Database Release & Changelog

CnidoSite is versioned. This page states which release you are using, when it was built, what changed in it, and when the next updates are due — so that any result you obtain here can be traced back to a specific version of the database.

Current release
CnidoSite r1.1
Build / last-update date
2026-09-16  (all dates on this page are ISO 8601, UTC)
Previous release
r1.0  — if you used CnidoSite before 2026-09-16, you were on this or an earlier version
First public release
2025-11-18
Archived snapshot
Not yet deposited in an external archive. The live release is self-describing through this page and through the version endpoint.
How to cite this release
CnidoSite r1.1 (build 2026-09-16). Accessed 2026-09-16.

Update schedule

Content releases are scheduled twice a year, in June and December. Corrective releases (bug fixes, security fixes and metadata corrections) are deployed as soon as they are verified and are recorded in the changelog below with their own date.

Each release is identified by the version string above, which is also shown in the footer of every page of the site. The machine-readable form of this information is available at api.php?resource=release.

Changelog

Newest first. Entries describe changes that are visible to a user of the site; internal refactoring is not listed.

r1.1 2026-09-16 Revision release — peer-review response
  • All species and taxonomic-class selectors are now rendered by the server instead of being built in JavaScript. Species lists are populated from the database in every module, so the selectors work with JavaScript disabled and no longer show an empty or stale list.
  • The deprecated JavaScript option-list library was removed from all 43 pages that still loaded it. It rebuilt every dependent drop-down on page load from hard-coded arrays, which is why child selectors could empty themselves or disagree with the species actually selected.
  • Proteomic Analysis: the species selector submitted a short code (for example "SPIST") while the underlying data tables are keyed by the full species name ("Stylophora_pistillata"), so those selections produced an empty table and a raw database error. The page now resolves either form through the species table, only queries a table that exists, and states plainly which dataset it is showing when the requested one is unavailable.
  • The duplicate copy of the Proteomic Analysis page under /submit/ was replaced by a permanent redirect to the live tool. It was reachable but not linked, used a separate and equally stale code path, and discarded the user's input.
  • Pfam and BUSCO result pages: the species parameter is now validated and escaped before being used in a query, and the pfam accession likewise. Both pages previously interpolated these values into SQL unescaped, which allowed an arbitrary-table read, and echoed them into the page unescaped, which allowed script injection. A malformed link on the Pfam table was also corrected.
  • Gene-set enrichment result pages: the job identifier, species code and gene-set name are now validated against their real value ranges before any use. The job identifier is restricted to digits and the species and gene-set names to their permitted character sets, closing a path-traversal and an injection route reachable from a crafted result URL.
  • Download handler hardened: the file parameter is reduced to a base name, resolved with realpath() and refused unless it lies inside the download directory. Requests for files that do not exist now return 404 instead of a silent zero-byte download, and large files are streamed rather than read into memory.
  • New Data Coverage Matrix page: a species-by-data-type availability table covering all species and all 15 data types, with each populated cell linking directly to the corresponding module for that species. Downloadable as tab-separated text.
  • New Functional Domain Search page and new per-species portal pages.
  • New release and changelog page (release.php) with the database version number, last-update date, update schedule and this changelog, plus a machine-readable metadata interface (api.php) and a downloadable file manifest for scripted access. The version stamp now appears in the footer of every page.
r1.0 2026-05-28 Content release
  • Mitochondrial datasets added to the Mitogenomic Data module.
  • Pan-geneset analysis added.
  • Species description pages added.
  • Cnidarian phylogeny made available in the Species Tree module.
  • Phenotype datasets added.
  • Multi-omics pages brought online (genome, transcriptome, single-cell, proteome, epigenome, metagenome).
  • Dynamic expression view added to the network module.
  • Gene-set enrichment analysis made available.
  • BLAST search tool integrated.
  • Taxonomic browsing implemented across the catalogue.
  • Co-expression networks added.
  • Primer design tool added.
  • JBrowse genome browser deployed.
r0.9 2025-11-18 Initial public release
  • CnidoSite first released, with the cnidarian genome and fossil-record modules.

Bulk download and programmatic access

Every dataset behind these pages can be retrieved without using a browser. The site exposes a read-only metadata interface that returns JSON or tab-separated text, and a file manifest that lists the entire download collection so it can be fetched with a single loop.

What you want Request Notes
Version, build date, full changelog api.php?resource=release Also available as TSV, one row per change.
Every species with its class and abbreviation api.php?resource=species TSV; add &class=Hydrozoa to restrict to one class.
Which species have which data api.php?resource=coverage The same matrix as the Data Coverage Matrix page, as data rather than HTML.
Site-wide totals api.php?resource=stats Species count, per-module coverage, number of download files and total volume.
The list of every downloadable file api.php?resource=downloads&format=tsv One row per file: name, species, class, data type, size in bytes and the direct download URL.

To mirror the whole collection, take the manifest and follow it:

curl -O 'https://cnidosite.org/api.php?resource=downloads&format=tsv'
awk -F'\t' 'NR>1 {print $6}' cnidosite-downloads.tsv | xargs -n1 -P4 curl -C - -O

Files are streamed by download_fun.php rather than read into memory, and curl -C - resumes an interrupted transfer, so the 31 GB collection can be mirrored reliably over a slow link. The same interface is documented, with all parameters, at api.php.

Where the data and their provenance are documented

QuestionWhere it is answered
Which sequences and annotations can I download, per species? Download — per-species table of genome, CDS, protein, GFF3, repeat and gene-family files, plus api.php?resource=downloads for the full list.
Which software and parameters produced each dataset? Statistics — a Software and Analytical Tools table, per module, with tool versions and command-line parameters.
Which species have which data types? Data Coverage Matrix, downloadable as tab-separated text.
Taxonomy, assembly statistics and accession numbers Each species has a portal page reachable from Taxonomy, carrying its assembly level, size, N50, BUSCO summary and accession.

Dataset-level provenance for the manuscript — original accession number, source publication, reference genome and genome version used for processing, processing pipeline version and date of incorporation for each incorporated dataset — is provided as a supplementary table with the paper. This page covers what the website itself makes visible.

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