Seq Design BuddyGitHub

A practical guide for students

A beginner guide to the SeqTrainer tool ecosystem

Learn how to prepare a benchmark, annotate possible promoters in a plasmid, validate the resulting design, and view it in SBOL Canvas.

Explore the four tools View the complete workflow

Instructions only

This website does not upload files, run models, validate SBOL, provide GPU resources, connect to HPC, or store experiment results.

Your files and models run in the original tools, not on this website.

The ecosystem

Four tools, four jobs

They are separate applications. Use all four for the full journey, or stop after the tool that answers your question.

Start here

SeqTrainer BenchLab

Inspect labeled DNA datasets, plan a benchmark, run small baselines, and export reproducibility files.

When to use it
Use it first when you need to understand a labeled CSV/TSV or prepare a benchmark plan.
Do not use it when
Do not use it as a DNABERT2, iPro-MP, GPU, or HPC runner.
Expected input
Labeled CSV or TSV with sequence and label columns.
Expected output
run_config.json, benchmark_plan.json, manifests, and optional baseline metrics.
Where it runs
Your local computer; heavy training happens separately.
Part of this site?
Local web app, not part of this site.
Open repositoryRead instructions
Start here

SeqTrainer

Run sequence model workflows and scan GenBank plasmids for computationally predicted promoters.

When to use it
Use it when you have a compatible checkpoint and want to annotate a plasmid or run a benchmark.
Do not use it when
Do not use dummy mode for scientific conclusions.
Expected input
GenBank plasmid, model checkpoint, and benchmark manifest for annotation.
Expected output
Annotated GenBank, predictions CSV, annotation manifest, and branch-specific SBOL files.
Where it runs
Local Python, Google Colab, or HPC, depending on the model.
Part of this site?
External fork and branch-specific Python project; this site only documents commands.
Open repositoryRead instructions
Later step

SBOL Validator

Check SBOL and related biological files and convert between supported formats.

When to use it
Use it after producing an SBOL design and before opening that design in Canvas.
Do not use it when
Do not treat it as a simulator or a model quality checker.
Expected input
SBOL, GenBank, FASTA, or GFF3 file, depending on the supported Validator version.
Expected output
Validation messages and, when requested, a converted file.
Where it runs
The official external Validator website.
Part of this site?
External web tool; no files pass through this site.
Open repositoryOpen websiteRead instructions
Later step

SBOL Canvas

View and edit genetic designs using SBOL symbols and visual glyphs.

When to use it
Use it as the final visualization step after validating an SBOL file.
Do not use it when
Do not upload SeqTrainer's SBOL3 .nt file when the Canvas workflow expects SBOL2 .rdf.
Expected input
A validated SBOL2 RDF/XML .rdf compatibility file imported through Canvas itself.
Expected output
A visual design that you save or export from Canvas.
Where it runs
The separate SBOL Canvas application.
Part of this site?
External design application; layout may need manual inspection.
Open repositoryOpen websiteRead instructions

Suggested path

How the tools connect

Read the detailed workflow
  1. 01

    Plan and benchmark

    SeqTrainer BenchLab

  2. 02

    Annotate a plasmid

    SeqTrainer

  3. 03

    Validate the design

    SBOL Validator

  4. 04

    Visualize the design

    SBOL Canvas

File handoffs

What moves between tools?

The handoffs happen on your computer or in the original services. Seq Design Buddy only explains what to expect and which file to carry forward.

  1. Labeled CSV/TSV

    SeqTrainer BenchLab

  2. run_config.json and benchmark bundle

    External training job or a completed checkpoint

  3. SeqTrainer promoter annotation

    Annotated .gb + predictions.csv + annotation_manifest.json

  4. Optional SBOL3 .nt export

    SBOL Validator for validation

  5. Optional SBOL2 .rdf compatibility file

    SBOL Canvas import

Learn the vocabulary

Use the glossary when train, validation, test, checkpoint, or SBOL feels new.

Open glossary

Keep artifacts understandable

Read what each JSON, CSV, manifest, and design file is for.

See BenchLab outputs

Open the real tools

Every external link opens the original repository or official application in a new tab.

View the educational guide

Open the SeqTrainer teaching slides in a new tab.

View educational guide