Data files
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Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creators: None
Submitter: Dikshant Pradhan
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Data file for PLaSMo accesssion ID PLM_23, version 1
Creators: BioData SynthSys, Robert Muetzelfeldt
Submitter: BioData SynthSys
Creators: Franco du Preez, Jacky Snoep
Submitter: Franco du Preez
Creators: Franco du Preez, Jacky Snoep
Submitter: Franco du Preez
Creator: Alexey Kolodkin
Submitter: Alexey Kolodkin
WT (Cy5) vs. trxB (Cy3)_stationary growth phase_DyeFlip
Creator: Daniel Hönicke
Submitter: Daniel Hönicke
WT (Cy3) vs. trxB (Cy5)_stationary growth phase
Creator: Daniel Hönicke
Submitter: Daniel Hönicke
WT (Cy3) vs. trxB (Cy5)_exp. growth phase
Creator: Daniel Hönicke
Submitter: Daniel Hönicke
WT (Cy5) vs. trxB (Cy3)_exp. growth phase_DyeFlip
Creator: Daniel Hönicke
Submitter: Daniel Hönicke
HSD11B1 was inhibited by CBX and the effect on the conversion of cortisone and 11KA4 in HSD11B1/AKR1C3 incubations was followed.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Experiment conducted in early April 2014 Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale. Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat.
Areas are then measured in image processing.
Creator: Yin Hoon Chew
Submitter: Andrew Millar
Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale. Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat. Areas are then measured in image processing.
Creator: Yin Hoon Chew
Submitter: Andrew Millar
E. faecalis was gucose-pulsed after resuspension in 100 mM MES buffer at pH 6.5 Intra- and extracellular metabolites concentrations were followed in time
Creator: Martijn Bekker
Submitter: Martijn Bekker
Growth curves of the PA1008 strain of Pseudomonas aeruginosa with multiple concentrations of meropenem. Data set 1 is used to parametrise the model in our project. This consists of three biological replicates, each with three technical repeats. The meropenem concentrations used for this data set were: 0, 2, 4, 10, 20, 40, 200 ug/ml.
Creators: Chloe Spalding, Sara Jabbari
Submitter: Chloe Spalding
Growth curves of the PA1008 strain of Pseudomonas aeruginosa with multiple concentrations of meropenem. Data set 1 is used to parametrise the model in our project. This consists of three biological replicates, each with three technical repeats. The meropenem concentrations used for this data set were: 0, 0.5, 1, 5, 10, 50, 100 ug/ml.
Creators: Chloe Spalding, Sara Jabbari
Submitter: Chloe Spalding
just cell counts, the area of the grains is separate.
Creator: Antoine Buetti-Dinh
Submitter: Antoine Buetti-Dinh
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Data used for training or testing of the model
Creator: Hannah Kinmonth-Schultz
Submitter: Hannah Kinmonth-Schultz
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
raw data of Figure 2
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages/stickleback
Creator: Xiaokang Zhang
Submitter: Xiaokang Zhang
More information can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages/zebrafish
Creator: Xiaokang Zhang
Submitter: Xiaokang Zhang
Python script allowing the user to define the names of the input files to be used. Together with "wrapper.py" this script requires input files to be located in a folder called "input" in the same directory.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
NHA1 ENA1-5 TOK1 TRK1 TRK2
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
Complete list of differentially expressed proteins between sub-anatomical regions. Non significant results were filtered out.
Creators: None
Submitter: Julia Scheel
Complete list of differentially expressed proteins between sub-anatomical regions. Non significant results were filtered out.
Creators: None
Submitter: Julia Scheel
CML dictionary for compchem conventions allowing representation of thermophysical properties of deep eutectic solvents (DES) with CML. Examples of thermophysical properties are: density, viscosity, conductivity and water activity
Creators: Gudrun Gygli, Xinmeng Xu, Juergen Pleiss
Submitters: Gudrun Gygli, Xinmeng Xu
CML unit dictionary for mili pascal * second and microSiemens per cm
Creators: Gudrun Gygli, Xinmeng Xu, Juergen Pleiss
Submitters: Gudrun Gygli, Xinmeng Xu
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
PhD thesis research by Joost W Aerts under supervision of Hans V. Westerhoff, Rob J van Spanning and Pascale Ehrenfreund
In this folder one has the: thesis summary a pdf of the thesis supplemental material per chapter, for chapters 3, 4, 6, and 7
Creators: Hans V. Westerhoff, Joost Aerts
Submitter: Hans V. Westerhoff
Creator: Helge Stark
Submitter: Helge Stark
At the GenoSysFat startup meeting 2015-04-22, Dominic Nanton of EWOS described the feeds they made for GenoSysFat.
Describes recipes with linseed oil (LNO) and palm oil (PO) to provide the 18:3n-3 precursor to EPA and DHA and match saturation of 100% fish oil (FO) control diet at ca 0.7 mass% EPA+DHA.
Page 2: Overview Page 3-4: Description of feeds. Feed no., Code, Initial fish weight (g), Feed size (mm), Fish number (3000), Feed (kg) Page 5-7: Feed formulations. Feed number, Feed name, Feed size ...
Creators: Jon Olav Vik, Dominic Nanton
Submitter: Jon Olav Vik
Data file for PLaSMo accesssion ID PLM_6, version 1
Creators: BioData SynthSys, Alexandra Pokhilko, Andrew Millar
Submitter: BioData SynthSys
Creators: None
Submitter: Lars Wöhlbrand
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
Data file for PLaSMo accesssion ID PLM_24, version 1
Creators: BioData SynthSys, Jonathan Massheder
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_42, version 1
Creators: BioData SynthSys, Jonathan Massheder
Submitter: BioData SynthSys
This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.
Creator: Matthew Rolfe
Submitter: The JERM Harvester
This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.
Creator: Matthew Rolfe
Submitter: The JERM Harvester
The distribution of enzymes involved in oxidative Stickland reactions among archaea was estimated using BLAST searches (BLOSUM62) with the protein sequences of acetate-CoA ligase (EC 6.2.1.13, ACS), ketoisovalerate oxidoreductase (EC 1.2.7.7, BC-OR) and indolepyruvate oxdoreductase (EC 1.2.7.8, AR-OR) from Pyrococcus furiosus (Pfu) and Sulfolobus solfataricus (Sso) against all archaea. Positive results are indicated by a '+' (homologue found, e-value < 1e-20) and negative results by a '-' (no ...
Creator: Helge Stark
Submitter: Helge Stark
Supplementary movie of the distribution of nuclear pores in the nuclear envelope of P. cordatum
Creators: None
Submitter: Jana Kalvelage
Raw data of the measurements obtained via DLS measurements. Can be opened with the Zetasizer software.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Raw data of the measurements obtained via DLS measurements. Can be opened with the Zetasizer software.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Simulation of double mutants and perturbations and time series samples using for Sample 1 only OE mutants of which we update the enzyme concentrations. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model. Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.
Creator: Niels Zondervan
Submitter: Niels Zondervan
Creator: Xiaokang Zhang
Submitter: Xiaokang Zhang
COBRA Matlab toolbox was used.
Creators: Xiaokang Zhang, Eileen Marie Hanna
Submitter: Xiaokang Zhang
gadMorTrinity can be found at: https://doi.org/10.6084/m9.figshare.13067354.v1
Creator: Xiaokang Zhang
Submitter: Xiaokang Zhang
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Andrej Blejec
Submitter: Andrej Blejec
Contains a Jupyter notebook file that uses libroadrunner and tellurium to run all simmulations and analysis based on the 40 independent samples. The Readme.txt file contains information on how to recreate the complete modelling environment used for all simmulations and analysis using Anaconda.
Creator: Niels Zondervan
Submitter: Niels Zondervan
Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, ...
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev