Investigations
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Collection of models submitted to PLaSMo by Chris Davey and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: AFRC Wheat 2 evapw submodel - PLM_33, AFRC Wheat 2 jdaydif submodel - PLM_34, AFRC Wheat 2 julday submodel - PLM_35, AFRC Wheat 2 ldim submodel - PLM_36, AFRC Wheat 2 photpd submodel - PLM_37, AFRC Wheat 2 tdays submodel - PLM_38, AFRC Wheat 2 vappres submodel - PLM_39, AFRC Wheat 2 vernal submodel - PLM_40, AFRC Wheat 2 weathr submodel - PLM_41, AFRC Wheat2 dev submodel - PLM_32, AFRCtest2 - PLM_25, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, Miscanmod - PLM_3
Assays: AFRC Wheat 2 evapw submodel - PLM_33, version 1, AFRC Wheat 2 jdaydif submodel - PLM_34, version 1, AFRC Wheat 2 julday submodel - PLM_35, version 1, AFRC Wheat 2 ldim submodel - PLM_36, version 1, AFRC Wheat 2 photpd submodel - PLM_37, version 1, AFRC Wheat 2 tdays submodel - PLM_38, version 1, AFRC Wheat 2 vappres submodel - PLM_39, version 1, AFRC Wheat 2 vernal submodel - PLM_40, version 1, AFRC Wheat 2 weathr submodel - PLM_41, version 1, AFRC Wheat2 dev submodel - PLM_32, version 1, AFRCtest2 - PLM_25, version 1, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, version 1, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1, Miscanmod - PLM_3, version 1
Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: 3PG - PLM_12, CENTURY_Rowe_daily - PLM_22, DALEC - PLM_23, LINTUL - PLM_4, McMurtrie vegetation model - PLM_11, TRIFFID - PLM_5
Assays: 3PG - PLM_12, version 1, CENTURY_Rowe_daily - PLM_22, version 1, DALEC - PLM_23, version 1, LINTUL - PLM_4, version 1, McMurtrie vegetation model - PLM_11, version 1, McMurtrie vegetation model - PLM_11, version 2, TRIFFID - PLM_5, version 1
Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.
Submitter: Jacqueline Wolf
Studies: Comparison of Sulfolobus solfataricus P2 grown on caseinhydrolysate and ...
Assays: Metabolic modelling of S. solfataricus during growth on casaminoacids, Metabolome analysis: Casaminoacids versus D-Glc, Proteome analysis: Casaminoacids versus D-Glc, RNA sequencing: Casaminoacids vs D-glc
Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.
Submitter: Andrew Millar
Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model
Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).
Submitter: Andrew Millar
Studies: Construction of Framework Model v1, Test of FMv1, growth study of Col-0 accession in 12L:12D, Test of FMv1, growth study of Col-0 accession in 5 photoperiods, Test of FMv1, growth study of other accessions and transgenic line in 12...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version, Gas exchange of Fei-0 and Ler plants in 12hL:12hD, Growth of Col-0 and 35S:miR156 plants in 12hL:12hD, Growth of Col-0 in 12hL:12hD, Growth of Col-0 plants in 5 photoperiods, Growth of Fei-0 and Ler plants in 12hL:12hD
Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits
Submitter: Jacky Snoep
Studies: Figure 1C: Biphasic control can resist mutant invasion of feedback circu..., Figure 1D: Biphasic control can resist mutant invasion of feedback circu..., Figure 1G: Biphasic control can resist mutant invasion of feedback circu..., Figure 1H: Biphasic control can resist mutant invasion of feedback circu..., Figure 2: Frequency-dependent selection of mutant pancreatic beta cells., Figure 4C: Biphasic control can provide mutant resistance to stem-cell h..., Figure 4D: Biphasic control can provide mutant resistance to stem-cell h...
Assays: Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Frequency-dependent selection of mutant pancreatic beta cells.
Frequency doubling in the cyanobacterial circadian clock
Submitter: Jacky Snoep
Studies: Figure 4B: A minimal mathematical model, containing an incoherent feedfo..., Figure 6C and D: The clock-sigC circuit represents a general mechanism t...
Assays: Frequency doubling in the cyanobacterial circadian clock, Frequency doubling in the cyanobacterial circadian clock
Submitter: Dawie van Niekerk
Studies: Allosteric regulation of phosphofructokinase controls the emergence of g..., Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: gustavsson1-4 models, gustavsson5 model
Submitter: Jacky Snoep
Studies: Entrainment of heterogeneous glycolytic oscillations in single cells
Assays: No Assays
Submitter: Jacky Snoep
Studies: Substrate preferences for AKR1C3, and implications of varying AKR1C3:17B...
Assays: No Assays
The objectives of WP1 within the colosys project are:
- Produce resources of data and information that will be used for the identification of CC driver genes (WP2) and for the construction and configuration of computational models of cancer-related biological processes (WP2 and WP3)
- Integrate information from public patient data and cancer cell line data repositories with information from project specific clinical and model data
- Convert information from public cellular signalling databases ...
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT". changed ID
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
Submitter: Malte Herold
Studies: Omics_data_analysis
Assays: Experimental methods, Genomics, Proteomics, RNAseq
Gene co-epxression network analyses are common in the study of large scale biological data sets. In this study, we have developed a methodology for the comparison of pairs of co-expression networks using the s-core network peeling approach. We apply the methodology to gene-expression data for human and mouse.
The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde ...
Submitter: Jacky Snoep
Studies: BPG stability, PGK-30C, PGK-70C, PGK-GAPDH 30C & 70C
Assays: BPG degradation, BPG stability analysis, PGK - GAPDH models, PGK 30C data, PGK 30C model, PGK 70 data, PGK 70C model, PGK-GAPDH 30, PGK-GAPDH 70
Drug detoxification dynamics explain the postantibiotic effect
Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches.
Submitter: Matthias König
Studies: A Multiscale Computational Model of Human Galactose Metabolism, PKDB Caffeine Study
Assays: Digitized pharmacokinetics data (Akinyinka2000), Digitized pharmacokinetics data (Amchin1999), Digitized pharmacokinetics data (Blanchard1983a), Digitized pharmacokinetics data (Haller2002), Digitized pharmacokinetics data (Healy1991), Digitized pharmacokinetics data (Hetzler1990), Digitized pharmacokinetics data (Jeppesen1996), Digitized pharmacokinetics data (Kakuda2014), Digitized pharmacokinetics data (Kaplan1997), Digitized pharmacokinetics data (Magnusson2008), Digitized pharmacokinetics data (Oh2012), Digitized pharmacokinetics data (Perera2011), Digitized pharmacokinetics data (Spigset1999a), Digitized pharmacokinetics data (Tanaka2014), Galactose Modelling
Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.
One of these activities is antibiotic production and is widespread in streptomycetes ...
Submitter: Jay Moore
Studies: ScoCyc metabolic pathway curation, Timeseries 1
Assays: Metabolic pathway curation, Online/offline measurements, metabolomics, proteomics, transcriptomics
Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.
Submitter: Theresa Kouril
Studies: Comparison of S. solfataricus grown on l-fucose and d-glucose
Assays: Cell free extract activity measurements: L-fuc/d-glc, Metabolic model of Sulfolobus solfataricus, Proteome analysis: d-fuc / l-glu, RNA sequencing:l-fuc/d-glu, intracellular metabolome analysis: l-fucose vs d-glucose