Build itPaste the brief into OpenCode and check that colouring by CD3E lights up the T-cell clusters.
OpenCode · development brief
Build a single-cell explorer from the exported JSON: UMAP scatter coloured by cluster, gene search that colours cells by expression with a sequential scale, a per-cluster marker table, and cell counts. State the processi▎
Single-cell mini explorerSource & credit
Single-cell mini explorer: Trace one cluster: cells → UMAP position → cluster label → top markers → expression of one gene.
Single-cell mini explorer Owner-supplied illustrative interface; source figures credited below.
Builds on: scanpy (BSD-3) precompute; PBMC 3k dataset (10x, CC BY 4.0)
Hero recipe: Rendered UMAP with eight cluster colours from the reference palette
Must not claim: No cell-type identity beyond marker-based labels; no differential-expression significance without the test named.
Owner-supplied illustrative interface; source figures credited below.
Cell biology & imaging
OME-Zarr cloud image browser
Paste the brief into OpenCode, open the IDR URL and toggle channels at two zoom levels.
Understand itTrace one image: URL → multiscale metadata → pick a resolution level → channels, z, t → display.
Input: OME-Zarr URL
↓Process: read metadata, fetch chunks for the current view
↓Output: viewer with channel toggles, sliders, metadata panel
Choose toolsvizarr or a small custom viewer, ome-zarr-py for validation, no LLM.
vizarr (MIT) — browser viewerome-zarr-py — validation and metadataIDR — public data (CC BY 4.0)
Build itPaste the brief into OpenCode, open the IDR URL and toggle channels at two zoom levels.
OpenCode · development brief
Build an OME-Zarr browser: paste a Zarr URL, read multiscales and channel metadata, show the image with channel toggles and contrast controls, z and t sliders, a resolution-level indicator and a metadata panel. Cite the ▎
OME-Zarr cloud image browserSource & credit
OME-Zarr cloud image browser: Trace one image: URL → multiscale metadata → pick a resolution level → channels, z, t → display.
Builds on: ome-zarr-py (BSD-2), vizarr (MIT); IDR public Zarr (CC BY 4.0)
Hero recipe: IDR image 6001240 rendered with channel toggles in a viewer frame
Must not claim: Display only; intensities are not calibrated or comparable across channels.
Owner-supplied illustrative interface; source figures credited below.
Ecology & evolution
Camera-trap triage
Paste the brief into OpenCode, run the sample folder and review 50 frames with the keyboard.
Choose toolsMegaDetector for detection; a grid UI; no species ID.
MegaDetector v5/v6 (MIT) — class-level detectionReview grid — keyboard-driven accept/rejectNo LLM, no species classifier
Build itPaste the brief into OpenCode, run the sample folder and review 50 frames with the keyboard.
OpenCode · development brief
Build a camera-trap triage tool: run MegaDetector over a folder, show a review grid with boxes and confidence, a threshold slider, bins for empty/animal/person/vehicle, keyboard accept/reject, and export corrected labels▎
Camera-trap triageSource & credit
Camera-trap triage: Trace one frame: detector → boxes with class and confidence → threshold → bin → human review.
Builds on: MegaDetector (MIT); LILA Snapshot Serengeti (CDLA-Permissive)
Hero recipe: LILA sample frame with a rendered detection box and a review grid
Must not claim: Class-level only; no species ID; no population estimates.
Owner-supplied illustrative interface; source figures credited below.
Research workflows
Literature triage with citations
Paste the brief into OpenCode, run a query you know well and check five summaries against their abstracts.
Choose toolsEurope PMC API, an LLM under a quote-only rule, a board UI.
Europe PMC REST — search and abstracts (free)LLM — extracts quotes only; cannot paraphraseBoard UI — include / maybe / exclude
Build itPaste the brief into OpenCode, run a query you know well and check five summaries against their abstracts.
OpenCode · development brief
Build a literature triage app: run a Europe PMC query, show each result with title, abstract and PMID, generate a summary that consists only of verbatim quotes from the abstract with the PMID attached, let a reviewer mar▎
Literature triage with citationsSource & credit
Literature triage with citations: Trace one paper: search → abstract → LLM summary limited to quoted sentences → human decision → log.
Literature triage with citations Owner-supplied illustrative interface; source figures credited below.
Builds on: Europe PMC REST (free, keyless), Crossref; note OpenAlex now needs an API key with usage pricing
Hero recipe: Rendered screening board with include/exclude columns and quoted-evidence cards linking to PMIDs
Must not claim: No completeness claims; nothing not traceable to a fetched abstract or full text.
Owner-supplied illustrative interface; source figures credited below.
Research workflows
Protocol → bench checklist
Paste the brief into OpenCode, load a protocol you have run and check the reagent tally against your own calculation.
Understand itTrace one step: original text → derived checklist item + duration + reagents → progress state → print view.
Input: protocol steps (CC BY)
↓Process: LLM derives items, durations and reagent tallies; each item links to its step
↓Output: checklist with timers, reagent totals, printable view
Choose toolsprotocols.io API, an LLM for extraction, a checklist UI with local state.
protocols.io API — public protocolsLLM — extracts items, durations, reagents; flagged as derivedChecklist UI — progress, timers, print
Build itPaste the brief into OpenCode, load a protocol you have run and check the reagent tally against your own calculation.
OpenCode · development brief
Build a protocol-to-checklist app: fetch a public protocols.io protocol, show the original steps, derive a checklist with durations and a reagent tally, start timers per item, keep progress locally, and print the checkli▎
Protocol → bench checklistSource & credit
Protocol → bench checklist: Trace one step: original text → derived checklist item + duration + reagents → progress state → print view.
Builds on: protocols.io API v3/v4 (public protocols are CC BY); free access token
Hero recipe: Rendered checklist with timers beside the original protocol steps; Wikimedia 'Pipetting.jpg' (public domain) as context
Must not claim: The checklist never replaces the protocol; no safety adequacy claims.
Owner-supplied illustrative interface; source figures credited below.