Krueger, Felix

1 files · 22 MB · zipdeclared

Trim Galore is a single-binary adapter and quality trimmer for FASTQ files, with built-in support for bisulfite sequencing (RRBS, WGBS, EM-seq), poly-G / poly-A trimming, paired-end validation, UMI-aware specialty modes (--clock, --implicon), inline demultiplexing, and an integrated FastQC report. The v2.x line is a Rust rewrite of the original Perl Trim Galore (v0.6.x) and is byte-for-byte compatible with v0.6.11 on the core flag paths covered by CI.

Markkanen, Melina · Putkuri, Heidi · Kičiatovas, Dovydas · et al.

1 files · 3.7 MB · zipdeclared

Analysis scripts for the manuscript "Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities".

Shim, S.-H. Dan

1 files · 742 KB · zipdeclared

RamPo is a Python desktop application for processing Raman spectroscopy data, with workflows adapted for high-pressure Raman experiments.

SPARC Europe

1 files · 23 MB · pngdeclared

This SPARC Europe illustration and accompanying text form a visual argument for structural change toward a more sustainable OA scholarly communication ecosystem in Europe. It is designed as a conversation-starter for national and regional OA policymakers, research funders, and other advocates working toward systemic change in European OA scholarly communications. We hope this illustration fuels the conversations needed to move from the open access world we have to the world we want. Please share any thoughts or questions you might have: info@sparceurope.org

Lindgren, Eric · Rahm, J. Magnus · Fransson, Erik · et al.

1 files · 4.5 MB · zipdeclared

calorine is a Python library for constructing and sampling neuroevolution potentials (NEPs) via GPUMD . It provides ASE calculators, IO functions for reading and writing GPUMD input and output files, as well as a Python interface that allows inspection NEP models.

Hernangómez, Diego

1 files · 2.4 MB · zipdeclared

Provides access to public spatial data from the Cadastre of Navarre through its 'INSPIRE' ATOM, WFS and WMS services. Supports complete municipal dataset downloads, bounding box feature queries and georeferenced map image downloads for addresses, buildings and cadastral parcels.

Phan, Viet Anh · Jerabek, Jan

1 files · 2.9 MB · zipdeclared

Reproducible artifact for the article "Executed Security Analysis of Dual-Stack Lite: Full-Stack Attack Execution, a Five-Dimensional Taxonomy, and Mitigation Strategies" (submitted to Computers & Security). Contains the one-command Docker testbed realizing the DS-Lite (RFC 6333) reference architecture across the data, control, and management planes; 15 attack tools spanning softwire spoofing/interception/injection, fragment-reassembly poisoning, PCP abuse, DHCPv6/DNS AFTR-discovery hijacking, and DS-Lite MIB access over SNMP; an independent verifier (packet captures plus direct reads of the AFTR and B4 state, and observed device behavior) with the per-attack reference captures for the baseline, every attack, and every mitigation before and after it is applied; the five-dimensional attack taxonomy (Landing Surface, Impact, Architectural Layer Dependency, Affected-Population Scope, Attacker Position) with its classifier and quality-verification scripts; one attack-defense tree per attack rendered with QuADTool, the PRISM reachability check, and the binary mitigation-coverage matrix; and the 11 verified, reversible mitigations with their apply/verify scripts. The article is self-contained; this archive holds the exhaustive supporting detail and regenerates every numerical result and capture from one command.

Langermann, Florence · Blaschta, Stephanie · Dietze, Klara · et al.

3 files · 731 KB · geopackagedeclared

Beschreibung (Deutsch) Diese Datenpublikation enthält archäologische Geodaten aus den Forschungsprojekten "The Cultic Centre of the Sun-God of Heliopolis (Egypt)" und „Eclipse and Mutation: The end of the sun temple of Heliopolis" zu den ergrabenen und aufgefundenen Befunden im altägyptischen Heiligtum in Heliopolis im heutigen Kairo. Die Befunde wurden innerhalb einer Reihe von Grabungskampagnen zwischen 2012 bis 2024 ergraben und dokumentiert. Diese Datensammlung stellt eine Zusammenstellug dieser Befunde dar und soll als Grundlage für eine Gesamtkartierung dienen. An der Zusammenstellung der Daten waren maßgeblich die drei verantwortlichen Ausgräberi:innen Stephanie Blaschta , Klara Dietze und Florence Langermann beteiligt. Für die Erstellung der Datenstrukturen und Schemata und dem Zusammenführen der Daten war Michael Schleier verantwortlich. Das Projekt wurde von der Deutschen Forschungsgemeinschaft (DFG) sowie weiteren akademischen und privaten Förderinstitutionen unterstützt. Weitere Informationen: Projektwebseite DAI Datendokumentation des i3mainz, Hochschule Mainz Description (English) This data publication contains archaeological geodata from the research projects "The Cultic Center of the Sun-God of Heliopolis (Egypt)" and "Eclipse and Mutation: The end of the sun temple of Heliopolis" on the excavated and discovered features in the ancient Egyptian sanctuary in Heliopolis in present-day Cairo. The features were excavated and documented during a series of excavation campaigns between 2012 and 2024. This data collection represents a compilation of these features and is intended to serve as the basis for an overall mapping. The three excavators responsible, Stephanie Blaschta , Klara Dietze and Florence Langermann , played a key role in compiling the data. Michael Schleier was responsible for creating the data structures and schemas and merging the data. The dataset is published under a CC BY-SA 4.0 license . The project is funded by the German Research Foundation (DFG) and a wide network of institutional and private sponsors. Further information: Project website at DAI Datendokumentation of the i3mainz, Mainz University of Applied Sciences

Schnaitter, Hannes

1 files · 781 KB · zipdeclared

Diese Anleitung bietet Lernenden, die QUADRIGA OER nutzen, Empfehlungen und Anleitungen zu verschiedenen Bestandteilen von QUADRIGA OER. Dies betrifft insbesondere die verschiendenen Interaktionsmöglichkeiten von Lesen über Ausführen in der Cloud bis zur lokalen Entwicklung. Dieses interaktive Lehrbuch kann als Web-Version verwendet, zur individuellen Anpassung heruntergeladen werden und steht darüber hinaus auch auf GitHub zur Verfügung. Die QUADRIGA-OER sind nach einem einheitlichen Template gestaltet, werden nach einem standardisierten Verfahren qualitätsgeprüft und mit Metadaten nach dem QUADRIGA-Metadatenschema ausgezeichnet. QUADRIGA Datenkompetenzzentrum QUADRIGA ist das Datenkompetenzzentrum der Wissenschaftsregion Berlin-Brandenburg. Für die beiden Anwendungsdomänen Digital Humanities und Verwaltungswissenschaft entstehen unter der Einbindung der Expertise der beiden Disziplinen Informatik und Informationswissenschaft Selbstlernangebote, die als OER in Form von Jupyter Books zur freien Nachnutzung zur Verfügung gestellt werden. Um den Forschungsprozess möglichst realistisch abzubilden, basieren die OER auf Fallstudien, denen wiederum ein eigens für das Projekt entwickeltes Datenkompetenzframework zugrunde liegt. Die Fallstudien nehmen drei für die Anwendungsdomänen repräsentativen Datentypen in den Blick: Bewegtes Bild, Tabelle und Text. Zu den Zielgruppen von QUADRIGA zählen insbesondere promovierende und promovierte Wissenschaftler*innen der genannten Disziplinen, die den Umgang mit digitalen Daten, Methoden und Werkzeugen erlernen und weiterentwickeln wollen. QUADRIGA ist eins von 11 Datenkompetenzzentren in Deutschland und wird vom Bundesministerium für Forschung, Technologie und Raumfahrt (BMFTR) und von der Europäischen Union im Rahmen von NextGenerationEU finanziert. Zu den Verbundpartnern zählen: Universität Potsdam (Verbundkoordination) (Förderkennzeichen: 16DKZ2034A) Filmuniversität Babelsberg KONRAD WOLF (Förderkennzeichen: 16DKZ2034B) Fachhochschule Potsdam (Förderkennzeichen: 16DKZ2034C) Fraunhofer FOKUS (Förderkennzeichen: 16DKZ2034D) Freie Universität Berlin (Förderkennzeichen: 16DKZ2034E) Technische Universität Berlin (Förderkennzeichen: 16DKZ2034F) Gesellschaft für Informatik (Förderkennzeichen: 16DKZ2034G) Humboldt-Universität zu Berlin (Förderkennzeichen: 16DKZ2034H) Mehr zum Aufbau und zur Umsetzung des Projekts können Sie im Umsetzungskonzept erfahren. Weitere Informationen sowie Publikationen finden Sie auf der Webseite , in der Zenodo-Community und der GitHub-Organisation des Projekts.

Sihler, Florian · Gerstl, Oliver · Schubert, Julian · et al.

1 files · 3.8 MB · zipdeclared

flowR is a sophisticated static program analysis framework for the R programming language.

Zurowietz, Martin · Langenkämper, Daniel · Nattkemper, Tim W.

1 files · 14 MB · zipdeclared

BIIGLE is a web service for the efficient and rapid annotation of still images and videos.

Fu, Yuming

1 files · 1.5 MB · zipdeclared

A simple tool to manipulate and visualize UV/optical/NIR spectra for astronomical research.

Kappelmann, Kevin

1 files · 255 KB · zipdeclared

An MCP interacting with Isabelle via Isabelle/PIDE

Gerlero, Gabriel S. · Kler, Pablo A.

1 files · 956 KB · zipdeclared

What's Changed Remove unused ty ignores by @gerlero in https://github.com/gerlero/foamlib/pull/783 Bump actions/checkout from 6 to 7 by @dependabot[bot] in https://github.com/gerlero/foamlib/pull/784 Fix some ty errors by @gerlero in https://github.com/gerlero/foamlib/pull/786 Test serialization of faces-like lists by @gerlero in https://github.com/gerlero/foamlib/pull/787 Update OpenFOAM version in CI workflow by @gerlero in https://github.com/gerlero/foamlib/pull/788 Change Python version to 3.14 in CI workflow by @gerlero in https://github.com/gerlero/foamlib/pull/789 Update OpenFOAM version to latest by @gerlero in https://github.com/gerlero/foamlib/pull/790 Fix benchmark foamlib version by @gerlero in https://github.com/gerlero/foamlib/pull/791 Update internal FIELD_KEYWORDS handling by @gerlero in https://github.com/gerlero/foamlib/pull/792 Fix ty errors in test files by @gerlero in https://github.com/gerlero/foamlib/pull/793 Fix ty errors in internal serialization module by @gerlero in https://github.com/gerlero/foamlib/pull/794 Fix ty error in internal parsing module by @gerlero in https://github.com/gerlero/foamlib/pull/795 Fix FoamFile ty errors by @gerlero in https://github.com/gerlero/foamlib/pull/797 Fix ty errors in parametricStudy example by @gerlero in https://github.com/gerlero/foamlib/pull/798 Fix ty errors by @gerlero in https://github.com/gerlero/foamlib/pull/799 Upgrade Ruff action to version 4 in CI workflow by @gerlero in https://github.com/gerlero/foamlib/pull/800 Update typing definitions by @gerlero in https://github.com/gerlero/foamlib/pull/801 Simplify typing definitions by @gerlero in https://github.com/gerlero/foamlib/pull/802 Fix type hint for function return in _serialization.py by @gerlero in https://github.com/gerlero/foamlib/pull/803 Refactor data normalization function by @gerlero in https://github.com/gerlero/foamlib/pull/804 Full Changelog : https://github.com/gerlero/foamlib/compare/v1.6.1...v1.6.2

Pavel V. Dimens

1 files · 72 MB · zipdeclared

Fixes Reports preprocess GIH uses log-scaled binning to reduce data significantly and prevent altair crashes align aggregate linked read Total vs. plot uses reversed tubro palette and a dropdown selector instead of radio samtools stats stats-boxes sets more realistic cutoffs for %mapped, %properly paired, %optical dupes coerce bins in bcftools report into numeric type force columns pertaining to contigs into String types fixes altair compatability for nominal data fixes table parsing errors that arise when contigs are both named as a number and as strings (e.g. a contig named '1' and another named 'X') Full Changelog : https://github.com/pdimens/harpy/compare/4.1.2...4.1.3

Xudong Zou

1 files · 30 KB · zipdeclared

codes used in the 5'aQTL study

Bartul Mimica · David Turner

1 files · 52 MB · zipdeclared

v0.11.2 Metadata-integrity fix. In the recording GUI, pressing "Add Subject" silently erased an animal's saved interventions from subject_presets.json . The loss surfaced only in the next session, when the animal was recalled and its intervention "failed to load". ⚠️ Who is affected Anyone using the Record → subject metadata page who stores interventions (optogenetics, chemogenetics, electrophysiology, lesion) against a remembered animal. Two distinct losses, depending on how the animal was entered: | flow | session _metadata.yaml | remembered animal ( subject_presets.json ) | |---|---|---| | picked from the autocomplete dropdown | intact | intact | | picked from the dropdown, then any field edited, then "Add Subject" | intact | interventions erased | | subject id typed by hand, then "Add Subject" | interventions missing | interventions erased | So a recording made by typing the animal's id has a _metadata.yaml without its interventions . That file cannot be repaired automatically — if you have affected sessions, the intervention fields must be re-entered by hand. subject_presets.json itself heals as soon as you re-add the intervention through its dialog. Root cause _add_subject assembles its dict from the subject form widgets . There is no widget for interventions , so the key is simply absent from that dict. It was then handed to _update_subject_in_repository , which stored it as the complete animal: self.subject_repository[existing_subject_index] = repository_entry # wholesale replace Every key the form does not represent — interventions — was destroyed. The session record survived only because _add_subject merges into it with .update() . The repository got replace , the session got merge ; that asymmetry was the entire bug. The autocomplete made it worse: QCompleter was constructed from a plain list, which Qt copies into a private model. A newly remembered animal therefore never appeared in the dropdown during that visit, pushing users to type the id by hand — straight onto the path that also loses interventions from the session record. Behaviour verified by driving the real GUI offscreen, not by reading the code. Fixed _update_subject_in_repository now merges into the stored preset instead of replacing it, so a caller passing a partial dict cannot destroy keys it never mentioned. A key the caller does pass still wins — deleting an intervention through its dialog still persists correctly. _add_subject seeds from the remembered preset (falling back to the record already in the session) and overlays the form data, so interventions reach the session record and therefore the recording's metadata. The completer is backed by a retained QStringListModel , refreshed on every repository change via a new _refresh_subject_completer() . Animals remembered during a visit now appear in the dropdown immediately. Four regression tests were written before the fix: three failed against the old code and pass now; the fourth pins that merging never resurrects a deleted intervention. Full suite green (2184 passed, 92% coverage). Provenance Not introduced by an automated code sweep. The partial-dict/replace mismatch dates to ba1dd49 (2025-10-16). A later fix ( 4189e5a , 2026-05-14) hardened dict aliasing one line away without noticing it. Full changelog: v0.11.1...v0.11.2

Hanno Rein · Dan Tamayo · Shangfei Liu · et al.

1 files · 6.0 MB · zipdeclared

Optimized Lazy Kernel method in WHFast. Fixed bug in WHFast512 when GR is enabled, related to backreaction. Fixed size of integers in collision structure in python.

Francesco Padovani · Ajinkya Kulkarni · Francois El-Daher

1 files · 28 MB · zipdeclared

SpotMAX version used in the Padovani, et al. - Science Advances 2026 publication.