Mani-Tlusty2021 - generative development model

  public model
Model Identifier
MODEL2103180001
Short description
Codes for simulating the minimal generative model for organismal development, analysing data, and making plots. Also contains data generated with the model which was used for publication.
Format
MATLAB (Octave)
Related Publication
  • A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration
  • somya mani, Tsvi Tlusty
  • BMC Biology , 4/ 2021 , DOI: 10.1186/s12915-021-01013-4
  • IBS-CSLM, Ulsan, South Korea
  • Background: Multicellular organisms are characterized by a wide diversity of forms and complexity despite a restricted set of key molecules and mechanisms at the base of organismal development. Development combines three basic processes—asymmetric cell division, signaling, and gene regulation—in a multitude of ways to create this overwhelming diversity of multicellular life forms. Here, we use a generative model to test the limits to which such processes can be combined to generate multiple differentiation paths during development, and attempt to chart the diversity of multicellular organisms generated. Results: We sample millions of biologically feasible developmental schemes, allowing us to comment on the statistical properties of cell differentiation trajectories they produce. We characterize model-generated “organisms” using the graph topology of their cell type lineage maps. Remarkably, tree-type lineage differentiation maps are the rarest in our data. Additionally, a majority of the “organisms” generated by our model appear to be endowed with the ability to regenerate using pluripotent cells. Conclusions: Our results indicate that, in contrast to common views, cell type lineage graphs are unlikely to be tree-like. Instead, they are more likely to be directed acyclic graphs, with multiple lineages converging on the same terminal cell type. Furthermore, the high incidence of pluripotent cells in model-generated organisms stands in line with the long-standing hypothesis that whole body regeneration is an epiphenomenon of development. We discuss experimentally testable predictions of our model and some ways to adapt the generative framework to test additional hypotheses about general features of development.
Contributors
Somya Mani, Krishna Kumar Tiwari

Metadata information


Curation status
Non-curated

Modelling approach(es)

Tags
Name Description Size Actions

Model files

get_lineagemaps1.m Model for biological development that takes in parameter values and initial condditions to generate corresponding lineage maps 8.09 KB Preview | Download

Additional files

lineage_maps_genome04_N7.mat lineage map data: 7 node system 776.43 KB Preview | Download
lineage_maps_genome09_N6.mat lineage map data: 6 node system 374.11 KB Preview | Download
write_trajectories.m writes properties of developmental trajectories to a text file 2.26 KB Preview | Download
lineage_maps_genome08_N5.mat lineage map data: 5 node system 197.79 KB Preview | Download
lineage_maps_genome15_N4.mat lineage map data: 4 node system 110.58 KB Preview | Download
lineage_maps_genome17_N3.mat lineage map data: 3 node system 43.19 KB Preview | Download
main_fig5D_data.csv data values used for fig5D of the main manuscript. csv file 7.90 MB Preview | Download
lineage_maps_genome15_N6.mat lineage map data: 6 node system 330.78 KB Preview | Download
lineage_maps_genome20_N6.mat lineage map data: 6 node system 257.98 KB Preview | Download
lineage_maps_genome10_N3.mat lineage map data: 3 node system 20.42 KB Preview | Download
lineage_maps_genome04_N3.mat lineage map data: 3 node system 50.25 KB Preview | Download
randomize_edges.py python code to randomize lineage graphs 3.09 KB Preview | Download
lineage_maps_genome13_N4.mat lineage map data: 4 node system 113.82 KB Preview | Download
lineage_maps_genome11_N3.mat lineage map data: 3 node system 37.05 KB Preview | Download
supp_fig10_data.csv data for Fig S10 in additional file 1 981.28 KB Preview | Download
lineage_maps_genome14_N6.mat lineage map data: 6 node system 393.97 KB Preview | Download
lineage_maps_genome08_N4.mat lineage map data: 4 node system 104.03 KB Preview | Download
lineage_maps_genome05_N7.mat lineage map data: 7 node system 859.64 KB Preview | Download
write_reproducibility.m writes properties of regenerative organisms to a text file. matlab code 1.93 KB Preview | Download
lineage_maps_genome03_N6.mat lineage map data: 6 node system 289.67 KB Preview | Download
lineage_maps_genome06_N5.mat lineage map data: 5 node system 154.77 KB Preview | Download
lineage_maps_genome14_N5.mat lineage map data: 5 node system 208.41 KB Preview | Download
lineage_maps_genome13_N7.mat lineage map data: 7 node system 839.89 KB Preview | Download
lineage_maps_genome17_N4.mat lineage map data: 4 node system 99.53 KB Preview | Download
lineage_maps_genome07_N5.mat lineage map data: 5 node system 206.38 KB Preview | Download
lineage_maps_genome13_N5.mat lineage map data: 5 node system 164.78 KB Preview | Download
lineage_maps_genome15_N7.mat lineage map data: 7 node system 1.10 MB Preview | Download
lineage_maps_genome04_N4.mat lineage map data: 4 node system 107.89 KB Preview | Download
lineage_maps_genome05_N3.mat lineage map data: 3 node system 31.15 KB Preview | Download
lineage_maps_genome17_N5.mat lineage map data: 5 node system 184.33 KB Preview | Download
lineage_maps_genome05_N4.mat lineage map data: 4 node system 116.28 KB Preview | Download
lineage_maps_genome20_N3.mat lineage map data: 3 node system 34.44 KB Preview | Download
lineage_maps_genome07_N3.mat lineage map data: 3 node system 33.49 KB Preview | Download
lineage_maps_genome17_N7.mat lineage map data: 7 node system 999.61 KB Preview | Download
lineage_maps_genome04_N6.mat lineage map data: 6 node system 259.90 KB Preview | Download
lineage_maps_genome20_N5.mat lineage map data: 5 node system 205.43 KB Preview | Download
Adj_asym_sig_seeds.mat seeds for the random number generator for generating developmental rules matrices used in get_lineagemaps1.m. binary file. .mat format 15.40 KB Preview | Download
genome_initialcondition_seeds.mat seeds for the random number generator for generating initial conditions used in get_lineagemaps1.m. binary file. .mat format 1.12 MB Preview | Download
lineage_maps_genome08_N3.mat lineage map data: 3 node system 49.26 KB Preview | Download
lineage_maps_genome18_N6.mat lineage map data: 6 node system 358.42 KB Preview | Download
lineage_maps_genome10_N7.mat lineage map data: 7 node system 904.51 KB Preview | Download
lineage_maps_genome16_N7.mat lineage map data: 7 node system 970.10 KB Preview | Download
lineage_maps_genome07_N7.mat lineage map data: 7 node system 887.25 KB Preview | Download
explore_reproducibility.m calculates properties of regenerative organisms generated by the model 8.07 KB Preview | Download
lineage_maps_genome02_N6.mat lineage map data: 6 node system 333.24 KB Preview | Download
lineage_maps_genome09_N7.mat lineage map data: 7 node system 1.02 MB Preview | Download
supp_fig11_data.csv data for Fig S11 in additional file 1 12.52 MB Preview | Download
lineage_maps_genome16_N5.mat lineage map data: 5 node system 196.85 KB Preview | Download
lineage_maps_genome17_N6.mat lineage map data: 6 node system 291.02 KB Preview | Download
lineage_maps_genome12_N5.mat lineage map data: 5 node system 218.34 KB Preview | Download
lineage_maps_genome12_N6.mat lineage map data: 6 node system 422.87 KB Preview | Download
lineage_maps_genome07_N6.mat lineage map data: 6 node system 341.04 KB Preview | Download
supp_fig16_data.csv data for Fig S16 in additional file 1 29.12 MB Preview | Download
lineage_maps_genome03_N7.mat lineage map data: 7 node system 972.87 KB Preview | Download
lineage_maps_genome08_N6.mat lineage map data: 6 node system 380.72 KB Preview | Download
main_fig2_data.csv data values used for fig2 of the main manuscript. csv file 331.68 MB Preview | Download
lineage_maps_genome18_N5.mat lineage map data: 5 node system 178.00 KB Preview | Download
lineage_maps_genome16_N3.mat lineage map data: 3 node system 36.89 KB Preview | Download
lineage_maps_genome03_N5.mat lineage map data: 5 node system 186.56 KB Preview | Download
lineage_maps_genome06_N3.mat lineage map data: 3 node system 29.52 KB Preview | Download
lineage_maps_genome11_N7.mat lineage map data: 7 node system 973.41 KB Preview | Download
lineage_maps_genome02_N4.mat lineage map data: 4 node system 108.81 KB Preview | Download
lineage_maps_genome10_N4.mat lineage map data: 4 node system 76.29 KB Preview | Download
supp_fig3B_data.csv data for Fig S3(B) in additional file 1 1.80 GB Preview | Download
write_linmap_properties_table.m writes properties of lineage maps to text file. 6.70 KB Preview | Download
supp_fig19_data.csv data for Fig S19 in additional file 1 187.95 MB Preview | Download
lineage_maps_genome03_N4.mat lineage map data: 4 node system 102.50 KB Preview | Download
lineage_maps_genome06_N7.mat lineage map data: 7 node system 740.96 KB Preview | Download
lineage_maps_genome14_N3.mat lineage map data: 3 node system 28.73 KB Preview | Download
lineage_maps_genome20_N7.mat lineage map data: 7 node system 947.08 KB Preview | Download
lineage_maps_genome12_N3.mat lineage map data: 3 node system 19.59 KB Preview | Download
lineage_maps_genome08_N7.mat lineage map data: 7 node system 1.09 MB Preview | Download
process_data.py python code to calculate properties of lineage graphs 23.09 KB Preview | Download
lineage_maps_genome18_N3.mat lineage map data: 3 node system 39.95 KB Preview | Download
get_trajectory_length_plots.py python code to calculate length of developmental trajectory from initial condition to final organism 1.32 KB Preview | Download
jitterplot.py python code to create scatter plots that have some jitter added to points 334.00 Bytes Preview | Download
lineage_maps_genome13_N3.mat lineage map data: 3 node system 36.21 KB Preview | Download
check_reproducibility.m checks whether homeostatic organisms generated by model can regenerate 2.98 KB Preview | Download
lineage_maps_genome14_N4.mat lineage map data: 4 node system 103.96 KB Preview | Download
lineage_maps_genome14_N7.mat lineage map data: 7 node system 944.60 KB Preview | Download
supp_fig14_data.csv data for Fig S14 in additional file 1 76.35 MB Preview | Download
lineage_maps_genome09_N5.mat lineage map data: 5 node system 156.24 KB Preview | Download
lineage_maps_genome19_N6.mat lineage map data: 6 node system 295.83 KB Preview | Download
lineage_maps_genome01_N4.mat lineage map data: 4 node system 87.83 KB Preview | Download
lineage_maps_genome19_N7.mat lineage map data: 7 node system 710.67 KB Preview | Download
lineage_maps_genome09_N3.mat lineage map data: 3 node system 26.92 KB Preview | Download
lineage_maps_genome15_N3.mat lineage map data: 3 node system 40.76 KB Preview | Download
lineage_maps_genome19_N5.mat lineage map data: 5 node system 195.63 KB Preview | Download
supp_fig8_data.csv data for Fig S8(B,C,D) in additional file 1 75.90 MB Preview | Download
supp_fig15_data.csv data for Fig S15 in additional file 1 73.62 MB Preview | Download
supp_fig3_9_13_data.csv data values for Fig S3(A,C), S4, S5, S6, S7, S8(A), S9, S13 in additional file 1 476.45 MB Preview | Download
lineage_maps_genome01_N5.mat lineage map data: 5 node system 190.89 KB Preview | Download
lineage_maps_genome01_N6.mat lineage map data: 6 node system 365.17 KB Preview | Download
lineage_maps_genome11_N5.mat lineage map data: 5 node system 188.69 KB Preview | Download
main_fig4A_data.csv data values used for fig4A of the main manuscript, and fig s12 of additional file-1. csv file 152.05 MB Preview | Download
lineage_maps_genome18_N4.mat lineage map data: 4 node system 106.34 KB Preview | Download
lineage_maps_genome01_N7.mat lineage map data: 7 node system 1.06 MB Preview | Download
lineage_maps_genome15_N5.mat lineage map data: 5 node system 209.15 KB Preview | Download
lineage_maps_genome12_N4.mat lineage map data: 4 node system 117.41 KB Preview | Download
lineage_maps_genome11_N6.mat lineage map data: 6 node system 334.68 KB Preview | Download
main_fig3_data.csv data values used for fig3 of the main manuscript. csv file 18.44 MB Preview | Download
lineage_maps_genome01_N3.mat lineage map data: 3 node system 30.64 KB Preview | Download
get_graph_prop.m calculates properties of lineagemaps generated by get_lineagemaps1.m 2.72 KB Preview | Download
supp_fig18_data.csv data for Fig S18 in additional file 1 64.59 MB Preview | Download
lineage_maps_genome02_N5.mat lineage map data: 5 node system 185.77 KB Preview | Download
lineage_maps_genome03_N3.mat lineage map data: 3 node system 33.17 KB Preview | Download
lineage_maps_genome12_N7.mat lineage map data: 7 node system 635.96 KB Preview | Download
lineage_maps_genome05_N5.mat lineage map data: 5 node system 199.54 KB Preview | Download
lineage_maps_genome06_N4.mat lineage map data: 4 node system 85.38 KB Preview | Download
lineage_maps_genome16_N4.mat lineage map data: 4 node system 103.82 KB Preview | Download
main_fig4B_data.csv data values used for fig4B of the main manuscript. csv file 202.48 MB Preview | Download
lineage_maps_genome09_N4.mat lineage map data: 4 node system 93.95 KB Preview | Download
lineage_maps_genome07_N4.mat lineage map data: 4 node system 95.60 KB Preview | Download
lineage_maps_genome20_N4.mat lineage map data: 4 node system 127.01 KB Preview | Download
lineage_maps_genome02_N3.mat lineage map data: 3 node system 41.56 KB Preview | Download
lineage_maps_genome04_N5.mat lineage map data: 5 node system 192.45 KB Preview | Download
get_final_paper_plots.py python code to analyse lineage map data and produce plots used in final manuscript 72.03 KB Preview | Download
lineage_maps_genome05_N6.mat lineage map data: 6 node system 471.12 KB Preview | Download
get_randomized_stacked_topology_hist.py python code to analyse and make stacked histogram of graph topologies of randomized graphs 3.55 KB Preview | Download
lineage_maps_genome02_N7.mat lineage map data: 7 node system 773.57 KB Preview | Download
lineage_maps_genome16_N6.mat lineage map data: 6 node system 302.59 KB Preview | Download
check_randomization_topology_swaps.py python code. checks whether graph topology of lineage maps change following graph randomization 4.95 KB Preview | Download
lineage_maps_genome19_N3.mat lineage map data: 3 node system 30.04 KB Preview | Download
lineage_maps_genome10_N6.mat lineage map data: 6 node system 440.40 KB Preview | Download
lineage_maps_genome11_N4.mat lineage map data: 4 node system 73.20 KB Preview | Download
lineage_maps_genome06_N6.mat lineage map data: 6 node system 285.09 KB Preview | Download
explore_trajectories.m calculates properties of development trajectories from initial conditions to final homeostatic organisms 6.26 KB Preview | Download
lineage_maps_genome10_N5.mat lineage map data: 5 node system 152.03 KB Preview | Download
lineage_maps_genome18_N7.mat lineage map data: 7 node system 834.28 KB Preview | Download
lineage_maps_genome19_N4.mat lineage map data: 4 node system 137.13 KB Preview | Download
main_fig5C_data.csv data values used for fig5C of the main manuscript. csv file 32.16 MB Preview | Download
lineage_maps_genome13_N6.mat lineage map data: 6 node system 400.15 KB Preview | Download

  • Model originally submitted by : Somya Mani
  • Submitted: 24-May-2021 15:00:30
  • Last Modified: 24-May-2021 15:00:30
Revisions
  • Version: 7 public model Download this version
    • Submitted on: 24-May-2021 15:00:30
    • Submitted by: Krishna Kumar Tiwari
    • With comment: updated model name and corrected doi notation.