cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14722224
title: Simulated networks from "Gene regulatory network structure informs the distribution of perturbation effects"

description: Data overview

This is the data release for "Gene regulatory network structure informs the distribution of perturbation effects" (Aguirre M, Spence JP, Sella G, and Pritchard JK, bioRxiv 2024). Here, we provide data from each synthetic gene regulatory network produced in our study, including summary statistics from gene-level perturbations. 

Synthetic networks

We provide two files for each of the 1,920 synthetic GRNs in our study. One is a plaintext log file which contains the graph generating parameters used to simulate each network. These log files are also aggregated into the plaintext tab-separated table, `networks.tsv`.

The other file is a python object (in gpickle format) that contains the instantiated network. This object is of type "grn", which is implemented in our project repository. All modeling parameters and summary statistics for the network (e.g., model betas which specify regulatory effects, and log2 fold-changes from knockout experiments) are stored as attributes in this object. Please refer to the main page of our repository for further documentation. 

These two files for each network (3,840 in total) are provided as a gzipped tarball, which can be extracted by running the command 

tar -xzf grns.tar.gz

The uncompressed data will occupy ~94GB of space on disk. Please refer to the project repository for information on how to process these data into summary matrixes.

Intermediate data used for figures

We also provide processed data files which can be used to replicate figures for our manuscript. These files are referenced in figure notebooks on our project repository, and include, for example, graphs and summary statistics used to show that various graph properties are controlled by parameters of our generating algorithm (see the second cell of the Fig. 2 notebook). 

These files are also provided as a gzipped tarball, which can be extracted by running the command

tar -xzf figdata.tar.gz

and whose contents will occupy ~38GB of space on disk when uncompressed.
DOI: 10.5281/zenodo.14722225
title: Simulated networks from "Gene regulatory network structure informs the distribution of perturbation effects"

description: Data overview

This is the data release for "Gene regulatory network structure informs the distribution of perturbation effects" (Aguirre M, Spence JP, Sella G, and Pritchard JK, bioRxiv 2024). Here, we provide data from each synthetic gene regulatory network produced in our study, including summary statistics from gene-level perturbations. 

Synthetic networks

We provide two files for each of the 1,920 synthetic GRNs in our study. One is a plaintext log file which contains the graph generating parameters used to simulate each network. These log files are also aggregated into the plaintext tab-separated table, `networks.tsv`.

The other file is a python object (in gpickle format) that contains the instantiated network. This object is of type "grn", which is implemented in our project repository. All modeling parameters and summary statistics for the network (e.g., model betas which specify regulatory effects, and log2 fold-changes from knockout experiments) are stored as attributes in this object. Please refer to the main page of our repository for further documentation. 

These two files for each network (3,840 in total) are provided as a gzipped tarball, which can be extracted by running the command 

tar -xzf grns.tar.gz

The uncompressed data will occupy ~94GB of space on disk. Please refer to the project repository for information on how to process these data into summary matrixes.

Intermediate data used for figures

We also provide processed data files which can be used to replicate figures for our manuscript. These files are referenced in figure notebooks on our project repository, and include, for example, graphs and summary statistics used to show that various graph properties are controlled by parameters of our generating algorithm (see the second cell of the Fig. 2 notebook). 

These files are also provided as a gzipped tarball, which can be extracted by running the command

tar -xzf figdata.tar.gz

and whose contents will occupy ~38GB of space on disk when uncompressed.
DOI: 10.5281/zenodo.14748699
title: All-atom cytoPlus model of mammalian cell plasma membranes

description: All-atom trajectory of a data-driven model of mammalian plasma membranes. The phospholipid compositions of the two leaflets were modeled after data from lipidomics analysis of the individual leaflets of red blood cell membranes. The overall cholesterol concentration was also taken from lipidomics analysis, but its interleaflet distribution was determined from a long atomistic simulation of the bilayer on Anton (15 us) followed by a shorter simulation in NAMD (2 us, uploaded here). The converged membrane  model has fewer phospholipids and more cholesterol in the exoplasmic (sphingomyelin-rich) leaflet, and more phospholipids and less cholesterol in the cytoplasmic (PUFA-rich) leaflet. Detailed information about the lipid and cholesterol compositions of the two leaflets, together with experimental validation of the model and direct illustrations of its biophysical and physiological effects can be found in https://doi.org/10.1101/2023.07.30.551157.

Uploaded files include: a structure file for the system (.psf), an all-atom trajectory centered on the average z position of the terminal methyl carbons of all lipids (.dcd), the parameter files and a sample NAMD input file used for the simulation. The uploaded trajectory is the last 1.2 us from the NAMD run with frames output every 120 ps.
DOI: 10.5281/zenodo.14748700
title: All-atom cytoPlus model of mammalian cell plasma membranes

description: All-atom trajectory of a data-driven model of mammalian plasma membranes. The phospholipid compositions of the two leaflets were modeled after data from lipidomics analysis of the individual leaflets of red blood cell membranes. The overall cholesterol concentration was also taken from lipidomics analysis, but its interleaflet distribution was determined from a long atomistic simulation of the bilayer on Anton (15 us) followed by a shorter simulation in NAMD (2 us, uploaded here). The converged membrane  model has fewer phospholipids and more cholesterol in the exoplasmic (sphingomyelin-rich) leaflet, and more phospholipids and less cholesterol in the cytoplasmic (PUFA-rich) leaflet. Detailed information about the lipid and cholesterol compositions of the two leaflets, together with experimental validation of the model and direct illustrations of its biophysical and physiological effects can be found in https://doi.org/10.1101/2023.07.30.551157.

Uploaded files include: a structure file for the system (.psf), an all-atom trajectory centered on the average z position of the terminal methyl carbons of all lipids (.dcd), the parameter files and a sample NAMD input file used for the simulation. The uploaded trajectory is the last 1.2 us from the NAMD run with frames output every 120 ps.
DOI: 10.6084/m9.figshare.28284377.v4
title: Data files: Reference genome of European whitefish (<i>Coregonus lavaretus L.</i>) from Finland

description: <b>Datafile 2: Summary of the European whitefish assemblies.</b> The main assembly includes both PacBio and OmniC sequence data, while the alternative assembly was based on PacBio sequence data only. The main assembly is publicly available at the ENA under the accession PRJEB69218. The alternative assembly is available upon request from Antti Kause.<b>Datafile 3: Smudgeplot of European whitefish</b>. The k-mer based smudgeplot analysis was performed using PacBio Hi-Fi reads to assess the heterozygosity and ploidy of the European whitefish genome. The analysis indicated that 35% of the genome is fully diverged diploid, indicated by the “AB” pattern. Conversely, 63% of the genome is either tetraploid or highly similar diploid paralogs as evidenced by “AABB” pattern, suggesting that the diploid resolution in these regions is not complete. In the smudgeplot, the x-axis represents the coverage ratio, while the y-axis indicates the total coverage. “A” and “B” represent different alleles, 1n = haploid, 2n = diploid, 3n = triploid, 4n = tetraploid, and so on.
DOI: 10.5281/zenodo.13309332
title: The datest, Aerosol Radiation Effect Outweighs VOCs Reactivity Effect on Vertical Ozone Photochemical Features

description: 该数据集包括所有使用的原始和过滤后的VOCs和NO2观测数据,以及模型输入数据和从模拟实验中提取的所有结果。
DOI: 10.5281/zenodo.13309333
title: The datest, Aerosol Radiation Effect Outweighs VOCs Reactivity Effect on Vertical Ozone Photochemical Features

description: 该数据集包括所有使用的原始和过滤后的VOCs和NO2观测数据,以及模型输入数据和从模拟实验中提取的所有结果。
DOI: 10.5281/zenodo.14752899
title: The datest, Aerosol Radiation Effect Outweighs VOCs Reactivity Effect on Vertical Ozone Photochemical Features

description: 该数据集包括所有使用的原始和过滤后的VOCs和NO2观测数据,以及模型输入数据和从模拟实验中提取的所有结果。
DOI: 10.15468/dl.3qqxgb
title: Occurrence Download

description: A dataset containing 582 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthopagrus schlegelii (Bleeker, 1854)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 582 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001518-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xztmca
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chrysophrys schlegelii Bleeker, 1854",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001519-250127130748423/datasets/export for details.
DOI: 10.6084/m9.figshare.28284377.v5
title: Data files: Reference genome of European whitefish (<i>Coregonus lavaretus L.</i>) from Finland

description: <b>Datafile 2: Summary of the European whitefish assemblies.</b> The main assembly includes both PacBio and OmniC sequence data, while the alternative assembly was based on PacBio sequence data only. The main assembly is publicly available at the ENA under the accession PRJEB69218. The alternative assembly is available upon request from Antti Kause.<b>Datafile 3: Smudgeplot of European whitefish</b>. The k-mer based smudgeplot analysis was performed using PacBio Hi-Fi reads to assess the heterozygosity and ploidy of the European whitefish genome. The analysis indicated that 35% of the genome is fully diverged diploid, indicated by the “AB” pattern. Conversely, 63% of the genome is either tetraploid or highly similar diploid paralogs as evidenced by “AABB” pattern, suggesting that the diploid resolution in these regions is not complete. In the smudgeplot, the x-axis represents the coverage ratio, while the y-axis indicates the total coverage. “A” and “B” represent different alleles, 1n = haploid, 2n = diploid, 3n = triploid, 4n = tetraploid, and so on.
DOI: 10.15468/dl.vqec6y
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carcharhinus falciformis (Müller & Henle, 1839)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001520-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tu7njs
title: Occurrence Download

description: A dataset containing 2958875 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Philippines"
 ]
}

 The dataset includes 2958875 records from 1639 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001505-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqe1nl
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Botia almorhae Gray, 1831",
 "Country is India"
 ]
}

 The dataset includes 19 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009428-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6h2399
title: Occurrence Download

description: A dataset containing 523 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Orthion Standl. & Steyerm."
 ]
}

 The dataset includes 523 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013388-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7t5atx
title: Occurrence Download

description: A dataset containing 702 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vrydagzynea Blume"
 ]
}

 The dataset includes 702 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0248424-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygwt23
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cuphea reitzii Lourteig"
 ]
}

 The dataset includes 31 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155695-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nqo3cz
title: Occurrence Download

description: A dataset containing 1660 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nepsera aquatica (Aubl.) Naudin",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 1660 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009428-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dv6ktv
title: Occurrence Download

description: A dataset containing 3078 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Taraxacum scanicum Dahlst., Taraxacum schroeterianum Hand.-Mazz., Taraxacum scolopendrinum (Heldr. ex Halácsy) Dahlst., Glacies Millière, Arctica Schumacher, 1817, Coryphella J.E.Gray, 1850, Celtica F.M.Vázquez & Barkworth, Dioszegia Zsolt, 1957, Hamata Cao, Dmitriev, Dietrich & Zhang, 2019, Albinaria Vest, 1867)",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "DatasetKey is one of (Pl@ntNet automatically identified occurrences, Pl@ntNet observations, iNaturalist Research-grade Observations, Observation.org, Nature data from around the World, naturgucker, Artportalen (Swedish Species Observation System), Norwegian Species Observation Service, Programme d'observation naturaliste participative avec l'application mobile INPN Espèces - Application INPN Espèces: Observations naturalistes, participatives et opportunistes, fondées sur des photographies, Species recordings from the Danish National portal Arter.dk, Lajitietokeskus/FinBIF - Notebook, general observations, Vascular plant records verified via iRecord, iRecord Surveys)",
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 500",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 3078 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071136-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pudazh
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Aster likiangensis Franch."
 ]
}

 The dataset includes 144 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0271617-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lddaze
title: Occurrence Download

description: A dataset containing 1387 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cistus libanotis L."
 ]
}

 The dataset includes 1387 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002422-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k3r4et
title: Occurrence Download

description: A dataset containing 2102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Mus musculus Linnaeus, 1758"
 ]
}

 The dataset includes 2102 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0246851-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfk8uw
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is NMNH Extant Specimen Records (USNM, US)",
 "TaxonKey is Chiloscyllium hasseltii Bleeker, 1852"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071134-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cjwy3u
title: Occurrence Download

description: A dataset containing 7002 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is Germany",
 "DecimalLongitude is greater than or equal to 10.1313471390463",
 "DecimalLongitude is less than 10.1344066922307",
 "DecimalLatitude is greater than or equal to 47.27011",
 "DecimalLatitude is less than or equal to 55.05864"
 ]
}

 The dataset includes 7002 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010159-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qlmzbm
title: Occurrence Download

description: A dataset containing 2522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Country is Kenya",
 "Country is Uganda",
 "Country is Tanzania, United Republic of"
 ]
 },
 "Year is less than or equal to 2016",
 "TaxonKey is Sphingidae"
 ]
}

 The dataset includes 2522 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002458-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.psdwrp
title: Occurrence Download

description: A dataset containing 354728 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-170.70736 3.12994,-36.29264 3.12994,-36.29264 56.87006,-170.70736 56.87006,-170.70736 3.12994))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chamaea fasciata (Gambel, 1845)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 354728 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233381-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxq7zm
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Desmodium amplistipulaceum L.Torres-Colín & L.O.Alvarado"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155696-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6d87zt
title: Occurrence Download

description: A dataset containing 21212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is Germany",
 "DecimalLongitude is greater than or equal to 10.128287585862",
 "DecimalLongitude is less than 10.1313471390463",
 "DecimalLatitude is greater than or equal to 47.27011",
 "DecimalLatitude is less than or equal to 55.05864"
 ]
}

 The dataset includes 21212 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010158-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.otkz0k
title: Occurrence Download

description: A dataset containing 1738 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula nutans Georgi"
 ]
}

 The dataset includes 1738 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009428-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yspxjq
title: Occurrence Download

description: A dataset containing 493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Clarkia cylindrica subsp. cylindrica, Clinopodium douglasii (Benth.) Kuntze, Elymus condensatus J.Presl, Elymus triticoides Buckley, Mimulus guttatus Fisch., Mimulus guttatus Fisch. ex DC., Mimulus nudatus Curran, Mimulus nudatus Curran ex Greene, Grindelia camporum Greene, Lupinus formosus var. formosus, Lupinus microcarpus var. microcarpus, Peritoma arborea (Nutt. ex Torr. & A.Gray) Iltis, Pseudognaphalium biolettii Anderb., Rhamnus californica Eschsch., Sambucus nigra L., Sambucus nigra Lour., Sambucus nigra Marshall, 1785, Scrophularia californica Cham. & Schltdl., Stipa lepida Hitchc., Sida lepida F.Muell., Stipa pulchra Hitchc., Stipa pulchella Munro, Stipa pulchella Munro ex Ball, Sida pulchra Bertero, Sida pulchra Bertero ex Colla)",
 "HasCoordinate is true",
 "Geometry POLYGON((-119.11692 34.12002,-118.99469 34.17798,-118.74613 34.15696,-118.87384 34.18025,-118.80518 34.21944,-118.63077 34.22568,-118.63077 34.16605,-118.50443 34.16378,-118.36504 34.14673,-118.27646 34.16037,-118.25449 34.11149,-118.36779 34.08192,-118.50512 34.04723,-118.56142 34.02788,-118.74476 34.01422, -118.8093 33.98633, -119.0867 34.09387,-119.11692 34.12002))"
 ]
}

 The dataset includes 493 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233354-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.