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1,307 results for “libraries”
Towards a DNA barcode library for Madagascar's threatened ichthyofauna
<p>Supplementary documents, trees and curated DNA barcode library dataset for freshwater and marine fishes from Madagascar, in XLSX, tab-delimited and Fasta formats.</p>
Supplemental files to "A COI DNA Barcode Library for Anastrepha Schiner (Diptera: Tephritidae)"
<p>The attached files are the supplemental material from Moore et al., "A COI DNA Barcode Library for <em>Anastrepha </em>Schiner (Diptera: Tephritidae)". They contain various DNA sequence alignments, calculation tables, tree files, taxonomic information on <em>Anastrepha</em>, and a R script.</p>
Bacteria and archaea of the Columbia and Willamette Rivers, 16S rRNA gene amplicon library metadata
<p>Bacterial and archaeal communities in the Columbia and Willamette Rivers in the Portland, OR, USA, region were characterized by 16S rRNA gene amplicon sequencing as part of the Lewis & Clark College spring 2022 Microbial Ecology course. Whole-water (>0.2 µm) samples were collected from: the Willamette River; the Columbia River above the confluence with the Willamette; and the Columbia River just downstream of the confluence with the Willamette.</p> <p>This dataset provides additional metadata to supplement the DNA sequences archived with the NCBI SRA at <a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA865380">https://www.ncbi.nlm.nih.gov/sra/PRJNA865380</a></p>
Books in a bubble : assessing the OAPEN Library collection
<p>Open access infrastructure for books is becoming more mature, and it is being used by an increasing number of people. The growing importance of open access infrastructure leads to more interest in sustainability, governance and impact assessment. For this paper, we will assess the OAPEN Library. In the spring of 2022, it passed the milestone of 20,000 titles. This was a good moment to evaluate the core asset of the OAPEN Library: its collection.</p> <p>How well meets the collection the needs of its users? The OAPEN Library sees global usage; the collection reflects this by offering titles in over 50 languages. The collection is not focused on a specific subject area, but the choice of medium – books and chapters, not journals and articles – is more strongly associated with the humanities and social sciences. It does not track its users, but the supporters of the OAPEN Libraries are globally distributed academic institutions, scientific and scholarly funders and publishers. An assessment of the OAPEN Library should therefore take into account the diversity of languages, subjects and users.</p>
CZI (Carl Zeiss Image) dataset with artificial test camera images with various dimension for testing libraries reading
<p>Set of CZI test images created by using a simulated microscope with a test grayscale camera (no LSM or AiryScan or RGB). The filename indicates the used dimension(s) for the acquisition experiment. The files can be used to test the basic functionality of libraries reading CZI files.</p> <p>Examples:</p> <ul> <li>S=2_T=3_CH=1.czi = 2 Scenes, 3 TimePoints and 1 Channel <ul> <li>Z-Stack <strong>was not</strong> activated inside acquisition experiment</li> </ul> </li> <li>S=2_T=3_Z=5_CH=2.czi = 2 Scenes, 3 TimePoints, 5-Z-Planes and 1 Channels <ul> <li>Z-Stack <strong>was </strong>activated inside acquisition experiment</li> </ul> </li> </ul> <p>The test files (so far) contain not any data with more "advanced" dimensions like AiryScan rawdata, illumination angles etc. Also no CZI files with pixel type RGB are included yet.</p> <p> </p> <p> </p> <p> </p>
Library of multivariate time series
<p>A database of many different types of multivariate time series, each with between 5-25 processes and between 100-2500 observations.</p> <p>The database contains a serialized Python dictionary of 1053 datasets, where the key for the dictionary is the dataset name, and each value is another dictionary of: "data", an MxT numpy array of processes-by-observations; and "labels", a list of descriptive labels for the dataset.</p>
Asynchronous Workload Balancing through Persistent Work-Stealing and Offloading for a Distributed Actor Model Library
<p>With dynamic imbalances caused by both software and ever more complex hardware, applications and runtime systems must adapt to dynamic load imbalances. We present a diffusion-based, reactive, fully asynchronous, and decentralized dynamic load balancer for a distributed actor library. With the asynchronous execution model, features such as remote procedure calls, and support for serialization of arbitrary types, UPC++ is especially feasible for the implementation of the actor model. While providing a substantial speedup for small- to medium-sized jobs with both predictable and unpredictable workload imbalances, the scalability of the diffusion-based approaches remains below expectations in most presented test cases.</p> <p>Actor-UPCXX is a high-performance computing library based on the actor model to enable the use of the actor model for HPC simulations. The source code can be found at: https://github.com/TUM-I5/Actor-UPCXX</p>
FIG. 4 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 4. — Some examples of endemic earthworm species sampled in Corsica and their habitats (to their right): A, Scherotheca portonana L4 Qiu & Bouché, 1998; B, alpine pasture at Col de Vergio (Bouché#466); C, Scherotheca albomaculata Qiu & Bouché, 1998; D, open Mediterranean chaparral at Sainte-Lucie de PortoVecchio (Bouché#414); E, Eumenescolex emiliae L1 Qiu & Bouché, 1998; F, Pinus laricio L. forest at Zonza (Bouché#2932); G, Hormogaster insularis Bouché, 1970; H, Quercus suber L. open wood at Volpajola (Bouché#480). Scale bars: 5 cm.
FIG. 2 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 2. — Bayesian inference of the phylogenetic relationships of earthworms from Corsica based on their COI sequences. Species-level genetic lineages (as delimited by ASAP, barcode gap analysis and morphological data) are shown as black triangles in order to facilitate visualization and to display the amount of intra-lineage genetic divergence (indicated by the height of the triangle). Green circles: posterior probability values over 90; all the species-level clades showed values close to 100.
FIG. 1 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 1. — Distribution map of the sampling localities in Corsica Island. Locality codes refer to Table 1. Map base: Qgis.
FIG. 5 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 5. — Observed and estimated species diversity of earthworms in the island of Corsica: A, incidence-based rarefaction and extrapolation curves of species numbers;B, Chao asymptotic estimator of species numbers. The figure compares the results obtained when considering all species-level lineages obtained with DNA barcodes (All), when considering non-cryptic lineages only (NC) and when considering all endemic lineages (End). Solid lines represent rarefaction curves, whereas dashed lines represent extrapolation curves; shaded areas are 95% and error bars confidence intervals based on a bootstrap with 200 replications.
FIG. 3 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 3. — Graphical representation of the number of earthworm species known from Corsica. Rectangle surfaces are proportional to species numbers.
Figure 3 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 3. Mounted specimens illustrating the species of Microgastrinae recovered in this study. A, Cotesia glabrata Telenga ex Carcharodus alceae, Italy. Adult plus cocoons. Gregarious parasitoid; brood sizes vary considerably, host usually well grown or prepupal when killed. The other Cotesia species (near glabrata) look similar and behave in the same way. B, Dolichogenidea sp. near sicaria Marshall, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, killing the host while still quite young. C, Microgaster australis Thomson, ex Muschampia stauderi, Greece. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. D, Microgaster nobilis Reinhard, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. All specimens are in the collection of the National Museums of Scotland.
Figure 4 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 4. Interaction matrices showing the recorded interactions of Hesperiidae and their hostplants (A), Hesperiidae and their parasitoids (B) and parasitoids and hostplants of Hesperiidae (C). White squares indicate recorded interactions between the taxa in the corresponding row and column, while blue squares indicate lack of interaction.
Figure 2 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 2. Circular cladogram showing ecological interactions among European and North African Hesperiidae, their hostplants, and their microgastrine parasitoids, recovered through DNA barcoding for Hesperiidae and/or parasitoids. Hesperiid, parasitoid and plant cladograms are coloured in orange, blue and green, respectively. Lines representing interactions with parasitoids are coloured in blue, while lines involving hostplant interactions are coloured in green.
Figure 1 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 1. Representation of the study system. Hesperiid larvae feeding on their hostplants can be attacked by a number of parasitoids, which can in turn be attacked by various hyperparasitoids. A, Spialia rosae on its hostplant Rosa sicula. B, third instar larva of Sp. rosae on a silk shelter. C, Microgaster australis parasitizing an L3 Sp. rosae larva. D, Gelis sp. parasitizing M. australis on its cocoon after emerging from the Sp. rosae larva. Drawings by Martí Franch.
Composition and electrical resistance results of a Ir-Pd-Pt-Rh-Ru composition spread thin film materials library
<p>The dataset contains the results of electrical resistance measurement and composition analysis of a thin film composition spread materials library. </p> <p>342 measurement areas were evaluated for chemical composition using energy dispersive X-ray spectroscopy and electrical resistance using a 4-point probe.</p> <p>CSV columns:</p> <p>x: x-coordinate of materials library in µm</p> <p>y: y-coordinate of materials library in µm</p> <p>Ir: relative chemical composition in at.%</p> <p>Pd: relative chemical composition in at.%</p> <p>Pt: relative chemical composition in at.%</p> <p>Rh: relative chemical composition in at.%</p> <p>Ru: relative chemical composition in at.%</p> <p>Resistance: electrical resistance in Ohm</p> <p> </p> <p>This dataset is supplementary information for an associated publication. A link to the publication will be provided after publishing.</p>
PanDDA analysis of PTP1B screened against fragment libraries
<p>Tyrosine phosphatase, PTP1B, screened against multiple fragment libraries via X-ray crystallography.</p>
Georgetown Outbreak Activity Library (GOAL) dataset
<p>The Georgetown Outbreak Activity Library (GOAL) dataset is a research effort led by Dr. Rebecca Katz at the Georgetown University Center for Global Health Science and Security. The data is designed to support responders in understanding what needs to get done, by whom, and when in the context of an event, providing information on existing guidance and authorities and to define response requirements for new and emerging events. GOAL can also be used for preparedness and planning efforts to ensure that this work is comprehensive and based in the practical realities of outbreak response.</p> <p>The GOAL dataset is available as an Excel file (.xlsx) which includes data coded about response activities needed throughout all phases of an outbreak, with case studies available to exemplify these activities during preparedness, response, and recovery efforts. The GOAL dataset contains a comprehensive set of fields describing what needs to be done for each response activity, when, by whom, and under what circumstances. A Data Dictionary and Glossary are included in the Excel file download.</p> <p>In addition to the coded data, the GOAL Case Study PDF Files (.zip) folder contains the original case studies written by Georgetown researchers which exemplify many of the activities described in the GOAL dataset. </p> <p>To learn more about the project and interact with the data, visit <a href="https://outbreaklibrary.org/">https://outbreaklibrary.org/.</a> The complex data contained within the GOAL dataset have also been translated for a public audience into <em>The Outbreak Atlas, </em>a book by Rebecca Katz and Mackenzie S. Moore. </p>
SurrogateLIB: An extendable library of mixed-integer programs with embedded machine learning predictors
<p>We constructed a set of Mixed-Integer Programming (MIP) instances with embedded Machine Learning (ML) predictors. The generators for these instances are available at: <a href="https://github.com/Opt-Mucca/PySCIPOpt-ML">https://github.com/Opt-Mucca/PySCIPOpt-ML</a>. The full paper which introduces SurrogateLIB and the larger Python framework PySCIPOpt-ML is available at: <a href="https://arxiv.org/abs/2312.08074">https://arxiv.org/abs/2312.08074</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.