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11 results for “free software”
The Debsources Dataset: Two Decades of Free and Open Source Software
<p>This is the Debsources Dataset: source code and related metadata spanning two decades of Free and Open Source Software (FOSS) history, seen through the lens of the Debian distribution.</p> <p>The dataset spans more than 3 billion lines of source code as well as metadata about them such as: size metrics (lines of code, disk usage), developer-defined symbols (ctags), file-level checksums (SHA1, SHA256, TLSH), file media types (MIME), release information (which version of which package containing which source code files has been released when), and license informa-<br> tion (GPL, BSD, etc).</p> <p>The Debsources Dataset comes as a set of tarballs containing deduplicated unique source code files organized by their SHA1 checksums (the source code), plus a portable PostgreSQL database dump (the metadata).</p> <p>The Debsources Dataset is described in full in the paper The Debsources Dataset: Two Decades of Free and Open Source Software, published on the Empirical Software Engineering journal with DOI 10.1007/s10664-016-9461-5 . A preprint of the paper is available at https://upsilon.cc/~zack/research/publications/debsources-ese-2016.pdf .</p>
Data and Software for "Complex Dynamics in a Synchronized Cell-Free Genetic Clock"
<p>Contains raw data, analysis scripts, simulation scripts, device operation software for the publication: "Complex Dynamics in a Synchronized Cell-Free Genetic Clock".</p>
Free Open Source Communities Sustainability: Does It Make a Difference in Software Quality?
<p><strong>Context:</strong> Free and Open Source Software (FOSS) communities' ability to stay viable and productive over time is pivotal for society as they maintain the building blocks that digital infrastructure, products, and services depend on. Sustainability may, however, be characterized from multiple aspects, and less is known how these aspects interplay and impact community outputs, and software quality specifically.</p> <p><strong>Objective: </strong>This study, therefore, aims to empirically explore how the different aspects of FOSS sustainability impact software quality.</p> <p><strong>Method: </strong>16 sustainability metrics across four categories were sampled and applied to a set of 217 OSS projects sourced from the Apache Software Foundation Incubator program. The impact of a decline in the sustainability metrics was analyzed against eight software quality metrics using Bayesian data analysis, which incorporates probability distributions to represent the regression coefficients and intercepts.</p> <p><strong>Results: </strong>Findings suggest that selected sustainability metrics do not significantly affect defect density or code coverage. However, a positive impact of community age was observed on specific code quality metrics, such as risk complexity, number of very large files, and code duplication percentage. Interestingly, findings show that even when communities are experiencing sustainability, certain code quality metrics are negatively impacted.</p> <p><strong>Conclusion:</strong> Findings imply that code quality practices are not consistently linked to sustainability, and defect management and prevention may be prioritized over the former. Results suggest that growth, resulting in a more complex and large codebase, combined with a probable lack of understanding of code quality standards, may explain the degradation in certain aspects of code quality.</p>
Data for Precursor intensity-based label-free quantification software tools for Galaxy Platform.
<p><strong>Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the Galaxy Platform.</strong></p> <p> </p> <p><strong>ABRF:</strong> Data was generated through the collaborative work of the ABRF Proteomics Research Group (<a href="https://abrf.org/research-group/proteomics-research-group-prg">https://abrf.org/research-group/proteomics-research-group-prg</a>). See Reference for details: Van Riper, S. et al. ‘<a href="http://cbs.umn.edu/sites/cbs.umn.edu/files/public/downloads/2016_ABRF_PRG_Poster_for_ASMS_20160501.pdf">An ABRF-PRG study: Identification of low abundance proteins in a highly complex protein sample</a>’ at the 64th Annual Conference of American Society of Mass Spectrometry and Allied Topics" at San Antonio, TX."</p> <p><strong>UPS:</strong> <strong>MaxLFQ Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M.<a href="https://www.ncbi.nlm.nih.gov/pubmed/24942700/"> Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.</a> Mol Cell Proteomics. 2014 Sep;13(9):2513-26. doi: 10.1074/mcp.M113.031591. Epub 2014 Jun 17. PubMed PMID: 24942700; PubMed Central PMCID: PMC4159666;</strong></p> <p><strong>PRIDE #5412; ProteomeXchange repository PXD000279: </strong>ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000279</p>
Data and software for "Metal Pad Sensing: exploiting the electrical double layer to improve resistance-based microfluidic cell tracking, with applications to label-free mechanophenotyping"
<p>Data and software for "Metal Pad Sensing: exploiting the electrical double layer to improve resistance-based microfluidic cell tracking, with applications to label-free mechanophenotyping"</p>
Somatosensory data for group analyses in the Frontiers Reseach Topic: From raw MEG/EEG to publication: how to perform MEG/EEG group analysis with free academic software.
<p><strong>If you use the data or the analysis pipeline, please refer to:</strong></p> <p>Andersen, L.M., 2018. Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation. Front. Neurosci. 12. <a href="https://doi.org/10.3389/fnins.2018.00006">https://doi.org/10.3389/fnins.2018.00006</a></p> <p><strong>and/or</strong></p> <p>Andersen, L.M., 2018. Group Analysis in FieldTrip of Time-Frequency Responses: A Pipeline for Reproducibility at Every Step of Processing, Going From Individual Sensor Space Representations to an Across-Group Source Space Representation. Front. Neurosci. 12. <a href="https://doi.org/10.3389/fnins.2018.00261">https://doi.org/10.3389/fnins.2018.00261</a></p> <p><strong>IMPORTANT</strong><br> Version 2 only contains subjects 1, 18, 20 and a new version of the FreeSurfer folder. This is due to a (very) wrong co-registration for subject 1 and due to 18 and 20 having had their anatomy files mixed up. This has now been fixed. For all other subjects, please see version 1. Also, get the updated scripts from github instead at: <a href="https://github.com/ualsbombe/omission_frontiers.git">https://github.com/ualsbombe/omission_frontiers.git</a></p> <p><br> </p> <p>Dataset with tactile expectations to be analysed with pipelines for either <a href="https://mne.tools/stable/index.html">MNE-Python</a> or <a href="http://www.fieldtriptoolbox.org/">FieldTrip</a>, aiming to follow the MEG-BIDS structure</p> <p><br> <strong>Unzipping the data</strong></p> <p>Data is compressed into twenty-two different zip-files, one for each of the twenty subjects, one for the FreeSurfer data, one for the scripts files . The easiest way to uncompress and prepare the analysis directories is to create a directory in your home folder called "analyses", which has a sub-directory called "omission_frontiers_BIDS-FieldTrip", which has a sub-directory called "data".<br> Thus, as an example, in my case, I should have the path: /home/lau/analyses/omission_frontiers_BIDS-FieldTrip/data</p> <p><strong>Path:</strong><br> on a Linux system the path would be /home/your_name/analyses/omission_frontiers_BIDS-FieldTrip/data<br> on a macOS system the path would be /Users/your_name/analyses/omission_frontiers_BIDS-FieldTrip/data<br> on a Windows system the path would be C:\Users\your_name\analyses\omission_frontiers_BIDS-FieldTrip\data</p> <p><strong>Steps for unzipping:</strong></p> <p>1. Set up the folder above according to your operating system, following the examples above and substitute "your_name" for your user name.<br> 2. Unzip each of the subject folders into the data folder (sub-01 - sub-20) (/home/your_name/analyses/omission_frontiers_BIDS-FieldTrip/data)<br> 3. Also unzip the FreeSurfer folder into the data folder (/home/your_name/analyses/omission_frontiers_BIDS-FieldTrip/data)<br> 4. Finally, unzip the scripts folder into /home/your_name/analyses/omission_frontiers_BIDS-FieldTrip/</p> <p>Now you are ready to run the analyses.</p> <p><br> <strong>The MEG data</strong></p> <p>Raw fif files are contained in the data folder, ordered by subject (n=20)<br> There is one recording for each subject, MaxFiltered, called oddball_absence-tsss-mc_meg.fif. These are split into three files with -1 and -2 being the remainder of the recording</p> <p><strong>Processed MRI data </strong></p> <p>For the MRI, only the segmented data are provided. This is to sufficient to make the volume conduction model and the source model, while protecting the subjects' identity</p> <p>For Fieldtrip, there is an mri_segmented.mat for each subject, which is found in the meg (sic!) folder for each subject. This has been co-registered to the MEG data<br> For MNE-Python, the FreeSurfer directory should also be used, which contains a folder for each subject that contains surfaces (surf) and boundary element methods models (bem) that are used for source reconstruction in MNE-python. There is also a trans-file for each subject (oddball_absence_dense-trans.fif) in the meg folder specifying the co-registration between MEG and MRI coordinate systems for the MNE-Python analysis. Finally, the FreeSurfer folder also contains the labels for the cortical surface. This is not used in any of the analyses, but are supplied for interested users.</p> <p><br> <strong>Metadata</strong></p> <p>Each subject has a number of tsv-files:<br> *channel.tsv contain information about the channels in that recording<br> *events.tsv contain information about the events in that recording<br> removed_trial_indices.tsv contains information about which events were removed manually (NB! this is only used for the FieldTrip analysis)<br> ica_components.tsv contains information which independent component were removed manually (NB! this is only used for the FieldTrip analysis)<br> *scans_tsv contain information about the scans conducted</p> <p><br> <strong>Scripts </strong></p> <p>Please see Github for the updated scripts at: <a href="https://github.com/ualsbombe/omission_frontiers.git">https://github.com/ualsbombe/omission_frontiers.git</a></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>
Public Money? Public Code: What 'Free' Software Really Means in Research
<p><strong>Episode Summary:</strong></p> <p>Our guest Dr Christian Busse spoke to us about the Free Software Foundation Europe and the challenges and opportunities connected to Open and Free Software...and what the differences between those two things might be. Christian has very kindly supplied some notes for us to add this week.</p> <p><strong>Links: </strong> </p> <p>First, the main website of the "Public Money, Public Code" campaign is: <a href="https://publiccode.eu/">https://publiccode.eu</a> </p> <p>Second, the "Legal activities" section of the FSFE website, which includes further links for licensing questions, workshops and the Legal Network, can<br> be accessed via <a href="https://fsfe.org/activities/ftf/activities.en.html">https://fsfe.org/activities/ftf/activities.en.html</a> </p> <p>Finally, there is an position paper by the FSFE on Free Software in Horizon2020: <a href="https://fsfe.org/activities/ftf/activities.en.html">https://fsfe.org/activities/ftf/activities.en.html</a> </p> <p><strong>Quotes:</strong></p> <p>'Free as in freedom and free as in beer'</p>
Replication Package for: "Redundancy-free Analysis of Multi-revision Software Artifacts"
<p>Researchers often analyze several revisions of a software project to obtain historical data about its evolution. For example, they statically analyze the source code and monitor the evolution of certain metrics over multiple revisions. The time and resource requirements for running these analyses often make it necessary to limit the number of analyzed revisions, e.g. by only selecting major revisions or by using a coarse-grained sampling strategy, which could remove significant details of the evolution. Most existing analysis techniques are not designed for the analysis of multi-revision artifacts and they treat each revision individually. However, the actual difference between two subsequent revisions is typically very small. Thus, tools tailored for the analysis of multiple revisions should only analyze these differences, thereby preventing re-computation and storage of redundant data, improving scalability and enabling the study of a larger number of revisions. In this work, we propose the Lean Language-Independent Software Analyzer (LISA), a generic framework for representing and analyzing multi-revisioned software artifacts. It employs a redundancy-free, multi-revision representation for artifacts and avoids re-computation by only analyzing changed artifact fragments across thousands of revisions. The evaluation of our approach consists of measuring the effect of each individual technique incorporated, an in-depth study of LISA's resource requirements and a large-scale analysis over 7 million program revisions of 4,000 software projects written in four languages. We show that the time and space requirements for multi-revision analyses can be reduced by multiple orders of magnitude, when compared to traditional, sequential approaches.</p>
Data from: Image Calibration and Analysis Toolbox – a free software suite for measuring reflectance, colour, and pattern objectively and to animal vision
1. Quantitative measurements of colour, pattern, and morphology are vital to a growing range of disciplines. Digital cameras are readily available and already widely used for making these measurements, having numerous advantages over other techniques, such as spectrometry. However, off-the-shelf consumer cameras are designed to produce images for human viewing, meaning that their uncalibrated photographs cannot be used for making reliable, quantitative measurements. Many studies still fail to appreciate this, and of those scientists who are aware of such issues, many are hindered by a lack usable tools for making objective measurements from photographs. 2. We have developed an image processing toolbox that generates images that are linear with respect to radiance from the RAW files of numerous camera brands, and can combine image channels from multispectral cameras, including additional ultraviolet photographs. Images are then normalised using one or more grey standards to control for lighting conditions. This enables objective measures of reflectance and colour using a wide range of consumer cameras. Furthermore, if the camera's spectral sensitivities are known, the software can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox also provides image analysis tools that can extract luminance (lightness), colour, and pattern information. Furthermore, all processing is performed on 32-bit floating point images rather than commonly used 8-bit images. This increases precision and reduces the likelihood of data loss through rounding error or saturation of pixels, while also facilitating the measurement of objects with shiny or fluorescent properties. 3. All cameras tested using this software were found to demonstrate a linear response within each image and across a range of exposure times. Cone-catch mapping functions were highly robust, converting images to several animal visual systems and yielding data that agreed closely with spectrometer-based estimates. 4. Our imaging toolbox is freely available as an addition to the open source ImageJ software. We believe that it will considerably enhance the appropriate use of digital cameras across multiple areas of biology, in particular researchers aiming to quantify animal and plant visual signals.
Data from: Image Calibration and Analysis Toolbox – a free software suite for measuring reflectance, colour, and pattern objectively and to animal vision
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