cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8273590
title: Dataset and scripts for "Non-zero temperature study of spin 1/2 charmed baryons using lattice gauge theory"

description: charmJ12Scripts

A set of scripts and folders to reproduce the analysis and plots in the spin 1/2 charm baryon paper which can be found at EPJA

 

This repository includes the raw correlator data, the scripts and software used to analyse them as well as a script which can be run in order to reproduce the entire analysis, and particularly the figures in the manuscript.

 

correlators

Correlators from openqcd-fastsum-hadspec are zipped in the correlators folder. These are unzipped automatically by the script. The correlators are plain text files.

 

output

Analysis output is placed here. You do not need to look here in order to see the figures in the paper

 

code

The python code and scripts that do the analysis. There is some modularity here with the libraries in the lib folder

 

paperPlots

The plots from the paper will be generated here. They are not supplied with this repo as they can be found in the paper

 

plotXYData

The x-y and y-error data of each plot in the paper. Only 'scatter' style data is included. This is generated by the run script, but also supplied herein. It will be overwritten by the runscript

 

run

The folder where the main script needed to run all the analysis is.

 

Conda Notes

Install your favourite conda solution, such as https://docs.conda.io/en/latest/miniconda.html

 

Switch to a faster environment solver

This is optional, but likely will solve the dependencies much much faster. See https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community conda update -n base conda conda install -n base conda-libmamba-solver conda config --set solver libmamba

 

Install Environment

conda env create -f environment.yml

 

Activate/Use

conda activate charm

 

Update (w. new packages)



Edit environment.yml

Deactivate conda environment with conda deactivate

Update conda environment with conda env update -f=environment.yml
description: M.N.A. acknowledges support from The Royal Society Newton International Fellowship. This work used the DiRAC Extreme Scaling service at the University of Edinburgh, operated by the Edinburgh Parallel Computing Centre and the DiRAC Data Intensive service operated by the University of Leicester IT Services on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BEIS capital  unding via STFC capital grants ST/R00238X/1, ST/K000373/1 and  T/R002363/1 and STFC DiRAC Operations grants ST/R001006/1 and ST/R001014/1. DiRAC is part of the UK National e-Infrastructure. We acknowledge the support of the Swansea Academy for Advanced  omputing, the Supercomputing Wales project, which is part-funded by the  European Regional Development Fund (ERDF) via Welsh Government, and the University of Southern Denmark and ICHEC, Ireland for use of computing facilities. This work was performed using PRACE resources at Cineca (Italy), CEA (France) and Stuttgart (Germany) via grants 2015133079, 2018194714, 2019214714 and 2020214714.
DOI: 10.5281/zenodo.8275973
title: Dataset and scripts for "Non-zero temperature study of spin 1/2 charmed baryons using lattice gauge theory"

description: charmJ12Scripts

A set of scripts and folders to reproduce the analysis and plots in the spin 1/2 charm baryon paper which can be found at EPJA

 

This repository includes the raw correlator data, the scripts and software used to analyse them as well as a script which can be run in order to reproduce the entire analysis, and particularly the figures in the manuscript.

 

correlators

Correlators from openqcd-fastsum-hadspec are zipped in the correlators folder. These are unzipped automatically by the script. The correlators are plain text files.

 

output

Analysis output is placed here. You do not need to look here in order to see the figures in the paper

 

code

The python code and scripts that do the analysis. There is some modularity here with the libraries in the lib folder

 

paperPlots

The plots from the paper will be generated here. They are not supplied with this repo as they can be found in the paper

 

plotXYData

The x-y and y-error data of each plot in the paper. Only 'scatter' style data is included. This is generated by the run script, but also supplied herein. It will be overwritten by the runscript

 

run

The folder where the main script needed to run all the analysis is.

 

Conda Notes

Install your favourite conda solution, such as https://docs.conda.io/en/latest/miniconda.html

 

Switch to a faster environment solver

This is optional, but likely will solve the dependencies much much faster. See https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community conda update -n base conda conda install -n base conda-libmamba-solver conda config --set solver libmamba

 

Install Environment

conda env create -f environment.yml

 

Activate/Use

conda activate charm

 

Update (w. new packages)



Edit environment.yml

Deactivate conda environment with conda deactivate

Update conda environment with conda env update -f=environment.yml
description: M.N.A. acknowledges support from The Royal Society Newton International Fellowship. This work used the DiRAC Extreme Scaling service at the University of Edinburgh, operated by the Edinburgh Parallel Computing Centre and the DiRAC Data Intensive service operated by the University of Leicester IT Services on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BEIS capital  unding via STFC capital grants ST/R00238X/1, ST/K000373/1 and  T/R002363/1 and STFC DiRAC Operations grants ST/R001006/1 and ST/R001014/1. DiRAC is part of the UK National e-Infrastructure. We acknowledge the support of the Swansea Academy for Advanced  omputing, the Supercomputing Wales project, which is part-funded by the  European Regional Development Fund (ERDF) via Welsh Government, and the University of Southern Denmark and ICHEC, Ireland for use of computing facilities. This work was performed using PRACE resources at Cineca (Italy), CEA (France) and Stuttgart (Germany) via grants 2015133079, 2018194714, 2019214714 and 2020214714.
DOI: 10.15468/dl.5g5v7u
title: Occurrence Download

description: A dataset containing 281 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((25.88751 -25.63007,26.17715 -25.61733,26.17876 -25.34507,25.88056 -25.35317,25.88751 -25.63007))",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 281 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029707-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syqwmg
title: Occurrence Download

description: A dataset containing 378448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lampranthus densifolius (L.Bolus) L.Bolus, Lampranthus debilis (Haw.) N.E.Br., Lepidium ecklonii Schrad., Leptospermum rotundifolium (Maiden & Betche) F.A.Rodway, Linaria bordiana Santa & Simonn., Lycium afrum L., Melaleuca densa R.Br., Melaleuca diosmifolia Andrews, Melaleuca incana R.Br., Melaleuca nesophila F.Muell., Melaleuca styphelioides Sm., Melaleuca viminea Lindl., Melilotus siculus (Turra) Steud., Mesembryanthemum guerichianum Pax, Moraea fugacissima (L.f.) Goldblatt, Moraea spathulata (L.f.) Klatt, Moraea virgata Jacq., Nassella charruana (Arechav.) M.E.Barkworth, Nassella hyalina (Nees) Barkworth, Nerine undulata (L.) Herb., Onopordum nervosum Boiss., Salmonopuntia schickendantzii (F.A.C.Weber) Font & M.Köhler, Oxalis glabra Thunb., Oxalis obtusa Jacq., Panicum racemosum (P.Beauv.) Spreng., Passerina corymbosa Eckl. ex C.H.Wright, Pauridia capensis (L.) Snijman & Kocyan, Persicaria odorata (Lour.) Soják, Phillyrea latifolia L., Piptochaetium bicolor (Vahl) É.Desv., Piptochaetium montevidense (Spreng.) Parodi, Piptochaetium uruguense Griseb., Plantago triandra Berggr., Plectranthus ecklonii Benth., Polygonatum multiflorum (L.) All., Populus yunnanensis Dode, Potamogeton acutifolius Link, Prostanthera ovalifolia R.Br., Psoralea arborea Sims, Puccinellia ciliata Bor, Romulea flava (Lam.) M.P.de Vos, Rubus cissburiensis W.P.C.Barton & Ridd., Ruschia geminiflora (Haw.) Schwantes ex H.Jacobsen, Sagittaria macrophylla Zucc., Salvia aurea L., Schoenoplectiella lineolata (Franch. & Sav.) J.Jung & H.K.Choi, Sclerolaena bicornis Lindl., Sedum cespitosum (Cav.) DC., Sedum ×rubrotinctum R.T.Clausen, Selago corymbosa L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 378448 records from 2056 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012732-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m88p8f
title: Occurrence Download

description: A dataset containing 21334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calyptocarpus vialis Less.",
 "HasCoordinate is True"
 ]
}

 The dataset includes 21334 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044116-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u6ekz9
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Lupinus paraguariensis Chodat & Hassl."
 ]
}

 The dataset includes 27 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102454-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n33vbc
title: Occurrence Download

description: A dataset containing 35012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Capsicum L.",
 "HasCoordinate is True"
 ]
}

 The dataset includes 35012 records from 602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044117-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zljxye
title: Occurrence Download

description: A dataset containing 127716 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Amphibia",
 "TaxonKey is Aves",
 "TaxonKey is Insecta",
 "TaxonKey is Reptilia",
 "TaxonKey is Mammalia",
 "TaxonKey is Chilopoda",
 "TaxonKey is Diplopoda",
 "TaxonKey is Arachnida"
 ]
 },
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "HasCoordinate is true",
 "DecimalLongitude is greater than or equal to -140.000000",
 "DecimalLongitude is less than -135.000000",
 "DecimalLatitude is greater than or equal to 55.000000",
 "DecimalLatitude is less than 60.000000",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2018"
 ]
}

 The dataset includes 127716 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048353-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97mpzr
title: Occurrence Download

description: A dataset containing 22710 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Lycorma delicatula (White, 1845)",
 "Year 2003-2024"
 ]
}

 The dataset includes 22710 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078456-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2motk
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Thyrsanthera suborbicularis Pierre ex Gagnep.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048357-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4z5qvq
title: Occurrence Download

description: A dataset containing 363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Protea longifolia Andrews"
 ]
}

 The dataset includes 363 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092828-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6p5v6b
title: Occurrence Download

description: A dataset containing 35012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Capsicum L.",
 "HasCoordinate is True"
 ]
}

 The dataset includes 35012 records from 602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044119-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6gyjgb
title: Occurrence Download

description: A dataset containing 17228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Copaifera L."
 ]
}

 The dataset includes 17228 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078464-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jkr74s
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Amphibia",
 "TaxonKey is Aves",
 "TaxonKey is Insecta",
 "TaxonKey is Reptilia",
 "TaxonKey is Mammalia",
 "TaxonKey is Chilopoda",
 "TaxonKey is Diplopoda",
 "TaxonKey is Arachnida"
 ]
 },
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "HasCoordinate is true",
 "DecimalLongitude is greater than or equal to -140.000000",
 "DecimalLongitude is less than -135.000000",
 "DecimalLatitude is greater than or equal to -10.000000",
 "DecimalLatitude is less than -5.000000",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2018"
 ]
}

 The dataset includes 121 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048360-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzzhbf
title: Occurrence Download

description: A dataset containing 12354 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteris cretica L."
 ]
}

 The dataset includes 12354 records from 347 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0345373-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30302835
title: Additional file 2 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30302835.v1
title: Additional file 2 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30302838
title: Additional file 3 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.30302838.v1
title: Additional file 3 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.30302841
title: Additional file 4 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.30302841.v1
title: Additional file 4 of Alcohol exposure significantly influences gene expression in the hypothalamus, highlighting complex links with gonadotropin-releasing hormone signaling and thyroid hormone production in adolescent mice

description: Supplementary Material 4.
DOI: 10.82144/2c045249
title: MIRC NAVFAC Incidental Sightings - Aerial 1965-2014

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent incidental sightings from airplanes between 1965 and 2014.
DOI: 10.82144/e5db0624
title: Manx Basking Shark Watch 2017-2018 (aggregated per 1-degree cell)

description: Original provider:
Manx Basking Shark atch

Dataset credits:
Data provider
Manx Basking Shark Watch
Originating data center
&lt;a href='http://www.seaturtle.org/tracking/' target='_blank'&gt;Satellite Tracking and Analysis Tool (STAT)&lt;/a&gt;
Project partner
Dr Matt Witt of Exeter University has also been tagging basking sharks. He and his team very kindly analyse our tag data with theirs, adding huge value to our work. We have jointly published papers about this work in Nature Scientific Papers. See the paper here https://www.nature.com/articles/srep42837
Project sponsor or sponsor description
The Manx Government's Department of Environment, Fisheries and Agriculture (DEFA) generously supports the running costs of Happy Jack, the MBSW research boat.&lt;br&gt;&lt;br&gt;The Manx Lottery Trust very kindly sponsored Mae's SPOT tag.

Abstract:
Manx Basking Shark Watch is a charity with two aims &lt;br&gt;1: To study basking sharks.&lt;br&gt;2: To help the public to understand as much as possible about these enigmatic endangered animals and our work with them.
 This dataset is a summarized representation of the telemetry locations aggregated per species per 1-degree cell.
DOI: 10.82144/93c20831
title: MIRC NAVFAC Incidental Sightings - Shore 1965-2014

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent incidental sightings from shores between 1965 and 2014.
DOI: 10.82144/ca612b14
title: IMMS Ridley 9 (aggregated per 1-degree cell)

description: Original provider:
Institute for Marine Mammal Studies

Dataset credits:
Data provider
Institute for Marine Mammal Studies
Originating data center
&lt;a href='http://www.seaturtle.org/tracking/' target='_blank'&gt;Satellite Tracking and Analysis Tool (STAT)&lt;/a&gt;

Abstract:
Turtles are an important component of the ecosystem, and may serve as a key biological indicator of the health of their environments. They are constantly impacted by a variety of both natural and anthropogenic factors.&lt;br&gt;Satellite telemetry is a powerful tool for examining short- and long-term movements of these protected species and enhancing conservation and management efforts. These observations will allow us to examine how much time these turtles actually spend in the Mississippi Sound and what microhabitats they utilize. The use of satellite tags on recently rehabilitated and released sea turtles will increase our knowledge about the daily activities and habitat fidelity of these animals.
 This dataset is a summarized representation of the telemetry locations aggregated per species per 1-degree cell.
DOI: 10.82144/58801804
title: MIRC NAVFAC MISTCS Vessel Surveys Jan-Apr 2007

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent sightings from the NAVFAC MISTCS Vessel Surveys Jan-Apr 2007.
DOI: 10.82144/b9379b90
title: MIRC Valiant Shield Aerial Survey Aug 2007

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent sightings during large ship, small boat, aerial, shore-based between 2007 and 2013
DOI: 10.82144/a0ae2a2e
title: MIRC PIFSC Large Vessel Surveys Jan-May 2010

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent sightings from the PIFSC Large Vessel Surveys Jan-May 2010.
DOI: 10.82144/bf7a12a8
title: MIRC PIFSC Small Vessel Surveys Jun-Aug 2013

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent sightings from the PIFSC Small Vessel Surveys Jun-Aug 2013.
DOI: 10.82144/c9c8711a
title: MIRC PIFSC CNMI Vessel Surveys May-Jul 2012

description: Original provider:
HDR Environmental, Operations and Construction, Inc.

Dataset credits:
The U.S. Navy Marine Species Monitoring Program

Abstract:
Features in this feature class represent sightings from the PIFSC CNMI Vessel Surveys May-Jul 2012.
DOI: 10.15468/dl.tm8rcr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diluvarca ferruginea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060149-250920141307145/datasets/export for details.
DOI: 10.15468/dl.xy6hew
title: Occurrence Download

description: A dataset containing 1372184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Columbiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((90 0,120 0,120 30,90 30,90 0))"
 ]
}

 The dataset includes 1372184 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060095-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.