Our Work

peff_uniprot_fetcher generates PEFF (PSI Extended FASTA Format) files from the UniProt REST API. It fetches protein sequences and GFF annotations (natural variants, PTMs, processed forms) and writes t…

peff_uniprot_fetcher generates PEFF (PSI Extended FASTA Format) files from the UniProt REST API. It fetches protein sequences and GFF annotations (natural variants, PTMs, processed forms) and writes them as annotated PEFF using pefftacular, with modification mapping backed by psimodpy, unimodpy, and uniprotptmpy. It requires Python 3.12 or later.

tdfextractor reads Bruker timsTOF .d folders (DDA, DIA, and PRM acquisitions) via tdfpy and writes MS2, MGF, and mzML spectrum files for downstream search engines and processing pipelines. It supports…

tdfextractor reads Bruker timsTOF .d folders (DDA, DIA, and PRM acquisitions) via tdfpy and writes MS2, MGF, and mzML spectrum files for downstream search engines and processing pipelines. It supports precursor filtering by intensity, charge, m/z, retention time, CCS, and neutral mass, configurable peak centroiding and noise filtering, and per-array compression and encoding for mzML output. It requires Python 3.12 or later.

This is a complete, pre-configured Raspberry Pi OS disk image containing the working software and configuration for the Ecophysiometer, an open-hardware environmental monitoring device. It accompanies…

This is a complete, pre-configured Raspberry Pi OS disk image containing the working software and configuration for the Ecophysiometer, an open-hardware environmental monitoring device. It accompanies the manuscript "The Ecophysiometer: an open science approach to improve environmental monitoring" and reproduces the working system used to generate the results reported there. The image can be written directly to a microSD card (e.g. with Raspberry Pi Imager, balenaEtcher, or dd) and booted on compatible Raspberry Pi hardware without installing any software manually. It corresponds to the source code and hardware design archived at 10.5281/zenodo.22906767 or https://github.com/australScientist/PEF1

Version 1.1 (23 septembre 2026). Marge équatoriale brésilienne reclassée de « revendiqué » à « reconnu » (recommandations de la CLPC approuv&…

Version 1.1 (23 septembre 2026). Marge équatoriale brésilienne reclassée de « revendiqué » à « reconnu » (recommandations de la CLPC approuvées le 27 février 2025). Encadré du panneau B : plateau reconnu ≈ 0,55 M km² ; plateau soumis ≈ 1,5 M km². Mention « dénomination proposée » au panneau A. Nouveau fichier : panneau C seul. Côté brésilien, « reconnu » désigne les zones ayant fait l'objet de recommandations de la CLPC (région sud 2019, marge équatoriale 2025). Côté français, les limites du plateau sont en outre fixées par décret (n° 2020-376). L'Élévation du Rio Grande et la marge orientale-méridionale restent en soumission. La CLPC décrit le rebord externe de la marge comme partant « from the border with France in respect of the area of French Guiana » et s'abstient de recommander une limite dans ce secteur pour ne pas préjuger de la délimitation France–Brésil (§§ 71 et 78 du résumé). Figure originale en trois panneaux comparant les espaces maritimes français au large de la Guyane (« Guyane bleue », dénomination proposée par l'auteur) et les espaces maritimes brésiliens (« Amazônia Azul ») : mer territoriale, zone économique exclusive (200 milles) et plateau continental au-delà de 200 milles (reconnu par la CLPC / décret, ou seulement soumis). Le dépôt contient : (1) la figure complète ; (2) une note de données (sources des géométries, définitions, écarts de surfaces MarineRegions–Shom) ; (3) un tableau CSV des surfaces de référence ; (4) le panneau C seul ; (5) les notes de version. Le fichier surfaces_reference.csv n'a pas été modifié en v1.1 ; pour le plateau brésilien, l'encadré du panneau B et les notes de version priment (reconnu ≈ 0,55 M km² ; soumis ≈ 1,5 M km²). Géométries : MarineRegions / VLIZ, Maritime Boundaries Geodatabase v12 (doi:10.14284/632, doi:10.14284/697) et Natural Earth. Marge équatoriale brésilienne : CLPC, résumé des recommandations du 27 février 2025, table 4. Surfaces françaises de référence : Shom, tableau des superficies au 26 janvier 2023 (limitesmaritimes.gouv.fr). Surfaces brésiliennes de référence : Marinha / LEPLAC / CIRM ; marge équatoriale ≈ 360 000 km² (note conjointe MRE / Marinha, 3 avril 2025). Écart principal documenté : le polygone « EEZ » MarineRegions de Guyane (~131 506 km²) agrège eaux intérieures + mer territoriale + ZEE ; le Shom isole une ZEE stricto sensu de 121 746 km². Contrôle : 2 950 + 6 810 + 121 746 = 131 506 km². Plateau français au-delà de 200 milles : 69 955 km² (Shom 2023), fourchette de lecture de la figure 62–72 000 km² (communication EXTRAPLAC / recommandation CLPC 2009 ~72 000 km² ; décret n° 2020-376). La figure n'est pas une délimitation officielle. Au-delà de 200 milles, les droits portent sur le sol et le sous-sol seulement (art. 77 CNUDM). English — Version 1.1: Brazil's Equatorial Margin reclassified from submitted to CLCS-recommended (recommendations approved 27 February 2025); the Rio Grande Rise and the Eastern-Southern Margin remain under review. Panel B box: recognised shelf ≈ 0.55 M km², submitted ≈ 1.5 M km². Original three-panel figure comparing French maritime spaces off French Guiana ("Guyane bleue", a name proposed by the author) and Brazilian maritime spaces ("Amazônia Azul"): territorial sea, EEZ (200 nautical miles), and continental shelf beyond 200 nm (CLCS-recommended / decreed versus submitted only). Main documented discrepancy: MarineRegions' French Guiana "EEZ" polygon (~131,506 km²) aggregates internal waters + territorial sea + EEZ; Shom reports a strict EEZ of 121,746 km². Check: 2,950 + 6,810 + 121,746 = 131,506 km². Not an official delimitation. Beyond 200 nm: sovereign rights over the seabed and subsoil only.

This artifact contains the code and inputs needed to reproduce selected experimental results from the MagicFlow paper. It runs fresh magic-state cultivation, factory, utilization, routing, circui…

This artifact contains the code and inputs needed to reproduce selected experimental results from the MagicFlow paper. It runs fresh magic-state cultivation, factory, utilization, routing, circuit-level error, and Shor case-study experiments, then generates Figures 17–22, 24–25, and 27–28 and Tables 3–4 from the resulting data. The included README provides setup and execution commands and maps each generated result to the paper.

paper-scaffold is a Typst manuscript scaffold in which every number in the prose is read by id from a declaration file written by the analysis, with a checksum, a record of the code and data behind it…

paper-scaffold is a Typst manuscript scaffold in which every number in the prose is read by id from a declaration file written by the analysis, with a checksum, a record of the code and data behind it, and guards on what the prose assumes about it. A static gate reports stale figures, tables and builds without re-running the analysis, and checks prose rules, word limits and journal profiles. Word export goes through pandoc with native equations. An edit guard lets a wording pass drop a number but never invent one, and a set of packaged agent skills audits claims and methods against the code that computes them.

What's Changed Upgrade all Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1248 Adopt SchemaFrame::Mode::Root from Blaze by @jviotti in https://github.com/sourcemeta/one…

What's Changed Upgrade all Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1248 Adopt SchemaFrame::Mode::Root from Blaze by @jviotti in https://github.com/sourcemeta/one/pull/1249 Upgrade Blaze to d911fa085995ce3c4fe3d7027cf9252a4c16c47f by @jviotti in https://github.com/sourcemeta/one/pull/1250 Start benchmarking server operations by @jviotti in https://github.com/sourcemeta/one/pull/1247 Revise benchmark location by @jviotti in https://github.com/sourcemeta/one/pull/1251 Start decreasing dependence on Blaze's foundation module by @jviotti in https://github.com/sourcemeta/one/pull/1252 Upgrade Blaze to 079b9d438b37ee40966730c79a498abda84c04f8 by @jviotti in https://github.com/sourcemeta/one/pull/1253 Upgrade uWebSockets to v20.80.0 by @jviotti in https://github.com/sourcemeta/one/pull/1254 Upgrade Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1255 Stop exposing pointer locations on the locations endpoint by @jviotti in https://github.com/sourcemeta/one/pull/1256 Upgrade all Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1257 Fix ClangTidy warnings on the Community build by @jviotti in https://github.com/sourcemeta/one/pull/1258 Implement a new schema trace playground endpoint by @jviotti in https://github.com/sourcemeta/one/pull/1259 Fix KraftCloud public deployment timeouts by @jviotti in https://github.com/sourcemeta/one/pull/1261 Support the new trace playground endpoint over MCP by @jviotti in https://github.com/sourcemeta/one/pull/1260 Expose whether a schema is a meta-schema in its metadata by @jviotti in https://github.com/sourcemeta/one/pull/1262 Make the metaschema metadata flag independent of the view by @jviotti in https://github.com/sourcemeta/one/pull/1263 Support converting schemas into newer official dialects (Enterprise) by @jviotti in https://github.com/sourcemeta/one/pull/1264 Upgrade all Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1265 Reject boolean schemas with a clear error instead of crashing by @jviotti in https://github.com/sourcemeta/one/pull/1266 Never convert meta-schemas, and say why in the docs by @jviotti in https://github.com/sourcemeta/one/pull/1267 Cite Dr. JSON-LD in the RDF API docs by @jviotti in https://github.com/sourcemeta/one/pull/1271 Cite the API Evangelist new post on the guide by @jviotti in https://github.com/sourcemeta/one/pull/1272 Explain in the docs why ingested schemas get a new $id by @jviotti in https://github.com/sourcemeta/one/pull/1269 Add one-ui as a top-level ui/ folder by @itvi-1234 in https://github.com/sourcemeta/one/pull/1270 Report the base dialect of each dependency and dependent by @jviotti in https://github.com/sourcemeta/one/pull/1268 Declare the conversion in a converted schema's identifier by @jviotti in https://github.com/sourcemeta/one/pull/1274 Make the ./ui build not depend on any third-party CDN by @jviotti in https://github.com/sourcemeta/one/pull/1276 Point a converted schema's references at matching conversions by @jviotti in https://github.com/sourcemeta/one/pull/1275 Build and install the experimental web UI (share/sourcemeta/one/ui) by @jviotti in https://github.com/sourcemeta/one/pull/1277 Support an experimental web UI behind a configuration option by @jviotti in https://github.com/sourcemeta/one/pull/1278 Allow asking for a schema in the dialect it already declares by @jviotti in https://github.com/sourcemeta/one/pull/1280 Add manifest.webmanifest and icon assets to the UI, like the old one by @itvi-1234 in https://github.com/sourcemeta/one/pull/1282 Upgrade Sourcemeta dependencies by @jviotti in https://github.com/sourcemeta/one/pull/1283 Always bundle converted schemas by @jviotti in https://github.com/sourcemeta/one/pull/1281 Better explain auto-upgrades by @jviotti in https://github.com/sourcemeta/one/pull/1285 New Contributors @itvi-1234 made their first contribution in https://github.com/sourcemeta/one/pull/1270 Full Changelog: https://github.com/sourcemeta/one/compare/v7.1.0...v7.2.0

Changes inspectdf dependency removed: inspectdf was archived from CRAN on 2026-04-10, which made the package impossible to install from a clean library (any dependency resolution against the CRAN sou…

Changes inspectdf dependency removed: inspectdf was archived from CRAN on 2026-04-10, which made the package impossible to install from a clean library (any dependency resolution against the CRAN source index, e.g. pak in GitHub Actions, failed with "Can't find package called inspectdf") New plot_na_percentage(): bar plot with the percentage of NA values per column, computed with naniar::miss_var_summary() (naniar was already a dependency). It replaces the inspectdf::inspect_na() %>% show_plot() chart in the metabolomics, olink, and proteomics QC plots, producing the same chart (same values, column order, and text labels) Bug Fixes Olink QC plots failed with ggplot2 4.0: the id-count plots of plot_basic_olink_qc() labelled the bars with aes(label = n) instead of olink_count, so ggplot2 resolved n to a function. ggplot2 4.0 rejects that ("Aesthetics are not valid data columns"), so the olink QC plots failed for any dataset with 200 samples or fewer Tests Unit tests for plot_na_percentage() and end-to-end tests of plot_basic_metabolomics_qc() (bundled data) and plot_basic_olink_qc() (synthetic data) writing the QC pdfs