{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:10:36Z","timestamp":1763809836588,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,2,1]],"date-time":"2018-02-01T00:00:00Z","timestamp":1517443200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Swammerdam Institute for Life Science Starting"},{"DOI":"10.13039\/501100001827","name":"University of Amsterdam","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001827","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Systems Biology Research Priority Area"},{"DOI":"10.13039\/501100001827","name":"University of Amsterdam","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001827","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Multi-scale modeling of biological systems requires integration of various information about genes and proteins that are connected together in networks. Spatial, temporal and functional information is available; however, it is still a challenge to retrieve and explore this knowledge in an integrated, quick and user-friendly manner.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins\/genes in Saccharomyces cerevisiae. GEMMER creates network visualizations that integrate information on function, temporal expression, localization and abundance from various existing databases. GEMMER supports modeling efforts by effortlessly gathering this information and providing convenient export options for images and their underlying data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>GEMMER is freely available at http:\/\/gemmer.barberislab.com. Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at https:\/\/github.com\/barberislab\/GEMMER.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty052","type":"journal-article","created":{"date-parts":[[2018,1,30]],"date-time":"2018-01-30T20:11:42Z","timestamp":1517343102000},"page":"2147-2149","source":"Crossref","is-referenced-by-count":7,"title":["GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for<i>Saccharomyces cerevisiae<\/i>"],"prefix":"10.1093","volume":"34","author":[{"given":"Thierry D G A","family":"Mondeel","sequence":"first","affiliation":[{"name":"Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, XH Amsterdam, The Netherlands"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Cr\u00e9mazy","sequence":"additional","affiliation":[{"name":"Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, XH Amsterdam, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5640-7422","authenticated-orcid":false,"given":"Matteo","family":"Barberis","sequence":"additional","affiliation":[{"name":"Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, XH Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2018,2,1]]},"reference":[{"key":"2023012713413178300_bty052-B1","doi-asserted-by":"crossref","first-page":"W529","DOI":"10.1093\/nar\/gkw363","article-title":"APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks","volume":"44","author":"Alonso-L\u00f3pez","year":"2016","journal-title":"Nucleic Acids Res"},{"year":"2009","author":"Bastian","key":"2023012713413178300_bty052-B2"},{"key":"2023012713413178300_bty052-B3","doi-asserted-by":"crossref","first-page":"902545.","DOI":"10.1155\/2014\/902545","article-title":"Modeling biology spanning different scales: an open challenge","volume":"2014","author":"Castiglione","year":"2014","journal-title":"Biomed Res. 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