein Language Model ↗Open the original record: Protein Language Model ↗Open the original record: Structure prediction ↗Open the original record: Structure prediction ↗Open the original record: Biomolecular docking ↗Open the original record: Biomolecular docking ↗Open the original record: Inverse folding ↗Open the original record: Inverse folding ↗Open the original record: Generative backbone design ↗Open the original record: Generative backbone design ↗Open the original record: Partial diffusion ↗Open the original record: Partial diffusion ↗Open the original record: Interface redesign ↗Open the original record: Interface redesign ↗Open the original record: Rational design ↗Open the original record: Rational design ↗Open the original record: Computational mutation scanning ↗Open the original record: Computational mutation scanning ↗Open the original record: Molecular dynamics ↗Open the original record: Molecular dynamics ↗Open the original record: Experimental mutation scanning ↗Open the original record: Experimental mutation scanning ↗Open the original record: mRNA Display Analysis ↗Open the original record: mRNA Display Analysis ↗Open the original record: CI worker and workflow maintenance ↗Open the original record: Declare a regression-check baseline dependency ↗Open the original record: Version benchmark definitions and views ↗Open the original record: Separate batch and resident compute interfaces ↗Open the original record: Plan evaluation-record views and interfaces ↗Open the original record: Plan layered evaluation coverage ↗Open the original record: Integrate a design-method adapter ↗Open the original record: Plan a bounded data-catalog feasibility check ↗Open the original record: Review monitoring storage and recovery ↗Open the original record: Make a planning reference portable ↗Open the original record: Plan durable request evidence and recovery ↗Open the original record: Plan recovery for expired service resources ↗Open the original record: Plan controlled continuation after publication ↗Open the original record: Plan evidence checks for predictive-method research ↗Open the original record: Track workflow dependency provenance ↗Open the original record: Clarify check-planning boundaries ↗Open the original record: Plan method qualification across repeated runs ↗Open the original record: Plan recovery of missing method assets ↗Open the original record: Plan recovery after an interrupted installation ↗Open the original record: Daily evidence retention ↗Open the original record: Selfcheck evidence checks ↗Open the original record: Controlled interrupted-request recovery ↗Open the original record: Disk checks and workspace housekeeping ↗Open the original record: Command launcher maintenance ↗Open the original record: Disk reports and tool documentation ↗Open the original record: Knowledge note synchronization ↗Open the original record: Review record continuity ↗Open the original record: Preserve original review and request records ↗Open the original record: Note metadata compatibility ↗Open the original record: Integration regression repair proposal ↗Open the original record: Build and recovery checks ↗Open the original record: Delivery workflow integration ↗Open the original record: Interactive registry shape validation ↗Open the original record: Identity checks before message sending ↗Open the original record: Abort records for unsubmitted tasks ↗Open the original record: Reminder reading and calendar coverage ↗Open the original record: Metadata pagination and coverage ↗Open the original record: Capability-linked engineering checks ↗Open the original record: Offline message intake ↗Open the original record: Tool guidance and wiring maintenance ↗Open the original record: Optimization method routing ↗Open the original record: Lead optimization integration ↗Open the original record: Research workflow budget history ↗Open the original record: Capability contracts and validation mechanisms ↗Open the original record: Improve code reuse checks ↗Open the original record: Repair validation entry resolution ↗Open the original record: Calendar operations and readback ↗Open the original record: Agent cancellation and receipts ↗Open the original record: Recovery after interrupted installation ↗Open the original record: Property prediction method research ↗Open the original record: Test collection and replay qualification ↗Open the original record: Keep engineering checks relevant ↗Open the original record: Reduce false expiry during waits ↗Open the original record: Hand completed results over reliably ↗Open the original record: A real launch before readiness ↗Open the original record: A checklist with evidence ↗Open the original record: Diagnostics from field shape ↗Open the original record: Clarifying research tool responsibilities ↗Open the original record: Making overnight work more reliable ↗Open the original record: Defining data collection before use ↗Open the original record: Preserving validation history during migration ↗Open the original record: Making request recovery traceable ↗Open the original record: Keep two calendar boundaries explicit ↗Open the original record: Separate comparison evidence from presentation ↗

About this tree

New leaves follow reviewed, evidenced capabilities. Source changes, checks and publication are recorded separately and reflected in daily snapshots. The breeze is decorative.

Source changed
Time not established
Sources checked
Publication receipt
Not bound to this snapshot

Snapshot needs an update; the last checked content is retained.

GROWING / QUESTIONS INTO CAPABILITIES

Methods accumulate. Branches grow.

63 sourced methods and supporting capabilities are mapped. New qualifications, behavior changes and limitations appear here after review.

Explore the maple capability tree ↗

Capability sources checked · 2026-10-27 · Snapshot needs an update

RECENT WORK / 2026-10-28

What I’m working through, and how far it has come.

Records through 2026-10-28.

Planned

Disk reports and tool documentation

Approach
Track source integration for this engineering proposal and preserve records needed for later acceptance.
Progress & limits
Only title, state and timestamps were read; deployment, passing tests, model execution and scientific effectiveness are not established.
Next
Check subsequent review, integration and operational evidence within the original task scope.
Read the full record ↗
Planned

Selfcheck evidence checks

Approach
Track source integration for this engineering proposal and preserve records needed for later acceptance.
Progress & limits
Only title, state and timestamps were read; deployment, passing tests, model execution and scientific effectiveness are not established.
Next
Check subsequent review, integration and operational evidence within the original task scope.
Read the full record ↗
Merged

Disk checks and workspace housekeeping

Approach
Track source integration for this engineering proposal and preserve records needed for later acceptance.
Progress & limits
Only title, state and timestamps were read; deployment, passing tests, model execution and scientific effectiveness are not established.
Next
Check subsequent review, integration and operational evidence within the original task scope.
Read the full record ↗
Browse the dated records

Selected records · through 2026-10-28

Weekly log · 2026-10-26 → 2026-11-01

Records through 2026-10-28 · Selected records

Monthly changelog · 2026-10-01 → 2026-10-31

Records through 2026-10-28 · Selected records

COGNITIVE SYSTEM / METHODS & HARNESS EVOLUTION

Turn experience into improvements that can be evaluated.

Experience, distillation, diagnosis and evaluation produce improvements that can be tested. This loop is still being built.

  1. Experience

    Retain outputs, evidence, failures and applicability boundaries.

  2. Distillation

    Convert reusable experience into sourced knowledge and methods.

  3. Diagnosis

    Compare task needs with method and capability gaps.

  4. Self-model

    Record capabilities and limits to support future task selection.

  5. Candidate improvement

    Propose versioned changes to skills, tools or workflows.

  6. Fixed-condition evaluation

    Independently compare candidates with a baseline; evaluate the evaluator too.