cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12567873
title: MADE-WIC: Multiple Annotated Datasets for Exploring Weaknesses In Code and Replication Package

description: MADE-WIC is a large dataset of functions and their comments with multiple annotations for technical debt and code weaknesses leveraging different state-of-the-art approaches. This package contains the dataset and the code needed to recreate it.

 

This is an updated version. The previous one had correct labellings but some entries missed some comments.
DOI: 10.5281/zenodo.15126132
title: MADE-WIC: Multiple Annotated Datasets for Exploring Weaknesses In Code and Replication Package

description: MADE-WIC is a large dataset of functions and their comments with multiple annotations for technical debt and code weaknesses leveraging different state-of-the-art approaches. This package contains the dataset and the code needed to recreate it.

 

This is an updated version. The previous one had correct labellings but some entries missed some comments.
DOI: 10.17637/rh.27020611
title: Accompanying data for "Chiral superfluid helium-3 in the quasi-two-dimensional limit"

description: This dataset includes the measured values of the superfluid transition temperature and the energy gap of the A phase of superfluid helium-3 confined in a 80 nm high slab-shaped cavity with specular quasiparticle scattering boundary conditions. Also corresponding calculations of the suppression of the superfluid transition temperature with almost fully specular boundaries are included. The article detailing the findings of this study, and the used methods and techniques, has been published in <i>Physical Review Letters</i> <b>134,</b> 136001 (2025) available at https://doi.org/10.1103/PhysRevLett.134.136001.<b>Data from the experiments</b>'80nm_cavity_Tc_suppression_specular.dat' lists the measured superfluid transition temperatures in the confined cavity relative to the bulk-marker transition temperature corresponding to specular boundary condition and various pressures, i.e., various values of effective cavity height. These values are included in Figure 1 in the article.'80nm_cavity_A_phase_gap_specular_[pressure]bar.dat' files give the measured temperature dependence of the energy gap of superfluid A phase of helium-3 corresponding to specular boundary condition and various pressures. Values of the gap are based on the measured NMR frequency shift in the superfluid state as described in the article. Four pressures are included in Figure 3 in the article. All five pressures are shown in Supplementary Figure S3.'80nm_cavity_initial_slopes_specular.dat' gives the measured initial slopes of the superfluid frequency shift versus temperature determined within different ranges below the measured superfluid transition temperature in the cavity for specular boundary conditions and various pressures. These values are needed in conversion between the frequency shift and the energy gap and are plotted in Figure 2(b) and Supplementary Figure S2 in the article.The values of superfluid transition temperature and the initial slopes measured using 192 nm high cavity are shown in couple of figures in the manuscript. Those values come from the earlier work, data of which can be found here: https://doi.org/10.17637/rh.12777620.<b>Calculations:</b>'calc_Tc_suppression_S[specularity].dat' show the calculated suppressed superfluid transition temperatures as a function of effective cavity height for two specularities close to being fully specular. The corresponding lines are shown in Figure 1(c) in the manuscript.In all the calculations we have used the quasiclassical weak-coupling approach, as cited in the manuscript.Literature values of bulk (or fully specular) superfluid transition temperature are given by D. S. Greywall in Phys. Rev. B <b>33,</b> 7520 (1986) (https://doi.org/10.1103/PhysRevB.33.7520).Values of the weak-coupling bulk energy gap of <sup>3</sup>He-A can be found, for example, by using E. V. Thuneberg's calculator from https://users.aalto.fi/~thunebe1/theory/qc/bcsgap.html.The values as a function of temperature are also given in https://doi.org/10.17637/rh.12777620.
DOI: 10.15468/dl.p6q3tx
title: Occurrence Download

description: A dataset containing 20584 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.6161 40.41577,-3.59031 40.40914,-3.5872 40.4117,-3.58202 40.41901,-3.57657 40.42848,-3.57217 40.43992,-3.5859 40.43992,-3.59031 40.44012,-3.59679 40.44406,-3.60612 40.4488,-3.60301 40.44091,-3.60615 40.43372,-3.60108 40.42157,-3.6161 40.41577))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 20584 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000319-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14971280
title: Dataset of light microscopy and image processing - The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions

description: This dataset contains mainly brightfield and widefield fluorescence microscopy images from FDA (Viability dye) and Calcofluor (cell wall) stained Arabidopsis thaliana cells after prtoplasting, along with the prossessing and quantified data (including segmented masks, raw quantification and processed quantification), as well as other miscelaneous data and scripts used in the study "The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions" (https://doi.org/10.1101/2025.03.05.641611). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the Q-Warg workflow (10.5281/zenodo.14973382).
DOI: 10.5281/zenodo.14971281
title: Dataset of light microscopy and image processing - The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions

description: This dataset contains mainly brightfield and widefield fluorescence microscopy images from FDA (Viability dye) and Calcofluor (cell wall) stained Arabidopsis thaliana cells after prtoplasting, along with the prossessing and quantified data (including segmented masks, raw quantification and processed quantification), as well as other miscelaneous data and scripts used in the study "The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions" (https://doi.org/10.1101/2025.03.05.641611). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the Q-Warg workflow (10.5281/zenodo.14973382).
DOI: 10.15468/dl.vwpu2h
title: Occurrence Download

description: A dataset containing 513 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Mycobacterium lepromatosis, Dasypus septemcinctus Linnaeus, 1758)"
 ]
}

 The dataset includes 513 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000320-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15125745
title: Theta: Modular Model Checker Built For Diverse Algorithm Configurations (Accompanying Artifact)

description: Theta Benchmarking Artifact

Accompanying artifact for our paper entitled "Theta: Modular Model Checker Built For Diverse Algorithm Configurations".

We used Theta version 6.12.2, available under v6.12.2.

Overview

This Zenodo artifact accompanies our paper on benchmarking Theta, a model checker framework. The artifact includes all necessary files for reproducing our benchmarking experiments and analyzing the results.

Artifact Structure

The artifact consists of the following directories and files:





binary/: Contains Theta's JAR files, solvers, and required shared libraries.




benchmarks/: Includes all benchmarks used in the evaluation, with expected verdicts where known.




benchexec/: Contains the version of BenchExec used for the experiments.




results/: Stores the benchmarking results.




tooldefs/: Holds BenchExec tool definitions for Theta (slightly modified from the official tool info module).




variants.csv: Lists all configurations used in the experiments.




create-variants.py: Generates benchmark definition files (pre-generated in this artifact).




get-latest-files.sh: Helper script to retrieve the latest result files.




get-portfolios.py: Script to generate quantile plots.




get-results.py: Script to parse results and generate the summary table.




run-all.sh: Main script to execute all benchmark runs.




run-benchmark.sh: Script to execute a specific benchmark configuration.




svcomp.def: Benchmark definition file.



Reproducing Results

To reproduce the results, follow these steps:





Modify run-benchmark.sh (if necessary) to use a non-Slurm-based BenchExec setup.




Navigate to the binary/ folder and execute:

source ../run-all.sh


This will re-run all experiments that do not have a corresponding folder in results/. To fully reproduce the results, delete the results of specific configurations before rerunning.



Analyzing Results





To generate the results table, run:

python get-results.py





To generate the quantile plot, run:

get-latest-files.sh | python get-portfolios.py



Threats to Validity

The following factors may threaten the validity of this experiment: 

Internal Validity.

Reliability of the experiments were ensured by using the BenchExec framework. The number of solved tasks may be influenced by environmental effects, therefore, small differences are disregarded.

External Validity.

The generalizability of the experimental results may be limited by the relatively small number of benchmarks used. 

 Construct Validity.

Academic competitions like SV-COMP showcase the performance of tools after extensive tuning and repeated testing on a fixed benchmark set. As a result, our findings may not be easily reproducible on a different, less used set of benchmarks.
DOI: 10.5281/zenodo.15124213
title: Theta: Modular Model Checker Built For Diverse Algorithm Configurations (Accompanying Artifact)

description: Accompanying artifact for our paper entitled "Theta: Modular Model Checker Built For Diverse Algorithm Configurations".

We used Theta version 6.12.2, available under v6.12.2.

README: Theta Benchmarking Artifact

Overview

This Zenodo artifact accompanies our paper on benchmarking Theta, a model checker framework. The artifact includes all necessary files for reproducing our benchmarking experiments and analyzing the results.

Artifact Structure

The artifact consists of the following directories and files:





binary/: Contains Theta's JAR files, solvers, and required shared libraries.




benchmarks/: Includes all benchmarks used in the evaluation, with expected verdicts where known.




benchexec/: Contains the version of BenchExec used for the experiments.




results/: Stores the benchmarking results.




tooldefs/: Holds BenchExec tool definitions for Theta (slightly modified from the official tool info module).




variants.csv: Lists all configurations used in the experiments.




create-variants.py: Generates benchmark definition files (pre-generated in this artifact).




get-latest-files.sh: Helper script to retrieve the latest result files.




get-portfolios.py: Script to generate quantile plots.




get-results.py: Script to parse results and generate the summary table.




run-all.sh: Main script to execute all benchmark runs.




run-benchmark.sh: Script to execute a specific benchmark configuration.




svcomp.def: Benchmark definition file.



Reproducing Results

To reproduce the results, follow these steps:





Modify run-benchmark.sh (if necessary) to use a non-Slurm-based BenchExec setup.




Navigate to the binary/ folder and execute:

source ../run-all.sh


This will re-run all experiments that do not have a corresponding folder in results/. To fully reproduce the results, delete the results of specific configurations before rerunning.



Analyzing Results





To generate the results table, run:

python get-results.py





To generate the quantile plot, run:

get-latest-files.sh | python get-portfolios.py



Threats to Validity

The following factors may threaten the validity of this experiment: 

Internal Validity.

Reliability of the experiments were ensured by using the BenchExec framework. The number of solved tasks may be influenced by environmental effects, therefore, small differences are disregarded.

External Validity.

The generalizability of the experimental results may be limited by the relatively small number of benchmarks used. 

 Construct Validity.

Academic competitions like SV-COMP showcase the performance of tools after extensive tuning and repeated testing on a fixed benchmark set. As a result, our findings may not be easily reproducible on a different, less used set of benchmarks.
DOI: 10.15468/dl.mvysva
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aster ericoides Lam., 1783",
 "Geometry POLYGON((-102 35, -91 35, -91 44, -102 44, -102 35))"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000321-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m7tpjy
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "TaxonKey is Lamellibrachia Webb, 1969"
 ]
}

 The dataset includes 45 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000324-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ns8wvt
title: Occurrence Download

description: A dataset containing 3131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asclepias viridis Walter",
 "Geometry POLYGON((-102 35, -91 35, -91 44, -102 44, -102 35))"
 ]
}

 The dataset includes 3131 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000323-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pc6484
title: Occurrence Download

description: A dataset containing 4201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ireland",
 "TaxonKey is Meles meles (Linnaeus, 1758)"
 ]
}

 The dataset includes 4201 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000322-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sk7jka
title: Occurrence Download

description: A dataset containing 72074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-109.06553 7.24065,-28.77141 7.24065,-28.77141 64.15242,-109.06553 64.15242,-109.06553 7.24065))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Liquidambar styraciflua L."
 ]
}

 The dataset includes 72074 records from 207 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000313-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9r6nz2
title: Occurrence Download

description: A dataset containing 1932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.59179 40.40297,-3.58872 40.40823,-3.6038 40.41212,-3.61581 40.41348,-3.62168 40.41095,-3.62756 40.39967,-3.63191 40.3948,-3.63574 40.39402,-3.62296 40.3913,-3.61657 40.38935,-3.6176 40.38487,-3.613 40.38507,-3.60763 40.38546,-3.5992 40.37845,-3.59153 40.37923,-3.58821 40.38624,-3.60993 40.39752,-3.60737 40.40278,-3.5992 40.40181,-3.59179 40.40297))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 1932 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000325-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nv2byu
title: Occurrence Download

description: A dataset containing 2333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.6161 40.41577,-3.59031 40.40914,-3.5872 40.4117,-3.58202 40.41901,-3.57657 40.42848,-3.57217 40.43992,-3.5859 40.43992,-3.59031 40.44012,-3.59679 40.44406,-3.60612 40.4488,-3.60301 40.44091,-3.60615 40.43372,-3.60108 40.42157,-3.6161 40.41577))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Arthropoda"
 ]
}

 The dataset includes 2333 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000327-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jpqxt
title: Occurrence Download

description: A dataset containing 2064 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "TaxonKey is Nicomache Malmgren, 1865"
 ]
}

 The dataset includes 2064 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000329-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m6hq69
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Andorra",
 "TaxonKey is Bombus Latreille, 1802"
 ]
}

 The dataset includes 178 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000328-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvbdac
title: Occurrence Download

description: A dataset containing 3271122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-1156.73471 -56.18652,-1143.41192 -56.18652,-1143.41192 -41.77425,-1156.73471 -41.77425,-1156.73471 -56.18652))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3271122 records from 1063 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000237-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gw5cvh
title: Occurrence Download

description: A dataset containing 18213 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sympetrum danae (Sulzer, 1776)"
 ]
}

 The dataset includes 18213 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000473-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zps67p
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Encholirium magalhaesii L.B.Sm."
 ]
}

 The dataset includes 96 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192410-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gt3h5p
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vampyrodes caraccioli caraccioli",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000473-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9gth2
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Watermelon mosaic virus",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 117 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013477-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j4e8go
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myosotis azorica H.C.Watson ex Hook.",
 {
 "or" : [
 "Country is Portugal",
 "Country is United States of America",
 "Country is United Kingdom of Great Britain and Northern Ireland"
 ]
 }
 ]
}

 The dataset includes 16 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000473-160802083343578/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhfp6e
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Encholirium maximum Forzza & Leme"
 ]
}

 The dataset includes 33 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192411-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94mun9
title: Occurrence Download

description: A dataset containing 258530 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "TaxonKey is Haliaeetus leucocephalus (Linnaeus, 1766)"
 ]
}

 The dataset includes 258530 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192416-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkpenc
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 2. Aspacher GEO-Tag der Artenvielfalt"
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000473-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcdyr3
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Encyclia adenocarpos (Lex.) Schltr."
 ]
}

 The dataset includes 297 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192428-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.