QSDB - a graphical Quorum Sensing Database: VANTED add-on source code (doi:10.18419/darus-3242)

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QSDB - a graphical Quorum Sensing Database: VANTED add-on source code

doi:10.18419/darus-3242

DaRUS

2022-11-21

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Klein, Karsten; Garkov, Dimitar; Rütschlin, Sina; Böttcher, Thomas; Schreiber, Falk, 2022, "QSDB - a graphical Quorum Sensing Database: VANTED add-on source code", https://doi.org/10.18419/darus-3242, DaRUS, V1

QSDB - a graphical Quorum Sensing Database: VANTED add-on source code

doi:10.18419/darus-3242

Klein, Karsten (University of Konstanz)

Garkov, Dimitar (University of Konstanz)

Rütschlin, Sina (University of Konstanz)

Böttcher, Thomas (University of Vienna)

Schreiber, Falk (University of Konstanz)

251654672

DaRUS

Klein, Karsten

Schreiber, Falk

Garkov, Dimitar

2022-10-25

https://doi.org/10.18419/darus-3242

Chemistry, Computer and Information Science, Medicine, Health and Life Sciences, Web Databases, Quorum Sensing (Microbiology), Quorum Quenching (Microbiology), Systems Biology, Systems Biology Graphical Notation, SBGN

The add-on had been designed for the <a href="http:\\vanted.org">VANTED framework</a> and used to create QSDB Database's collection of clickable networks. Each network is laid out according to SBGN standards, showing quorum sensing and quorum quenching interactions between organisms and signaling molecules. This data set constitutes the source code of the add-on, developed to visualise the SBGN graphs of the QSDB Database using as input tabular aggregated data collected from existing literature.<br><br> <p><b>Paper abstract:</b> The human microbiome is largely shaped by the chemical interactions of its microbial members, which includes cross-talk via shared signals or quenching of the signalling of other species. Quorum sensing is a process that allows microbes to coordinate their behaviour in dependence of their population density and to adjust gene expression accordingly. We present the Quorum Sensing Database (QSDB), a comprehensive database of all published sensing and quenching relations between organisms and signalling molecules of the human microbiome, as well as an interactive web interface that allows browsing the database, provides graphical depictions of sensing mechanisms as Systems Biology Graphical Notation diagrams and links to other databases.<br><br> <b>Database URL:</b> QSDB (Quorum Sensing DataBase) is freely available via an interactive web interface and as a downloadable csv file at <a href="http://qsdb.org">http://qsdb.org</a>.</p>

<p><b>Build instructions:</b></p> <ol><li> Clone the repository and import the project as an existing project in Eclipse.</li> <li> Make sure you also have <a href="https://github.com/LSI-UniKonstanz/vanted">Vanted</a> and the <a href="https://github.com/LSI-UniKonstanz/vanted-libraries">Vanted-Libraries</a> repositories as existing projects in Eclipse. </li> Detailed information how to do so can be found at the <a href="https://github.com/LSI-UniKonstanz/vanted/wiki/Sourcecode">Vanted Sourcecode Wiki page</a>. <li> Start the add-on by the running main from <b>org.vanted.addons.SBGN_QS.StartVantedWithAddon.java.</b></li></ol>

Please <b>also</b> cite: <br/><br/> Karsten Klein, Dimitar Garkov, Sina Rütschlin, Thomas Böttcher, Falk Schreiber, QSDB—a graphical Quorum Sensing Database, Database, Volume 2021, 2021, baab058, <a href="https://doi.org/10.1093/database/baab058">doi:10.1093/database/baab058</a>.

The published produced data is available to access and download at: <a href="http:\\qsdb.org">http:\\qsdb.org</a>.

Klein, Karsten, Garkov, Dimitar, Rütschlin, Sina, Böttcher, Thomas, Schreiber, Falk (2021). QSDB - a graphical Quorum Sensing Database. Database, Volume 2021, baab058.

10.1093/database/baab058

Klein, Karsten, Garkov, Dimitar, Rütschlin, Sina, Böttcher, Thomas, Schreiber, Falk (2021). QSDB - a graphical Quorum Sensing Database. Database, Volume 2021, baab058.

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