Data files

What is a Data file?
30 Data files visible to you, out of a total of 86
No description specified

Creator: Amatus Beyer

Submitter: Amatus Beyer

No description specified

Creator: Aaron Laier

Submitter: Aaron Laier

The Results of the analysis are structured in three parts:

  1. The results of the main analysis
  2. The results with a broader prior (Sensitivity analysis)
  3. The Results of the multiple period comparison

For each part, full posterior traces for all analysis and visualizations of the paper are avalable.

Furthermore the diagnostics and traces were added for the different analysis. The trace for the mulitple comparison was to large to upload it and is available on request.

The classification in reproducible and not reproducible models was made by Tiwari et al.

Citations were looked up in Scopus, Web of Science and Google Scholar.

The following journals had to be excluded, as Journal Impact Factors (JIF) were missing or papers were discontinued:

  • Experientia was closed 1996 and continued as Cellular and Molecular Life Sciences 1997
  • The American journal of physiology – split into fields 1977, further splits in 1980 and 1989
  • IFAC Proceedings Volumes – last issue ...

This code uses the PEtab problem (written in the yaml file) to perform MCMC sampling with pyPESTO. Afterwards an ensemble is created, that allows to compute the posterior predictive distribution and therefore the credibility intervals for the model output.

The sampling.py scipt of pyPESTO visulize was adjusted for an improved visualization. The used code was also uploaded.

A Conda environment file (.yml) containing the specific version of Python and installed packages with the according versions, ...

Creators: None

Submitter: Sebastian Höpfl

Complete posterior distributions for each drug and condition.

The files are in the hdf5 format and contain the complete information of the analysis for a FAIR data sharing.

Creators: None

Submitter: Sebastian Höpfl

The parameters A and B were estimated for the function f(x)=x⋅e^(B-Ax) and the AUC was calculated for the decay phase only. For OH-Midazolam the fourth replicate in the 2 weeks condition has an outlier in the measurement after six hours (more than 2SD above the mean of this condition) and was omitted for the AUC calculation as this could not be fitted to an exponential decay.

Creators: None

Submitter: Sebastian Höpfl

One example of a ReStoRunT sheet.

Creators: None

Submitter: Wolfgang Müller

This file is part of a tutorial for the Gesellschaft für Ökologie and the NFDI4Biodiversity.

Creators: None

Submitter: Wolfgang Müller

No description specified

Creator: Birger Wolter

Submitter: Birger Wolter

No description specified

Creator: Ulrike Wittig

Submitter: Maja Rey

No description specified

Creators: Maja Rey, Ulrike Wittig

Submitter: Maja Rey

No description specified

Creators: Maja Rey, Ulrike Wittig

Submitter: Maja Rey

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.

The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)

The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model

The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model

The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model

The stoichiometric matrix of the multi-compartment metabolic model of growing Arabidopsis thaliana

The ASCII file includes complete information on used transformers / compounds / genes and their inter-connection in the model. The Transformer information includes: Identifier name, Trivial name, Stoichiometric equation, Compartment, EC number, Pathway, Associated genes). The Compound information includes: Identifier name, Trivial name, Kegg ID, Compartment. The Gene information includes: ATG code of the genes whose products participate in transformations accounted in the model, Association with ...

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