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However, utilising the wide array of clinical, genomic, epidemiological, and spatial data collected globally is difficult due to differences in data preprocessing, data science capacity, and access to hardware and cloud resources. To facilitate large-scale and routine analyses of infectious disease data at the local level (i.e. without sharing data across borders), we developed GRAPEVNE (Graphical Analytical Pipeline Development Environment), a platform enabling the construction of modular pipelines designed for complex and repetitive data analysis workflows through an intuitive graphical interface. Built on the\n                    <ns3:italic>Snakemake<\/ns3:italic>\n                    workflow management system, GRAPEVNE streamlines the creation, execution, and sharing of analytical pipelines. Its modular approach already supports a diverse range of scientific applications, including genomic analysis, epidemiological modeling, and large-scale data processing. Each module in GRAPEVNE is a self-contained Snakemake workflow, complete with configurations, scripts, and metadata, enabling interoperability. The platform\u2019s open-source nature ensures ongoing community-driven development and scalability. GRAPEVNE empowers researchers and public health institutions by simplifying complex analytical workflows, fostering data-driven discovery, and enhancing reproducibility in computational research. Its user-driven ecosystem encourages continuous innovation in biomedical and epidemiological research but is applicable beyond that. Key use-cases include automated phylogenetic analysis of viral sequences, real-time outbreak monitoring, forecasting, and epidemiological data processing. For instance, our dengue virus pipeline demonstrates end-to-end automation from sequence retrieval to phylogeographic inference, leveraging established bioinformatics tools which can be deployed to any geographical context. For more details, see documentation at:\n                    <ns3:ext-link xmlns:ns4=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns4:href=\"https:\/\/grapevne.readthedocs.io\">https:\/\/grapevne.readthedocs.io<\/ns3:ext-link>\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.23824.1","type":"journal-article","created":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T12:20:09Z","timestamp":1748348409000},"page":"279","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["GRAPEVNE - Graphical Analytical Pipeline Development Environment for Infectious 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Kifle","family":"Tessema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John T.","family":"McCrone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samir","family":"Bhatt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4420-0656","authenticated-orcid":false,"given":"Abhishek","family":"Dasgupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Ratcliffe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8838-7147","authenticated-orcid":false,"given":"Moritz 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.26280.r124600, Anderson F Brito, Instituto Todos pela Sa\u00fade (ITpS), S\u00e3o Paulo, 16 Jun 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-279\/v1#referee-response-124600","order":0,"name":"referee-response-124600","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.26280.r126316, Kayode Oshinubi, Northern Arizona University, Flagstaff, Arizona, 28 Jun 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-279\/v1#referee-response-126316","order":1,"name":"referee-response-126316","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [226052] [228186]; The United Kingdom Research and Innovation (#APP8583), the Medical Research Foundation (MRF-RG-ICCH-2022-100069, , UK International Development (301542-403), the Bill & Melinda Gates Foundation (INV-063472) and Novo Nordisk Foundation (NNF24OC0094346, The Centre for Epidemic Response and Innovation acknowledges funding in part by grants from the Rockefeller Foundation (HTH 017), the National Institute of Health USA (U01 AI151698) for the United World Antiviral Research Network, and the INFORM Africa project through the Institute of Human Virology Nigeria (U54 TW012041), the SAMRC South African mRNA Vaccine Consortium (SAMVAC), Global Health EDCTP3 Joint Undertaking and its members and the Bill & Melinda Gates Foundation (101103171), European Union (EU) Horizon Europe Research and Innovation Programme (101046041), the Health Emergency Preparedness and Response Umbrella Program, managed by the World Bank Group (TF0B8412). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}