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311 results for “Open source”
[Tool demo] Prospector: a Tool to Find Fixes to Known Vulnerabilities of Open-Source Projects
<p> </p> <p><strong>>>>> TOOL DEMO SCREENCAST</strong>: please download file <strong><a href="https://zenodo.org/record/7974442/files/tool_demo_final.mp4?download=1">tool_demo_final.mp4</a></strong>. <strong><<<<</strong></p> <p> </p> <p><strong>ABSTRACT</strong>: Though vulnerability databases are key for monitoring known vulnerabilities in open-source projects, they rarely contain information about the code changes that fix the flaws they describe. Finding them is time-consuming and error-prone as it involves the analysis of multiple, unstructured resources. </p> <p>In this paper we present \prospector, a tool that supports mapping<br> vulnerability advisories from vulnerability databases onto the corresponding fix in the source code. \prospector employs a set of heuristics that mimics and automates the<br> strategies that would be employed by human security experts.</p> <p>Given an advisory expressed in natural language, \prospector processes the commits found in the target source code repository, ranks them based on a set of predefined rules, and produces a report that the user can inspect to<br> determine which commits to retain as the actual fix.<br> The tool is publicly available and is released under the Apache 2.0 license.</p>
QAnubis - open source coding tool
<p>QAnubis - open source coding tool</p> <p>The main activity of qualitative research is data analysis, which involves a process of collecting and analyzing narrative data, including texts, photos, audiovisual elements, and various digital file formats. Different approaches and methodologies are available for qualitative data investigation, with a greater emphasis on coding, where artifacts and their contents are categorized under a finite set of categories. Similar to other fields, efforts are made to develop and enhance computerized tools known as Computer-Assisted Qualitative Data Analysis Software (CAQDAS) that aim to increase the efficiency and effectiveness of the analysis process by providing means to assist in data identification, organization, interpretation, exploration, and integration.</p> <p>To contribute to the field of qualitative analysis, this work presents an open-source web tool called QAnubis for performing coding on PDF files while preserving their original content and formatting.</p>
Supplementary material for "A Rapid, Open-Source CCT Predictor for Low Alloy Steels, and its Application to Compositionally Heterogeneous Material"
<p>The complete collection of measured, modelled and analysed data associated with the work "A Rapid, Open-Source CCT Predictor for Low Alloy Steels, and its Application to Compositionally Heterogeneous Material" and includes:</p> <ol> <li>Measured and analysed dilatometry data.</li> <li>Optical micrographs of as-cooled microstructures.</li> <li>Microhardness measurements of the as-cooled samples.</li> <li>PAG size analysis.</li> <li>Modelled CCT data.</li> <li>SA-540 EPMA data.</li> <li>Modelled results from adapting the model to consider SA-540 chemical heterogeneity.</li> <li>Full chemical analysis for each alloy examined.</li> <li>Modelled Thermo-Calc CCT data.</li> <li>Modelled JMatPro CCT data.</li> </ol>
An analysis of the impact of domain debt in open-source projects
<p>Datasets related to the thesis paper:</p> <ul> <li><em>original_boa.txt</em> contains the intial output given by <a href="https://boa.cs.iastate.edu/boa/index.php">BOA</a>, while <em>filtered_boa.txt</em> comprises the set of repositories with at most five domain entity packages</li> <li><em>original_seart.txt</em> included data as returned by <a href="https://seart-ghs.si.usi.ch/">SEART</a></li> <li><em>database_structure.sql</em> is the SQL file that may be exploited to perform further analysis on the two datasets</li> <li><em>repos.json</em> contains the final list of repositories, as chosen in the study</li> </ul>
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>
EvoSL: A Large Open-Source Corpus of Changes in Simulink Models & Projects
<p>EvoSL is a corpus of 924 Simulink repositories useful to perform model evolutionary studies. <a href="https://zenodo.org/api/files/cbb76da1-1077-4020-8d7c-1c6f4f7b3d36/dataset_er_derived_full_schema.pdf?versionId=a9270932-acca-40d8-b5aa-88330525ade8">dataset_er_derived_full_schema</a> shows the full schema design of the EvoSL_v1 SQLite database. Refer to the paper for full details of the dataset.</p> <p>EvoSL.sqlite (Table: Model_element_changes) contains over 2+ million element-level change raw data extracted from 14k+ Simulink model snapshots. Refer to the tool (https://github.com/50417/EvoSL-Tool) to discard duplicates using its cleaning module.</p> <p>"EvoSL: A Large Open-Source Corpus of Changes in Simulink Models & Projects" is accepted in <a href="https://conf.researchr.org/track/models-2023/models-2023-technical-track">MODELS 2023</a> (CORE A, acceptance rate: 24.6%)</p> <p> </p>
Open‐source workflow approaches to passive acoustic monitoring of bats
<ol> <li>The affordability, storage, and power capacity of compact modern recording hardware has evolved passive acoustic monitoring (PAM) of animals and soundscapes into a non-invasive, cost-effective tool for research and ecological management and is particularly effective for bats and toothed whales that consistently echolocate. The use of PAM at large scales hinges on effective automated detectors and species classifiers which, combined with distance sampling approaches, have enabled species abundance estimation of toothed whales. But standardized, user-friendly, and open-access automated detection and classification workflows are in demand for this key conservation metric to be realized for bats.</li> <li>We used the PAMGuard toolbox including its new deep learning classification module to test the performance of four open-source workflows for automated analyses of acoustic datasets from bats. Each workflow used a different initial detection algorithm followed by the same deep learning classification algorithm and was evaluated against the performance of an expert manual analyst.</li> <li>Workflow performance depended strongly on the signal-to-noise ratio and detection algorithm used: the full deep learning workflow had the best classification accuracy (≤67%) but was computationally too slow for practical large-scale bat PAM. Workflows using PAMGuard's detection module or triggers onboard an SM4BAT or AudioMoth accurately classified up to 47%, 59% and 34%, respectively, of calls to species. Not all workflows included noise sampling critical to estimating changes in detection probability over time, a vital parameter for abundance estimation. The workflow using PAMGuard's detection module was 40 times faster than the full deep learning workflow and missed as few calls (recall for both ~0.6), thus balancing computational speed and performance. </li> <li>We show that complete acoustic detection and classification workflows for bat PAM data can be efficiently automated using open-source software such as PAMGuard and exemplify how detection choices, whether pre- or post-deployment, hardware or software-driven, affect the performance of deep learning classification and <span>the downstream ecological information that can be extracted from acoustic recordings. In particular, understanding, and quantifying detection/classification accuracy and the probability of detection are key to avoid introducing biases that may ultimately affect the quality of data for ecological management. </span> </li> </ol>
Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection
<p>Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.</p>
Free Open Source Communities Sustainability: Does It Make a Difference in Software Quality?
<p> Free and Open Source Software (FOSS) communities' sustainability is important to maintain and promote access to technology and innovation. While considerable effort has been invested on the topic of FOSS sustainability, limited attention has been given to its impact on community outcomes, e.g., software quality. We conducted an empirical study to examine the influence of FOSS sustainability on software quality. We used projects' data sourced from the Apache Software Foundation Incubator. A total of 236 projects were originally selected. Our final list included a total of 217 projects after applying our exclusion criteria. We used Bayesian data analysis, which incorporates probability distributions to represent the regression coefficients and intercepts. Our findings suggest that our selected sustainability metrics do not significantly affect defect density or code coverage. However, we observed a positive impact of community age on specific code quality metrics, such as risk complexity, number of very large files, and code duplication percentage. Interestingly, our findings show that even when communities are experiencing sustainability, certain code quality metrics are negatively impacted. This implies that code quality practices are not consistently linked to sustainability, and defect management and prevention may be prioritized over the former.</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>
Open Source Software Package, Version and Dependency Metadata
<p>This dataset contains metadata about 7 million open source packages, versions and dependencies from 34 different software ecosystems in 4 different csv files exported from <a href="https://packages.ecosyste.ms/">https://packages.ecosyste.ms</a>. This can be seen as a spiritual successor to https://zenodo.org/records/3626071, up to date for 2023, including more packages and an expanded array of metadata fields.</p><p>Full copies of the postgresql database this data was extracted from are also available: <a href="https://packages.ecosyste.ms/open-data">https://packages.ecosyste.ms/open-data</a> </p><h4>Files</h4><p>Expanded csv sizes:</p><ul><li>packages-1.0.0-2023-10-17.csv - 2.6GB - 7,015,326 rows</li><li>packages_with_repository_fields-1.0.0-2023-10-17.csv - 4.3GB - 7,019,492 rows</li><li>versions-1.0.0-2023-10-17.csv - 14GB - 84,953,382 rows</li><li>dependencies2-1.0.0-2023-10-17.csv - 124GB - 976,944,543 rows</li></ul><p>Contact</p><p>If you would like any help, support or more data from Ecosyste.ms please do get in touch via email: hello@ecosyste.ms or open an issue on GitHub: <a href="https://github.com/ecosyste-ms/packages/issues">https://github.com/ecosyste-ms/packages/issues</a></p>
Open‐source workflow approaches to passive acoustic monitoring of bats
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Data from: An inexpensive and open-source method to study large terrestrial animal diet and behavior using time-lapse video and GPS
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Data from: A look inside a flexible open-source scanning electrochemical probe microscope
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Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection
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MALDI-MS dataset for use with open-source untargeted metabolomic workflow for complex biological samples
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Quantitative analysis of subcellular distributions with an open-source, object-based tool
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Mapping built infrastructure in semi-arid systems using data integration and open-source approaches for image classification
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Data from: The BumbleBox: An open-source platform for quantifying behavior in bumblebee colonies
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Dataset and scripts for "Sentiment Analysis over Collaborative Relationships in Open Source Software Projects"
<p>Dataset and scripts for "Sentiment Analysis over Collaborative Relationships in Open Source Software Projects".</p> <p>README is included in the files</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.