cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10594283
title: Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

description: This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format.

File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy<n>", where <n> from 1 to 8 is an identifier for the experiment. The images under the xy<n>_Phase folders are the raw images taken of the experiment, those under the xy<n>_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper.

Alternatively, the density data is also provided in csv format. In the csv_data folder, xy<n>/t<k>.csv encodes a matrix representing cell density for experiment <n> at time t_k.

The code for processing and analysing these data are provided in the "code" folder. It is also available at https://github.com/liuyue002/woundhealing .

Abstract of the paper:

When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.
DOI: 10.5281/zenodo.8367272
title: Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

description: This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format.

File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy<n>", where <n> from 1 to 8 is an identifier for the experiment. The images under the xy<n>_Phase folders are the raw images taken of the experiment, those under the xy<n>_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper.

Alternatively, the density data is also provided in csv format. In the csv_data folder, xy<n>/t<k>.csv encodes a matrix representing cell density for experiment <n> at time t_k.

The code for processing and analysing these data are provided in the "code" folder. It is also available at https://github.com/liuyue002/woundhealing .

Abstract of the paper:

When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.
DOI: 10.5281/zenodo.8367273
title: Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

description: This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format. File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy&lt;n&gt;", where &lt;n&gt; from 1 to 8 is an identifier for the experiment. The images under the xy&lt;n&gt;_Phase folders are the raw images taken of the experiment, those under the xy&lt;n&gt;_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper. Abstract of the paper: When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.
DOI: 10.5281/zenodo.8377953
title: Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

description: This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format. File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy&lt;n&gt;", where &lt;n&gt; from 1 to 8 is an identifier for the experiment. The images under the xy&lt;n&gt;_Phase folders are the raw images taken of the experiment, those under the xy&lt;n&gt;_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper. Alternatively, the density data is also provided in csv format. In the csv_data folder, xy&lt;n&gt;/t&lt;k&gt;.csv encodes a matrix representing cell density for experiment &lt;n&gt; at time t_k. The code for processing and analysing these data are provided at https://github.com/liuyue002/woundhealing . Abstract of the paper: When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.
DOI: 10.7925/drs1.duchas_5136115
title: Fairies

description: Story collected by a student at Baile Dháithí, Dunlavin school (Davidstown, Co. Wicklow) from 2 informants.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Róisín Bhreathnach.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815631
title: Local Marriage Customs

description: Story collected by Maura Patterson, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mrs J. Mooney.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815642
title: Old Crafts

description: Story collected by Maura Costigan, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mr Thomas Dooley.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136116
title: Hidden Treasure

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant Oliver Fitzharris.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815644
title: Ogham Alphabet from the Book of Ballymote

description: Story collected by May Mc Dermott, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136117
title: Harvesters

description: Story collected by a student at Baile Dháithí, Dunlavin school (Davidstown, Co. Wicklow) from informant Michael Murphy.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Róisín Bhreathnach.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136118
title: Old School

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant John Shiel.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815660
title: Saint Brigid's Cross

description: Story collected by Aine Dunne, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815665
title: Stage Coach

description: Story collected by Aine Dunne, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mr J. Miller.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136119
title: Old School

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant Mr Sharkey.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136120
title: Old Stories

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant James Byrne.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815670
title: Mountrath Town

description: Story collected by Aine Dunne, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mr J. Miller.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815673
title: Old Crafts

description: Story collected by Aine Dunne, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mr Thomas Dooley.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136121
title: Old Stories

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant James Byrne.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815708
title: Legends of Clonenagh

description: Story collected by Aine Dunne, a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) from informant Mr Thomas Dooley.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136122
title: Old Stories

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant James Byrne.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136123
title: Old Stories

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant James Byrne.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815719
title: Friar of the Hollow, Father Quigley

description: Story collected by a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136124
title: Methods of Tillage

description: Story collected by a student at Baile Dháithí, Dunlavin school (Davidstown, Co. Wicklow) from informant Patrick O' Toole.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Róisín Bhreathnach.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815726
title: The Synod of Rathbreasail

description: Story collected by a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136125
title: Cures

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant John Shiel.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815736
title: Leinster Steel at Waterloo - The Tale of a Town

description: Story collected by a student at St Brigid's Convent, Mountrath school (Mountrath, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Sr. Aquinas.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815751
title: Buried Treasure

description: Story collected by Mary Conroy, a student at The Oak, Portlaoighse school (Clondouglas, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Seán Bairéad.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5136126
title: Cures

description: Story collected by a student at Rathcoyle, Kiltegan school (Rathcoyle Lower, Co. Wicklow) from informant Peter Byrne.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Aodh Ó Broin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4815753
title: Buried Treasure

description: Story collected by Mary Conroy, a student at The Oak, Portlaoighse school (Clondouglas, Co. Laois) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Seán Bairéad.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.