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This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by replacing it with immediate light input. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by setting its value to 1. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally submitted to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Metabolic control analysis of glyceraldehyde 3-...
Targeted lipidomic analysis was performed on plasma and isolated liver microsomes of eight male fish from solvent control (Control) and High-Dose groups (n = 8) at Cinta Porte’s lab at CSIC, Spain, using Flow Injection Analysis High-Resolution Mass Spectrometry (FIA-HRMS).
The data is submitted to the MetaboLights repository.
Submitter: Marta Eide
Assay type: Metabolomics
Technology type: Mass Spectrometry
Investigation: 1 hidden item
TBARS assay measured oxidative stress as levels of malondialdehyde in samples. Performed in cod liver samples.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Temperature degradation of BPG, GAP and DHAP
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
test
Submitter: Holger Janssen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Systems Biology of Clostridium acetobutylicum -...
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Submitter: John Raedts
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods. Cell leakage and metabolite recovery was determined by ATP measurements
Submitter: John Raedts
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
Using TFinfer2 to analyse data from "Characterization of MG1655 and mutant strains under conditions of glucose excess and limitation"
Submitter: Botond Cseke
Biological problem addressed: Model Analysis Type
Investigation: Analysis of the glucose transport in Escherichi...
Submitter: Yi Chen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Exploring the Evolution of the Gene Ontology an...
Submitter: Sebastian Curth
Biological problem addressed: Model Analysis Type
Investigation: General Method Development
Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col.
In this study, thiamine vitamers were quantified to test whether the essential cofactor TDP had altered enzyme activities to affect the malate and fumarate levels, using existing plant samples harvested from am earlier L&H study.
Submitter: Andrew Millar
Assay type: Metabolite Profiling
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
B. subtilis was grown in SMM media with glucose as carbon source and the samples for RNA were harvested OD578nm- 1.0). The stress conditions that were applied over here are growthat 57°C, 16°C, 1.2M Nacl and 37°C(control). All the samples were analysed for transcriptome as biological triplicates.
Submitter: Praveen kumar Sappa
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Redefining the Complete Transcriptome of Bacill...
B. subtilis was grown in M9 media with glucose as carbon source and the samples were harvested during exponential phase (OD600nm- 0.4), early stationary phase(OD600nm- 1.3), late stationary phase(OD600nm- 1.0). All the samples were analysed for transcriptome as biological triplicates.
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Falko Krause
Assay type: Transcriptomics
Technology type: Microarray
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
Time courses of the internal pH changes under the conditions of Navarrete et al. (2010) will be obtained. The usage of different mutants (transport systems and regulation factors) will reveal the influence and key systems of pH regulation.
To estimate the changes of internal pH, the pH-dependent variant of GFP pHluorin is expressed in cells from a multicopy plasmid, and the changes in cell fluorescence are monitored during 5 hours of incubation in YNB-F growth media without added potassium.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
Submitter: Sara Jabbari
Biological problem addressed: Metabolic Network
Investigation: The effect of pH upon the metabolic shift in Cl...
TiMet flower specific protein detection network
Originally submitted to PLaSMo on 2012-03-02 12:39:54
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
Trial upload of the pollen netwrok from TiMet
Originally submitted to PLaSMo on 2012-02-27 12:17:46
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
Trial upload of the pollen netwrok from TiMet
Version Comments
Live pollen upload test
Originally submitted to PLaSMo on 2012-02-27 12:17:46
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
PP interaction network exported from Cytoscape in XGMML
Originally submitted to PLaSMo on 2012-03-02 12:32:33
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
Test for root network
Originally submitted to PLaSMo on 2012-02-27 14:24:59
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
The seed network, uploaded as a test from Cytoscape
Version Comments
Saving second/third version as a live test
Originally submitted to PLaSMo on 2012-02-24 11:41:50
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
The seed network, uploaded as a test from Cytoscape
Version Comments
Uploading new version for testing
Originally submitted to PLaSMo on 2012-02-24 11:41:50
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
Cytoscape shoot specific diurnal transcript oscillation.
Originally submitted to PLaSMo on 2012-03-02 12:42:30
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
Cytoscape silqueue specific protein detection
Originally submitted to PLaSMo on 2012-03-02 12:44:13
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Graf, Alexandra
RNA timeseries data for Arabidopsis Col wild-type plants and clock mutants, as separate mean and SD files. The raw data is available on BioDare.ed.ac.uk, and is linked as 'Attribution' from elsewhere on FAIRDOMHub.
The starting models are included here in their original forms, the P2011 model as an SBML L3V1 model file, and the KF2014 model of Fogelmark et al. shared as SBML; both prepared by Uriel Urquiza.
Submitter: Andrew Millar
Biological problem addressed: Gene Regulatory Network
Investigation: Absolute units in Arabidopsis clock models up t...
RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL
Submitter: Andrew Millar
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Prediction and analysis of phenotypes in the Ar...
Metabolite analysis in clock mutants: Col-0 parent and mutants gi-201, toc1-101 and prr7prr9; WS parent and lhy/cca1 double mutant. Plants grown in Golm and harvested at End of Day and End of Night, , assays 22 major metabolites. More detail on TiMet wiki if required. Heteroscedastic t-tests to highlight most significant changes, without multiple-testing correction.
Submitter: Andrew Millar
Assay type: Metabolite Concentration
Technology type: Chromatography
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Kinetic characterisation of triose phosphate isomerase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Kinetic characterisation en mathematical modelling of TPI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Metabolic control analysis of glyceraldehyde 3-...
Submitter: Daniel Hönicke
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Altering the expression pattern in Clostridium ...
This assay involved the determination of transcriptional profiles at 0, 2, 5, 10, 15 and 20 minutes through aerobic to anaerobic gas transitions and anaerobic to aerobic gas transitions. In each case an aerobic or anaerobic steady state was created, RNA sampled (0 min) and then the gas supply changed. RNA samples were then taken from the time at which the gas supply was changed.
For anaerobic conditions 5% CO2, 95% N2 was used.
The full transcriptional dataset is available from ArrayExpress ...
Submitter: Matthew Rolfe
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Dynamical studies for different oxygen availabi...
The transcriptional profiles of steady state E. coli cultures at a range of aerobiosis levels were determined. Two biological replicates and two technical replicates were carried out. Microarrays were carried out in a reference style (i.e. RNA vs a gDNA reference).
Submitter: Matthew Rolfe
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Steady state studies for different oxygen avail...
Transcriptome analysis for the samples harvested from Chemostat cultivated samples.
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Multiomics study of Bacillus subtilis under osm...
Submitter: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Patrick Becker
Assay type: Transcriptomics
Technology type: Rna-seq
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Jay Moore
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
Transcriptomics results from liver of cod exposed to chlorpyrifos-methyl
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Submitter: Ziva Ramsak
Assay type: Gene Expression Profiling
Technology type: Custom Array
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Niels Zondervan
Assay type: Transcriptional Profiling
Technology type: Technology Type
Investigation: Modelling of M. pneumoniae metabolism
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Identification of targets of the essential RNas...
These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
"TRIFFID (Top-down Representation of Interactive Foliage and Flora Including Dynamics)" is a dynamic global vegetation model, which updates the plant distribution and soil carbon based on climate-sensitive CO2 fluxes at the land-atmosphere interface. The surface CO2 fluxes associated with photosynthesis and plant respiration are calculated in the MOSES 2 tiled land-surface scheme (Essery et al (In preparation)), on each atmospheric model timestep (normally 30 minutes), for each of 5 plant functional ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Muetzelfeldt, Robert
Study: TRIFFID - PLM_5
This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments Not formulated to easily allow addition of the ISSF to replace the present light ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments Not formulated to easily allow addition of the ISSF to replace the present light ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Troein, Carl
Assay for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
This assay is designed to obtain the in vitro kinetic data of T. brucei recombinant trypanothione synthetase. The enzyme catalyzes the ATP-dependent ligation of spermidine (Spd) and GSH to generate glutathionylspermidine (Gsp) and also of Gsp and GSH to finally produce trypanothione (T(SH)2). The data was obtained in an spectrophotometric assay that links ADP production with NADH consumption through the piruvte kinase and lactate dehydrogenase.
Submitter: Alejandro Leroux
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Investigation: Kinetic understanding of the T. brucei trypanot...
TbTryS activity was measured at 37°C in the in vivo-like buffer. All substrate stock solutions were prepared in the in vivo-like buffer and the pH was adjusted to 7.0. The assays were performed in a final volume of 2 ml and contained 0.2 mM NADH, 1 mM phosphoenolpyruvate, 4 units pyruvate kinase, 4 units L-lactate dehydrogenase, 0.17 µM TbTryS, 2.1 mM ATP and varying amounts of glutathione, and spermidine.
Submitter: Alejandro Leroux
Assay type: Discontinuous Enzymatic
Technology type: HPLC
Investigation: Kinetic understanding of the T. brucei trypanot...
Compound data and computational prediction of physicochemical properties
Submitter: Pasquale Linciano
Biological problem addressed: Chemical characterization
Investigation: Phenotypic and machine learning approaches for ...