cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13770006
title: A simple framework for agent-based modeling with extracellular matrix: Simulation results

description: Data for "A simple framework for agent-based modeling with extracellular matrix"

 

Metzcar, J., Duggan, Ben S., Fischer, B., Murphy, M., Heiland, R., Macklin, P. A simple framework for agent-based modeling with extracellular matrix. bioRxiv. doi: 10.1101/2022.11.21.514608

 

Link to preprint



This repository contains the data for each subfigure (and video) in the preprint cited and linked abvoe, as well as the original figures and videos themselves. We have tried to include original model file (PhysiCell_settings.xml or other *.xml file) used to generate each results with each file set as well as the code (see python scripts) to make images and videos that appear in the pre-print - both within the files and base modules and examples in a separate folder.

The data can be regenerated using release 2.0, 2.1, and 2.2.1. Release 2.1 is recommended for reproducing more exactly the results for the fibrosis, invasive carcinoma, and series of leader-follower results as the results archived here were produced using a set of two random number generators (one from PhysiCell and one from BioFVM). 2.2.1, used to produce the invasive cellular front results, consolidates the use of random number generators to just one (the PhysiCell one). As such, in 2.2.1, the random number generator seed may need changed to produce stochastic replicates, even when multithreading.


 

The following file sets are in this download:



Fig2_SM_3_simple_tests.zip



Has results for Figure 2 and SM Figure 3



Fig3_fibrosis.zip



Results from fibrosis simulation (originally Figure 3, now Figure 4)



Fig4_invasive_carcinoma.zip



Results from invasive carcinoma simulation (originally Figure 4, now Figure 5)



Fig5_collective_migration_initial_tests.zip



Results from initial leader follower model development (originally Figure 5, now Figure 6)



Fig6_instant_remodeling.zip



Results from instant remodeling leader follower model scenariods (originally Figure 6, now Figure 7)



Fig7b_leader_follower.zip



Results from leader-follower collective migration scenario (origianlly Figure 7b, now Figure 8b)



images_and_vidoes_for_paper.zip



has all the images, videos, and some figures from the main body of the paper and the supplmental material. Updated in this version.



Invasive_cellular_front.zip



Has results for each ECM scenario: random, parallel, and perpindicular orientations and mixed ECM conditions. New to this data repository.



python_imaging.zip



Base modules and examples for producing images (tested on Python 3.9). Updated in in this verison



SM_Fig_4b_leader_follower_decreased_remodeling.zip

stochastic_replicates.zip



Contains stochastic replicates for the collective migration, fibrosis, and invasive carcinoma models and source code for all.



stochastic_replicates_invasive_cellular_front.zip



Contains stochastic replicates for the invasive cellular front scenarios. New to this data repository.
DOI: 10.15468/dl.pjwwxu
title: Occurrence Download

description: A dataset containing 5582304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Year 2000-2024"
 ]
}

 The dataset includes 5582304 records from 3670 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020456-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wa4blg
title: Occurrence Download

description: A dataset containing 5396 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1980-2019",
 "HasCoordinate is true",
 "TaxonKey is Papilio troilus Linnaeus, 1758",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5396 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035550-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wqj5uk
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.425852 25.651097,-100.416705 25.691013,-100.461548 25.709436,-100.465772 25.701447,-100.519873 25.719246,-100.517685 25.707465,-100.524226 25.709797,-100.559513 25.690881,-100.498746 25.681681,-100.500516 25.675908,-100.495338 25.674190,-100.463186 25.665103,-100.463048 25.653683,-100.428582 25.649504,-100.425852 25.651097))",
 "HasCoordinate is true",
 "TaxonKey is Prosopis L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000318-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uajex5
title: Occurrence Download

description: A dataset containing 2457 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maytenus senegalensis (Lam.) Exell"
 ]
}

 The dataset includes 2457 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021293-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zblwhg
title: Occurrence Download

description: A dataset containing 1127 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gerrhonotus liocephalus Wiegmann, 1828"
 ]
}

 The dataset includes 1127 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005442-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yapzjc
title: Occurrence Download

description: A dataset containing 11833 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Solanum carolinense L."
 ]
}

 The dataset includes 11833 records from 135 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045841-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t7kz52
title: Occurrence Download

description: A dataset containing 81591 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Georgia"
 ]
}

 The dataset includes 81591 records from 356 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006638-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7speyt
title: Occurrence Download

description: A dataset containing 127417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Piciformes"
 ]
}

 The dataset includes 127417 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0328886-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hb45b8
title: Occurrence Download

description: A dataset containing 20366 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sphyrna lewini (Griffith & Smith, 1834)"
 ]
}

 The dataset includes 20366 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022411-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vny2am
title: Occurrence Download

description: A dataset containing 447 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xenoglossa strenua (Cresson, 1879)"
 ]
}

 The dataset includes 447 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0342960-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dvv7hy
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepus corsicanus de Winton, 1898)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 147 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054259-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5egrc
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Morina nepalensis D.Don",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 75 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0322898-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7ers7
title: Occurrence Download

description: A dataset containing 3054 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sphagnum subsecundum Nees",
 "HasCoordinate is true",
 "Year 1990-2022",
 "Geometry POLYGON((-13 35,48 35,48 72,-13 72,-13 35))",
 {
 "or" : [
 {
 "not" : {
 "CoordinateUncertaintyInMeters" : [
 "is not null"
 ]
 }
 },
 "CoordinateUncertaintyInMeters is less than or equal to 250"
 ]
 }
 ]
}

 The dataset includes 3054 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019472-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfekvm
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Michelia martini (H.Lév.) H.Lév.",
 "TaxonKey is Michelia martini (H.Lév.) Dandy"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 50 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016450-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5w4vh
title: Occurrence Download

description: A dataset containing 708 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Juglans neotropica Diels"
 ]
}

 The dataset includes 708 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035552-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a2dnuz
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lipotes vexillifer Miller, 1918",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "DatasetKey is Paleobiology Database"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000319-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pyagtp
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.73149 36.29778,-0.70387 36.29778,-0.70387 39.11028,-7.73149 39.11028,-7.73149 36.29778))",
 "HasCoordinate is true",
 "TaxonKey is Acacia dealbata Link",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 48 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030292-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxtst8
title: Occurrence Download

description: A dataset containing 624 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Borreria verticillata (L.) G.Mey."
 ]
}

 The dataset includes 624 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042609-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7efgxc
title: Occurrence Download

description: A dataset containing 854160 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Malurus cyaneus (Ellis, 1782)"
 ]
}

 The dataset includes 854160 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054031-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqzddw
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrophylax barrettiae Fawc. & Rendle"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000320-150811131857512/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ob1hdy
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tetrastigma hemsleyanum Diels & Gilg"
 ]
}

 The dataset includes 450 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003595-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5q6t64
title: Occurrence Download

description: A dataset containing 12478 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Solanum pimpinellifolium L.",
 "TaxonKey is Solanum tuberosum L.",
 "TaxonKey is Lupinus piurensis C.P.Sm.",
 "TaxonKey is Cucurbita maxima Duchesne",
 "TaxonKey is Capsicum eximium Hunz.",
 "TaxonKey is Canavalia plagiosperma Piper",
 "TaxonKey is Arracacia xanthorrhiza Bancr.",
 "TaxonKey is Ananas ananassoides (Baker) L.B.Sm.",
 "TaxonKey is Agave tequilana F.A.C.Weber",
 "TaxonKey is Fragaria ×ananassa (Weston) Rozier",
 "TaxonKey is Amaranthus caudatus L.",
 "TaxonKey is Fagopyrum esculentum Moench",
 "TaxonKey is Cynara cardunculus subsp. flavescens Wiklund",
 "TaxonKey is Carum roxburghianum (DC.) Kurz",
 "TaxonKey is Psophocarpus tetragonolobus (L.) DC.",
 "TaxonKey is Cynara cardunculus L."
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12478 records from 290 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008302-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-27457
title: Correspondence book No. 1 of Pentecostal Missionary Union [PMU], 1914-1920

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 2 including 61 pages of subject index; 2011 pages of PMU outgoing correspondence;
DOI: 10.15468/dl.4dsabk
title: Occurrence Download

description: A dataset containing 1840 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Occurrence evidence",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Material citation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Observation"
 ]
 },
 {
 "or" : [
 "Continent is Africa",
 "Continent is Asia",
 "Continent is Europe",
 "Continent is Oceania",
 "Continent is Antarctica"
 ]
 },
 "TaxonKey is Phoenix L."
 ]
}

 The dataset includes 1840 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127809-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8zbg5
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lonicera sempervirens L.)",
 "HasCoordinate is true",
 "Continent is North America",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 214 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405728-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wu7cuz
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stanhopea haseloviana Rchb.f."
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140701-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78m39j
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia gasparrinii Boiss."
 ]
}

 The dataset includes 49 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205324-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdcxa5
title: Occurrence Download

description: A dataset containing 2738 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bison bonasus (Linnaeus, 1758)"
 ]
}

 The dataset includes 2738 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023683-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-235115
title: Page Normal school photograph album, Hearne, 1920s-1930s

description: [description english/roman)] Photograph album on the Page Normal school, Hearne, Texas, 1920s-1930s. Included are 35 photographs. The few photographs with dates are dated between 1922 and 1933.
DOI: 10.15468/dl.6xhqaz
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stanhopea gibbosa Rchb.f."
 ]
}

 The dataset includes 79 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140693-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g6f5n6
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pissodes terminalis Hopping, 1920",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127808-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cnw2g7
title: Occurrence Download

description: A dataset containing 57342 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centropus bengalensis (Gmelin, 1788)"
 ]
}

 The dataset includes 57342 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0433001-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vg4vdb
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum aphrogenes Meikle"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005265-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-235441
title: 17th Annual Leadership Conference, COGIC, Women's International Convention, General Session, minutes, 2005

description: [description english/roman)] Minutes of the General Session, Women's International Convention, COGIC (Church of God in Christ), 17th Annual Leadership Conference, Atlanta, Georgia, 2005 May 30.
DOI: 10.15468/dl.jr3fbb
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cryptophlebia illepida (Butler, 1882)",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 92 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127832-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hsy49j
title: Occurrence Download

description: A dataset containing 5909 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "TaxonKey is Vigna Savi"
 ]
}

 The dataset includes 5909 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0176530-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-234867
title: Saints Industrial Faith Hall, 1974

description: [description english/roman)] Packet 22: photograph of Saints Industrial School Faith Hall, Lexington, Mississippi, 1974 February.
DOI: 10.15468/dl.jytbbu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dyspersa apicalis (Foerster, 1848)",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127826-210914110416597/datasets/export for details.