cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.82539a
title: Occurrence Download

description: A dataset containing 780 records in GBIF matching the query:
SELECT catalogNumber, scientificName, eventDate, recordedBy, countryCode, institutionCode FROM occurrence WHERE "year" = 1979 AND recordNumber IN ('19315', '19129', '19155', '18945', '19170', '19227', '19073', '19016', '19016', '19225', '19228', '19150', '19208', '18955', '18955', '19278', '19299', '19005', '19271', '18961', '19324', '18984', '19056', '19070', '19169', '19307', '19261', '19031', '19184', '19223', '19066', '19084', '19338', '19085', '19087', '19145', '18981', '19001', '19029', '19023', '19219', '19034', '19083', '19326', '19114', '19159', '19249', '19281', '19038', '18948-A', '18948', '18938', '19130', '18952', '19309', '19188', '18948', '19148', '19294', '19163', '19298', '19186', '19202', '18967', '19120', '19217', '18959', '19325', '18946', '18957', '19291', '19204', '19260', '19236', '19314', '19302', '19240', '19240', '19245', '19106', '19200', '19265', '18938-A', '18938', '19000', '19101', '19081', '19172', '19081');

 The dataset's 780 records were derived from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001291-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10574988
title: Arrayed CRISPR/Cas9 Loss-Of-Function Screen in a Neuronal Model of Adaptor Protein Complex 4 Deficiency Identifies Modulators of ATG9A Trafficking
title: R Code And Supplementary Files

description: R code and supplementary files for "Arrayed CRISPR/Cas9 Loss-Of-Function Screen in a Neuronal Model of Adaptor Protein Complex 4 Deficiency Identifies Modulators of ATG9A Trafficking" by Ziegler et al.

 

 
description: Supplementary Files

Supplementary File 1:

Complete dataset for the primary screen

Supplementary File 2:

Complete dataset for the secondary screen

Supplementary File 3:

List of GO terms derived from Ensemble (downloaded: 09/19/2022)

Supplementary File 4:

Complete dataset of significant pathways

Supplementary File 5:

Significant pathways in relevant pathway clusters associated with secondary screen hits

Supplementary File 6:

Raw data for Figures 4 C, E, F and G

 

R Script:

Ziegler_et_al_Analysis_Script.R

Calculations of Pathway Impact Scores (PI-Scores) for pathways (using GO ontology terms) based on primary screen data. Simulation of PI-Score calculation (10,000 times) to derive normality distribution and p-value.

Identification of pathway clusters based on PI-Scores using average linkage hierarchical clustering and the DynamicTreeCut algorithm.

Identification of most prevalent protein classes within relevant clusters based on Uniprot family domain.

Chord plot to cross-match significant pathways in relevant pathway clusters with secondary screen hits.
DOI: 10.5281/zenodo.10574989
title: Arrayed CRISPR/Cas9 Loss-Of-Function Screen in a Neuronal Model of Adaptor Protein Complex 4 Deficiency Identifies Modulators of ATG9A Trafficking
title: R Code And Supplementary Files

description: R code and supplementary files for "Arrayed CRISPR/Cas9 Loss-Of-Function Screen in a Neuronal Model of Adaptor Protein Complex 4 Deficiency Identifies Modulators of ATG9A Trafficking" by Ziegler et al.

 

 
description: Supplementary Files

Supplementary File 1:

Complete dataset for the primary screen

Supplementary File 2:

Complete dataset for the secondary screen

Supplementary File 3:

List of GO terms derived from Ensemble (downloaded: 09/19/2022)

Supplementary File 4:

Complete dataset of significant pathways

Supplementary File 5:

Significant pathways in relevant pathway clusters associated with secondary screen hits

Supplementary File 6:

Raw data for Figures 4 C, E, F and G

 

R Script:

Ziegler_et_al_Analysis_Script.R

Calculations of Pathway Impact Scores (PI-Scores) for pathways (using GO ontology terms) based on primary screen data. Simulation of PI-Score calculation (10,000 times) to derive normality distribution and p-value.

Identification of pathway clusters based on PI-Scores using average linkage hierarchical clustering and the DynamicTreeCut algorithm.

Identification of most prevalent protein classes within relevant clusters based on Uniprot family domain.

Chord plot to cross-match significant pathways in relevant pathway clusters with secondary screen hits.
DOI: 10.15468/dl.pdff77
title: Occurrence Download

description: A dataset listing the 233 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Colección Científica de Referencia Zoológica del Chocó- Herpetología",
 "Geometry POLYGON((-95.64723 -1.75579,-59.35277 -1.75579,-59.35277 12.75579,-95.64723 12.75579,-95.64723 -1.75579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 233 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001294-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p3jwp2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.83912 40.46729,-8.46723 40.46729,-8.46723 40.88886,-8.83912 40.88886,-8.83912 40.46729))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Potamogeton crispus L."
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001296-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10824274
title: Deceptive Patterns
DOI: 10.15468/dl.v6e8yz
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Olindias muelleri Haeckel, 1879",
 "Year 2020-2025"
 ]
}

 The dataset includes 92 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001297-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.42sb79
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Macroprotodon cucullatus (Geoffroy Saint-Hilaire, 1827)"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001299-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bt2gyz
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.81675 40.43497,-8.46384 40.43497,-8.46384 40.88891,-8.81675 40.88891,-8.81675 40.43497))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stuckenia pectinata (L.) Börner"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001300-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pe46kh
title: Occurrence Download

description: A dataset containing 780 records in GBIF matching the query:
SELECT recordNumber, catalogNumber, scientificName, eventDate, recordedBy, countryCode, institutionCode FROM occurrence WHERE "year" = 1979 AND recordNumber IN ('19315', '19129', '19155', '18945', '19170', '19227', '19073', '19016', '19016', '19225', '19228', '19150', '19208', '18955', '18955', '19278', '19299', '19005', '19271', '18961', '19324', '18984', '19056', '19070', '19169', '19307', '19261', '19031', '19184', '19223', '19066', '19084', '19338', '19085', '19087', '19145', '18981', '19001', '19029', '19023', '19219', '19034', '19083', '19326', '19114', '19159', '19249', '19281', '19038', '18948-A', '18948', '18938', '19130', '18952', '19309', '19188', '18948', '19148', '19294', '19163', '19298', '19186', '19202', '18967', '19120', '19217', '18959', '19325', '18946', '18957', '19291', '19204', '19260', '19236', '19314', '19302', '19240', '19240', '19245', '19106', '19200', '19265', '18938-A', '18938', '19000', '19101', '19081', '19172', '19081');

 The dataset's 780 records were derived from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001298-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jsdh8
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Peromyscus pseudocrinitus Burt, 1932"
 ]
}

 The dataset includes 79 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001301-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eygt32
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "not" : {
 "InstitutionCode" : [
 "is one of (iNaturalist)"
 ]
 }
 },
 "SpeciesKey is one of (Apis mellifera Linnaeus, 1758)",
 "Country is United States of America",
 "StateProvince is Georgia"
 ]
}

 The dataset includes 91 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001302-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kg6r3r
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.81829 40.47676,-8.46969 40.47676,-8.46969 40.90021,-8.81829 40.90021,-8.81829 40.47676))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ruppia maritima L."
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001303-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ssz5xr
title: Occurrence Download

description: A dataset containing 492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Trichocentrum ascendens (Lindl.) M.W.Chase & N.H.Williams"
 ]
}

 The dataset includes 492 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001304-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.edz7pp
title: Occurrence Download

description: A dataset containing 342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pteris vittata L."
 ]
}

 The dataset includes 342 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001305-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14907818
title: Composition of simple computational tasks captures the inductive biases of animals in network models

description: This is the data is associated with a Nature Machine Inteligence manuscript: "Composition of simple computational tasks captures the inductive biases of animals in network models."

The repository contains partially processed data that was used to generate manuscript figures, as well as PyTorch .model files associated with trained networks. This data is associated with a github codebase: David Hocker. (2025). Savin-Lab-Code/kind_cl: Nature Machine Intelligence code (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14907734

Data organization

rnndata: folder containing  RNN model and wait-time stats files for four types of pretraining curriculum methods. 



full_cl: performs all kindergarten tasks and behavioral shaping. (note: additional file type provided for this curriculum)

nok_cl: performs just behavioral shaping phases of pretraining

nok_nocl: performs no pretraining at all

pkind_mem: performs the memory pretraining task, followed by behavioral shaping


the model and stats files are for networks at the end of their training. the full_cl maniuplation contains additional data, as it was the main form of curriculum learning studied in the manuscript. python-compatible forms of the behavior over training are provided (rnn_#_allbeh.json files). RNN 33 also has additional files. it contains model files over the full course of learning, as well as a sample set of simulated data at the end of training (full_cl/33/rnn_curric_33_block_10_1k.json)

processed4plots: folder containing intermediate-level processed data for visualizing results presented in the manuscript. These files are called from visualization scripts in the corresponding github repo (https://github.com/Savin-Lab-Code/kind_cl/)



behdat_rnn_full_cl_end/: subfolder containing matlab files for behavior of each network from full_cl at end of training

behdat_rnn_full_cl_overtraining/: subfolder containing matlab files that aggregate behavior of each network from full_cl across training

behdat*: aggregated features of RNN behavior over training, for a given curriculum type

flowfields*: .mat matlab files that provide 2D flow fields for RNNs 33 and 23

ke_overtraining*: aggregated dynamical systems features measures (number of slow features, dimensionality) over training, for a given curriculum type

ke_results*: distributions of slow features and dimsionality for 3 main curricula presented in Figure 6E

kemin_rnn_curric*: converted .mat version of results of kinetic energy minimization. provides location of slow points in low-dimensional PC space

rrate*: aggregated reward rates of RNNs over training, for a given curriculum type
DOI: 10.5281/zenodo.14907819
title: Composition of simple computational tasks captures the inductive biases of animals in network models

description: This is the data is associated with a Nature Machine Inteligence manuscript: "Composition of simple computational tasks captures the inductive biases of animals in network models."

The repository contains partially processed data that was used to generate manuscript figures, as well as PyTorch .model files associated with trained networks. This data is associated with a github codebase: David Hocker. (2025). Savin-Lab-Code/kind_cl: Nature Machine Intelligence code (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14907734

Data organization

rnndata: folder containing  RNN model and wait-time stats files for four types of pretraining curriculum methods. 



full_cl: performs all kindergarten tasks and behavioral shaping. (note: additional file type provided for this curriculum)

nok_cl: performs just behavioral shaping phases of pretraining

nok_nocl: performs no pretraining at all

pkind_mem: performs the memory pretraining task, followed by behavioral shaping


the model and stats files are for networks at the end of their training. the full_cl maniuplation contains additional data, as it was the main form of curriculum learning studied in the manuscript. python-compatible forms of the behavior over training are provided (rnn_#_allbeh.json files). RNN 33 also has additional files. it contains model files over the full course of learning, as well as a sample set of simulated data at the end of training (full_cl/33/rnn_curric_33_block_10_1k.json)

processed4plots: folder containing intermediate-level processed data for visualizing results presented in the manuscript. These files are called from visualization scripts in the corresponding github repo (https://github.com/Savin-Lab-Code/kind_cl/)



behdat_rnn_full_cl_end/: subfolder containing matlab files for behavior of each network from full_cl at end of training

behdat_rnn_full_cl_overtraining/: subfolder containing matlab files that aggregate behavior of each network from full_cl across training

behdat*: aggregated features of RNN behavior over training, for a given curriculum type

flowfields*: .mat matlab files that provide 2D flow fields for RNNs 33 and 23

ke_overtraining*: aggregated dynamical systems features measures (number of slow features, dimensionality) over training, for a given curriculum type

ke_results*: distributions of slow features and dimsionality for 3 main curricula presented in Figure 6E

kemin_rnn_curric*: converted .mat version of results of kinetic energy minimization. provides location of slow points in low-dimensional PC space

rrate*: aggregated reward rates of RNNs over training, for a given curriculum type
DOI: 10.15468/dl.hvmnzn
title: Occurrence Download

description: A dataset containing 37448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-97.38745 32.96223,-96.84503 32.95932,-96.87003 33.44515,-97.47451 33.46141,-97.38745 32.96223))",
 "Month is one of (April, May, June, July)",
 "OccurrenceStatus is Present",
 "Year 2023-2025"
 ]
}

 The dataset includes 37448 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001306-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqc5uy
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.80639 40.48338,-8.44772 40.48338,-8.44772 40.88108,-8.80639 40.88108,-8.80639 40.48338))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ruppia cirrhosa (Petagna) Grande"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001307-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14910633
title: Sirviente_etal_2025_egusphere-2024-2451_

description: Dataset used in  Sirviente, S., Gomiz-Pascual, J. J., Bolado-Penagos, M., Sauvage, S., Sánchez-Pérez, J. M., and Bruno, M.: Anthropogenic pressures driving the salinity intrusion in the Guadalquivir Estuary: Insights from 1D Numerical Simulations, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-2451, 2024.
DOI: 10.5281/zenodo.14910634
title: Sirviente_etal_2025_egusphere-2024-2451_

description: Dataset used in  Sirviente, S., Gomiz-Pascual, J. J., Bolado-Penagos, M., Sauvage, S., Sánchez-Pérez, J. M., and Bruno, M.: Anthropogenic pressures driving the salinity intrusion in the Guadalquivir Estuary: Insights from 1D Numerical Simulations, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-2451, 2024.
DOI: 10.15468/dl.ta645a
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Country is Philippines",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Schismatoglottis plurivenia Alderw."
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001309-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6t6bz
title: Occurrence Download

description: A dataset containing 1840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is one of (Apis mellifera Linnaeus, 1758)",
 "Country is United States of America",
 "StateProvince is Georgia"
 ]
}

 The dataset includes 1840 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001310-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwzhdj
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.80606 40.48449,-8.4706 40.48449,-8.4706 40.88491,-8.80606 40.88491,-8.80606 40.48449))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ulva lactuca L."
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001311-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.by5ekx
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-148.93613 -21.66295,-18.06387 -21.66295,-18.06387 30.66295,-148.93613 30.66295,-148.93613 -21.66295))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aechmea magdalenae (André) André ex Baker"
 ]
}

 The dataset includes 25 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001312-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9khccx
title: Occurrence Download

description: A dataset containing 780 records in GBIF matching the query:
SELECT recordNumber, catalogNumber, scientificName, eventDate, recordedBy, countryCode, institutionCode, stateProvince, county, locality, collectionCode, occurrenceID, basisOfRecord FROM occurrence WHERE "year" = 1979 AND recordNumber IN ('19315', '19129', '19155', '18945', '19170', '19227', '19073', '19016', '19016', '19225', '19228', '19150', '19208', '18955', '18955', '19278', '19299', '19005', '19271', '18961', '19324', '18984', '19056', '19070', '19169', '19307', '19261', '19031', '19184', '19223', '19066', '19084', '19338', '19085', '19087', '19145', '18981', '19001', '19029', '19023', '19219', '19034', '19083', '19326', '19114', '19159', '19249', '19281', '19038', '18948-A', '18948', '18938', '19130', '18952', '19309', '19188', '18948', '19148', '19294', '19163', '19298', '19186', '19202', '18967', '19120', '19217', '18959', '19325', '18946', '18957', '19291', '19204', '19260', '19236', '19314', '19302', '19240', '19240', '19245', '19106', '19200', '19265', '18938-A', '18938', '19000', '19101', '19081', '19172', '19081');

 The dataset's 780 records were derived from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001308-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.