cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.styywr
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aechmea pallida L.B.Sm."
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140688-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abodje
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Côte d’Ivoire",
 "TaxonKey is Indigofera terminalis Baker"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019666-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztqk7u
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Croatia",
 {
 "or" : [
 "TaxonKey is Coenonympha oedippus Fabricius, 1787",
 "TaxonKey is Euphydryas maturna (Linnaeus, 1758)",
 "TaxonKey is Lycaena dispar (Haworth, 1803)",
 "TaxonKey is Euphydryas aurinia (Rottemburg, 1775)",
 "TaxonKey is Colias myrmidone (Esper, 1781)",
 "TaxonKey is Nymphalis vaualbum (Denis & Schiffermüller, 1775)",
 "TaxonKey is Phengaris nausithous (Bergsträsser, 1779)",
 "TaxonKey is Phengaris teleius (Virgstrassir, 1779)",
 "TaxonKey is Leptidea morsei Fenton, 1881"
 ]
 }
 ]
}

 The dataset includes 80 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173907-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wpmcq
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hoya acuminata (Wight) Benth. ex Hook.fil."
 ]
}

 The dataset includes 18 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022226-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3eehs
title: Occurrence Download

description: A dataset containing 711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Colección Hidrobiológica del Chocó",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 711 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019667-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g64e6q
title: Occurrence Download

description: A dataset containing 517002 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Greece",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 517002 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173912-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdfc6x
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium hogdalense (Dahlst. ex Zahn) Dahlst. ex Johanss."
 ]
}

 The dataset includes 41 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022231-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v27ow6
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amerotyphlops tenuis (Salvin, 1860)"
 ]
}

 The dataset includes 11 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019667-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jy5qtm
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is China",
 "Country is Chinese Taipei",
 "Country is Hong Kong"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cathaya argyrophylla Chun & Kuang"
 ]
}

 The dataset includes 81 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173929-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1krxy5
title: Occurrence Download

description: A dataset containing 10891 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nicotiana glauca Graham"
 ]
}

 The dataset includes 10891 records from 274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019668-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4pjsr
title: Occurrence Download

description: A dataset containing 2217 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Cemophora coccinea (Blumenbach, 1788)"
 ]
}

 The dataset includes 2217 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083553-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4p8gu6
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alstroemeria arnicana Ravenna"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140689-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pr79ey
title: Occurrence Download

description: A dataset containing 988 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Morpho polyphemus Westwood",
 "Year 2010-2021"
 ]
}

 The dataset includes 988 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005969-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8a293v
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Cynisca leonina (Müller, 1885)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083570-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.atdgiz
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puya tillii Manzan."
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019668-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gukbd7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sphagnum magellanicum Brid.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140691-240321170329656/datasets/export for details.
DOI: 10.15468/dl.p6c2be
title: Occurrence Download

description: A dataset containing 13981508 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Colombia"
 ]
}

 The dataset includes 13981508 records from 3066 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006852-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcfk3j
title: Occurrence Download

description: A dataset containing 357705 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sambucus L.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 357705 records from 869 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013264-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p5582u
title: Occurrence Download

description: A dataset containing 979268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Literature Occurrence"
 ]
}

 The dataset includes 979268 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285720-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mtfjn9
title: Occurrence Download

description: A dataset containing 1567 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((102 77.08599, 107.8886 77.08599, 107.8886 78.39351, 102 78.39351, 102 77.08599))"
 ]
}

 The dataset includes 1567 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042560-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wortkv
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sorex araneus Linnaeus, 1758",
 "Country is Ukraine",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013264-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkbkv9
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((30.86975 -30.07859,30.87292 -30.07859,30.87292 -30.07651,30.86975 -30.07651,30.86975 -30.07859))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 29 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0317733-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhj6mh
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stylotrichium sucrei R.M.King & H.Rob."
 ]
}

 The dataset includes 19 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013264-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.as835f
title: Occurrence Download

description: A dataset containing 210310 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tyrannus savana Vieillot, 1808"
 ]
}

 The dataset includes 210310 records from 326 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042563-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z8qnzd
title: Occurrence Download

description: A dataset containing 376 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Gonatodes caudiscutatus (Günther, 1859)"
 ]
}

 The dataset includes 376 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0317784-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5encd0
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygraphus miser Blandford, 1894"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013265-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nezxt
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is OAXAcA",
 "TaxonKey is Anthocerotophyta"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051618-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aczapg
title: Occurrence Download

description: A dataset containing 844 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, United Kingdom of Great Britain and Northern Ireland, Portugal, Spain, France, Germany, Belgium, Netherlands, Italy, Greece, Switzerland, Austria, Türkiye, Russian Federation, Belarus, Ukraine, Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Romania, Bulgaria, North Macedonia, Albania, Slovenia, Croatia, Bosnia and Herzegovina, Hungary, Slovakia, Czechia, Poland)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aremonia agrimonoides (L.) DC."
 ]
}

 The dataset includes 844 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0164500-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbhwhy
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ipomoea lachnaea Spreng."
 ]
}

 The dataset includes 13 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0164501-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lh4iuz
title: Occurrence Download

description: A dataset containing 835 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bufo californicus Camp, 1915"
 ]
}

 The dataset includes 835 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013265-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmyxz3
title: Occurrence Download

description: A dataset containing 67091 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ribes nigrum L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 67091 records from 325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0305002-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxbtzs
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bufotes siculus (Stöck, Sicilia, Belfiore, Buckley, Lo-Brutto, Lo-Valvo & Arculeo, 2008)"
 ]
}

 The dataset includes 206 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020496-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ey7t9h
title: Occurrence Download

description: A dataset containing 715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is one of (Abronia deppii (Wiegmann, 1828), Abronia graminea (Cope, 1864))"
 ]
}

 The dataset includes 715 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020498-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10806507
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: 10.5281/zenodo.10806508
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 or 2.1 (recommended). 



 

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

Fig4_invasive_carcinoma.zip

Fig5_collective_migration_initial_tests.zip

Fig6_instant_remodeling.zip

Fig7b_leader_follower.zip

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



python_imaging.zip

Base modules and examples for producing images (tested on Python 3.9)

README

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.