The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.
Get full access to this article
View all access options for this article.
References
1.
AghamirzaieD., BatraD., HeathL.S., et al.2015. Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics. 16, 928.
2.
CollakovaE., KlumasC., SurenH., et al.2013. Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biol. 13, 72.
3.
CzaudernaT., KlukasC., and SchreiberF.2010. Editing, validating and translating of SBGN maps. Bioinformatics, 26, 2340–2341.
4.
KakumanuA., AmbavaramM.M.R., KlumasC., et al.2012. Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol. 160, 846–867.
5.
KrauseF., SchulzM., RipkensB., et al.2013. Biographer: Web-based editing and rendering of SBGN compliant biochemical networks. Bioinformatics, 29, 1467–1468.
6.
MiH., SchreiberF., MoodieS., et al.2015. Systems biology graphical notation: Activity flow language level 1 version 1.2. J. Integr. Bioinform. 12, 265.
7.
NiY., AghamirzaieD., ElmarakebyH., et al.2016. A machine learning approach to predict gene regulatory networks in seed development in Arabidopsis. Front. Plant Sci. 7, 1936.
8.
RohnH., JunkerA., HartmannA., et al.2012. VANTED v2: A framework for systems biology applications. BMC Syst. Biol. 6, 139.
9.
van IerselM.P., VillegerA.C., CzaudernaT., et al.2012. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics, 28, 2016–2021.