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47 results for “open tools”
1. Files containing data from each sample studied and ready to be open in Thellier Tool 4.0 software (Leonardt et al., 2004) for evaluation and determination of archaeointensity and archaeoinclination.
<p>Files containing data from each sample studied and ready to be open in Thellier Tool 4.0 software (Leonardt et al., 2004) for evaluation and determination of archaeointensity and archaeoinclination.</p> <p>Data supporting manuscript entitled “Archaeomagnetic studies of bricks from ancient buildings sampled in SE Poland (Central Europe)” by J. Nawrocki, K. Standzikowski, M. Chadima, T. Werner, M. Łanczont, J. Gancarski, Z. Gil submitted to Journal of Archaeological Science: Reports (JASREP-D-23-00078).</p>
Dataset to publication: ''Magnetstein: An open source tool for quantitative NMR mixture analysis robust to low resolution, distorted lineshapes and peak shifts''
<p>MANIQ (plugin for Mnova 14.3.1 software (Mestrelab Research, S. L., Spain)) and ACD/TP (Targeted Profiling tool for ACD/Spectrus 2020.1.1 (Advanced Chemistry Development, Inc., ACD/Labs Ontario, Toronto, ON, Canada)) project files and raw experimental NMR data to:</p> <table> <caption>Experiments obtained to Magnetstein with optimized parameters, Magnetstein with default parameters, ACD/TP and MANIQ.</caption> <tbody> <tr> <td>Exp. no.</td> <td>Problem</td> <td>Ingredients</td> </tr> <tr> <td>1</td> <td>large intensity differences<br> between peaks</td> <td>α-pinene<br> benzyl benzoate<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>2</td> <td>peak overlap<br> & contamination (extra peaks)</td> <td>imonene<br> α-pinene<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>3</td> <td>low resolution (43 MHz<br> benchtop NMR spectrometer)</td> <td>benzyl benzoate<br> isopropyl myristate<br> limonene<br> pinene</td> </tr> <tr> <td>4</td> <td>lineshape distortion<br> (shim z1 & z2)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> <tr> <td>5</td> <td>peak position<br> mismatch<br> between library<br> and mixture<br> (different<br> temperatures)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> <tr> <td>6</td> <td>test sample</td> <td>α-pinene<br> benzyl benzoate<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>7</td> <td>large intensity<br> differences<br> & peak overlap</td> <td><br> benzyl benzoate<br> m-anisaldehyde<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>8</td> <td><br> peak overlap &<br> different solvents<br> for single<br> ingredients (in CDCl<sub>3</sub>)<br> and mixture (DMSO-d<sub>6</sub>)</td> <td>benzyl benzoate<br> m-anisaldehyde</td> </tr> <tr> <td>9</td> <td>ineshape<br> distortion<br> (shim z2)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> </tbody> </table> <p> </p>
List of PRECINCT Open Source Tools and Assets
<p>This is a list of open source tools developed by the PRECINCT project for stakeholders to engage with.</p>
Quantitative analysis of subcellular distributions with an open-source, object-based tool
Open the record for dataset details and reuse information.
On Strong Scaling and Open Source Tools for Analyzing Atom Probe Tomography Data
<p>This repository contains supplemental results to the paper "On Strong Scaling and Open Source Tools<br> for Analyzing Atom Probe Tomography Data".</p> <p>Specifically, the input parameter and result files from all synthetic benchmark studies.<br> The results file for all synthetic specimen benchmark studies are available from the<br> authors upon serious request.</p> <p><strong>The repository content is as follows:</strong></p> <p><strong>Real world data:<br> Three triplets of *.tar.gz archive files document the settings and analysis files for the real world case studies</strong><br> 3013902 is the incipient specimen,<br> 2763207 the intermediate specimen, and<br> 3345501 the mature specimen.</p> <p><strong>Scripts.zip</strong><br> Contains all batch scripts we used for performing the analyses as a queue</p> <p><strong>Synthetic data:</strong></p> <p><strong>APTCrystallography.zip</strong><br> Contains all results from the benchmarking of the reimplemented Vicente Araullo-Peters et al. method</p> <p><strong>FullVolumeTessellation.zip</strong><br> Contains all results from the benchmarking of the Voro++ Voronoi volume tessellation method except for the HDF5/XDMF volume tessellation files of the 200 and 2000 million ion datasets</p> <p><strong>TwoPointStatistics.zip</strong><br> Contains all results from benchmarking the computing of 2-point spatial statistics</p> <p><strong>TipSurfaceDescrSpatialStatistics.zip</strong><br> Contains all results from benchmarking the alpha shape computation, descriptive spatial statistics, and clustering analyses</p> <p><strong>PARAPROBE.Results.2Mio.tar.gz<br> PARAPROBE.Results.20Mio.tar.gz</strong><br> <strong>PARAPROBE.Results.200Mio.tar.gz</strong><br> Contains all settings files and some results from benchmarking the hybrid implementation.</p> <p><strong>Unpack the individual repositories using tar through Linux console as follows:</strong><br> tar -xvf <archivename> <br> where <archivename> is a placeholder for the respective tar gz compressed archives within the ZIP file.<br> Alternatively WinRAR can be used on a Windows system.</p> <p><strong>We would kindly like to ask you to use the following repository<br> to access source code of PARAPROBE in the future:</strong></p> <p><strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong><br> <br> <strong>Only above repository will be updated in the future! </strong><br> <strong>Only there new code additions and bugfixes are posted!<br> The examples folder of this repository contains a folder examples/tasks/paper14 which shows how<br> to run a workflow of paraprobe tools from this above repository to run analyses akin as reported in this paper.</strong></p> <p>Recommendations and bug reports to M. Kühbach are appreciated! Happy APT analyzing!</p> <p>------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <strong>The PARAPROBE source code version we used for analyzing the synthetic and real world APT<br> specimens in the paper used an earlier development version of the PARAPROBE tool, the source code</strong><br> <strong>is here:</strong></p> <p>PARAPROBE_20190117_VersionUsedForPaper.zip</p> <p>https://github.com/mkuehbach/PARAPROBE<br> https://paraprobe.readthedocs.io/en/latest/</p> <p> </p>
Re-usable Survey Tools and Data for Advancing Open Science
<p>Re-usable Survey Tools and Data for Advancing Open Science</p>
Replication package for "Blended Modeling in Commercial and Open-source Model-Driven Software Engineering Tools: A Systematic Study"
<p>Replication package for the paper <em>Blended Modeling in Commercial and Open-source Model-Driven Software Engineering Tools: A Systematic Study</em>.</p> <p>Protocol</p> <ul> <li><code>/01-protocol/protocol.pdf</code></li> </ul> <p>Data & analysis scripts</p> <p>This replication package is structured as follows:</p> <ul> <li><code>/02-search</code> - Detailed data on the <code>/academic</code> and <code>/grey literature</code> search.</li> <li><code>/03-tools</code> - Identified tools and inclusion/exclusion decisions.</li> <li><code>/04-classification_schema</code> - Classification framework and the corresponding data extraction form.</li> <li><code>/05-data</code> - Clean data in a processable form.</li> <li><code>/06-analysis</code> - Analysis scripts and results.</li> </ul>
Different community open-source evaluation and benchmarking tools with their respective characteristics
<p>Schematic of different community open-source evaluation and benchmarking tools with their respective characteristics.</p>
Orbit Image Analysis: An open-source whole slide image analysis tool
<p>This is a whole slide image (WSI) dataset for glomeruli segmentation on kidney tissue, in total 88 images.</p> <p>The train-set (58 images) and test-set (32 images) has been used in the publication "Orbit Image Analysis: An open-source whole slide image analysis tool" to train and test the<br> glomeruli segmentation model.</p>
Open source and open hardware: developing tools that are accessible and customisable
<p><strong>The following video describes how ROMI uses open source hardware to support communities through customisation and adaptation. Funded by EU Grant 773875.</strong></p> <p><em>Videos are available in:</em></p> <ul> <li>Hi-res (1080p Apple ProRes)</li> <li>Mid-res (1080p H265)</li> </ul> <p><strong>Video script:</strong></p> <p>(MINCHIN) A key aspect and component of the ROMI project is that it should be open source so there is no proprietary software there's no ownership over the designs in fact it's created to be hacked customised and adapted to any farm.<br> <br> (HANAPPE) One of the aspects of the ROMI project is open hardware and we started from scratch like buying a motor buying a motor-controller programming the motor controller and which is maybe different than many of the projects you might see more industrial projects who might rely more on say high-end standard components from from the industry but i think there's a real advantage in trying to build everything up is that first you understand everything you can explain everything you can fix anything you can you know document anything for you know DIY farmers that they you know if they want to replace one motor with another and understanding that all allows you to quickly experiment stuff without having to depend on someone else who's working with say a closed source component and it allows you to be quite reactive and of course in the end allows you to be fairly cost effective.<br> <br> (BAORI) One of the things we set out to do with this project was to make it accessible and the idea is that at the end of the project everything will be open source so from the frame to the software the designs the cad everything will be open source so if you're a maker if you're somebody who is an engineer and wants to build one of these robots yourself you'll be able to download everything including the software to be able to make it run and because we wanted it to be accessible we started out with one thought that was everything that we put into this rover should also be accessible.<br> <br> (CAMPRODON) So we are trying to bring that philosophy that is embedded within Fab Labs slash (/) maker movement at large the open hardware movement, of how you design for distributed manufacturing. Which means that you take design decisions on the way that you build things which are meant for others replicated in new laboratories using new machines and you do that on top of a network such as a Fab Lab network which is a robust yet heterogeneous.<br> <br> (BARBERAN) It seems like someone tinkered with it. The idea when we design this is to constrain ourselves to do it in a way that anyone else can build it easily. So we try to keep the type and the complexity of the tools we use as small and simple as we can, so we use 3d printers that today are really accessible, we use CNC machines that's maybe the the most complex machine we use but it was it was needed because we need to build something that can stand the weather in a harsh environment in a farm. So we use aluminium and plastic and the rest of the components are mostly commercial components so the the process of designing it is a common go between the computer and the farm and the fab lab we tried here with the cable on the office to hang the first versions of the of the cable bot then we come back to redesign the pieces and then we adjust the sizes of the pulleys and the springs and then we do another model. And so this ability to reiterate so fast is also provided by the simplicity of the tools we use. Using a really simple 3d printer to build a robot is allows you to do in one month several versions and iterations of the same robot.<br> <br> (HANAPPE) In the end our goal is sustainability it's not technology, and what is the best way for whatever we build to have an impact on on say farmers in Europe or wider, and if if what we do is good then we would like them to have access to these tools, and there's some sort of a confidence that then there will be some financing flowing back to us.<br> <br> (MINCHIN) When we open source this knowledge and these tools it allows for an abundance of researchers of practitioners to come together to find the solutions, we don't have to depend on a small development team so the the library of tools that are developed are really a public library for others to to use and to adapt.<br> <br> (BARBERAN) At the end I think the the most important part that we don't even realise because we just do it because we are on the on the inertia of doing it is that we are setting rocks for the future. At the end we are not making right now the the the best robot the best tool what we are doing is setting ground to build on the future the best robot and the best thing built by people not by us because we don't we are not farmers we are not going to design the best robot and we are not a big company with resources as crazy to to make the ultra high-tech thing. But we are able to do something to share with people and a lot of heads think better than a couple of heads you know. The the model that that linux a lot of people in the linux community use is we are dumber than them but we are hundreds of thousands. Hundreds of thousands of heads think better than 10 heads so being able to share that knowledge and to include people in in the development of their own tools i think is the best part on a mid and long term way of seeing this.</p>
Tools_Visual Analysis_SSH Open Marketplace
<p>A dataset of visual-analysis-tools based on the <a href="https://marketplace.sshopencloud.eu/">SSH Open Marketplace</a> created for the <a href="https://zfmedienwissenschaft.de/online/open-media-studies-blog">Open-Media-Studies-Blog</a>.</p>
Open tools
<p>List of open tools to support scientific research</p>
The Threatened Species No-Go Mapping Tool: An online open-access land-use decision support tool that identifies areas of importance for highly sensitive species of conservation concern
Open the record for dataset details and reuse information.
Orbit Image Analysis: an open-source whole slide image analysis tool
Open the record for dataset details and reuse information.
An Orthogonal Dynamic Covalent Chemistry Tool for Ring-Opening Polymerization of Cyclic Oligochalcogenides on Detachable Helical Peptide Templates
<p>Original data</p>
The Open Field test as a tool for behavior analysis in pigs - is a standardization of setup necessary? A systematic review.
<p>Systematic review.</p>
Are automated static analysis tools worth it? An investigation into relative warning density and external software quality on the example of Apache open source projects
<p>This is the dataset for the publication "Are automated static analysis tools worth it? An investigation into relative warning density and external software quality on the example of Apache open source projects".</p> <p>It contains just-in-time defect-prediction style data in jit_data2.tar.gz as well as warnings generated by PMD 6.31.0 in warnings_data3.tar.gz.</p> <p>Further information and scripts for generating the plots and tables can be found in the <a href="https://github.com/atrautsch/emse2021a_replication">replication kit</a>.</p>
Data from: The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies
Open the record for dataset details and reuse information.
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.