Find research datasets worth reusing

opencc-zeroNov 2024View details →

UOC Data Science M2.851.PR1 data set

Dataset for testing Film Affinity Top Movies 2024

opencc-by-4.0Mar 2024View details →

vScreenML v2.0 training set

New training set of vScreenML 2.0 that contains minimized protein structures in complex with active and decoys structures, as well as corresponding new calculated features.

opencc-zeroDec 2013View details →

Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)

Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compare interspecific variation between ptSSRs and nucleotide sequences of ycf1 then test intraspecific variation for ptSSRs using 911 samples in the P. ponderosa species complex. Results: The ptSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The ptSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for ptSSR loci in a plastome alignment for the target group.

opencc-zeroDec 2017View details →

Data from: Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets

The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets. Our study (which used more than 230 CPU years for the BAli-Phy analyses alone) shows that BAli-Phy has better precision and recall (with respect to the true alignments) than the other alignment methods on the simulated data sets, but has consistently lower recall on the biological benchmarks (with respect to the reference alignments) than many of the other methods. In other words, we find that BAli-Phy systematically under-aligns when operating on biological sequence data, but shows no sign of this on simulated data. There are several potential causes for this change in performance, including model misspecification, errors in the reference alignments, and conflicts between structural alignment and evolutionary alignments, and future research is needed to determine the most likely explanation. We conclude with a discussion of the potential ramifications for each of these possibilities.

opencc-zeroAug 2019View details →

Data from: Testing the benefits of conservation set-asides for improved habitat connectivity in tropical agricultural landscapes

1. Habitat connectivity is important for tropical biodiversity conservation. Expansion of commodity crops, such as oil palm, fragments natural habitat areas, and strategies are needed to improve habitat connectivity in agricultural landscapes. The Roundtable on Sustainable Palm Oil (RSPO) voluntary certification system requires that growers identify and conserve forest patches identified as High Conservation Value Areas (HCVAs) before oil palm plantations can be certified as sustainable. We assessed the potential benefits of these conservation set-asides for forest connectivity. 2. We mapped HCVAs and quantified their forest cover in 2015. To assess their contribution to forest connectivity, we modelled range expansion of forest-dependent populations with five dispersal abilities spanning those representative of poor dispersers (e.g., flightless insects) to more mobile species (e.g., large birds or bats) across 70 plantation landscapes in Borneo. 3. Because only 21% of HCVA area was forested in 2015, these conservation set-asides currently provide few connectivity benefits. Compared to a scenario where HCVAs contain no forest (i.e., a no-RSPO scenario), current HCVAs improved connectivity by ~3% across all dispersal abilities. However, if HCVAs were fully reforested, then overall landscape connectivity could improve by ~16%. Reforestation of HCVAs had the greatest benefit for poor to intermediate dispersers (0.5-3 km per generation), generating landscapes that were up to 2.7 times better connected than landscapes without HCVAs. By contrast, connectivity benefits of HCVAs were low for highly mobile populations under current and reforestation scenarios, because range expansion of these populations was generally successful regardless of the amount of forest cover. 4.Synthesis and applications. The RSPO requires that HCVAs be set aside to conserve biodiversity, but HCVAs currently provide few connectivity benefits because they contain relatively little forest. However, reforested HCVAs have the potential to improve landscape connectivity for some forest species (e.g., winged insects), and we recommend active management by plantation companies to improve forest quality of degraded HCVAs (e.g., by enrichment planting). Future revisions to the RSPO's Principles and Criteria (P&C) should also ensure that large (i.e., with a core area >2 km2) HCVAs are reconnected to continuous tracts of forest to maximise their connectivity benefits.

opencc-by-4.0Jun 2021View details →

Bait sets for Atlantic salmon, Atlantic cod and Tiger shark

Bait sets for Atlantic salmon, Atlantic cod and Tiger Shark, in FASTA file format. Each line string starting with ">" corresponds to the name of the contig/chromosome/linkage group where the bait sequence is designed from, followed by the base pairs where the bait sequence starts and ends. For salmon/cod, we include 20 extra sequences for the Random regions.

opencc-by-4.0Jun 2021View details →

Model settings and surface measurements for air quality study

<ol> <li>Source code, run directories and initial condition for GEOS-Chem model simulations.</li> <li>Surface O3, NO2 and PM2.5 measurements in China in 2014-2019</li> </ol>

opencc-zeroDec 2017View details →

Data from: Selective sets of mRNAs localize to extracellular paramural bodies in the rice glup6 mutant line

The transport of rice glutelin storage proteins to the storage vacuoles requires Rab5 and its cognate guanine nucleotide exchange factor (Rab5-GEF). Loss of function of these membrane vesicular trafficking factors results in the initial secretion of storage proteins and later their partial engulfment by the plasma membrane to form an extracellular paramural body (PMB); an aborted endosome complex. Here we show that in the Rab5-GEF mutant glup6 line, glutelin RNAs are specifically mis-localized from their normal location on the cisternal-ER to the protein body-ER and also apparently translocated to the PMBs. We substantiated the association of mRNAs with this aborted endosome complex by RNA-seq of PMBs purified by flow cytometry. Two PMB-associated RNA groups are readily resolved: those that are specifically enriched in this aborted complex and those that are highly expressed in the cytoplasm. Examination of the PMB-enriched RNAs indicates that they were not a random sampling of the glup6 transcriptome but, instead, encompassed only a few functional mRNA classes. Although specific autophagy is also an alternative mechanism, these studies support the view that RNA localization may co-opt membrane vesicular trafficking and that many RNAs, which share function or intracellular location, are co-transported in developing rice seeds.

opennotspecifiedJul 2005View details →

FIGURE 3. Discriminant analysis. Data set included 140 in Morphometric analysis to differentiate taxonomically seven species of Eleutherodactylus (Amphibia: Anura: Leptodactylidae) from an Andean cloud forest of Colombia

FIGURE 3. Discriminant analysis. Data set included 140 of four species (Eleutherodactylus douglasi, E. merostictus, E. miyatai and E. prolixodiscus) and 11 quantitative variables. The model utilized stepwise discrimination in which all variables were included in the model and then, at each step, the variable that contributed least to the prediction of group memberships was eliminated.

opencc-by-4.0Jun 2021View details →

Assemblies of the CAMI 2 challenge data sets

Assembly submissions, including participants' submissions, of the CAMI 2 challenge data sets. The gold standards can be found either on the CAMI 2 challenge website: <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a> or in publisso alongside the data sets: https://repository.publisso.de/resource/frl:6425521 Also see <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a>

openepl-2.0Jul 2021View details →

Architectural Uncertainty Analysis for Access Control Scenarios in Industry 4.0 - Data Set

This data set contains additional information to the master's thesis of Nicolas Boltz. Included are the implementation, tests, and model instances of sample scenarios.

opencc-by-4.0Mar 2021View details →

Data set for phase-field studies of crystal growth in single-seal syntaxial veins in limestone

The numerical data in this repository consists of the simulation data of single-seal syntaxial calcite vein formation in limestone. The simulations were performed using  the software package named "Pace3D (v. 2.5.1)". The data is organized, the way it appears in the figures in the manuscript and the folders are named accordingly. <ul> <li>The simulation data shows intermediate growth stages and was converted from Pace3D output data format to VTK data format. The VTK files can be visualized using open source software packages like Paraview. The data files in each subfolder are also compressed (file format *.gz). For visualization the data has to be decompressed (e.g. with gzip, 7zip).</li> </ul>

CASINO V2 data sets

Raw data (*.dat format, basically text file) files directly exported from simulations of CASINO V2.

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

Data set for 'Remote control of neural function by X-ray-induced scintillation'

Data set for: Matsubara T, Yanagida T, Kawaguchi N, Nakano T, Yoshimoto J, Sezaki M, Takizawa H, Tsunoda SP, Horigane S, Ueda S, Takemoto-Kimura S, Kandori H, Yamanaka A, Yamashita T (2021) Remote control of neural function by X-ray-induced scintillation. Nature Communications 12: 4478, doi 10.1038/s41467-021-24717-1 There are 2 files in this upload: 1. The file named "Matsubara_data.zip" (~18 GB) is a zipped version of a folder "Dataset" (~27 GB), which contains images, movies, and other data analyzed in the study. When unzipped, the folder contains subfolders categorized based on experiment types.  A 'read me' text file is associated with each small dataset. 2. The file named "Matsubara_published.zip" (~5 MB) contains the Open Access pdf of the paper, the Supplementary Information file, and the Source Data file.

opencc-zeroApr 2022View details →

Malinae481 exonic probe set

The subtribe Malinae (Rosaceae) comprises close to 1,000 species and up to 30 genera. It is defined, among other characters, by a derived base chromosome number of x = 17. A parsimonious pattern of chromosome breakage and fusion explains the derivation of the x = 17 karyotype from a polyploidisation event of two x = 9 genomes. High collinearity between the genetic and physical maps of Pyrus and Malus as well as their identical karyotypes suggest that the reorganization of the Malinae genome occurred before the divergence of the two genera, and presumably before speciation of the whole subtribe. The preservation of extensive duplicated chromosomal segments in the genome of members of the Malinae, dating back to the genome-wide duplication, necessitates an assessment of the homology of markers used in phylogenetic studies. First, we identified single-copy orthologs and relatively recently diverged paralogs in the genome of Malus domestica. Average sequence divergence among orthologs was 3.65% in a genome-wide comparison of Malus and Pyrus, which is about one third of the average sequence divergence of 9.36% between Maleae and Amygdaleae orthologs and around half of the divergence based on fourfold degenerate site transversion of 8% between paralogs from the most recent WGD within each of these genomes. Based on this information, we developed a strategy to identify in the Malus genome (1) single-copy loci (presumably located within non-duplicated regions, or hidden paralogs due to differential gene loss) and (2) loci only duplicated once (one paralog only present in the genome; avoidance of multi-gene families). We further constrained our locus selection by imposing the minimum divergence between them to 6% as minimum sequence divergence between orthologs and paralogs. Specifically, we blasted 28,695 mRNAs (queries thereafter) in the range of 800–3,000 bp from the Malus domestica 'Golden Delicious' (GDDH13) genome v.1.1, downloaded from the Genome Database for Rosaceae, against the Malus domestica GDDH13 genome v.1.1 (subject thereafter) using the nucleotide BLAST search. Default settings were used except for the e-value, which was lowered to 0.00001. In an initial filtering step, we only kept the hits exceeding 70 bp and 10% of query length with ≥80% sequence similarity between query and subject. We then assigned the hits (usually corresponding to exons) to loci based on the criterion that the length of introns separating the hits does not exceed 10,000 bp. Queries that showed hits with >6 loci were not taken into account. In a second, refined filtering step we only kept loci that fulfilled the following criteria: length cover and sequence similarity of the sum of all hits for a particular locus ≥90%, length of single hits ≥100 bp (in accordance with the bait length of 100 bp), intron length ≤1,200 bp, number of loci per query ≤2, sequence divergence among loci ≥6%. We then blasted the 1,280 Malus queries that fulfilled our selection criteria against the Pyrus communis Bartlett DH genome v.2.0 and applied the same selection criteria. 616 of these queries fulfilled them. Subject sequences from the Malus (799) and Pyrus (764) genomes, matching chosen mRNAs and representing full loci, were then extracted and exon-intron boundaries inferred based on the alignments together with the blasted queries. After filtering for identical numbers of loci in both genomes, sequence divergence between exons of single-copy loci in Malus and Pyrus ≤15% and exon length ≥80 bp, we ended up with 713 loci (481 loci if pairs of paralogous loci are treated as single loci), which corresponded to the 546 mRNAs. Extracted sequences were collapsed at ≥95% similarity and used for bait design. The final exonic probe set covers 2,008,479 bp in total. This way, we expect to get baits with good correspondence to the Malinae genomes, i.e. both orthologs and paralogs are targeted.

Data and code for "Characterizing mid-circuit measurements on a superconducting qubit using gate set tomography" v1.0.2

This is the supplemental code and data for arXiv:2103.03008 "Characterizing mid-circuit measurements on a superconducting qubit using gate set tomography".

opencc-by-4.0Aug 2021View details →

Test data set for Aquaria

Data sets for testing zenodo in Aquaria.

opencc-by-4.0Aug 2021View details →

Data Set S1. Microplastic properties and Data Set S2. Sediment grain size

The data for microplastic properties (including abundance, shape, colour, polymer type and size) and sediment grain size (including the grain size and the content of clay, silt and sand) in Core CCYY1.