Replication Data for: HOPS: high-performance library for (non-)uniform sampling of convex-constrained models (ICPSR doi:10.26165/JUELICH-DATA/YXLFKJ)

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Replication Data for: HOPS: high-performance library for (non-)uniform sampling of convex-constrained models

doi:10.26165/JUELICH-DATA/YXLFKJ

Jülich DATA

2020-12-18

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Johann F. Jadebeck; Axel Theorell; Samuel Leweke; Katharina Nöh, 2020, "Replication Data for: HOPS: high-performance library for (non-)uniform sampling of convex-constrained models", https://doi.org/10.26165/JUELICH-DATA/YXLFKJ, Jülich DATA, V1

Replication Data for: HOPS: high-performance library for (non-)uniform sampling of convex-constrained models

doi:10.26165/JUELICH-DATA/YXLFKJ

Johann F. Jadebeck (Forschungszentrum Jülich GmbH)

Axel Theorell (Forschungszentrum Jülich GmbH)

Samuel Leweke (Forschungszentrum Jülich GmbH)

Katharina Nöh (Forschungszentrum Jülich GmbH)

Jülich DATA

Johann F. Johann

Katharina Nöh

Jadebeck, Johann Fredrik

2020-10-27

Medicine, Health and Life Sciences, Metabolic Network Model HOPS Sampling MCMC Rounding

This collection contains showcased models and pre-processing results (determining an independent flux space and rounding) that are used as basis for benchmarking the uniform sampling performance of the CHHR implementations of the HOPS library [10.1093/bioinformatics/btaa872] (https://github.com/modsim/hops) and the COBRA toolbox [doi.org/10.1038/s41596-018-0098-2]. Here, the pre-processing was performed with the COBRA toolbox for all benchmarks to guarantee fair comparability. The models are split in two classes: 1) simplices with 64, 256, 512, 1024, and 2048 dimensions; 2) metabolic network models (e_coli_core, iAT_PLT_256, iJO1366, RECON1, Recon2, Recon3D_301) [http://bigg.ucsd.edu/], [doi.org/10.1038/nbt.2488] formulated in SBML format [doi.org/10.1093/bioinformatics/btg015]. For each of these models, the left hand side of the constraint system (called <b>A</b>), the right hand side (called <b>b</b>), a shift of the transformation from sampling space, meaning the null space, to parameter space, meaning the full space of the model (called <b>p_shift</b>), the linear transformation from sampling space to parameter space (called <b>N</b>) and the Chebyshev center (called <b>start</b>) are provided. These files come in <b> rounded </b> and <b> unrounded </b> types, indicating if the rounding algorithm has been applied. For convenience, sometimes the rounding transformation is also given (indicated by <b>T</b>). The rounding transformation is only given in the <b>rounded</b> form, because it is identity otherwise. Additionally, the dataset contains an <i>E. coli </i> WT model with carbon atom transitions and isotope labelling measurements [10.1038/nprot.2009.58] used in the Bayesian inference non-uniform sampling example. The <i>E. coli</i> WT model is contained in a single FluxML file [doi.org/10.3389/fmicb.2019.01022]. To reproduce the data generated with the <i> E. coli WT </i> model, the rounding was calculated using the HOPS library and independent fluxes were provided by the high-performance simulator 13CFLUX2 [doi.org/10.1093/bioinformatics/bts646].

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10.1093/bioinformatics/btaa872

Johann F Jadebeck, Axel Theorell, Samuel Leweke, Katharina Nöh, HOPS: high-performance library for (non-)uniform sampling of convex-constrained models, Bioinformatics, 2020, btaa872

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A_e_coli_core_rounded.csv

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A_e_coli_core_unrounded.csv

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A_iAT_PLT_636_rounded.csv

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A_iAT_PLT_636_unrounded.csv

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A_iJO1366_rounded.csv

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A_iJO1366_unrounded.csv

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A_RECON1_rounded.csv

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A_RECON1_unrounded.csv

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A_Recon2_rounded.csv

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A_Recon2_unrounded.csv

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A_Recon3D_301_rounded.csv

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A_Recon3D_301_unrounded.csv

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A_simplex_1024D_rounded.csv

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A_simplex_1024D_unrounded.csv

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A_simplex_2048D_rounded.csv

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A_simplex_2048D_unrounded.csv

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A_simplex_256D_rounded.csv

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A_simplex_256D_unrounded.csv

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A_simplex_512D_rounded.csv

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A_simplex_512D_unrounded.csv

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A_simplex_64D_rounded.csv

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A_simplex_64D_unrounded.csv

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b_e_coli_core_rounded.csv

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b_e_coli_core_unrounded.csv

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b_iAT_PLT_636_rounded.csv

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b_iAT_PLT_636_unrounded.csv

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b_iJO1366_rounded.csv

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b_iJO1366_unrounded.csv

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b_RECON1_rounded.csv

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b_RECON1_unrounded.csv

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b_Recon2_rounded.csv

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b_Recon2_unrounded.csv

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b_Recon3D_301_rounded.csv

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b_Recon3D_301_unrounded.csv

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b_simplex_1024D_rounded.csv

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b_simplex_1024D_unrounded.csv

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b_simplex_2048D_rounded.csv

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b_simplex_2048D_unrounded.csv

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b_simplex_256D_rounded.csv

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b_simplex_256D_unrounded.csv

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b_simplex_512D_rounded.csv

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b_simplex_512D_unrounded.csv

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b_simplex_64D_rounded.csv

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b_simplex_64D_unrounded.csv

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e_coli_core.xml

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E.coli_Zamboni2009.fml

application/octet-stream

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iAT_PLT_636.mat

application/matlab-mat

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iJO1366.xml

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N_e_coli_core_rounded.csv

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N_e_coli_core_unrounded.csv

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N_iAT_PLT_636_rounded.csv

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N_iAT_PLT_636_unrounded.csv

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N_iJO1366_rounded.csv

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N_iJO1366_unrounded.csv

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N_RECON1_rounded.csv

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N_RECON1_unrounded.csv

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N_Recon2_rounded.csv

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N_Recon2_unrounded.csv

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N_Recon3D_301_rounded.csv

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N_Recon3D_301_unrounded.csv

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N_simplex_1024D_rounded.csv

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N_simplex_2048D_rounded.csv

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N_simplex_256D_rounded.csv

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N_simplex_512D_rounded.csv

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N_simplex_64D_rounded.csv

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N_simplex_64D_unrounded.csv

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p_shift_e_coli_core.csv

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p_shift_e_coli_core_rounded.csv

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p_shift_e_coli_core_unrounded.csv

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p_shift_iAT_PLT_636_rounded.csv

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p_shift_iAT_PLT_636_unrounded.csv

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p_shift_iJO1366_rounded.csv

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p_shift_iJO1366_unrounded.csv

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p_shift_RECON1_rounded.csv

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p_shift_RECON1_unrounded.csv

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p_shift_Recon2_rounded.csv

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p_shift_Recon2_unrounded.csv

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p_shift_Recon3D_301_rounded.csv

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p_shift_Recon3D_301_unrounded.csv

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p_shift_simplex_1024D_rounded.csv

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p_shift_simplex_2048D_rounded.csv

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p_shift_simplex_256D_rounded.csv

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p_shift_simplex_512D_rounded.csv

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p_shift_simplex_64D_rounded.csv

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p_shift_simplex_64D_unrounded.csv

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RECON1.mat

application/matlab-mat

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Recon2.xml

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Recon3D_301.mat

application/matlab-mat

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start_e_coli_core_rounded.csv

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start_e_coli_core_unrounded.csv

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start_iAT_PLT_636_rounded.csv

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start_iAT_PLT_636_unrounded.csv

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start_iJO1366_rounded.csv

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start_iJO1366_unrounded.csv

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start_RECON1_rounded.csv

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start_RECON1_unrounded.csv

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start_Recon2_rounded.csv

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start_Recon2_unrounded.csv

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start_Recon3D_301_rounded.csv

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start_Recon3D_301_unrounded.csv

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start_simplex_1024D_rounded.csv

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start_simplex_1024D_unrounded.csv

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start_simplex_2048D_rounded.csv

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start_simplex_2048D_unrounded.csv

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start_simplex_256D_rounded.csv

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start_simplex_256D_unrounded.csv

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start_simplex_512D_rounded.csv

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start_simplex_512D_unrounded.csv

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start_simplex_64D_rounded.csv

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start_simplex_64D_unrounded.csv

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T_e_coli_core_rounded.csv

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T_iAT_PLT_636_rounded.csv

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T_iJO1366_rounded.csv

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T_RECON1_rounded.csv

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T_Recon2_rounded.csv

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T_Recon3D_301_rounded.csv

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T_simplex_1024D_rounded.csv

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T_simplex_2048D_rounded.csv

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T_simplex_256D_rounded.csv

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T_simplex_512D_rounded.csv

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T_simplex_64D_rounded.csv

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T_simplex_64D_unrounded.csv

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