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8,537 results for “Openness”
BANP opens chromatin and activates CpG island regulated genes [RNA-Seq]
GEO Series GSE155664. Mus musculus. 44 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide open chromatin methylome profiles in colorectal cancer
GEO Series GSE149282. Homo sapiens. 24 samples. Type: Methylation profiling by array.
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function (DNase-hypersensitivity)
GEO Series GSE52179. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Open chromatin profile of primary and lymph node oral cancer cells
GEO Series GSE92479. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
INTERFLEX - EON (SWE) open access data
<p>Open access data for backing up results presented by EON within the Interflex-project.</p>
Utah Open Data - D4 Evaluation Datasets
<p><a href="https://opendata.utah.gov/">State of Utah</a> data used for the evaluation of our data-driven domain discovery algorithm (D4). This repository contains 1766 tables that were downloaded on 2019-09-27 from the <a href="http://api.us.socrata.com/api/catalog/v1">Socrata Open Data API</a>.</p> <p> </p>
NYC Open Data (Services) - D4 Evaluation Datasets
<p><a href="https://opendata.cityofnewyork.us/">NYC Open</a> Services data used for the evaluation of our data-driven domain discovery algorithm (D4). This repository contains 692 tables that were downloaded on 2016-11-22 from the <a href="http://api.us.socrata.com/api/catalog/v1">Socrata Open Data API</a>.</p> <p> </p>
Biodiversidata: An Open-Access Biodiversity Database for Uruguay
<p>We present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates and geographic location accuracy. The dataset provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country area. The total number of records collated is 69,380, including 673 species. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date, and it represents the first open repository for the country.</p>
Exploring the Security Awareness of the Python and JavaScript Open Source Communities
<p>Online appendix for "Exploring the Security Awareness of the Python and JavaScript Open Source Communities"</p>
Results of the Nanofront open science survey
<p>This dataset contains the results of the survey performed during the talk I gave about Open Science during the NanoFront Winter Retreat 2019 in Courchevel, France</p> <p>The talk, along with the questions and the context, can be found here:</p> <pre>https://doi.org/10.5281/zenodo.2600527</pre>
A Mixed Graph-Relational Dataset of Socio-technical Interactions in Open Source Systems
<p># Realtional Dataset</p> <p>- Downlaod Dump.sql <br> - Before importing Dump.sql icrease your max_allowed_packet=4M to 16M in your MySQL initialization usually located at C:\ProgramData\MySQL\MySQL Server 8.0\my.ini <br> - Import Dump.sql to your local MySQL server by MySQL Workbech->Server->Data Import -> Import from Self-Contained File -> Start Import<br> <br> ---------------------------------------------------------------------------------------------------------------------------------------<br> # Graph Dataset via graphs_cypher</p> <p># Download Neo4j Desktop</p> <p>Download link can be found here https://neo4j.com/</p> <p># Add Graph in Neo4j Desktop</p> <p>Run Neo4j Desktop application and follow instructions:</p> <p>- Click on Add Graph<br> - Set desired name and password<br> - Click on Create<br> - Start the Graph database</p> <p><br> # Loading Cypher scripts to Graph database</p> <p> </p> <p>Once the graph database is running, start Neo4j browser and execute cypher script for each project.<br> as show in the figure below<br> </p> <p>The script will insert the data of the graph in the database.</p> <p>OR</p> <p># Loading from graph.db</p> <p>- Download the graph.db <br> - graph.db contains subfolder DeveloperInteractionGraph.db and SubsystemInteractionGraph.db <br> - To visualize any desired graph from the graph.db/DeveloperInteractionGraph.db or SubsystemInteractionGraph.db <br> - Create a graph in Neo4j<br> - Click on Manage<br> - Click on Open Folder<br> - Paste the desired (project).db inside the data/databases folder<br> - Restart DB<br> - Neo4j credentials:<br> userid = neo4j<br> password = admin</p> <p>## Visualize graph</p> <p>The resultant graph can be visualized using following query:<br> Show only 25 nodes<br> ```<br> $ MATCH (n) RETURN n LIMIT 25<br> ```</p> <p>Show all nodes<br> ```<br> $ MATCH (n) RETURN n<br> ```<br> </p> <p> </p>
Need for Tweet: How Open Source Developers Talk About Their GitHub Work on Twitter
<p>This dataset contains 70,427 cross-linked Twitter-[GHTorrent](http://ghtorrent.org) user pairs identified as likely belonging to the same users. The dataset accompanies our research paper:</p> <p>@inproceedings{fang2020tweet,</p> <p> author = {Fang, Hongbo and Klug, Daniel and Lamba, Hemank and Herbsleb, James and Vasilescu, Bogdan},</p> <p> title = {Need for Tweet: How Open Source Developers Talk About Their GitHub Work on Twitter},</p> <p> booktitle = {International Conference on Mining Software Repositories (MSR)},</p> <p> year = {2020},</p> <p> pages = {to appear},</p> <p> publisher = {ACM},</p> <p>}</p> <p> </p> <p>The data <strong>cannot</strong> be used for any purpose other than conducting research. </p> <p>Due to privacy concerns, we only release the user IDs in Twitter and GHTorrent, respectively. We expect that users of this dataset will be able to collect other data using the Twitter API and GHTorrent, as needed. Please see below for an example.</p> <p>To query the Twitter API for a given user_id, you can:</p> <ul> <li> <p>Apply for Twitter developer account <a href="https://developer.twitter.com/en/apply-for-access">here</a>.</p> </li> <li> <p>Create an APP with your Twitter developer account, and create “API key” and “API secret key”.</p> </li> <li> <p>Obtain an access token. Given the previous <API key>:<API secret key>, run: </p> </li> </ul> <p>curl -u "<API key>:<API secret key>" --data "grant_type=client_credentials" "https://api.twitter.com/oauth2/token"</p> <p>The response looks like this: {"token_type":"bearer","access_token":"<...>"} </p> <p>Copy the "access_token".</p> <ul> <li> <p>Given the previous access token, run:</p> </li> </ul> <p>curl --request GET --url "https://api.twitter.com/1.1/users/show.json?user_id=<user_id>" --header "authorization: Bearer <access_token>"</p> <p>The GHTorrent user ids map to the users table in the MySQL version of GHTorrent. To use GHTorrent, please follow instructions on the <a href="https://ghtorrent.org">GHTorrent website</a>.</p>
Copulatory ducts reflexed outwards at anterior end and opening at base of atrium (b1) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift
Copulatory ducts reflexed outwards at anterior end and opening at base of atrium (b1)
Atrium heart-shaped (a5); copulatory openings long lateral slits (b5) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift
Atrium heart-shaped (a5); copulatory openings long lateral slits (b5)
Input data for manuscript "An open-source low-cost sensor for SNR-based GNSS reflectometry: Design and long-term validation towards sea level altimetry"
<p>Input data for Fagundes et al. (2021), "An open-source low-cost sensor for SNR-based GNSS reflectometry: Design and long-term validation towards sea level altimetry", GPS Solutions (in press). <a href="https://www.researchgate.net/publication/341946011">preprint</a></p>
A list of open access papers pertaining to racism
<p>This data file contains a listing >3,400 of open access papers published in Elsevier journals which pertain to racism in some capacity. The list was built through a Scopus keyword + title + abstract search for relevant keyowrds. The column "links" contians the url for each paper.</p>
Data supplement for: "Open Access für die Maschinen"
<p>Structured bibliographical metadata for the paper: "Open Access für die Maschinen".</p>
On the role of anthropogenic activity and sea level rise in tidal distortion on the open coast of the Yellow Sea Shelf
<p>This dataset is created for manuscript entitle of On the role of anthropogenic activity and sea level rise in tidal distortion on the open coast of the Yellow Sea Shelf submitted to JGR-OS. All rights reserved andreviewers cannot use the data here until the manuscript is officially published. Otherwise, they will bear legal responsibility.</p>
On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation
<p>This repository contains XML configuration files, POS and EPOS reconstructed APT datasets and RNG/RRNG range files, raw data, and synthetic dataset to follow our analysis made in the initial version of the paper <em>"On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation"</em></p> <p>We are continuously working on the atom probe crystallography tools of paraprobe and their corresponding configuration and analysis wizards in paraprobe-parmsetup and paraprobe-autoreporter. Also, we are currently working on an ontology for metadata of APT post-processing workflows. Therefore, changes in the structure of the HDF5 file are expected to come up.<br> <br> Therefore, we always recommend to work with the newest code of PARAPROBE on the GitLab:</p> <p><strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe.git<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong></p> <p>Therefore, the data in here serve as a reference to and documentation of the settings mainly.</p> <p><strong>This repository here contains the following pieces of information:</strong></p> <p><strong>VerifyCrystalStructures_Geo26Al.zip<br> VerifyCrystalStructures_Geo26Al3Sc.zip<br> VerifyCrystalStructures_Geo26W.zip</strong><br> Raw data and results for the assessment of the histograms and SDMs and corresponding amplitude spectra.</p> <p><strong>VerifySXIndexing.zip</strong><br> Raw data and results for the verification with synthetic single crystal datasets.</p> <p><strong>VerifyPXIndexing2_SimID.200.tar.gz<br> VerifyPXIndexing2_SimID.201.tar.gz<br> VerifyPXIndexing2_SimID.202.tar.gz</strong><br> Raw data and results for the verification with synthetic polycrystal datasets,<br> where 200 is without noise, 201 low noise, 202 high noise.</p> <p><strong>VerifyAlBicrystalZirong_ExampleROIs.tar.gz<br> VerifyAlBicrystalZirong_Library.tar.gz</strong><br> <strong>VerifyAlBicrystalZirong_Setup.tar.gz<br> VerifyAlBicrystalZirongRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering.</p> <p><strong>VerifyAlLiMgBaptiste_ExampleROIs.tar.gz<br> VerifyAlLiMgBaptiste_Library.tar.gz<br> VerifyAlLiMgBaptiste_Setup.tar.gz<br> VerifyAlLiMgBaptisteRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering.</p> <p><strong>AlBicrystalAdaptiveROIGrid.tar.gz<br> AlLiMgAgAdaptiveROIGrid.tar.gz</strong><br> Raw data and results for the tutorial with adaptive refinement of the ROI grid, as it is detailed in the Jupyter notebook tutorials on the GitLab repository.</p> <p> </p>
The Varying Openness of Digital Open Science Tools
<p>Dataset accompanying the paper submitted to F1000 entitled <strong>The Varying Openness of Digital Open Science Tools.</strong></p> <p> </p> <p>Abstract of paper</p> <p>Digital tools that support Open Science practices play a key role in the seamless accumulation, archiving and dissemination of scholarly data, outcomes and conclusions. Despite their integration into Open Science practices, the providence and design of these digital tools are rarely explicitly scrutinized. This means that influential factors, such as the funding models of the parent organizations, their geographic location, and the dependency on digital infrastructures are rarely considered. Suggestions from literature and anecdotal evidence already draw attention to the impact of these factors, and raise the question of whether the Open Science ecosystem can realise the aspiration to become a truly “unlimited digital commons” in its current structure. </p> <p> </p> <p>In an online research approach, we compiled and analysed the geolocation, terms and conditions as well as funding models of 242 digital tools increasingly being used by researchers in various disciplines. Our findings indicate that design decisions and restrictions are biased towards researchers in North American and European scholarly communities. In order to make the future Open Science ecosystem inclusive and operable for researchers in all world regions including Africa, Latin America, Asia and Oceania, those should be actively included in design decision processes. </p> <p>Digital Open Science Tools carry the promise of enabling collaboration across disciplines, world regions and language groups through responsive design. We therefore encourage long term funding mechanisms and ethnically as well as culturally inclusive approaches serving local prerequisites and conditions to tool design and construction allowing a globally connected digital research infrastructure to evolve in a regionally balanced manner.</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.