Roadmap
Every area of the workbench (50), reported as it stands: what ships and works (shipped), what works with named gaps (partial), and what is designed but not started (planned). Drag a card between columns to sort the board for yourself: it does not change the status.
Shipped
25Cloning & molecular-biology engine
One engine reimplementing pydna, DnaCauldron, QUEEN, DnaChisel, SeqTrace/cfutils/sangerseqR, poapy, pyMSA, crisprScore, cas-offinder, phangorn, qpcR and more, each checked byte for byte against the original. It runs with no interface attached, so the editor, the API and the assistant all call the same code
Golden Gate / Type-IIS assembly
Type-IIS assembly with measured ligation fidelity.
Ligation & restriction-ligation
Sticky-end, blunt-end, and cut-and-ligate in one tube. The editor could cut DNA and had nowhere to put the fragments.
Recombination cloning
Gateway BP/LR, Cre-lox and other recombinases, and homologous recombination.
Restriction digest & virtual gel
Multi-lane digest tool backed by the ports gel and migration model.
Virtual gel bench
A free-standing gel where lanes come from anywhere in the project, not only from a digest.
Primer Library
The project primer inventory: does this oligo already exist?
Melting temperature
The one place the editor decides what Tm means, so every tool agrees on the answer.
qPCR & digital PCR
Seven analyses plus assay design, and the first surface to pass an explicit completeness gate.
Codon Optimizer
The full DnaChisel constraint solver, wired as an editor tool.
Back-translate (protein to DNA)
The DNA that would encode a protein, weighted by a real codon-usage table.
RBS & operon design
Ribosome-binding-site strength and operon layout against a real CDS target.
NGS barcode & index design
Error-correcting DNA barcode sets, as a table you edit rather than a result you regenerate.
Multiple sequence alignment
A real MSA tab on a ported partial-order aligner, not a viewer over someone else output.
Sequencing verification & compare to reference
Did the construct come back right?
Dot plot
Visual sequence comparison by three genuinely different algorithms, plus the all-against-all grid.
Phylogenetics
Tree inference from an alignment, including maximum likelihood and model selection.
Protein analysis (ProtParam)
Physicochemical properties of a protein or a translated CDS, computed locally.
Protease digest
Peptides, masses and an MS window from a real cleavage-rule engine.
Protein domains (InterProScan)
De-novo domain and motif annotation. The one tool that is deliberately not local-first.
File import & format support
One importer for the whole app, with content sniffing at the gate rather than extension trust.
Fetch from database
Pull a real record in by accession instead of hunting for a file.
Export, provenance & version history
Getting work out, and knowing how it got there.
Projects, workspace & persistence
Disk-authoritative projects with a rebuildable local cache.
User documentation site
apps/docs, a separate build.
Partial
20Plasmid / Sequence Editor
The plasmid editor: circular, linear and sequence views over one shared document. Every project opens through it, and every tool below docks into it.
Annotation feature-type coverage
Which GenBank/INSDC feature types the editor recognizes by name, with a curated color and a picker entry, checked against the live source that feeds the "Add feature" type picker.
Visualization layer
The shared plotting primitives every analysis panel draws through, so a chart is one component rather than one per tool.
Gibson Assembly
DnaCauldron-backed Gibson planning, docked in the editor right rail.
Grammar assembly (MoClo / GoldenBraid)
Standard-grammar hierarchical assembly, L0 through L3, with parts bins.
Primer Designer
Primer design against the live sequence, on the ported thermodynamic stack.
PCR simulation, fusion PCR & multiplex PCR
Three docked surfaces over one amplification engine.
Codon usage analysis & codon tables
Codon adaptation of the open sequence, plus the genetic-code catalog behind it.
CRISPR guide design
PAM search, guide scoring and off-target search against the open sequences.
Site-directed mutagenesis
Point mutations, saturation libraries and the primers to make them.
Sanger / chromatogram trace editor
A trace editor in its own project tab, not a read-only viewer.
Read alignment (BAM / SAM pileup)
Aligned reads as a real pileup canvas inside the workbench.
Variant table (VCF)
VCF as a first-class document kind, coupled to the sequence canvas.
BLAST & EMBL-EBI services
The remote analyses that genuinely cannot run in a browser tab.
Document renderers
The seam that decides what a file looks like when you open it, so a format is registered honestly even before it can be drawn.
Databases (federated authority search)
One search across the authoritative registries, measured against them rather than assumed.
Workflow builder
A non-linear pipeline over the tools, not a macro recorder.
Lab notebook
Notes that live with the project and can reference its objects.
Accounts, sharing & feedback
The parts that need a server, kept to the parts that need a server.
AI copilot
An assistant that can see the workbench and act inside it.
Planned
5Genome-scale genomics
Everything that needs a genome rather than a construct.
Knowledge & pathway layer
The databases exist; the experience does not.
Design & synthesis
Adjacent design stacks we have the engine for and not the surface.
Systems biology
The modeling half, entirely absent.
Nucleic-acid folding
One missing engine, and the reason several features above ship an honest proxy instead of a number.
jane* covers in one workspace what is normally split across a plasmid editor, a cloning planner, a sequence analyser, and a set of design tools. It provides circular, linear, and sequence views with live editing, annotation management, primer design, restriction analysis, feature editing, translation and ORF analysis, plasmid visualization, gel simulation, SnapGene and Serial Cloner file handling with full history, chromatogram inspection with quality analysis, Sanger verification, multiple-sequence alignment, phylogenetic inference, dot-plot comparison, read pileups, variant tables, provenance tracking, and search. It simulates and designs PCR, qPCR and digital PCR, Gibson Assembly, Golden Gate, ligation, homologous and site-specific recombination, BioBrick, BASIC, ligase cycling assembly, MoClo and GoldenBraid grammars, CRISPR guides, codon optimization under real constraint solving, RBS and operon design, NGS barcode sets, and cloning verification, each running on one shared algorithmic engine rather than a separate implementation per tool.
The governing constraint is a single data model behind editing, analysis, visualization, and construct engineering: one operation updates the whole project at once, from annotations and primers through restriction maps, assembly products, sequencing results, and provenance. Every algorithm the engine implements is reachable through the same interface, and every capability reads the live editor context instead of asking for the same sequence twice. Still to build, and named honestly rather than implied: whole-genome scale surfaces (CRISPR screens, spatial and single-cell workbenches) and the systems-biology layer.