Sequence design, and the tube in the freezer it turns into
Cloning, CRISPR, and primer design in the browser, with every construct still connected to the stock it became, the gel that confirmed it, and the figure it ends up in.
The molecular biology bench, in one browser tab
One project. Every map, oligo, gel, and figure stays linked to the construct it belongs to and the tube in the freezer it became.
Design
Plasmid maps, restriction analysis, and a cloning wizard with gel visualization in the browser, with versioning and lineage so a construct records which parent it came from.
How most labs do it today. The map is a file on one laptop. Three versions later, the version that actually got built is whichever one happened to be open that afternoon.
CRISPR
Guide design and primer design sit next to the sequence they target, and the oligos you order stay linked to the construct they were made for.
How most labs do it today. Guides are designed in one place, ordered in another, and the oligos land in a sheet that nothing else reads.
Catalogue
Constructs, strains, and cell lines are samples with structured metadata and lineage. The catalogue and the inventory are part of the product, not a separate tier.
How most labs do it today. Benchling now leaves Registry and Inventory out of new academic tenants, so the catalogue and the freezer go back to being spreadsheets maintained by hand.
Freezer stocks
Map freezers, shelves, and boxes so a construct's stock has a real location, attached to the sequence it holds.
How most labs do it today. The map says clone 7 works. The freezer has four tubes labelled 7, spread across three boxes.
Verify
View chromatograms and align the read against the designed sequence, with the verification attached to the construct it verifies.
How most labs do it today. The .ab1 stays in an inbox. Nothing durable records that clone 4 was the one that passed, so six months later you sequence it again.
Gels
Gel and microscopy images attach to the same sample as the construct, with intensity and area measurement in the browser.
How most labs do it today. The gel that confirmed the clone is a JPEG in a folder named by date, connected to the clone by nothing but the date itself.
Figures
Charts are built from the underlying data, and multi-panel figures are assembled from the analysis rather than screenshotted beside it.
How most labs do it today. Results are pasted into a stats package and plots into a figure, and the panel that comes out points back at nothing.
Writing
Notes, protocols, sequences, and figures sit in one project, so an entry can point at the construct it's about.
How most labs do it today. The notebook describes the cloning strategy in prose, and links to nothing that can be clicked.
See it on your own construct
Import a plasmid map and keep the sequence, the clones it produced, and the gel that confirmed them in one project.