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GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae

Mondeel, Thierry D G A, Crémazy, Frédéric and Barberis, Matteo (2018) GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae Bioinformatics, 34 (12). pp. 2147-2149.

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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.


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.

Availability and implementation

GEMMER is freely available at Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
Mondeel, Thierry D G A
Crémazy, Frédéric
Date : 1 February 2018
DOI : 10.1093/bioinformatics/bty052
Copyright Disclaimer : © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Depositing User : Clive Harris
Date Deposited : 11 Apr 2019 09:33
Last Modified : 11 Apr 2019 09:33

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