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published: 2024-02-08
Edmonds, Devin; Sam Edmonds, Samina (2024): Data for Compsophis infralineatus Predation Note. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8240276_V1
Photographs and video of the snake Compsophis infralineatus predating upon the chameleons Calumma crypticum and Calumma gastrotaenia near Mandraka, Madagascar.
keywords:
predation; reptile; diet
published: 2011-09-20
Swenson, M. Shel; Suri, Rahul; Linder, C. Randal; Warnow, Tandy; Nguyen, Nam-puhong; Mirarab, Siavash; Neves, Diogo Telmo; Sobral, João Luís; Pingali, Keshav; Nelesen, Serita; Liu, Kevin; Wang, Li-San (2011): Data for SuperFine, DACTAL, and BeeTLe. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2952208_V1
This page provides the data for SuperFine, DACTAL, and BeeTLe publications. - Swenson, M. Shel, et al. "SuperFine: fast and accurate supertree estimation." Systematic biology 61.2 (2012): 214. - Nguyen, Nam, Siavash Mirarab, and Tandy Warnow. "MRL and SuperFine+ MRL: new supertree methods." Algorithms for Molecular Biology 7 (2012): 1-13. - Neves, Diogo Telmo, et al. "Parallelizing superfine." Proceedings of the 27th Annual ACM Symposium on Applied Computing. 2012. - Nelesen, Serita, et al. "DACTAL: divide-and-conquer trees (almost) without alignments." Bioinformatics 28.12 (2012): i274-i282. - Liu, Kevin, and Tandy Warnow. "Treelength optimization for phylogeny estimation." PLoS One 7.3 (2012): e33104.
published: 2014-10-29
Nguyen, Nam-phuong; Mirarab, Siavash; Bo, Liu; Pop, Mihai; Warnow, Tandy (2014): Data for Taxonomic Identification and Phylogenetic Profiling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8783447_V1
This dataset provides the data for Nguyen, Nam-phuong, et al. "TIPP: taxonomic identification and phylogenetic profiling." Bioinformatics 30.24 (2014): 3548-3555.
published: 2012-07-01
Mirarab, Siavash; Ngyuen, Nam-Phuong; Warnow, Tandy (2012): Data for SEPP: SATé-Enabled Phylogenetic Placement.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9316702_V1
This dataset provides the data for Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. "SEPP: SATé-enabled phylogenetic placement." Biocomputing 2012. 2012. 247-258.
published: 2019-02-07
Nute, Michael; Yarlagadda, Karthik; Stumpf, Rebecca (2019): PICAN-PI Public Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1678505_V1
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
keywords:
microbiome; data visualization; graphics; phylogenetics; 16S
published: 2019-02-19
Imker, Heidi (2019): Funding and Operating Organizations for Long-Lived Molecular Biology Databases. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3993338_V1
The organizations that contribute to the longevity of 67 long-lived molecular biology databases published in Nucleic Acids Research (NAR) between 1991-2016 were identified to address two research questions 1) which organizations fund these databases? and 2) which organizations maintain these databases? Funders were determined by examining funding acknowledgements in each database's most recent NAR Database Issue update article published (prior to 2017) and organizations operating the databases were determine through review of database websites.
keywords:
databases; research infrastructure; sustainability; data sharing; molecular biology; bioinformatics; bibliometrics
published: 2019-02-22
Fernández, Roberto; Parker, Gary; Stark, Colin (2019): Experiments on patterns of alluvial cover and bedrock erosion in a meandering channel. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2-3044828_V1
This dataset includes measurements taken during the experiments on patterns of alluvial cover over bedrock. The dataset includes an hour worth of timelapse images taken every 10s for eight different experimental conditions. It also includes the instantaneous water surface elevations measured with eTapes at a frequency of 10Hz for each experiment. The 'Read me Data.txt' file explains in more detail the contents of the dataset.
keywords:
bedrock; erosion; alluvial; meandering; alluvial cover; sinuosity; flume; experiments; abrasion;
published: 2019-03-06
Makhnenko, Roman; Tarokh, Ali (2019): Experimental data on bulk and unjacketed moduli of porous rocks. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7478121_V2
This dataset is provided to support the statements in Tarokh, A., and R.Y. Makhnenko. 2019. Remarks on the solid and bulk responses of fluid-filled porous rock, Geophysics. The unjacketed bulk modulus is a poroelastic parameter that can be directly measured in a laboratory test under a loading that preserves the difference between the mean stress and pore pressure constant. For a monomineralic rock, the measurement of the unjacketed bulk modulus is ignored because it is assumed to be equal to the bulk modulus of the solid phase. To examine this assumption, we tested porous sandstones (Berea and Dunnville) and limestones (Apulian and Indiana) mainly composed of quartz and calcite, respectively, under the unjacketed condition. The presence of microscale inhomogeneities, in the form of non-connected (occluded) pores, was shown to cause a considerable difference between the unjacketed bulk modulus and the bulk modulus of the solid phase. Furthermore, we found the unjacketed bulk modulus to be independent of the unjacketed pressure and Terzaghi effective pressure and therefore a constant.
keywords:
Poroelasticity; anisotropic solid skeleton; unjacketed bulk modulus; non-connected porosity
published: 2019-03-13
Ando, Amy; Fraterrigo, Jennifer; Guntenspergen, Glenn; Howlader, Aparna; Mallory, Mindy; Olker, Jennifer; Stickley, Samuel (2019): Spatial Conservation and Investment Portfolios to Manage Climate-Related Risk. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2887291_V1
keywords:
climate change; conservation; diversification; environmental investments; MPT; porftfolio; risk; uncertainty
published: 2019-03-22
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1
This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)
keywords:
songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published: 2019-03-19
Fernandez, Roberto; Parker, Gary; Stark, Colin P. (2019): Meltwater Meandering Channels on Ice: Centerlines and Images. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4384362_V1
This dataset includes images and extracted centerlines from experiments looking at the formation and evolution of meltwater meandering channels on ice. The laboratory data includes centimeter- and millimeter-scale rivulets. Dataset also includes an image and corresponding centerlines from the Peterman Ice Island. All centerlines were manually digitized in Matlab but no distributable code was developed for the process. Once digitized, centerlines were smoothed and standardized following methods and routines developed by other authors (Zolezzi and Guneralp, 2016; Guneralp and Rhoads, 2008). Details about the preparation of the centerlines and processing with these methods is included in the dissertation by Fernández (2018) linked to this dataset. "Millimeter scale and Peterman Ice Island centerlines.pdf": This file includes the images of two mm-scale experimetns and the Peterman Ice Island image. Seventeen centerlines were digitized from the former and seven were digitized from the latter. Those centerlines are shown above the images themselves. "Centimeter scale rivulet images.pdf": This file includes images corresponding to all cm-scale centerlines used for the analysis presented in the dissertation by Fernandez (2018). Each image has a short caption indicating the run ID and the time at which it was captured. The images were used to extract centerlines to look at the planform evolution of cm-scale meltwater meandering rivulets on ice. Images include 26 centerlines from four different runs. "Meltwater meandering channel centerlines.xlsx": This spreadsheet contains the centerline data for all fifty centerlines. The workbook includes 51 sheets. The first 50 are related to each one of the channels. The mm scale and Peterman Ice Island ones are identified using the same IDs shown in "Millimeter scale and Peterman Ice Island centerlines.pdf". The cm-scale centerlines are identified by run ID and a number indicating the time in minutes (with t = 0 min being the time at which water started flowing over the ice block). The naming convention is also associated to the images in "Centimeter scale rivulet images.pdf". The last sheet in the workbook includes a summary of the channel widths measured from every image for each centerline. The 50 sheets with the centerline information have four columns each. The titles of the columns are X, Y, S, and C. X,Y are dimensionless coordinates of the centerline. S is dimensionless streamwise coordinate (location along the centerline). C is dimensionless curvature value. All these values were non-dimensionalized with the channel width. See Fernandez (2018), Zolezzi and Guneralp (2016), and Guneralp and Rhoads (2008) for more details regarding the process of smoothing, standardizing and non-dimensionalization of the centerline coordinates.
keywords:
Meltwater, Meandering, Ice, Supraglacial, Experiments
published: 2019-03-19
Molloy, Erin K.; Warnow, Tandy (2019): Data from: TreeMerge: A new method for improving the scalability of species tree estimation methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9570561_V1
This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-01
Balasubramanian, Srinidhi; Koloutsou-Vakakis, Sotiria; Rood, Mark (2019): Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4085385_V1
This dataset contains scripts and data developed as a part of the research manuscript titled “Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt”. This includes (1) Spatial and temporal factors for ammonia emissions from agricultural fertilizer usage developed using the hybrid ISS-DNDC method for the Midwest U.S., (2) CAMx job scripts and outputs of predictions of ambient ammonia and total and speciated PM2.5, (3) Observation data used to statistically evaluate CAMx predictions, and (4) MATLAB programs developed to pair CAMx predictions with ground-based observation data in space and time.
keywords:
Air quality; Ammonia; Emissions; PM2.5; CAMx; DNDC; spatial resolution; Midwest U.S.
published: 2019-05-16
Molloy, Erin K.; Warnow, Tandy (2019): Data from: Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0569467_V2
This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> • Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> • Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> • Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-10
Pradhan, Dikshant; Jensen, Paul (2019): Pradhan 2019 Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3352362_V1
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords:
Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-31
Krichels, Alexander (2019): Data for Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9733959_V1
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords:
denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-05-31
Hahn, Jim (2019): Frequent pattern subject transactions from the University of Illinois Library (2016 - 2018). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9440404_V1
The data are provided to illustrate methods in evaluating systematic transactional data reuse in machine learning. A library account-based recommender system was developed using machine learning processing over transactional data of 383,828 transactions (or check-outs) sourced from a large multi-unit research library. The machine learning process utilized the FP-growth algorithm over the subject metadata associated with physical items that were checked-out together in the library. The purpose of this research is to evaluate the results of systematic transactional data reuse in machine learning. The analysis herein contains a large-scale network visualization of 180,441 subject association rules and corresponding node metrics.
keywords:
evaluating machine learning; network science; FP-growth; WEKA; Gephi; personalization; recommender systems
published: 2019-06-03
Rando, Halie; Wadlington, William; Johnson, Jennifer; Stutchman, Jeremy; Trut, Lyudmila; Farré, Marta; Kukekova, Anna (2019): Red Fox (Vulpes vulpes) Y-Chromosome Sequence. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4447017_V1
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords:
Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-06-13
Rezapour, Rezvaneh; Diesner, Jana (2019): Expanded Morality Lexicon. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3805242_V1.1
This lexicon is the expanded/enhanced version of the Moral Foundation Dictionary created by Graham and colleagues (Graham et al., 2013). Our Enhanced Morality Lexicon (EML) contains a list of 4,636 morality related words. This lexicon was used in the following paper - please cite this paper if you use this resource in your work. Rezapour, R., Shah, S., & Diesner, J. (2019). Enhancing the measurement of social effects by capturing morality. Proceedings of the 10th Workshop on Computational Approaches to Subjectivity, Sentiment and Social Media Analysis (WASSA). Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), Minneapolis, MN. In addition, please consider citing the original MFD paper: <a href="https://doi.org/10.1016/B978-0-12-407236-7.00002-4">Graham, J., Haidt, J., Koleva, S., Motyl, M., Iyer, R., Wojcik, S. P., & Ditto, P. H. (2013). Moral foundations theory: The pragmatic validity of moral pluralism. In Advances in experimental social psychology (Vol. 47, pp. 55-130)</a>.
keywords:
lexicon; morality
published: 2019-06-22
MacDonald, Sean; Ward, Michael; Sperry, Jinelle (2019): Manipulating social information to promote frugivory by birds on a Hawaiian Island. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9223847_V1
keywords:
conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas
published: 2018-01-11
Pence, Justin; Mohaghegh, Zahra (2018): DT-BASE - Training Quality Causal Model. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3357538_V3
Dataset includes structure and values of a causal model for Training Quality in nuclear power plants. Each entry refers to a piece of evidence supporting causality of the Training Quality causal model. Includes bibliographic information, context-specific text from the reference, and three weighted values; (M1) credibility of reference, (2) causality determined by the author, and (3) analysts confidence level. (M1, M2, and M3) Weight metadata are based on probability language from <a href="https://www.ipcc.ch/ipccreports/tar/vol4/english/index.htm" style="text-decoration: none" >Intergovernmental Panel on Climate Change (IPCC), Climate Change 2001: Synthesis Report</a>. The language can be found in the “Summary for Policymakers” section, in the PDF format. Weight Metadata: LowerBound_Probability, UpperBound_Probability, Qualitative Language 0.99, 1, Virtually Certain 0.9, 0.99, Very Likely 0.66, 0.9, Likely 0.33, 0.66, Medium Likelihood 0.1, 0.33, Unlikely 0.01, 0.1, Very Unlikely 0, 0.01, Extremely Unlikely
keywords:
Data-Theoretic; Training; Organization; Probabilistic Risk Assessment; Training Quality; Causal Model; DT-BASE; Bayesian Belief Network; Bayesian Network; Theory-Building
published: 2018-01-03
Sweet, Andrew; Bush, Sarah; Gustafsson, Daniel; Allen, Julie; DiBlasi, Emily; Skeen, Heather; Weckstein, Jason; Johnson, Kevin (2018): Data from: host and parasite morphology influence congruence between host and parasite phylogenies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2011663_V1
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis. 1) Files from the MrBayes analyses: a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre c) a maximum clade credibility tree - mcc_tree_brueelia.tre The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication. 2) Files related to a BEAST analysis with COI data: a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre 3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre 4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
keywords:
bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
published: 2018-03-08
Imker, Heidi (2018): Molecular Biology Databases Published in Nucleic Acids Research between 1991-2016. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4311325_V1
This dataset was developed to create a census of sufficiently documented molecular biology databases to answer several preliminary research questions. Articles published in the annual Nucleic Acids Research (NAR) “Database Issues” were used to identify a population of databases for study. Namely, the questions addressed herein include: 1) what is the historical rate of database proliferation versus rate of database attrition?, 2) to what extent do citations indicate persistence?, and 3) are databases under active maintenance and does evidence of maintenance likewise correlate to citation? An overarching goal of this study is to provide the ability to identify subsets of databases for further analysis, both as presented within this study and through subsequent use of this openly released dataset.
keywords:
databases; research infrastructure; sustainability; data sharing; molecular biology; bioinformatics; bibliometrics
published: 2018-03-28
Hahn, James (2018): Bibliotelemetry data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2237685_V2
Bibliotelemetry data are provided in support of the evaluation of Internet of Things (IoT) middleware within library collections. IoT infrastructure within the physical library environment is the basis for an integrative, hybrid approach to digital resource recommenders. The IoT infrastructure provides mobile, dynamic wayfinding support for items in the collection, which includes features for location-based recommendations. A modular evaluation and analysis herein clarified the nature of users’ requests for recommendations based on their location, and describes subject areas of the library for which users request recommendations. The modular mobile design allowed for deep exploration of bibliographic identifiers as they appeared throughout the global module system, serving to provide context to the searching and browsing data that are the focus of this study.
keywords:
internet of things; IoT; academic libraries; bibliographic classification
published: 2018-04-06
Collins, Kodi; Warnow, Tandy (2018): PASTA For Proteins Data (BALiBASE). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4074787_V1
keywords:
protein; multiple sequence alignment; balibase