Reference
Beginner glossary
Short definitions for the terms you will see in BenchLab, SeqTrainer, Validator, and Canvas.
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- Dataset
- A collection of examples, such as DNA sequences and their labels.
- DNA sequence
- The A, C, G, and T letters that describe a biological sequence.
- Label
- The target value attached to a sequence, such as promoter (1) or non-promoter (0).
- Benchmark
- A repeatable comparison of model approaches using the same data policy.
- Benchmark plan
- A saved description of what you intend to run, even before model training.
- Baseline model
- A simple reference model used to establish a starting point.
- Train set
- Data used to fit model parameters.
- Validation set
- Data used to choose settings or thresholds without touching the final test report.
- Test set
- Held-back data reserved for final reporting.
- Threshold
- A score cutoff used to turn a model score into a predicted class.
- MCC
- Matthews correlation coefficient, a balanced metric for binary classification.
- AUPRC
- Area under the precision-recall curve, useful when classes are imbalanced.
- Checkpoint
- Saved model weights that can be reused for prediction or annotation.
- Manifest
- A metadata file recording inputs, settings, provenance, and outputs.
- GenBank
- A sequence file format that can hold a sequence and annotated biological features.
- FASTA
- A simple sequence format that usually contains sequences but not supervised labels.
- SBOL
- A standard for representing synthetic biology designs and their relationships.
- SBOL2
- Version 2 of SBOL; SBOL Canvas commonly uses SBOL2 RDF/XML for visual import.
- SBOL3
- Version 3 of SBOL; SeqTrainer's .nt export is the canonical machine-readable result.
- RDF/XML
- An RDF serialization commonly saved as .rdf or .xml.
- N-Triples
- A line-based RDF serialization commonly saved as .nt.
- Sequence Ontology role
- A standard term that tells SBOL tools what kind of biological feature an item is.
- Predicted promoter
- A promoter-like region proposed by a computational model, not confirmed by wet-lab evidence.
- Compatibility output
- A second file written to help another tool import the design, even when it is not the canonical output.
- Plan-only export
- A BenchLab export made without training; metrics or predictions can be empty.
- Smoke test
- A quick check that the command and file-writing path work, not proof of scientific accuracy.
- Promoter
- A DNA region involved in starting transcription.
- Computational prediction
- A model-based result that still needs biological interpretation and validation.
- Plasmid
- A circular or linear DNA molecule used to carry a genetic design.
- Colab
- Google's hosted notebook environment, often used for GPU model runs.
- HPC
- A high-performance computing system used for larger or longer jobs.