Andrew Hinton · Zenodo (CERN European Organization for Nuclear Research) · 2026
This paper introduces The Scientific Codebase, a framework designed to bridge the gap between messy, exploratory data science and stable, production-ready software. It addresses the fact that while AI now makes code generation easy, organizing and verifying that code remains a significant challenge. The Four Phases of Development The methodology breaks down the evolution of scientific code into four distinct stages: Lab Bench: Initial exploratory analysis and experimentation. Crystallization: Organizing and refining the initial logic. Manuscript: Documenting and stabilizing code for formal presentation or review. Graduation: Transitioning the code into a fully operational production environment. Key Innovations and Goals Managing AI-Generated Code: Since AI now accelerates code production, the framework focuses on organizing and stabilizing those artifacts rather than just writing them. Separation of Concerns: It promotes separating core scientific logic from the technical "orchestration" code (like cloud infrastructure or data pipelines). Reproducibility: The framework uses extraction and snapshot testing to ensure that scientific results remain consistent as the code moves through different stages. MLOps Alignment: It provides a structured path for modern machine learning operations while maintaining the rigor required for scientific research. Core Takeaway The Scientific Codebase moves beyond simple notebook-driven workflows. It provides a disciplined engineering path that allows researchers to use AI tools effectively without sacrificing the reliability or traceability of their final production models.
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geertvandeweyer, wings-public · Zenodo (CERN European Organization for Nuclear Research) · 2026
This release contains the centralized and federated repositories associated with the WiNGS API project, providing the source code and supporting materials necessary to deploy and evaluate both architectures.
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Slanináková, Terézia, Charlop-Powers, Zachary, Doshchenko, Viktoriia et al. · Figshare · 2025
Effectively communicating knowledge related to molecular structures and their associated data remains a challenge, as traditional static figures limit interactivity and professional visualization tools often require substantial expertise. MolViewStories addresses these limitations by providing an open-source, web-based platform for creating and sharing interactive, narrative-driven molecular visualizations.The platform uses the MolViewSpec standard for reproducible scene specification, extended to support animations, interactive descriptions, and synchronized audio commentary. Visualization is powered by the Mol* Viewer, which leverages Web Graphics Library (WebGL) for efficient 3D rendering and WebXR for immersive virtual and augmented reality experiences. Users can construct molecular narratives through an intuitive graphical interface or a command-line workflow, enabling both exploratory and automated use. Completed stories can be shared online, exported locally, or distributed as self-contained packages that remain functional indefinitely. Each story is assigned a persistent uniform resource locator (URL) and can be modified or reused as a template, promoting collaboration and community-driven content creation.We demonstrate the capabilities of MolViewStories through a diverse set of narratives illustrating its broad applicability to research communication, education, and public outreach. Together, these examples highlight how interactive, web-based storytelling can make molecular data more accessible, reproducible, and engaging.MolViewStories is freely available at https://molstar.org/mol-view-stories with open-source code accessible at https://github.com/molstar/mol-view-stories.
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Hyunkyu, Lee · Zenodo (CERN European Organization for Nuclear Research) · 2024
The LTPI Software Suite provides a comprehensive collection of tools and scripts to support the analysis, and visualization of results related to the LTPI manuscript. This repository integrates the original LTPI Python implementation with an replication package designed to facilitate reproducibility of the LTPI study. Key Features: Core Python code for LTPI analysis and simulations. Scripts to reproduce all figures and simulations presented in the LTPI manuscript.Includes modular and extensible code for figure generation and data analysis. Fully documented workflows with detailed instructions for running simulations and generating manuscript figures.
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Advani, Rishi, Papotti, Paolo, Abolfazl Asudeh · Zenodo (CERN European Organization for Nuclear Research) · 2023
added news website template, user study data, and statistical tests submission-ready state
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Rowe, Jason · Zenodo (CERN European Organization for Nuclear Research) · 2016
First Release of source code to match publications.
Cited by 12Open access
Rekunen, Roope · Theseus (Ammattikorkeakoulujen) · 2024
Ohjelmointirajapinnan eli API:n käyttö yleensä rajoittuu siihen ohjelmointikieleen, millä rajapinta on alun perin kirjoitettu. Käytön muilla ohjelmointikielillä voi sallia tekemällä halutulla kielellä rajapinnan, joka muistuttaa käytettävää APIa. Tätä kutsutaan myös kielisidokseksi. Vaikka kielisidoksia pystyy kirjoittamaan käsin, se lisää työmäärää, sillä jokainen päivitys alkuperäiseen APIin pitää tehdä myös kielisidoksiin. \n \nYrityksellä, jolle projekti tehtiin, oli ongelma, jossa heidän tuotteensa käsintehdyt kielisidokset eivät aina pysyneet ajan tasalla. Ongelman ratkaisemista varten aloitettiin projekti, jossa kehitettiin työkalu. joka tuottaa yrityksen tuotteelle kielisidoksia. Projektin tarkoitus oli varmistaa, että kun tuotteen APIin tehdään muutoksia, muutokset siirtyvät kielisidoksiin automaattisesti. \n \nYritykselle tehdyn työkalun lisäksi uuden avoimen lähdekoodin projektin nimeltä Autoglue kehitys aloitettiin. Autoglue on ohjelmointikirjasto, jonka tarkoituksena on antaa kehittäjille rajapinta, jota voi käyttää oman kielisidoksia tuottavan työkalun kehittämiseen. Sen sijaan että Autoglue toimisi kuin monet muut projektit, jotka tuottavat kielisidoksia yhdestä kielestä monelle kielelle, tämän työn esittelemiä käsitteitä hyödynnetään abstraktioihin, joita voidaan käyttää kielisidosten tuottamisseen mistä tahansa kielestä mille tahansa kielelle. \n \nTämän työn tarkoitus on tutkia kielisidoksia, niiden sisäistä toimintaa ja miten niitä pystyy generoimaan automaattisesti. Käsitteet käydään läpi mahdollisimman yleisellä tasolla, mutta niiden seasta löytyy tarkempia esimerkkejä, jotka antavat käsityksen oikeasta toteutuksesta.
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Slanináková, Terézia, Charlop-Powers, Zachary, Doshchenko, Viktoriia et al. · Figshare · 2025
Effectively communicating knowledge related to molecular structures and their associated data remains a challenge, as traditional static figures limit interactivity and professional visualization tools often require substantial expertise. MolViewStories addresses these limitations by providing an open-source, web-based platform for creating and sharing interactive, narrative-driven molecular visualizations.The platform uses the MolViewSpec standard for reproducible scene specification, extended to support animations, interactive descriptions, and synchronized audio commentary. Visualization is powered by the Mol* Viewer, which leverages Web Graphics Library (WebGL) for efficient 3D rendering and WebXR for immersive virtual and augmented reality experiences. Users can construct molecular narratives through an intuitive graphical interface or a command-line workflow, enabling both exploratory and automated use. Completed stories can be shared online, exported locally, or distributed as self-contained packages that remain functional indefinitely. Each story is assigned a persistent uniform resource locator (URL) and can be modified or reused as a template, promoting collaboration and community-driven content creation.We demonstrate the capabilities of MolViewStories through a diverse set of narratives illustrating its broad applicability to research communication, education, and public outreach. Together, these examples highlight how interactive, web-based storytelling can make molecular data more accessible, reproducible, and engaging.MolViewStories is freely available at https://molstar.org/mol-view-stories with open-source code accessible at https://github.com/molstar/mol-view-stories.
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Gincheva, Andrina, Royé, Dominic, Torres Vázquez, Miguel Ángel et al. · Zenodo (CERN European Organization for Nuclear Research) · 2024
We present the R code used to Development and Validation Codebase analyses detailed in our paper "ONFIRE Dataset: Monthly Gridded Burned Area data". For more information, please consult the following source: Gincheva, A., & Turco, M. (2023). ONFIRE dataset: Monthly Gridded Burned Area data (Version 1.0) [Data set]. Zenodo. Available at https://doi.org/10.5281/zenodo.8289245. Authors: Andrina Gincheva, University of Murcia (andrina@um.es) Marco Turco, University of Murcia (marco.turco@um.es) General instructions This project is designed to be executed with QGIS and with R codes. Execute script files in the order they are listed. Please refer to the 'Readme-Instructions_to_reproduce_the_study' before proceeding. Data sources -Fire in Australia: New South Wales: https://datasets.seed.nsw.gov.au/dataset/fire-history-wildfires-and-prescribed-burns-1e8b6 Queensland: https://qldspatial.information.qld.gov.au/catalogue/custom/ Northern Territory: https://firenorth.org.au/nafi3/downloads/firescars/ South Australia: https://data.sa.gov.au/data/dataset/fire-history Tasmania: http://listdata.thelist.tas.gov.au/opendata/ Victoria: https://discover.data.vic.gov.au/dataset/ Western Australia: https://catalogue.data.wa.gov.au/dataset/dbca-fire-history - Australian regions: https://www.abs.gov.au/statistics/standards/australian-statistical-geography-standard-asgs-edition-3/jul2021-jun2026/access-and-downloads/digital-boundary-files#downloads-for-gda2020-digital-boundary-files - EFFIS data: contact https://effis.jrc.ec.europa.eu/apps/data.request.form/ - European regions (NUTS3): http://ec.europa.eu/eurostat/web/nuts/history - NFDB dataset for Canada: https://cwfis.cfs.nrcan.gc.ca/downloads/nfdb/fire_pnt/current_version/NFDB_point_large_fires.zip - NBAC dataset for Canada: https://cwfis.cfs.nrcan.gc.ca/downloads/nbac/nbac_1986_to_2020_20210810.zip - CONAF dataset for Chile: https://www.conaf.cl/incendios-forestales/incendios-forestales-en-chile/estadisticas-historicas/ (download the document "Estadísticas - Daño (Superficie Afectada) por Incendios Forestales según Mes 1985 - 2022") - Chile regions shapefile: https://www.bcn.cl/obtienearchivo?id=repositorio/10221/10398/2/Regiones.zip - FPA-FOD dataset for the U.S.: https://www.fs.usda.gov/rds/archive/catalog/RDS-2013-0009.6 - MTBS dataset for the U.S.: https://mtbs.gov/direct-download - 1ºx1º grid: https://github.com/SantanderMetGroup/ATLAS/raw/main/reference-grids/land_sea_mask_1degree.nc4 Notes regarding reproducibility: Script files starting with "1_" in their name are for data preprocessing. Most of these script files will NOT run because we do not include the raw data because files are simply too large to conveniently share. We suggest you run scripts starting with "2_" which directly reproduces the results in the paper. Please refer to the 'Readme-Instructions_to_reproduce_the_study' before proceeding. If you have any questions or wish to express any comment to the authors, please contact Dr. Marco Turco or/and Andrina Gincheva at the email indicated above. A.G. thanks to the Ministerio de Ciencia, Innovación y Universidades of Spain for Ph.D. contract FPU19/06536. M.T. acknowledges funding by the Spanish Ministry of Science, Innovation, and Universities through the Ramón y Cajal Grant Reference RYC2019-027115-I and through the project ONFIRE, grant PID2021-123193OB-I00, funded by MCIN/AEI/ 10.13039/501100011033 and by "ERDF A way of making Europe".
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Schiffthaler, Bastian, NicolasDelhomme · Zenodo (CERN European Organization for Nuclear Research) · 2021
Public scripts for the second version of the European aspen assembly
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Ramirez, Alejandra · Zenodo (CERN European Organization for Nuclear Research) · 2022
Final codebase
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John Ruberto · 2012
This paper tells the story of how our organization introduced static analysis into its software development process. The static analysis process automatically finds bugs, assigns them to the engineer that most likely introduced the bug, and then automatically verifies the fix. This project began two years ago, when we started recording the root cause of bugs that were fixed. Once we had several hundred bugs analyzed, we found that the largest number of bugs was caused by coding errors. The good news, there are many best practices in industry to improve code quality. One survey of software quality practices (Jones 2011) shows that three practices, taken together, are capable of removing 97% of the defects. Those three practices are code review, static analysis, and unit testing. Our organization already had healthy processes for code review and unit testing, but we had spotty history with static analysis. So, we took a fresh look at static analysis. When engineering the process for static analysis, we took care to avoid some of the issues of the past; namely false positives, excessive effort required to manage the bug list (triage false positives, manage assignments, etc.), and the demotivation of analyzing a large backlog of defects. When we designed the new process, we decided to focus on automating the bug identification, assignment, and retest processes ‐ eliminating a lot of the effort that got in the way of previous attempts. We also focused on keeping new code clean, which is much easier to justify than clearing old bugs from the backlog. The process also was designed to provide fast feedback, directly to the developer that created the bug. Paying attention to new bugs has resulted in high levels of adoption by the developers, as compared to focus on backlog bugs. The engineers are fixing the new bugs that come in, plus have made a significant dent in the backlog.
Cited by 1
Shibaji Chakraborty · Zenodo (CERN European Organization for Nuclear Research) · 2023
Submarine cables have experienced problems during extreme geomagnetic disturbances because of geomagnetically induced voltages adding or subtracting from the power feed to the repeaters. This is still a concern for modern fiber-optic cables because they contain a copper conductor to carry power to the repeaters. This paper provides a new examination of geomagnetic induction in submarine cables and makes calculations of the voltages experienced by the TAT-8 trans-Atlantic submarine cable during the March 1989 magnetic storm. It is shown that the cable itself 28 experiences an induced electromotive force (emf) and that induction in the ocean also leads to changes of potential of the land at each end of the cable. The process for calculating the electric fields induced in the sea and in the cable from knowledge of the seawater depth and conductivity and subsea conductivity is explained. The cable route is divided into 9 sections and the seafloor electric field is calculated for each section. These are combined to give the total induced emf in the cable. In addition, induction in the seawater and leakage of induced currents through the underlying resistive layers are modelled using a transmission line model of the ocean and underlying layers to determine the change in Earth potentials at the cable ends. The induced emf in the cable and the end potentials are then combined to give the total voltage change experienced by the cable power feed equipment. This gives results very close to those recorded on the TAT-8 cable in March 1989.
Cited by 1Open access
D Kim · Zenodo (CERN European Organization for Nuclear Research) · 2026
This paper examines what happens when legacy Excel artifacts are treated not as static lesbut as repositories of executable business logic and are transformed into a structural intermediate representation (IR) and an executable codebase. Its unit of analysis is the document-to-codetransformation architecture itself, interpreted together with repository-level automation literature and o cial product documentation. In addition, a limited internal operationalexample is used to inspect how structured repository representations are consumed in a live LLMwork ow.The central claim is threefold. First, document codi cation turns a document-managementproblem into a software-engineering problem. Second, that shift externalizes tacit operationalknowledge into structural addresses, dependency edges, regeneration procedures, and durablechange history. Third, once the asset becomes a repository object rather than a raw document, repository-oriented automation tools gain materially stronger leverage for search, multile change planning, impact analysis, veri cation, and documentation. More speci cally, thevalue of Excel codi cation lies in producing a structured repository surface, and that structureimproves LLM work quality by improving retrieval relevance, grounding traceability, and outputstability. The paper analyzes that leverage along ve dimensions: structural addressability, dependency visibility, executable reproducibility, change traceability, and executable veri cation.
Cited by 0Open access
D Kim · Zenodo (CERN European Organization for Nuclear Research) · 2026
This paper examines what happens when legacy Excel artifacts are treated not as static lesbut as repositories of executable business logic and are transformed into a structural intermediate representation (IR) and an executable codebase. Its unit of analysis is the document-to-codetransformation architecture itself, interpreted together with repository-level automation literature and o cial product documentation. In addition, a limited internal operationalexample is used to inspect how structured repository representations are consumed in a live LLMwork ow.The central claim is threefold. First, document codi cation turns a document-managementproblem into a software-engineering problem. Second, that shift externalizes tacit operationalknowledge into structural addresses, dependency edges, regeneration procedures, and durablechange history. Third, once the asset becomes a repository object rather than a raw document, repository-oriented automation tools gain materially stronger leverage for search, multile change planning, impact analysis, veri cation, and documentation. More speci cally, thevalue of Excel codi cation lies in producing a structured repository surface, and that structureimproves LLM work quality by improving retrieval relevance, grounding traceability, and outputstability. The paper analyzes that leverage along ve dimensions: structural addressability, dependency visibility, executable reproducibility, change traceability, and executable veri cation.
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yfliu, gqbbbbb, shengdian jiang · Zenodo (CERN European Organization for Nuclear Research) · 2024
We release it formally to get a DOI
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Association for Computational Linguistics 2025, Ezzini, Saad, F. Bissyandé, Tegawendé et al. · Underline Science Inc. · 2025
Recent advancements in large language models (LLMs) have significantly improved software development automation, including bug localization, code synthesis, program repair, and test generation. However, most prior work on program repair focuses on isolated elements, such as classes or functions, neglecting their interdependencies, which limits repair accuracy. We present SynFix, a RelationGraph-based approach that integrates LLMs with structural search and synchronization techniques for coordinated program repair across codebases. SynFix constructs a \textbf{RelationGraph} to capture relationships among classes, functions, variables, and their interactions (e.g., imports, inheritance, dependencies). Each RelationGraph node includes detailed code descriptions to help LLMs understand root causes and retrieve relevant contexts. By analyzing one-hop nodes in the RelationGraph, SynFixensures repairs account for dependent updates across components. Patch validation is conducted using regression tests from the SWE-bench benchmark suite. Evaluated on SWE-bench datasets, SynFix resolves 52.33% of issues in \textbf{SWE-bench-lite} (300 GitHub issues), 55.8% in \textbf{SWE-bench-verified} (500 issues), and 29.86% in \textbf{SWE-bench-full} (2,294 issues), outperforming baselines such as Swe-Agent, Agentless and AutoCodeRover. The codebase is available at \url{https://anonymous.4open.science/r/AutoFix-EC86/}.
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Rajeeva Musunuri · Zenodo (CERN European Organization for Nuclear Research) · 2026
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Kaitlyn Johnson, Sam Abbott, Johannes Bracher · London School of Hygiene & Tropical Medicine · 2026
What's Changed Issue 133: tweak supplement by @kaitejohnson in https://github.com/epinowcast/baselinenowcast-paper/pull/134 Hot fix add changes to the supplement by @kaitejohnson in https://github.com/epinowcast/baselinenowcast-paper/pull/138 Update codemeta.json by @github-actions[bot] in https://github.com/epinowcast/baselinenowcast-paper/pull/135 Change color scheme by @kaitejohnson in https://github.com/epinowcast/baselinenowcast-paper/pull/139 Full Changelog: https://github.com/epinowcast/baselinenowcast-paper/compare/v1.0.1-pre-publication-update...v2.0
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Diaz-Maurin, François, Sun, Hilary C., Yu, Jerold et al. · Zenodo (CERN European Organization for Nuclear Research) · 2018
Code for https://doi.org/10.1557/adv.2018.636. Code produced by Hilary Sun (hsun3@cs.stanford.edu) and Jerold Yu (jeroldyu@stanford.edu).
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