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311 results for “Open source”
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
An Empirical Study on the Usage and Availability of Machine Learning Libraries in Open-Source Python Projects - Dataset
<p>This repository contains the dataset of the manuscript:</p> <p>"An Empirical Study on the Usage and Availability of Machine Learning Libraries in Open-Source Python Projects"</p>
How are Solidity smart contracts tested in open source projects? An exploratory study
<p>A dataset with 139 Github Solidity projects containing information about testing files, testing tools, and testnets that each project uses.</p>
Open Source Software Sustainability
<p>The reproducible code and dataset along with the paper submission.</p>
Dvoice : An open source dataset for Automatic Speech Recognition on African Languages and Dialects
<p>DVoice is a community initiative that aims to provide African languages and dialects with data and models to facilitate their use of voice technologies. The lack of data on these languages makes it necessary to collect data using methods that are specific to each language. Two different approaches are currently used: the DVoice platform, which is based on Mozilla Common Voice, for collecting authentic recordings from the community, and transfer learning techniques for automatically labeling the recordings. The DVoice platform currently manages 7 languages including Darija (Moroccan Arabic dialect) whose dataset appears on this version, Wolof, Mandingo, Serere, Pular, Diola and Soninke. The Swahili-labeled data present in this version was obtained after automatic labeling via the learning transfer of the Voxlingua107 dataset. For a first time, we also advocate for the increase of data given their small size that we currently have. Thus this version of the dataset contains easily identifiable augmented data.</p>
SoK: Taxonomy of Attacks on Open-Source Software Supply Chains - Visualization Tool Screenshots & Selected Papers
<p>This artifact complements the paper "SoK: Taxonomy of Attacks on Open-Source Software Supply Chains", submitted at IEEE S&P 2023.</p> <p>The papers selected during the Systematic Literature Review (SLR) are presented in the CSV file.</p> <p>This screenshots display the main features of the visualization tool that allows to explore the taxonomy of attacks on OSS supply chains, as well as the related safeguards and the selected references.</p>
TrainRuns.jl: an Open-Source Tool for Running Time Estimation - Supplement Data
<p>This additional data contains the initial data and the calculated results for comparing FBS and TrainRuns.jl.</p> <p><strong>File description</strong></p> <ul> <li><em>local.yaml</em>: input parameters for the local train</li> <li><em>freight.yaml</em>: input parameters for the freight train</li> <li><em>running_path.yaml</em>: input parameters for the path</li> <li><em>freight_FBS.csv</em>: export of calculation from FBS for the freight train</li> <li><em>freight_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the freight train</li> <li><em>freight_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the freight train</li> <li><em>local_FBS.csv</em>: export of calculation from FBS for the local train</li> <li><em>local_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the local train</li> <li><em>local_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the local train</li> <li><em>running_path.csv</em>: converted running_path.yaml for displaying</li> <li><em>comparison.tex</em>: LaTeX code for the graph in comparison.pdf</li> </ul> <p><strong>Sources</strong></p> <p>The calculations in FBS were done with the file 'Ostsachsen_V220.railml'. FBS needs a commercial license, which can be purchased. License for 'Ostsachsen_V220.railml' is Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0).<br> The file 'Ostsachsen_V220.railml' can be found at:<br> https://www.railml.org/en/user/exampledata.html (last accessed 2022-06-06 with login) -> "Real world railway examples from professional tools" -> "East Saxony railway network by FBS" -> "Ostsachsen_V220.railml"</p> <p>Other sources are mentioned in the files.</p>
CrossNet-Open-Unmix for Music Source Separation (X-UMXL)
<p>Weights of CrossNet-Open-Unmix (X-UMX) trained on the internal 100h dataset which is larger than <a href="https://sigsep.github.io/datasets/musdb.html">MUSDB18</a>, named X-UMX Large (X-UMXL). The weights can be used with <a href="https://github.com/asteroid-team/asteroid/tree/master/egs/musdb18/X-UMX">X-UMX on Asteroid (PyTorch)</a>. The details of X-UMX are described in <a href="https://ieeexplore.ieee.org/document/9414044">here</a>.</p>
Replication Kit for Paper: "Are There Any Unit Tests? An Empirical Study on Unit Testing in Open Source Python Projects"
<p>Replication Kit for the Paper "Are there any Unit Tests? An Empirical Study on Open Source Python Projects" by Fabian Trautsch, Jens Grabowski.</p> <p>You can cite the paper via:</p> <p>@inproceedings{trautsch2017there,<br> title={Are There Any Unit Tests? An Empirical Study on Unit Testing in Open Source Python Projects},<br> author={Trautsch, Fabian and Grabowski, Jens},<br> booktitle={Proceedings of the IEEE International Conference on Software Testing, Verification and Validation (ICST)},<br> pages={207--218},<br> year={2017},<br> organization={IEEE}<br> }</p> <p> </p> <p>Contents:<br> 1) Used version of the vcsSHARK<br> - located in “vcsSHARK”<br> 2) Used version of the testImpSHARK<br> - located in “testImpSHARK”<br> 3) Analysis implementations<br> - located in “testImpSHARK/testimpshark/analysis”<br> 4) Raw Data CSV Files<br> - located in “testImpSHARK/testimpshark/analysis/data<br> 5) Raw MongoDB<br> - located in “mongo_backup”</p> <p><br> Usage:<br> 1) Usage instructions for the vcsSHARK is given on its github homepage (http://ftrautsch.github.io/vcsSHARK/index.html) or directly in the “vcsSHARK/pyvcsshark/main.py” file</p> <p>2) Usage instructions for the testImpSHARK:<br> - if only one revision should be analyzed use “testImpSHARK/main.py”<br> - if all revisions should be analyzed use “testImpSHARK/execution.py”<br> - in both files concrete instructions can be found</p> <p>3) Each analysis file is commented. For some of them (rq1_boxplot.py and rq4.py the connection to the MongoDB must be changed). For the R files, the path to the data must be adapted. Otherwise, the files can be directly executed.</p> <p>4) The MongoDB can be restored via:<br> mongorestore --gzip --archive=smartshark040816.gz --db smartshark --host <HOST> --port <PORT> --username <USERNAME> --password <PASSWORD> --authenticationDatabase <AUTHENTICATION_DATABASE></p> <p><br> Tests:<br> 1) The tests can be run directly via the unittest framework of python: e.g., python -m unittest tests/test_common.py</p>
Open Source Software in Data Science
<p>This upload includes an anonymized data set of a survey first launched in 2022. The survey has been revised since. The data set. however, contains answers of the first launch.</p>
April 7, 2024 (v1) Image Open Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 5 relative to Figure 7 - Figure Supplement 4
<p>Source data file relative to <strong><span>Figure 7 – figure supplement 4 Panel A</span></strong></p> <p><span>Raw image of agarose gel showing the 2 alternative mRNAs encoding for ArhGEF11 in control animals (left track, control) and after injection of the MO at the one cell stage (right track, +MO at 2 and 5ng). The source data includes the raw files (native format .scn and open source format .tiff) as well as a pdf file showing both the full scale image and the cropped image selected for the figure.<br></span></p>
Reproducible Evaluation of Open-Source Tools for Prostate Segmentation on Public Datasets
<p>Segmentation of the prostate and surrounding regions is important for a variety of clinical and research applications. Our goal is to evaluate the generalizability of publicly available state-of-the-art AI models on publicly available datasets. To compare the AI generated segmentations to the available manually annotated ground-truth, quantitative measures such as Dice Coefficient and Hausdorff distance, along with shape radiomics features, were analyzed. Our study also aims to show how cloud-based tools can be used to analyze, store, and visualize evaluation results.<strong> </strong></p> <p>Three open-source pre-trained AI prostate segmentation tools were evaluated against expert annotations, on three publicly available MRI prostate collections, available in NCI Imaging Data Commons[1]. Two pre-trained models originate from the nnU-Net framework[2], the last pre-trained model originates from Prostate158 paper[4]. ProstateX[5], QIN-Prostate-Repeatability[6] and PROSTATE-MRI-US-Biopsy[7]. Expert annotations of the the whole prostate gland, peripheral zone (PZ) and transition zone (TZ) of the prostate are available for ProstateX collection, whole prostate gland and PZ for QIN-Prostate-Repeatability collection, and whole prostate gland for PROSTATE-MRI-US-Biopsy collection.</p> <p>We rely on the DICOM standard to encode our segmentation and radiomics results. The DICOM standard aims to achieve interoperability and FAIR[10] principles. Encoding our results in DICOM representation allows us to leverage DICOM-reliant tools, such as Google Cloud Computing tools for storage,computation, analysis and visualization. Open-source DICOM-based visualization tools such as OHIF[8] viewer can also be used to look qualitatively at the AI and expert annotations and the referenced images.. DICOM Segmentation objects are used to encode the AI models predictions, using dcmqi[11], DICOM Structured Reports on the other hand are used to encode radiomics features[3] extracted from the AI and expert annotations, using dcmqi and highdicom[12]. </p> <p>This dataset is organized in three parts: </p> <p>AI_SEGMENTATIONS_DICOM.zip, AI_STRUCTURED_REPORTS_DICOM.zip and EXPERT_SRUCTURED_REPORTS_DICOM..zip. All zip files contain DICOM objects only, sorted based on DICOM attributes, following this pattern:</p> <p>PatientID/<br> └───Modality-%StudyInstanceUID/<br> └───%SeriesInstanceUID-%SeriesDescription.dcm.</p> <p>AI_SEGMENTATIONS_DICOM.zip contains all the pre-trained AI models evaluated segmentation results, encoded as DICOM Segmentation objects. AI_STRUCTURED_REPORTS_DICOM..zip contains firstorder and shape radiomics features extracted for the AI segmentation results, such as Segmentation Volume, encoded as DICOM Structured Reports. EXPERT_SRUCTURED_REPORTS_DICOM.zip contains firstorder and shape radiomics features extracted for the expert annotations (for ProstateX, QIN-Prostate-Repeatability and PROSTATE-MRI-US-Biopsy collections) stored a DICOM Structured Reports objects.</p> <p>Code repository containing evaluation cloud-based notebooks and results/metadata .csv tables is available here:<br><a href="https://github.com/ImagingDataCommons/idc-prostate-mri-analysis">https://github.com/ImagingDataCommons/idc-prostate-mri-analysis</a></p> <h2>Additional Notes</h2> <p><strong> </strong>This project has been funded in whole or in part with Federal funds from the NCI, NIH, under task order no. HHSN26110071 under contract no. HHSN261201500003l.<br>https://portal.imaging.datacommons.cancer.gov/</p> <p>nnU-Net: <a href="https://github.com/MIC-DKFZ/nnUNet">https://github.com/MIC-DKFZ/nnUNet</a> <br>Prostate158: <a href="https://github.com/Project-MONAI/model-zoo/tree/dev/models/prostate_mri_anatomy">https://github.com/Project-MONAI/model-zoo/tree/dev/models/prostate_mri_anatomy</a><br>Pyradiomics: <a href="https://github.com/AIM-Harvard/pyradiomics">https://github.com/AIM-Harvard/pyradiomics</a> <br>Highdicom: <a href="https://github.com/herrmannlab/highdicom">https://github.com/herrmannlab/highdicom</a> <br>DCMQI: <a href="https://github.com/QIICR/dcmqi">https://github.com/QIICR/dcmqi</a> <br>Github repo: <a href="https://github.com/ImagingDataCommons/idc-prostate-mri-analysis">https://github.com/ImagingDataCommons/idc-prostate-mri-analysis</a></p> <h2>Related information</h2> <p>ProstateX - <a href="https://doi.org/10.7937/K9TCIA.2017.MURS5CL">https://doi.org/10.7937/K9TCIA.2017.MURS5CL </a><br><br>QIN-Prostate-Repeatability - <a href="https://doi.org/10.7937/K9/TCIA.2018.MR1CKGND">https://doi.org/10.7937/K9/TCIA.2018.MR1CKGND</a><br><br>PROSTATE-MRI-US-BIOPSY - <a href="https://doi.org/10.7937/TCIA.2020.A61IOC1A">https://doi.org/10.7937/TCIA.2020.A61IOC1A</a></p> <h2>References </h2> <p>[1] Fedorov A, Longabaugh WJ, Pot D, Clunie DA, Pieper S, Aerts HJ, Homeyer A, Lewis R, Akbarzadeh A, Bontempi D, Clifford W. NCI imaging data commons. Cancer research. 2021 Aug 8;81(16):4188.</p> <p>[2] Isensee F, Jaeger PF, Kohl SA, Petersen J, Maier-Hein KH. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature methods. 2021 Feb;18(2):203-11.</p> <p>[3] Van Griethuysen JJ, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V, Beets-Tan RG, Fillion-Robin JC, Pieper S, Aerts HJ. Computational radiomics system to decode the radiographic phenotype. Cancer research. 2017 Nov 1;77(21):e104-7.</p> <p>[4] Adams, Lisa C., Marcus R. Makowski, Günther Engel, Maximilian Rattunde, Felix Busch, Patrick Asbach, Stefan M. Niehues, et al. 2022. “Prostate158 - An Expert-Annotated 3T MRI Dataset and Algorithm for Prostate Cancer Detection.” Computers in Biology and Medicine 148 (September): 105817.</p> <p>[5] Natarajan, S., Priester, A., Margolis, D., Huang, J., & Marks, L. (2020). Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy) (version 2) [Data set]. The Cancer Imaging Archive. DOI: 10.7937/TCIA.2020.A61IOC1A</p> <p>[6] Fedorov, A; Schwier, M; Clunie, D; Herz, C; Pieper, S; Kikinis, R; Tempany, C; Fennessy, F. (2018). Data From QIN-PROSTATE-Repeatability. The Cancer Imaging Archive. DOI: 10.7937/K9/TCIA.2018.MR1CKGND</p> <p>[7] Natarajan, S., Priester, A., Margolis, D., Huang, J., & Marks, L. (2020). Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy) (version 2) [Data set]. The Cancer Imaging Archive. DOI: 10.7937/TCIA.2020.A61IOC1A</p> <p>[8] Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research. Erik Ziegler, Trinity Urban, Danny Brown, James Petts, Steve D. Pieper, Rob Lewis, Chris Hafey, and Gordon J. Harris</p> <p>[9] Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L. The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository. Journal of digital imaging. 2013 Dec;26(6):1045-57.</p> <p>[10] Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J. The FAIR Guiding Principles for scientific data management and stewardship. Scientific data. 2016 Mar 15;3(1):1-9.</p> <p>[11] Herz C, Fillion-Robin JC, Onken M, Riesmeier J, Lasso A, Pinter C, Fichtinger G, Pieper S, Clunie D, Kikinis R, Fedorov A. DCMQI: an open source library for standardized communication of quantitative image analysis results using DICOM. Cancer research. 2017 Nov 1;77(21):e87-90.</p> <p>[12] Bridge CP, Gorman C, Pieper S, Doyle SW, Lennerz JK, Kalpathy-Cramer J, Clunie DA, Fedorov AY, Herrmann MD. Highdicom: A python library for standardized encoding of image annotations and machine learning model outputs in pathology and radiology. Journal of Digital Imaging. 2022 Aug 22:1-9.</p> <p> </p>
Figure 1 in Use of open-source object detection algorithms to detect Palmer amaranth (Amoronthus polmeri) in soybean
Figure 1. Examples of images collected for soybean in the VE-VC (A) and R2 (B) growth stages.
eELib: Open-Source Model Library for Prosumer Power Systems and Energy Management Strategies (data)
<p>Dataset and results used for the simulations in following publication:</p> <p>Carsten Wegkamp, Henrik Wagner, Eike Niehs, Julien Essers, Marcel Lüdecke, Mattias Hadlak, Bernd Engel:<br>"<strong>eELib: Open-Source Model Library for Prosumer Power Systems and Energy Management Strategies</strong>",<br>Open Source Modelling and Simulation of Energy Systems (OSMSES) 2024, Vienna, Austria, 2024</p> <p> </p> <p>This contains the input (scenario) files for the building & grid scenario and the results of the two simulations.<br>It uses the elenia Energy Library (eELib) with release version 1.0.0: https://gitlab.com/elenia1/elenia-energy-library</p>
Figure 8. Comparison between the exact function v p in Reconstruction of a passive tracer boundary source in an open water area
Figure 8. Comparison between the exact function v p and the reconstructed vα h.
Figure 6 in Reconstruction of a passive tracer boundary source in an open water area
Figure 6. Solution of the optimal control problem.
Figure 7 in Reconstruction of a passive tracer boundary source in an open water area
Figure 7. Difference between φ p and φα h.
Figure 2. Velocity field U, t in Reconstruction of a passive tracer boundary source in an open water area
Figure 2. Velocity field U, t = 0.
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.