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1,773 results for “package”
Frictionless Tabular data package for GC-MS data from Rose Genome article published in Nature genetics, June, 2018
<p>This dataset, in the form of a Frictionless Tabular Data Package (https://frictionlessdata.io/specs/tabular-data-package/), holds the measurements of 61 known metabolites (all annotated with resolvable CHEBI identifiers and InChi), measured by gas chromatography mass-spectrometry (GC-MS) in 6 different Rose cultivars (all annotated with resolvable NCBITaxId) and 3 organism parts (all annotated with resolvable Plant Ontology identifiers). The data was extracted from a supplementary material table, available from https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip and published alongside the Nature Genetics manuscript identified by the following doi: https://doi.org/10.1038/s41588-018-0110-3, published in June 2018. This dataset is used to demonstrate how to make data Findeable, Accessible, Discoverable and Interoperable(FAIR) and how Tabular Data Package representations can be easily mobilized for re-analysis and data science. It is associated to the following project available from github at: https://github.com/proccaserra/rose2018ng-notebook with all necessary information and Jupyter notebooks.</p>
S48 | CPPDBLISTA | Database of Chemicals likely (List A) associated with Plastic Packaging (CPPdb)
<p>This is the collection associated with list S48 CPPDBLISTA on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>S48 | CPPDBLISTA | <strong>Database of Chemicals associated with Plastic Packaging (CPPdb)</strong></p> <p>CPPdb Original File (List A and B) <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListA_ListB_181009_ZenodoV1.xlsx">XLSX</a> (06/03/2019)<br> Mapped Files (06/03/2019):<br> Table 2 from Groh et al as <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/Table2_Groh_etal_stoten_mapped.xlsx">XLSX</a>, <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/Table2_Groh_etal_stoten_mapped.csv">CSV</a> <br> CPPdb List A <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListA_Mapped_06032019.xlsx">XLSX</a>, <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListA_Mapped_06032019.csv">CSV</a> <br> CPPdb List B <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListB_Mapped_06032019.xlsx">XLSX</a>, <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListB_Mapped_06032019.csv">CSV</a></p> <p>Table 2 Groh et al. <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/Table2_Groh_etal_InChIKeys.txt">InChIKeys</a><br> CPPdb List A <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListA_InChIKeys.txt">InChIKeys</a><br> CPPdb List B <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/220319Update/CPPdb_ListB_InChIKeys.txt">InChIKeys</a><br> (all 06/03/2019)</p> <p>A database of chemicals likely (List A, 903) and possibly (List B, 3353 - in another upload) associated with plastic packaging, with hazard data, from Groh et al 2019 DOI: <a href="https://doi.org/10.1016/j.scitotenv.2018.10.015">10.1016/j.scitotenv.2018.10.015</a>. Mapped to structures by CAS/Name by K. Groh & E. Schymanski.</p> <p>Latest version of original data (last update Oct 2018): DOI: <a href="http://doi.org/10.5281/zenodo.1287773">10.5281/zenodo.1287773</a></p> <p> </p>
metapsyData: R Package to Access the Metapsy Databases
<p>The <code>metapsyData</code> package allows to access the Metapsy meta-analytic psychotherapy databases direct in your <code>R</code> environment. Once installed, simply run the <code>data</code> function (e.g. <code>data(DepPsychDB)</code>) to save the data locally. The documentation of the package is also hosted by <a href="https://rdrr.io/github/metapsy-project/metapsyData/">rdrr.io</a>.</p> <p>The interactive Metapsy web application (<a href="https://www.metapsy.org/">metapsy.org</a>) uses <code>metapsyData</code> in the background. You can open the Metapsy website in <code>R</code> by running <code>open_app()</code>.</p> <p>The raw data files can be accessed in the associated GitHub repository under <code>data</code>. To search for available databases in <code>metapsyData</code>, type in <code>metapsyData::</code> in your RStudio console.</p>
Example data set for the R package riversCentralAsia
<p>This data set contains example data for demonstrating the functionality of the R package riversCentralAsia. riversCentralAsia (https://github.com/hydrosolutions/riversCentralAsia) includes several functions for pre-processing hydrological data to facilitate hydrological modelling with RS MINERVE (https://crealp.github.io/rsminerve-releases/). The package is used extensively in the open-source teaching course Modeling of Hydrological Systems in Semi-Arid Central Asia (https://hydrosolutions.github.io/caham_book/). </p>
Replication package for "Motivation in the Dynamics of European Youth Migration"
<p>Replication package for the paper "Motivation in the Dynamics of European Youth Migration". The package contains the data and the SPSS and Stata code for the the analyses presented in the paper. The original data from which the variables are extracted was collected within the EU Horizon 2020 project YMOBILITY (2015-2018).</p>
IISD Experimental Lakes Area: Bathymetry Data Package, 1968-2025
The IISD Experimental Lakes Area (IISD-ELA) bathymetry data package provides bathymetric data on IISD-ELA lakes in a variety of formats and degrees of processing. The data package has been organized into four parts: tabular, geospatial, maps, and additional metadata. Tabular data include cumulative and interval values for area and volume at specific depth ranges, summary statistics (perimeter, surface area, total volume, mean depth, and maximum depth), and metadata for the lakes (such as water level on date of survey and methods used to collect and process the data). Geospatial data are suitable for map-making and geospatial analysis. The geospatial folder includes raw coordinate data (CSV) and processed geospatial outputs: contour lines (geodatabase and geopackage), lake polygons (geodatabase and geopackage), and raster DEMs (geodatabase and TIFF). Maps are provided in PDF format in black and white or colour. Where current maps are not available, historical maps have been provided, which are black and white scans. Additional metadata files include the Info Sheet PDF, which provides details for interpreting column names and understanding surveying and processing methods. A materials overview CSV table is provided, outlining which data types are available for each lake. A lake polygon metadata CSV table specifies which satellite imagery providers and dates were used to refine lake polygon outlines. The data package is ongoing - updated data will be provided as more lakes are surveyed and data processed. If current data do not exist for the lake you are interested in, please get in touch with us - we may be able to add a survey of that lake to our bathymetry survey schedule.
Sherbo et al. 2023 Data Package. Data associated with study assessing effects of dissolved organic matter on phytoplankton productivity in boreal lakes. The majority of data was collected in 2018 at the IISD Experimental Lakes Area in Northwestern Ontario
Allochthonous dissolved organic matter (DOM) structures many physical, chemical, and biological properties of lakes, including key variables that control productivity at the base of freshwater food webs. We examined phytoplankton biomass and productivity and their drivers, across eight pristine boreal lakes with DOM ranging from 3.5 to 9.5 mg DOC L-1. Increases in DOM were associated with significant increases in epilimnetic nitrogen, phosphorus and chlorophyll a (Chl a) concentrations suggesting that nutrients associated with DOM stimulate phytoplankton biomass and productivity. Such results were misleading; there was no significant relationship between Chl a and phytoplankton biomass measured via microscopy, and results did not incorporate the effects of DOM on thermocline and euphotic depth. Chl a:biomass and Chl a: carbon ratios indicated that increases in Chl a with DOM were driven by photo-acclimation to declining light availability. Increases. Further, increases in DOM led to large declines in thermocline (~50 %) and euphotic (~75 %) depths, and depth-integrated phytoplankton biomass and primary production (~70 %).
Oregon Prioritization package for expanding the Motus network in the Pacific Flyway
Addressing survival and movement of priority migratory avian species of concern along the Pacific Flyway is paramount for their conservation. Yet, the migratory life stage is understudied in many avian species. The Motus radiotelemetry receiver network is an established system for tracking survival and movement of avian species. This network is an international collaborative that successfully identifies stopover site duration, connected migratory routes, post-fledging dispersal and survival, and adult survival and fidelity on a landscape-scale; parameters that cannot be easily estimated using non-tagged birds. While the Motus network is highly connected in eastern North America, the western part of the continent is lagging in coverage and connectivity, limiting the ability to obtain sample sizes large enough to robustly model demographic parameters from tagged birds. Thus, the expansion of the Motus network is a high priority for Pacific Flyway State Agencies. To date, no method exists for determining priority locations for new Motus receiving stations. With collaborations from States and the Canadian Province of British Columbia, we used eBird citizen scientist data to prioritize strategic locations for new Motus receiving stations throughout the Pacific Flyway. We model priority species’ co-occupancy of varying abundance states (i.e., absent, present, abundant, abundant in multiple weeks) with spatially varying Landsat (red and near infrared), water, land cover types, and weather covariates while accounting for variable detection with temporally varying survey effort covariates. Using occupancy model predictions, we identify high-use areas of the Pacific Flyway for establishing new Motus receiving towers that have high probabilities of intercepting high presence and /or abundance of multiple species of interest in a series of predictive occupancy maps. This package contains all data used to model high occurrence of multiple priority species as well as predictive m
Measuring Software Testability Modulo Test Quality - Replication Package
<p>This repository represents the replication package for the paper <em>Measuring Software Testability Modulo Test Quality</em>.</p> <p>It includes the dataset and the Jupyter Notebook we used for the analysis in our paper.</p>
Replication package of "Good Things Come In Threes: Improving Search-based Crash Reproduction With Helper Objectives"
<p>The replication package for the study about using new helper objectives (MOHO) for crash reproduction. This study has been accepted at ASE 2020.</p> <p> </p> <p>Abstract:</p> <p>Evolutionary intelligence approaches have been successfully applied to assist developers during debugging by generating a test case reproducing reported crashes. These approaches use a single fitness function called <em>Crash Distance</em> to guide the search process toward reproducing a target crash. Despite the reported achievements, these approaches do not always successfully reproduce some crashes due to a lack of test diversity (premature convergence). In this study, we introduce a new approach, called <em>MO-HO</em>, that addresses this issue via multi-objectivization. In particular, we introduce two new Helper-Objectives for crash reproduction, namely <em>test length</em> (to minimize) and <em>method sequence diversity</em> (to maximize), in addition to <em>Crash Distance</em>.</p> <p>We assessed <em>MO-HO</em> using five multi-objective evolutionary algorithms (NSGA-II, SPEA2, PESA-II, MOEA/D, FEMO) on 124 hard-to-reproduce crashes stemming from open-source projects. Our results indicate that SPEA2 is the best-performing multi-objective algorithm for <em>MO-HO</em>.</p> <p>We evaluated this best-performing algorithm for <em>MO-HO</em> against the state-of-the-art: single-objective approach (Single-Objective Search) and decomposition-based multi-objectivization approach (<em>De-MO</em>). Our results show that <em>MO-HO</em> reproduces five crashes that cannot be reproduced by the current state-of-the-art. Besides, <em>MO-HO</em> improves the effectiveness (+10% and +8% in reproduction ratio) and the efficiency in 34.6% and 36% of crashes (i.e., significantly lower running time) compared to Single-Objective Search and <em>De-MO</em>, respectively. For some crashes, the improvements are very large, being up to +93.3% for reproduction ratio and -92% for the required running time. </p>
UWB-IODA project, Work package 1: IR-UWB optimized pulses
<p>The data files contain optimized UWB waveforms using B-spline functions. The spectral efficiency of each waveform is maximized under the constraint of the spectral mask defined by the FCC/ECC regulation authorities.</p>
The Daily Life of Software Engineers during the COVID-19 Pandemic -- Replication Package
<p>Following the onset of the COVID-19 pandemic and subsequent lockdowns, software engineers' daily life was disrupted and abruptly forced into remote working from home. This change deeply impacted typical working routines, affecting both well-being and productivity. Moreover, this pandemic will have long-lasting effects in the software industry, with several tech companies allowing their employees to work from home indefinitely if they wish to do so. Therefore, it is crucial to analyze and understand how a typical working day looks like when working from home and how individual activities affect software developers' well-being and productivity. We performed a two-wave longitudinal study involving almost 200 globally carefully selected software professionals, inferring daily activities with perceived well-being, productivity, and other relevant psychological and social variables. Results suggest that the time software engineers spent doing specific activities from home was similar when working in the office. (e.g., coding > emails > code review > networking). However, we also found some meaningful mean differences. The amount of time developers spent on each activity was unrelated to their well-being, perceived productivity, and other variables. We conclude that working remotely is not per se a challenge for organizations or developers.</p>
Human Stromal Antigen 1 (STAG1) Cohesin Subunit SA-1; A Target Enabling Package
<p>Loss of function mutations in the cohesin subunit gene <a href="https://www.ncbi.nlm.nih.gov/gene/10735">STAG2</a> are common in a variety of cancers (1). These cells become dependent on the paralogous cohesin subunit <a href="https://www.ncbi.nlm.nih.gov/gene/10274">STAG1</a> (2-4). Mutants of STAG1 that disrupt the binding to the cohesin subunit <a href="https://www.ncbi.nlm.nih.gov/gene/5885">RAD21</a> cannot complement the loss of STAG2. This TEP examines the druggability of STAG1 as a synthetic lethal strategy to treat <em>stag2<sup>-</sup></em> cancers. The TEP includes crystal structures of two domains of STAG1, alone and in complex with Rad21-rderived peptides. We performed screens of a fragment library and identified small molecules bound to pockets in the two domains of STAG1. We also developed assays for binding of RAD21 peptides to STAG1, which can be used to screen for molecules that disrupt binding.</p>
Human Pleckstrin Homology domain Interacting Protein (PHIP); A Target Enabling Package
<p>SGC Oxford has expressed, purified and crystallized the second bromodomain of PHIP as part of the probe programme. Fragment screening and X-ray crystallography identified binders, some of which optimised to uM affinity. However, molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p>
Human With No Lysine Kinase 3 (WNK3); A Target Enabling Package
<p>Kinases WNK1-4 regulate cation-chloride cotransporters via phosphorylation of SPAK and OSR1 and thereby control salt homeostasis, cell volume and blood pressure. Gain of function mutations in WNK kinases are found in Gordon’s hypertension syndrome suggesting the WNK pathway as a therapeutic target. WNK3 inhibition in particular has also been shown to reduce cerebral injury after Ischemic stroke. Here we present assays and crystal structures that define (i) the molecular basis for disease mutations; (ii) the multiple functional domains of WNK kinases and their protein interactions; (iii) the binding of small molecule kinase inhibitors and a potential allosteric pocket.</p>
Gender Differences in Public Code Contributions: a 50-year Perspective - Replication Package
<p>This page details the steps needed to replicate the findings of the paper: <a href="https://upsilon.cc/~zack/">Stefano Zacchiroli</a>, <em>Gender Differences in Public Code Contributions: a 50-year Perspective</em>, <a href="https://www.computer.org/csdl/magazine/so">IEEE Software</a>, 2021.</p> <p>After retrieving the replication package, follow the instruction described in the README.html file.</p>
Human Hydroxyacid Oxidase (HAO1); A Target Enabling Package
<p>This project provides the tools and data to develop small molecule inhibitors for an inherited metabolic disorder (Primary hyperoxaluria type 1) due to the defective enzyme (<a href="https://www.ncbi.nlm.nih.gov/gene/189">AGXT</a>), by targeting the enzyme (<a href="https://www.ncbi.nlm.nih.gov/gene/54363">HAO1</a>) upstream of the glyoxylate metabolic pathway to mitigate the defect (i.e. substrate reduction approach). This TEP package includes recombinant human HAO1 purification protocols, structures of the HAO1 in different states, <em>in vitro </em>assays to detect ligand/inhibitor binding (DSF, SPR) and enzyme activity (amplex red assay) of human HAO1, as well as initial chemical matters identified from crystallography-based fragment screening.</p>
Human Methylene- tetrahydrofolate reductase (MTHFR) A Target Enabling Package (TEP)
<p>The folate and methionine cycles are essential metabolic pathways for life, involved respectively in DNA synthesis and generation of the ubiquitous methyl donor S-adenosylmethionine (SAM). The enzyme 5,10-methylenetetrahydrofolate reductase (<a href="https://www.ncbi.nlm.nih.gov/gene/4524">MTHFR</a>) represents a key regulatory connection between these cycles, hence exerting a strong influence on an array of diseases. This TEP presents the first structures for any eukaryotic MTHFR, revealing a novel SAM-binding fold. The TEP provides additional mass spectrometry, activity assay and biophysical binding methods yielding mechanistic insights into how phosphorylation and allosteric binding of SAM act in concert to inhibit MTHFR activity. This work further provides the starting point for the design of tool molecules (e.g. SAM-analogues) aimed at disrupting the SAM-induced inhibition of MTHFR activity.</p> <p> </p>
Human T-box transcription factor T (Brachyury); A Target Enabling Package
<p>Chordoma is a rare cancer occurring along the spinal cord (OMIM: <a href="https://www.omim.org/entry/215400">215400</a>). Chordoma is derived from an embryonic tissue, the notochord, and over-expresses the embryonic transcription factor T-box transcription factor T, the homologue of mouse Brachyury. Chordomas are “genomicaly silent” cancers that do not carry an extensive mutation load. Recent studies indicate that expression of TBXT is essential for persistence and growth of chordoma cells. As TBXT is not expressed in any post-embryonic tissues, it could be an excellent target for treatment of chordoma. The long-term aim of this project is to test whether TBXT can be targeted with small molecules with sufficient affinity and specificity to be therapeutically useful. In this TEP we have determined crystal structures of the DNA-binding domain (DBD) of TBXT with and without cognate DNA oligonucleotides. The DNA-free protein crystals were used in a high-throughput fragment screen to identify 29 fragments bound in 6 clusters. The crystal structures of the bound fragments provide starting points for development of stronger binders which could be used to disrupt TBXT activity or to induce the degradation of the protein through a Proteolysis-targeting chimeric molecule (PROTAC) approach.</p>
Human TMEM16K (ANO10); A Target Enabling Package
<p>There are ten members of the TMEM16/Anoctamin family of proteins in mammals. Although the first members of this family to be discovered, TMEM16A and TMEM16B, have a calcium-regulated chloride channel function, subsequently other members of the family, such as TMEM16F, were found to have lipid scramblase activity combined with non-selective ion channel activity. TMEM16K was a relatively understudied member of the family despite the observation that mutations in TMEM16K have been linked to the genetic disease autosomal recessive spinocerebellar ataxia Type 10 (Also known as SCAR10 or ARCA3). SCAR10 is a late-onset neurodegenerative disorder which causes marked atrophy of the cerebellum with consequential deterioration in limb co-ordination, speech and eye movement. We have solved several structures of human TMEM16K through X-ray crystallography and cryo-EM capturing both active and inactive conformational states. Through collaborations, we have investigated TMEM16K’s function and location in cells. We were able to show that TMEM16K acts as a lipid scramblase with non-selective ion channel activity that is sensitive to both Ca<sup>2+</sup> and lipid chain lengths. We also showed that TMEM16K mainly resides in the endoplasmic reticulum where it may be regulated by the ER’s unique lipid profile. Our highest resolution cryo-EM structure for TMEM16K allowed us to identify a bound lipid in the cavity behind the groove that transports the lipid headgroups and this lipid binding site may represent an allosteric modulator site, providing a direction for the design of binders which could modulate TMEM16K activity in cells.</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.