Investigations
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Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: F2014.1 - PLM_1030, PLM_67v3withTempPulse - PLM_81
Assays: F2014.1 - PLM_1030, version 1, PLM_67v3withTempPulse - PLM_81, version 1
Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED ...
Submitter: Maja Zagorscak
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
- To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
- To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization
- To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at genome scale, the metabolic ...
Submitter: Niels Zondervan
Studies: Core Model predictions, Core Model training, Core model predicting combined mutations and perturbations, Genome-scale, constraint-based metabolic modeling of M. hyopneumonia, Metabolomics measurements, Proteomics analysis, Transcriptomics of M. pneumoniae at different times of growth
Assays: 40 samples data analysis - metabolite correlation, 40 samples, OE mutants of glycolysis and pyruvate metabolism enzymes com..., All samples data, Comparison of Kcat values from the model and values from literature, Construction and training of the core model, Construction of a Genome Scale Metabolitic model of M. hyopneumoniae, Dynamic model simmulation pipeline, Metabolic control analysis (local and global), Metabolomics external metabolites measurements, Metabolomics internal metabolites, time series measurements, Proteomics assay, Transcriptomics assay of M. pneumoniae at diferent times of growth, Validation by simulating independent mutant and perturbation samples
Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.
Submitter: Andrew Millar
This is a collection of deep eutectic solvent (DES) experimental and simulation data that is stored in CML format and analysed using gradient boosting decision trees.
Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73, Chew_et_al_2014_Framework_Model - PLM_76, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75, Salazar Photoperiodism Model with T6P - PLM_82, Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1, Chew_et_al_2014_Framework_Model - PLM_76, version 1, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75..., Salazar Photoperiodism Model with T6P - PLM_82, version 1, Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.
Supplementary files for the submission: Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities with Approximate Bayesian Computation and Steady-State Signalling Simulations
Submitter: Malte Herold
Studies: Supplementary files
Assays: Proteome data, RNA data, Simulations for network engineering
Supplementary files for the publication: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
All the files available are published under the CC BY 4.0 license.
Publication data made available for Biotechnology Reports, supplementary data
Submitter: Antoine Buetti-Dinh
Studies: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizin...
Assays: No Assays
Collection of models submitted to PLaSMo by Tomasz Zielinski and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Checking upload for andrew - PLM_1040, Plasmo test model1 - PLM_80
Assays: CHecking if all works - PLM_1000, version 111, Checking upload for andrew - PLM_1040, version 1, Plasmo test model1 - PLM_80, version 1, Test created 1552502361596, Test created 1552502791700, Test created 1552503965203, Test created 1552503978484, Test created 1552504117107, Test created 1552504664537, Test created 1552504857803, Test created 1552505193451
Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: TiMet 2011 PP interaction network - PLM_56, TiMet 2011 Pollen network - PLM_54, TiMet 2011 Root network - PLM_55, TiMet 2011 flower specific protein detection network - PLM_57, TiMet 2011 seed network - PLM_53, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_58, TiMet 2011 silqueue specific protein detection network - PLM_59
Assays: TiMet 2011 PP interaction network - PLM_56, version 1, TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2, TiMet 2011 Root network - PLM_55, version 1, TiMet 2011 flower specific protein detection network - PLM_57, version 1, TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5..., TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, T2011 Ostreococcus clock, TOC1 act D - PLM_92, T2011 Ostreococcus clock, TOC1 act L - PLM_91, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, T2011 Ostreococcus clock, acc immediate - PLM_83, T2011 Ostreococcus clock, acc on - PLM_84, Troein Ostreococcus clock 1-loop - PLM_7
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1, T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1, T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2, T2011 Ostreococcus clock, acc immediate - PLM_83, version 1, T2011 Ostreococcus clock, acc on - PLM_84, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, Neurospora Circadian Clock 3-variable model - PLM_51, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Assays: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, version 1, Neurospora Circadian Clock 3-variable model - PLM_51, version 1, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: LINTUL_V2 - PLM_42, SUCROS1 - PLM_24
Assays: LINTUL_V2 - PLM_42, version 1, SUCROS1 - PLM_24, version 1
Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.
Collection of models submitted to PLaSMo by Martin Beaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Central plant metabolism - PLM_61, Glycolysis SBGN - PLM_60, Insulin-like growth factor signaling - PLM_62, Martin test - PLM_65, Neuronal muscle signalling - PLM_63
Assays: Central plant metabolism - PLM_61, version 1, Glycolysis SBGN - PLM_60, version 1, Insulin-like growth factor signaling - PLM_62, version 1, Martin test - PLM_65, version 1, Martin test - PLM_65, version 2, Neuronal muscle signalling - PLM_63, version 1
Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: arabidopsis_clock_biopepa - PLM_47
Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis_clock_2011 - PLM_43, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, Arabidopsis_clock_extend - PLM_6
Assays: Arabidopsis_clock_2011 - PLM_43, version 1, Arabidopsis_clock_2011 - PLM_43, version 2, Arabidopsis_clock_2011 - PLM_43, version 3, Arabidopsis_clock_2011 - PLM_43, version 4, Arabidopsis_clock_2011 - PLM_43, version 5, Arabidopsis_clock_2011 - PLM_43, version 6, Arabidopsis_clock_2011 - PLM_43, version 7, Arabidopsis_clock_2011 - PLM_43, version 8, Arabidopsis_clock_2011 - PLM_43, version 9, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 1, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 2, Arabidopsis_clock_extend - PLM_6, version 1, Arabidopsis_clock_extend - PLM_6, version 2, Arabidopsis_clock_extend - PLM_6, version 3
Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
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
