SynthSys
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SynthSys is the University of Edinburgh's Centre for Synthetic and Systems Biology, supporting interdisciplinary research projects that may involve many parts of the University. SynthSys hosts/has hosted major awards such as the UK Centre for Mammalian Synthetic Biology (2015-20). Individual research groups may share data via their own collection or via this SynthSys collection.
Items in this Collection
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Prediction and analysis of phenotypes in the Arabidopsis clock mutant prr7prr9 using the Framework Model v2 (FMv2)
This upload contains or links to the biological data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated 2022 as bioRxiv https://doi.org/10.1101/105437v2, mostly ... -
Absolute units in Arabidopsis clock models up to U2020.3
Starting from the P2011 model of the circadian clock in Arabidopsis thaliana, this project corrects theoretical issues (steady-state binding assumption for the Evening Complex, EC) to form an intermediate model (published ... -
Spatiotemporal clock patterns in the leaf blade
We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk ... -
Source data and scripts for "A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction"
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of ... -
SUPERSEDED - Source data and scripts for "Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering"
## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/3001 ## Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because ... -
Peptide occurrences dataset from UniProt Feb 2018
Peptide occurences at different lengths, found in UniProt Feb 2018 release (UniProtKB/Swiss-Prot 2018_02 - February 28, 2018). An output of the Leverhulme funded project: Understanding the biological ramifications of a ... -
Timeseries used in Zielinski et al. Strengths and Limitations of Period Estimation Methods
Dataset contains timeseries data used for testing period analysis methods. The full details of the data are described in the actual paper, here there is only a short summary of methods generation. The synthetic test ... -
Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay
Supplementary data for Koszela et.al. Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay, BMC Biology, 2018 -
Data files and analysis scripts for Seaton et al. "Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism", bioRxiv 2017, Mol. Syst. Biol. 2018
Dataset description: The dataset comprises transcriptome (RNA levels) and proteome (protein levels) data for samples of the plant Arabidopsis thaliana, the alga Ostreococcus tauri and the cyanobacterium Cyanothece, along ... -
The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species
(University of Edinburgh. SynthSys and School of Biological Sciences, 2014-06-24)## Background ## The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead ...
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