What it does
Synthetic biologists draw genetic designs with a shared set of symbols, the SBOL Visual glyphs: a bent arrow for a promoter, a half circle for a ribosome binding site (RBS), a block arrow for a coding sequence (CDS), a T for a terminator, and so on. This tool turns a plain text list of parts into such a diagram, with lines for repression (a flat bar end) and activation (an arrow head) between a gene and the promoter it regulates.
It also reads the design like a careful colleague would:
- Transcription units: from each promoter along its strand to the first terminator, with the genes in it.
- Checks: a gene with no RBS just upstream, a gene no promoter reaches, a promoter with no terminator after it (read-through), an interaction that names a part that is not there, a regulator acting on something that is not a promoter or operator, and duplicate names.
Glyph types: promoter, operator, rbs, cds (or gene), terminator, insulator, ori (origin of replication), spacer and generic.
How to use it
- Type the parts in order, as name:type, separated by commas or new lines, for example
pTet:promoter, B1:rbs, gfp:cds, T1:terminator. Put < before a part on the reverse strand:<lacI:cds. - Add interactions on their own lines:
tetR -| pTet(tetR represses pTet) oraraC -> pBAD(activates). - Or use the Add a part and Add an interaction boxes.
- Download the diagram as SVG (for papers and slides) or PNG, or the whole report as an image, PDF or Word file.
Worked example
The example is the repressilator: three genes, each repressing the next one’s promoter, in a ring. The parts are pLlacO1, rbs1, tetR, T1, pLtetO1, rbs2, cI, T2 and pR, rbs3, lacI, T3, with lacI -| pLlacO1, tetR -| pLtetO1 and cI -| pR. The page shows 12 parts, 3 transcription units, 3 interactions, three red repression arcs on separate levels so they do not cross, and “No problems found”. Delete rbs2 and the checks report that cI has no ribosome binding site just upstream; delete T3 and they report that pR reads through to the end.
Tips
- Names must be unique so interactions point at the right part.
- Operators and spacers between an RBS and its gene are allowed by the checks.
- The SVG uses plain shapes and text, so you can restyle it in any vector editor.
FAQ
Is this an official SBOL file? No: it draws pictures in the SBOL Visual style. It does not write SBOL data files.
Does it simulate the circuit? No. The checks catch drawing slips, not biology; a design that passes may still not behave as hoped.
Where the numbers come from
- Glyph shapes follow the descriptions in the SBOL Visual standard (Synthetic Biology Open Language Visual, sbolstandard.org); fibub draws its own versions of the shapes.
- The example is the repressilator design idea (Elowitz, M. B. and Leibler, S. (2000), Nature 403, 335), written with generic part names.
- Checked against hand-worked designs: the repressilator, a reverse-strand unit with an operator, and broken designs for each warning.
Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.
Last updated 2026-11-09.