cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26188/5c4227cb49476
title: Morrongiello etal 2019 Journal of Animal Ecology- purple wrasse otolith increments.csv

description: increment measurements and biological data associated with Morrongiello etal 2019 publication in Journal of Animal Ecology titled 'Fishing constrains phenotype responses of marine fish to climate variability'<br>
DOI: 10.26188/5c4517a482de2
title: HiTIME small test dataset

description: A pure protein that was reduced, reacted with heavy/light paracetamol and then digested. The BSA_SUBSET file is a single twin-ion (the APAP-Glutathione conjugate). The mass difference is 6.0201 in that case. There's no noise floor cutoff for this subset.
DOI: 10.26188/5c451a7ea7874
title: HiTIME large test dataset

description: It's a pure protein that was reduced, reacted with heavy/light paracetamol and then digested. The advantage is that there are lots of twin ions in there. Because these twin-ions are mostly peptide derivatives, they come in multiple charge states which effectively gives us a few different doublet spacings. There are many separated by 6.0201 as before, a good number separated by 3.01005 and a few separated by 2.0067. We have removed any points with intensity &lt;1000 to make the file smaller.
DOI: 10.26188/5c50c9ef0c5ee
title: Marsupial landmark data

description: Partial dataset from publication Feigin et al. 2018 Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nat. Eco. Evo. <br>Final dataset was combined with data from Goswami et al. 2011. Biting through constraints: Cranial morphology, disparity and convergence across living and fossil carnivorous mammals. Proc. Roy. Soc. B
DOI: 10.26188/5c5617c01383b
title: The Functional And Evolutionary Trait Heritability (FAETH) score of over 17 million cattle sequence variants

description: Please see attached 'FAETH.v1.1.data.descrip.docx' for how to use this dataset.<br>For citation: Xiang, R., Van Den Berg, I., MacLeod, I. M., Hayes, B. J., Prowse-Wilkins, C. P., Wang, M., ... Goddard, M.E. (2019). Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. <i>PNAS (2019), In Press</i>.<br>
DOI: 10.26188/5c6656eb6735c
title: Literature and survey data for: Psychology, not technology, is our biggest challenge to open digital morphology data.

description: Hipsley, C. A. & Sherratt, E. Literature and survey data for: <b>Psychology, not technology, is our biggest challenge to open digital morphology data</b>. <br><br>Excel file containing 3 worksheets:<b>1) Literature summary:</b> Data accompanying <b>Figure 1a</b>. Number of publications per year retrieved through Web of Science’s Science Citation Index Expanded using the topic search terms: x-ray comput* tomograph* OR CT; magnetic resonance imag* OR MRI; synchrotron; photogrammetr*. Articles were limited to the Web of Science categories Anatomy Morphology, Evolutionary Biology, Paleontology, and Zoology. Results for 2018 are not shown. Only three articles prior to 1980 were recovered. Search performed on 25 June 2018.<b>2) CT papers:</b> Data accompanying <b>Figure 1b</b>. 50 publications including CT data published in the past 5 years in <i>Anatomical Record</i>, <i>Journal of Anatomy</i>, <i>Journal of Morphology</i>, <i>Journal of Vertebrate Paleontology</i>, and <i>Zoological Journal of the Linnean Society</i> (10 papers each). These journals were among the top 10% of publishers including CT data recovered in our literature search.<b>3) Survey responses:</b> Includes data accompanying <b>Figure 2</b>. Responses to an online survey generated in Google Docs and posted to the MORPHMET and geomorph discussion groups. Results can also be found here:https://docs.google.com/forms/d/1hZr2QyN3a7Sh1BlaXOPumnUlqLm_MN-SkwmyuQLsO3c/edit#responses<br><br><br><br><br>
DOI: 10.26188/5c75f384c4502
title: Spatial distribution of working age adults with disabilities across Australia: a small area analysis of the 2016 Census.

description: When 23 million Australians filled in their Census forms in 2016, 3.3% of working age adults (15 to 64 years) were identified as having a disability as they reported needingassistance in their self care, mobility and communication in their daily living.<br>Our team at the Centre of Research Excellence in Disability and Health (CRE-DH) has released an Interactive Map, and an accompanying Technical Report.<br>Access the map here: http://go.unimelb.edu.au/pfv6<br><br>The Interactive Map shows the proportion of working age adults who were identified as having a disability across Australia. It shows that there is considerable variation in the prevalence of disability between small geographic areas. Users can explore specific geographic areas of interest through the built-in navigation.<br>The Technical Report documents some key decisions on the map specifications and covers topics on data and definition, selection of geographic unit, impact of small counts, missing values, age standardisation, and data stability over time. It also gives a series of snapshots of several regions across the country where very high proportions of working age adults resided.<br>The source of the data referred to in this report is the Census of Population and Housing 2016 collected by the Australian Bureau of Statistics (ABS). The team would like to acknowledge the work of the ABS.<br>NOTE: The geographic areas used in the map are the Statistical Area Level 2 (SA2) as defined in Australian Statistical Geography Standard (ASGS) by the Australian Bureau of Statistics (ABS). The SA2 is the smallest area used in the majority of ABS statistical releases and generally have a population range of 3,000 to 25,000 persons. On average they contain about 6,600 working age adults. <br><br><br><br>
DOI: 10.26188/5c78c8d4e8074
title: Sample information for Chapter 4

description: Details of E. coli and Salmonella strains whose WGS<br>data were used for Chapter 4. 
<br>
DOI: 10.26188/5c78cc692db57
title: Sample information for Chapter 5

description: EXCEL spreadsheets providing detailed information of Kp strains whose WGS data were used for Chapter 5. 
<br>
DOI: 10.26188/5c78cc6b76eaf
title: Sample information for Chapter 5

description: EXCEL spreadsheets providing detailed information of Kp strains whose WGS data were used for Chapter 5. 
<br>
DOI: 10.26188/5c91acb11b183
title: Intermediate files

description: Intermediate files produced during statistical analysis
DOI: 10.26188/5c91acc0b0e25
title: Cell Ranger output

description: Expression matrix produced by the Cell Ranger pipeline
DOI: 10.26188/5c91acc0b1d81
title: Misc files

description: Additional data files for my PhD thesis analysis
DOI: 10.26188/5c91acd082c7f
title: Alevin Org 3

description: Alevin output for Organoid 3
DOI: 10.26188/5c91acd0d5ca3
title: Alevin Org 2

description: Alevin output for Organoid 2
DOI: 10.26188/5c91ace02f0e8
title: Alevin Org 1

description: Alevin output for Oraganoid 1
DOI: 10.26188/5c91b3533b916
title: Annotation files

description: Additional annotation files required for command line tools used in the analysis
DOI: 10.26188/5c9764ead9eb9
title: Meteorological dataset

description: Comprehensive hydrometeorologcial dataset collected at experimental farms in the University of Melbourne's Dookie Campus.<br>
DOI: 10.26188/5c9767891557e
title: Spectral and other ancillary data

description: Comprehensive hydrometeorologcial dataset collected at experimental farms in the University of Melbourne's Dookie Campus.
DOI: 10.26188/5c9770196a831
title: Site information and photos

description: Daily photos of experimental field sites in The University of Melbourne's Dookie Campus
DOI: 10.26188/5ca5598fc594a
title: Updated gene content PCA files (zipped directory)

description: Updated data files for pan-genome and phage gene content PCAs. These files contain data for 463 and 210 PCs, respectively.<br>These data are described in Wyres et al "Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae."
DOI: 10.26188/5ca55c17c4fbb
title: Additional data shown in figures (zipped directory)

description: These data are described in Wyres et al "Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae." Much of the numerical data underlying the figures shown in this manuscript can be found in the associated supplementary tables, but the remainder is contained herein.
DOI: 10.26188/5cb01b55b4411
title: Se_HsdR_5.fasta

description: 5 variants of <i>Staphylococcus epidermidis</i> type I restriction modification system HsdR subunits<br>
DOI: 10.26188/5cb01fc089ab2
title: Sa_HsdS_48.fasta

description: 48 variants of <i>Staphylococcus aureus</i> type I restriction modification system HsdS subunits
DOI: 10.26188/5cb8049f593a6
title: 812 simulated expression datasets for differential co-expression analysis

description: Simulated expression data with knock-outs Description A dataset containing simulated expression dataset. Data is simulated using a dynamical systems model from a network sampled from the S. Cerevisiae regulatory network. The dataset is a list containing the results from the simulation, and other information generated subsequently. Format A named list with 14 elements: simitra numeric, indicating the iteration of the simulation (a total of 1000 were performed and 812 converged) scoresan S4 Matrix, containing vectorised inference scores of applying the methods implemented in the package. These are precomputed predictions inputmodelsa named list, storing the parameters used to sample the initial values of input genes. Proportions, means and variances of each gene is stored for each gene staticnetan igraph object, storing the initial regulatory network (150 node network) infnetan igraph object, representing the true differential network as determined using sensitivity analysis of the model netlayouta matrix (150 x 2), storing the (x, y) positions of nodes for laying out the graph infdensa numeric, network density of the true differential association network numinputa numeric, the number of input genes in the regulatory network. These are genes that have no regulators therefore need to be pre-defined numbimodala numeric, the number of input genes that are knocked-down therefore have a bimodal distribution numtfsa numeric, the number of genes in the network that regulate any other gene (are TFs) numcotargetsa numeric, the number of genes that are co-regulated, i.e. regulated by more than one TF dataan S4 Matrix, the expression data with samples along the columns and genes along the rows. Condition classification (KD vs WT) are stored as attributes of this object tripletsa data frame, consisting of gene triplets representing TF- Target associations conditioned on the gene knocked-down. Triplets are annotated for being in either the direct, influence and association networks sensmatan S4 Matrix, sensitivities of genes to TFs based on perturbation analysis of the simulation modelLoadThis dataset is in the form of an R RDS object. To load it, type the command below in an R console:<br><i>simdata = readRDS("sim812.rds")</i><br>
DOI: 10.26188/5c91acb12a5a8
title: Velocyto output

description: Loom file output from velocyto.py
DOI: 10.26188/5cb019b506f53
title: Se_HsdM_6.fasta

description: 6 variants of <i>Staphylococcus epidermidis</i> type I restriction modification system HsdM subunits
DOI: 10.26188/5cb01e8f23305
title: Se_HsdS_31.fasta

description: 31 variants of <i>Staphylococcus epidermidis</i> type I restriction modification system HsdS subunits
DOI: 10.26188/5cb0211e35098
title: Newman_UoM-M1.fasta

description: <i>Staphylococcus aureus</i> type I restriction modification system HsdM subunit. Representative extracted from Newman_UoM genome.
DOI: 10.26188/5cb021b7b8cff
title: Newman_UoM-R.fasta

description: <i>Staphylococcus aureus</i> type I restriction modification system HsdR subunit. Representative extracted from Newman_UoM genome.
DOI: 10.26188/5cbd1f18b2602
title: Input data for demonstrating utilities of R package GeneMates

description: Input data for demonstrating utilities of R package GeneMates. Usage of this data set can be found at https://github.com/wanyuac/GeneMates.<br>
DOI: 10.26188/5cbd22cd00780
title: Example output from GeneMates

description: Example output from GeneMates.<br>
DOI: 10.26188/5cd106f5b3a77
title: Point spread functions

description: PSFs generated as a normalised function of a multivariate Gaussian distribution applied in three dimensions. Used to simulate optical blurring from confocal microscope. FWHM of the default PSF is 410nm in xy, 1800nm in z. Used by code at: <br>https://github.com/dladd/CardiacCalcium_TestCaCLEAN<br>
DOI: 10.26188/5cd1134528803
title: Finite element mesh: low RyR density, no mitochondria

description: Mesh resource for a finite element model of calcium mechanics in an 8 sarcomere section of a cardiomyocyte. Used by code at: <br>https://github.com/dladd/CardiacCalcium_FiniteElement
DOI: 10.26188/5cd1220539e55
title: RyR distribution parameters

description: Matlab .mat files with parameters describing the density and time delay for calcium released from RyR cluster populations. Used by code at: <br>https://github.com/dladd/CardiacCalcium_FiniteElement
DOI: 10.26188/5cd1236908243
title: Finite element mesh: high RyR density, with mitochondria

description: Mesh resource for a finite element model of calcium mechanics in an 8 sarcomere section of a cardiomyocyte. Used by code at: <br>https://github.com/dladd/CardiacCalcium_FiniteElement
DOI: 10.26188/5cd123691e6c6
title: Finite element mesh: high RyR density, no mitochondria

description: Mesh resource for a finite element model of calcium mechanics in an 8 sarcomere section of a cardiomyocyte. Used by code at: <br>https://github.com/dladd/CardiacCalcium_FiniteElement
DOI: 10.26188/5cd1237a76fda
title: Finite element mesh: low RyR density, with mitochondria

description: Mesh resource for a finite element model of calcium mechanics in an 8 sarcomere section of a cardiomyocyte. Used by code at: <br>https://github.com/dladd/CardiacCalcium_FiniteElement
DOI: 10.26188/5cd12747d138a
title: Finite element results (archive): low RyR density, no mitochondria

description: Results from a reaction-diffusion finite element model of calcium signalling in a rat ventricular cardiomyocyte. Solved for the first 30 ms of the calcium transient in an 8 sarcomere section.<br>Calcium is released from RyR clusters with a minimum 1um spacing between them (50 clusters per z-disk). The intracellular space is a modeled as a homogeneously diffusing continuum. <br>To view the results of the calcium and fluorescence-bound calcium fields, visualisation of the results in the 'vtk' folder with ParaView is recommended. All field data is available in OpenCMISS exnode / exelem formats in the 'output' folder. Note this model was run on 8 parallel processes.
DOI: 10.26188/5cd127480b8f7
title: Finite element results (archive): high RyR density, with mitochondria

description: Results from a reaction-diffusion finite element model of calcium signalling in a rat ventricular cardiomyocyte. Solved for the first 30 ms of the calcium transient in an 8 sarcomere section.<br>Calcium is released from RyR clusters with spacings based on immuno-labeled microscopy data populations (123 clusters per z-disk). Regions representing mitochondria are excluded to produce barriers to diffusion in the intracellular space.<br>To view the results of the calcium and fluorescence-bound calcium fields, visualisation of the results in the 'vtk' folder with ParaView is recommended. All field data is available in OpenCMISS exnode / exelem formats in the 'output' folder. Note this model was run on 8 parallel processes.
DOI: 10.26188/5cd12759dd1ba
title: Finite element results (archive): high RyR density, no mitochondria

description: Results from a reaction-diffusion finite element model of calcium signalling in a rat ventricular cardiomyocyte. Solved for the first 30 ms of the calcium transient in an 8 sarcomere section.<br>Calcium is released from RyR clusters with spacings based on immuno-labeled microscopy data populations (123 clusters per z-disk). The intracellular space is a modeled as a homogeneously diffusing continuum. <br>To view the results of the calcium and fluorescence-bound calcium fields, visualisation of the results in the 'vtk' folder with ParaView is recommended. All field data is available in OpenCMISS exnode / exelem formats in the 'output' folder. Note this model was run on 8 parallel processes.
DOI: 10.26188/5cd1275a2d54d
title: Finite element results (archive): low RyR density, with mitochondria

description: Results from a reaction-diffusion finite element model of calcium signalling in a rat ventricular cardiomyocyte. Solved for the first 30 ms of the calcium transient in an 8 sarcomere section.<br>Calcium is released from RyR clusters with a minimum 1um spacing between them (50 clusters per z-disk). Regions representing mitochondria are excluded to produce barriers to diffusion in the intracellular space.<br>To view the results of the calcium and fluorescence-bound calcium fields, visualisation of the results in the 'vtk' folder with ParaView is recommended. All field data is available in OpenCMISS exnode / exelem formats in the 'output' folder. Note this model was run on 4 parallel processes.
DOI: 10.26188/5cd17ce790da5
title: Higher frequency of Central Pacific El Niño events in recent decades relative to past centuries

description: <b>Additional information and datasets</b>used in Freund et al. 2019, Higher frequency of Central Pacific El Niño events in recent decades relative to past centuries <b><br></b><br>rdcu.be/bAxOG<br><br>---------------------------------------------------------------------------<br>File format provided: netcdf (.nc) and text format (.txt)<br>---------------------------------------------------------------------------<br><b>Central Pacific El Niño events </b>abbreviated as CP events (El Niño Modoki, Dateline El Niño, Central Pacific El Niño)<br><b><br>Eastern Pacific El Niño events </b>abbreviated as EP events (Traditional El Niño, canonical El Niño, Eastern Pacific El Niño) <br><br>All <b>frequency</b> information is given as number of events per 30 year period. <br>All <b>intensity</b> information is given as intensity of individual El Niño events as the maximum SSTA in Niño 3 and Niño 4 region. <br>All <b>ratio</b> information is given as the number of Central Pacific El Niño events vs. Eastern Pacific El Niño events per 30 year periods. <br>All <b>uncertainty</b> information is estimate by obtaining 1000 realisation bootstrap approach. See more details in methods and Supplementary Information (https://static-content.springer.com/esm/art:10.1038/s41561-019-0353-3/MediaObjects/41561_2019_353_MOESM1_ESM.pdf)<br><b>1)</b> Instrumental data saved by : "Instrumental_"<b>2) </b>Reconstructed data saved by: "Reconstructed_"<b>3) </b>Uncertainty<b> </b>around reconstructed data saved as:"ReconstructedUncertainty_"<br><br><b>Find cite and find further information in: </b>Freund, M. B., Henley, B. J., Karoly, D. J., McGregor, H. V., Abram, N. J. and Dommenget, D.: Higher frequency of Central Pacific El Niño events in recent decades relative to past centuries, Nature Geoscience, 6, 450–455, doi:10.1038/s41561-019-0353-3, 2019.<br><br><br>
DOI: 10.26188/5cd4c6c945296
title: UniMelb_Thylacine_Refassem_1.fasta

description: Reference-guided assembly of the Tasmanian tiger a.k.a. thylacine (Thylacinus cynocephalus) against the genome assembly of the Tasmanian devil (Sarcophilus harrisii; Assembly: GCA_000189315.1 Devil_ref v7.0). From publication PMID: 29230027.
DOI: 10.26188/5cd4cd3ec44fd
title: UniMelb_Wolf_Refassem_1.fasta

description: Reference-guided assembly of the grey wolf (Canis lupus) against the genome assembly of the domestic dog (Canis lupus familiaris; Assembly: GCA_000002285.2 (CanFam3.1). From publication PMID: 29230027.
DOI: 10.26188/5cde4c26c8201
title: Code_for_modelling_gametocyte_population_dynamics.zip

description: The data contains computer code (R, Stan, MATLAB) for simulating the results presented in the manuscript "Modelling the population dynamics of Plasmodium falciparum gametocytes in humans during malaria infection" by Cao et al. (bioRxiv). Upon unzipping the file, you will find an instruction document which details how to use the code.
DOI: 10.26188/5cf09572bca2b
title: Tmor-Da GIS 2D map for year 2016 (Autocad dwg 2018 format)

description: This map was drawn from an overlaid of satellite image from Google earth, with measured dimensions from fieldwork in year 2016.
DOI: 10.26188/5cf097d31122b
title: Tmor-Da GIS Map - Year 2016 -Autocad v18

description: GIS Map- Year 2016 - Autocad v18 format (encoded CRS) of Tmor-Da, Phnom Penh, Cambodia<br>
DOI: 10.26188/5cf5e3af414a8
title: PONE_Firestone_D4_S1.zip

description: Supplementary Materials (S1):<br>Simulated FMD outbreak datasets<br>Multiple file types (zip archive)
DOI: 10.26188/5d0b083523c27
title: NHM capture data_Victoria 1970-2018

description: New Holland Mouse capture dataset used in Burns, P. A., McCall, C., Rowe, K. C., Parrott, M. L., and Phillips, B. L. (2019). Accounting for detectability and abundance in survey design for a declining species. <i>Diversity and Distributions</i>.
DOI: 10.26188/5d13fb401e305
title: Filtered m_values for all samples

description: Matrix of m-values associated with Natri et al, 2019. <br>
DOI: 10.26188/5d26aec1d817a
title: Differential expression testing results

description: Results from differential expression testing across all 13 contrasts discussed in Natri et al, 2019.<br>Key:ANK: AnakalangWNG: WungaSMB: SumbaMDB: MadobagTLL: TaileleluMTW: MentawaiKOR: Korowai
DOI: 10.26188/5d26b0b5230dd
title: Differential methylation testing results

description: Results from differential methylation testing across all 13 contrasts discussed in Natri et al, 2019.<br>Key: ANK: AnakalangWNG: WungaSMB: SumbaMDB: MadobagTLL: TaileleluMTW: MentawaiKOR: Korowai
DOI: 10.26188/5d26eef7d07c4
title: HiTIME synthetic test data 17 twin ions

description: Synthetic LC-MS data was produced that contain exactly 17 twin-ions of varying abundance in addition to a number of non-twin-ion signals.
DOI: 10.26188/5d281b35c624b
title: 17 synthetic twin ions for HiTIME

description: 17 synthetic twin ions for HiTIME
DOI: 10.26188/5d282b0c73ae3
title: BSA control data

description: A control BSA digest dataset containing no true twin ion signal
DOI: 10.26188/5d2b6cc18233c
title: 2015 Warramaba virgo data

description: A series of lab experiments conducted on the cohort of <i>Warramaba virgo</i> collected from Nowingi, NSW in summer 2014/2015 and F1 and F2 reared in the lab at the University of Melbourne. Including temperature validations of thermocyclers published in Kong et al. 2016 doi: 10.1111/2041-210X.12589
DOI: 10.26188/5d2b738b70951
title: Water relations of Warramaba virgo eggs

description: A series of experiments investigating the role of water in egg development of <i>Warramaba virgo </i>between 2015 - 2016<br>
DOI: 10.26188/5d3b9b0bbbc4d
title: scATAC-seq 5 cell lines

description: scATAC-seq of 5 lung cancer cell lines: A549, H838, HCC827, H1975, H2228. A follow up dataset of publication: https://www.nature.com/articles/s41592-019-0425-8. with scRNA-seq sequenced on the same batch using 10X v3 kit.
DOI: 10.26188/5d2b729194549
title: 2016 Warramaba data

description: Life history data and thermal response of egg development under constant and fluctuating temperatures for the 2016 cohort of Warramaba grasshoppers (6 species) from eastern and western Australia. Parental generation were collected summer 2015/2016. Experiments conducted 2016-2017.<br>
DOI: 10.26188/5d2b74e07f6e2
title: 2017 Warramaba data

description: A series of experiments conducted on the 2017 cohort of<i> Warramaba</i> grasshoppers, collected in summer 2016/2017. <br>