Lynnette Hui Xian Ng, Araz Taeihagh,
... quantitative research on the open-source code repositories GitHub and GitLab to understand the usage patterns of ... further information from open-source code repositories from GitHub and GitLab to understand how developers use APIs. ... data sources are the public access code repositories, GitHub and GitLab. We investigate only open-source code ... code in private repositories and the Dark Web. GitHub is the largest online code repository for shared ... over 50 million users and 100 million repositories (Github, 2020b), and is the fastest-growing open-source ...
Tópico(s): Advanced Malware Detection Techniques
2021 - Wiley | Policy & Internet
Zhebin Yu, Susan Peters, Loes van Boxmeer, George S. Downward, Gerard Hoek, Marianthi‐Anna Kioumourtzoglou, Marc G. Weisskopf, Johnni Hansen, Leonard H. van den Berg, Roel Vermeulen,
... et al. 2017) (see supporting information at https://github.com/kevininef/Airpollution-ALS). We averaged the air ... Core Team). Supporting information is available at https://github.com/kevininef/Airpollution-ALS. The PAN study was ... controls were included (see supporting information at https://github.com/kevininef/Airpollution-ALS), covering all of the ... are presented in the supporting information at https://github.com/kevininef/Airpollution-ALS.Table 1 Association between ... ALS were robust (see supporting information at https://github.com/kevininef/Airpollution-ALS).Figure 1. Two-pollutant ...
Tópico(s): Air Quality and Health Impacts
2021 - National Institute of Environmental Health Sciences | Environmental Health Perspectives
Thomas M. Pearce, Marina N. Nikiforova, Somak Roy,
... demonstrations of these widgets are publicly hosted using Github Pages (https://pearcetm.github.io, last accessed April 15, 2019). The source ... all three widgets is available in a public Github repository (https://github.com/pearcetm, last accessed April 15, 2019) under ... graphical visualization elements using SVG elements.d3-legendhttps://github.com/susielu/d3-legend (last accessed August 5, ... the Apache license version 2.0.d3-tiphttps://github.com/Caged/d3-tip (last accessed August 5, ... To try the widget, please visit https://pearcetm.github.io/jsproteinmapper. The widget fetches protein structure data, ...
Tópico(s): Gene expression and cancer classification
2019 - Elsevier BV | Journal of Molecular Diagnostics
Yu Wu, Na Wang, Jess Kropczynski, John M. Carroll,
GitHub is a widely used online collaborative software development environment. In this paper, we describe curation projects as a new category of GitHub project that collects, evaluates, and preserves resources for ... curate resources; (2) why curation has occurred on GitHub; (3) how curated resources are used by software developers; and (4) how the GitHub platform could better support these practices. We conduct ... developers, each of whom hosts curation projects on GitHub. Our results suggest that the motivators that inspire ...
Tópico(s): Scientific Computing and Data Management
2017 - PeerJ, Inc. | PeerJ Computer Science
Jacob Fiksel, Leah R. Jager, Johanna Hardin, Margaret A. Taub,
Git and GitHub are common tools for keeping track of multiple versions of data analytic content, which allow for more than one person to simultaneously work on a project. GitHub Classroom aims to provide a way for students ... on and submit their assignments via Git and GitHub, giving teachers an opportunity to facilitate the integration ... courses. In the Fall 2017 semester, we implemented GitHub Classroom in two educational settings—an introductory computational ... course. We found many educational benefits of implementing GitHub Classroom, such as easily providing coding feedback during ...
Tópico(s): Advanced Data Storage Technologies
2019 - American Statistical Association | Journal of Statistics Education
Shidan Wang, Donghan M. Yang, Ruichen Rong, Xiaowei Zhan, Guanghua Xiao,
... pathology image analysis toolYesManual labeling; automated cell detectionhttps://github.com/qupath/qupathNoJS Segment Annotator24Tangseng P. Wu Z. ... A web-based image annotation toolYesArea-based clickinghttps://github.com/kyamagu/js-segment-annotatorNoLabelMe25Russell B.C. Torralba ... tool providing iPhone/iPad (Apple, Cupertino, CA) applicationYesPolygonalhttps://github.com/CSAILVision/LabelMeAnnotationToolYesLabelme: A Python-based image annotation toolYesPolygonalhttps://github.com/wkentaro/labelmeNoOpenSurfaces26Bell S. Upchurch P. Snavely N. ...
Tópico(s): Medical Imaging and Analysis
2019 - Elsevier BV | American Journal Of Pathology
Hao Wu, Benjamin D. Humphreys,
... trimmomaticPicardCommand line tools for RNA-seq fileshttps://broadinstitute.github.io/picard/STARUltrafast read mapperTools: https://github.com/alexdobin/STARForum: https://groups.google.com/forum/#! ... reduction toolsMASTModel-based analysis of scRNA-seq datahttps://github.com/RGLab/MASTSCDEBayesian approach to model scRNA-seq datahttps://github.com/hms-dbmi/scdeZIFADimensionality reduction for scRNA-seq datahttps://github.com/epierson9/ZIFAtSNENonlinear dimensionality reduction approachhttp://lvdmaaten.github. ...
Tópico(s): Renal and related cancers
2017 - Elsevier BV | Kidney International
Mairieli Wessel, Joseph Vargovich, Marco Aurélio Gerosa, Christoph Treude,
... activities in the distributed software development process. Recently, GitHub introduced GitHub Actions , a feature providing automated workflows for software ... and management. Our research investigates how projects use GitHub Actions , what the developers discuss about them, and ... popular repositories (almost 30% of our sample) adopt GitHub Actions and that developers frequently ask for help ... Our findings also suggest that the adoption of GitHub Actions leads to more rejections of pull requests ( ... results when segmenting our results by categories of GitHub Actions . We suggest practitioners consider these effects when ...
Tópico(s): Open Source Software Innovations
2023 - Springer Science+Business Media | Empirical Software Engineering
Eric J. Duncavage, Joshua F. Coleman, Monica E. de Baca, Sabah Kadri, Annette Leon, Mark J. Routbort, Somak Roy, Carlos J. Suarez, Chad Vanderbilt, Justin M. Zook,
... html, last accessed September 1, 2022), rlsim (https://github.com/sbotond/rlsim, last accessed September 1, 2022), RNASeqReadSimulator (https://github.com/davidliwei/RNASeqReadSimulator, last accessed September 1, 2022), SimCT (https://github.com/jaudoux/simct, last accessed September 1, 2022), ... 10: e1003853Crossref PubMed Scopus (4) Google Scholar (https://github.com/BeyondTheSky/BSSim, last accessed September 1, 2022)], ... version given, last update July 30, 2020)https://github.com/pughlab/bamgineerSimulates haplotype-phased, allele-specific copy ...
Tópico(s): Genomics and Phylogenetic Studies
2022 - Elsevier BV | Journal of Molecular Diagnostics
Hannah Boekweg, Amanda J. Guise, Edward D. Plowey, Ryan Kelly, Samuel Payne,
... article can be found in our publicly available GitHub repository, https://github.com/PayneLab/SingleCellSampleSize. Below are listed specific scripts ... making simulated populations can be found in the GitHub repository in a file called simulate_data.R. ... in Figure 1 can be found in our GitHub repository in the file called makeFigure1.R. The ... in Figure 2 can be found in our GitHub repository in the file makeFigure2.R. To generalize ... in Figure 3 can be found in our GitHub repository in the files makeFigure3A.R and makeFigure3B. ...
Tópico(s): Cell Image Analysis Techniques
2021 - Elsevier BV | Molecular & Cellular Proteomics
Mohammad AlMarzouq, Abdullatif AlZaidan, Jehad Al Dallal,
... to highlight the challenges and opportunities of using GitHub as a data source in both research and ... and opportunities faced while conducting empirical research using GitHub as a data source. The challenges and opportunities ... process–output model of open-source software. Findings GitHub data accessed from the application programming interface (API) ... and GHTorrent. There are also several idiosyncrasies about GitHub that researchers need to be aware of to ... libra and open-source software communities hosted on GitHub. Originality/value This study provides a summary of ...
Tópico(s): Online Learning and Analytics
2020 - Emerald Publishing Limited | International Journal of Web Information Systems
Hudson Silva Borges, Marco Túlio Valente,
Besides a git-based version control system, GitHub integrates several social coding features. Particularly, GitHub users can star a repository, presumably to manifest interest or satisfaction with an open source project. ... on the meaning, characteristics, and dynamic growth of GitHub stars. First, by surveying 791 developers, we report ... of stars before using or contributing to a GitHub project. Then, we report a quantitative analysis on ... characteristics of the top-5,000 most starred GitHub repositories. We propose four patterns to describe stars ...
Tópico(s): Scientific Computing and Data Management
2018 - Elsevier BV | Journal of Systems and Software
... repositories on popular code sharing platforms such as GitHub provide another venue to follow the latest bioinformatics trends. The open source component of GitHub allows users to bookmark and copy repositories that ... This Perspective aims to demonstrate the utility of GitHub "stars," "watchers," and "forks" (GitHub statistics) as a measure of software impact. We ... software and analyzed commonly used impact metrics and GitHub statistics of 50 genomics-oriented bioinformatics tools. We ... community-selected best bioinformatics resources and show that GitHub statistics are distinct from the journal's impact ...
Tópico(s): Genetics, Bioinformatics, and Biomedical Research
2018 - Frontiers Media | Frontiers in Bioengineering and Biotechnology
... systems.In this paper, we specifically focus on GitHub, a source code hosting site and one of ... popular platforms for online collaborative coding and sharing.GitHub offers an opportunity for researchers to perform analysis ... providing REST-based APIs for downloading its data.GitHub hosts a vast amount of user repositories so it is quite difficult for a GitHub user to decide to which repository she should contribute on GitHub.So, our paper aims to review different approaches ... be used for creating a recommender system for GitHub, to provide personalized suggestions to GitHub users to ...
Tópico(s): Caching and Content Delivery
2017 - | International Journal of Information Technology and Computer Science
Liguo Yu, Alok Mishra, Deepti Mishra,
GitHub is a distributed code repository and project hosting web site. It is becoming one of the ... version control systems and study the dynamics of GitHub, i.e., the ability and scalability of GitHub to process different requests and provide different services to different GitHub projects and GitHub users. Our study shows that GitHub could handle hundreds of thousands of requests a ... of requests for one project. This capability of GitHub makes it suitable for supporting distributed software development.
Tópico(s): Software System Performance and Reliability
2014 - Springer Science+Business Media | Lecture notes in computer science
Tomás Dodds, Valeria Reséndez, Gerret von Nordheim, Theo Araujo, Judith Moeller,
... of low-cost code hosting platforms such as GitHub. GitHub is a well-known public code management system ... This study aims to map how newsrooms employ GitHub as a trading zone for collaborative journalism. We analyze the GitHub activities of leading media outlets from 27 countries. ... continue to be the primary code producers in GitHub. However, our results show that newsrooms in developing ... for understanding how newsrooms across the globe use GitHub for collaboration and the role journalistic code plays ...
Tópico(s): Expert finding and Q&A systems
2024 - Taylor & Francis | Digital Journalism
Paul Roepman, Ewart de Bruijn, Stef van Lieshout, Lieke Schoenmaker, Mirjam C. Boelens, Hendrikus J. Dubbink, Willemina R.R. Geurts-Giele, Floris H. Groenendijk, Manon M. H. Huibers, Mariëtte E.G. Kranendonk, Margaretha G.M. Roemer, Kris G. Samsom, Marloes Steehouwer, Wendy W.J. de Leng, Alexander Hoischen, Bauke Ylstra, Kim Monkhorst, Jacobus J. M. van der Hoeven, Edwin Cuppen,
... performed using STRELKA version 1.0.14 (https://github.com/Illumina/strelka, last accessed May 21, 2021), ... the tool GRIDSS version 2.8.3 (https://github.com/PapenfussLab/gridss, last accessed May 21, 2021) ... using the AMBER tool version 3.3 (https://github.com/hartwigmedical/hmftools/tree/master/amber, last accessed ... In combination with COBALT version 1.7 (https://github.com/hartwigmedical/hmftools/tree/master/count-bam-lines, ... were performed using LINX version 1.7 (https://github.com/hartwigmedical/hmftools/tree/master/sv-linx, last ...
Tópico(s): Genomics and Rare Diseases
2021 - Elsevier BV | Journal of Molecular Diagnostics
Roy M. Anderson, T. Déirdre Hollingsworth, Rebecca F. Baggaley, Rosie Maddren, Carolin Vegvari,
... Many sources of variability exist (figure).13Vegvari C GitHub caro-veg/covid-19-commentary-figures: code to generate figures for commentary. GitHub, July, 2020https://github.com/caro-veg/covid-19-commentary-figuresDate accessed: ... in the parameter Rt within a population. The GitHub repository contains the model code for the individual ... spreading, in the value of Rt.15Hardwick R GitHub umbralcalc/covid-simple: very simple stochastic COVID-19 ... using a compound Poisson process for population heterogeneity. GitHub, July, 2020https://github.com/umbralcalc/covid-simpleDate accessed: ...
Tópico(s): COVID-19 Clinical Research Studies
2020 - Elsevier BV | The Lancet
Zhifang Liao, Mengjie Yi, Wang Yan, Shengzong Liu, Hui Liu, Yan Zhang, Yun Zhou,
... sustainable development of open source communities, such as GitHub. This paper takes GitHub as an example to analyze the health condition ... Firstly, the paper presents the healthy definition of GitHub open source ecosystem health and, then, according to ... indicators evaluation method. Based on the above, the GitHub ecosystem health prediction method is proposed. By analyzing the projects and data collected in GitHub, it is found that, using the proposed evaluation ... can analyze the healthy development trend of the GitHub ecosystem and contribute to the stability of ecosystem ...
Tópico(s): Open Source Software Innovations
2019 - Multidisciplinary Digital Publishing Institute | Symmetry
... presented with a dialog box with the option “GitHub.” GitHub (Microsoft, Redmond, Wash) is a website that allows ... be downloaded (by the command “git clone https://github.com/...”). The data are then unzipped and ready ... then run by me, before being stored on github. When you run a cell, the output from ... are shown. If you download the notebook from GitHub again, your results will be erased, and the ... output, since that is what was saved on GitHub).Nearly all deep learning libraries for imaging tasks ... for patent or commercialization. (These are on public GitHub site to make it easy for readers to ...
Tópico(s): Education and Critical Thinking Development
2019 - Radiological Society of North America | Radiology Artificial Intelligence
Arkaprabha Sarangi, Amit Goel, Rakesh Aggarwal,
... rRNA Metagenome Analysis.PurposeToolsURLTrimming of primers and adaptersCutadapthttps://github.com/marcelm/cutadaptSicklehttps://github.com/najoshi/sicklecutPrimershttps://github.com/aakechin/cutPrimersAdaperRemovalhttps://github.com/MikkelSchubert/adapterremovalQuality controlNGS-QC ToolKithttp://www.nipgr. ... cms/?page=trimmomaticclinQChttps://sourceforge.net/projects/clinqc/AfterQChttps://github.com/OpenGene/AfterQCMerger of paired-end readsPandaseqhttps://github.com/neufeld/pandaseqPEARhttps://sco.h-its.org/exelixis/ ...
Tópico(s): Helicobacter pylori-related gastroenterology studies
2018 - Elsevier BV | Journal of Clinical and Experimental Hepatology
Yan Hu, Jun Zhang, Xiaomei Bai, Shuo Yu, Zhuo Yang,
... platforms have changed the style of software development. Github is now the most popular social coding platform ... service. Software developers of various levels keep entering Github, and use Github to save their public and private software projects. ... amounts of software developers and software repositories on Github are posing new challenges to the world of ... important problems: analyzing the importance and influence of Github repositories. We proposed a HITS based influence analysis on graphs that represent the star relationship between Github users and repositories. A weighted version of HITS ...
Tópico(s): Web Data Mining and Analysis
2016 - Springer International Publishing | SpringerPlus
Kelly Blincoe, Jyoti Sheoran, Sean Goggins, Eva Petakovic, Daniela Damian,
... ability to follow other users and projects on GitHub has introduced a new layer of open source ... explored how following others influences the actions of GitHub users. Objective: this paper studies the motivation behind ... approach was used including a survey of 800 GitHub users to uncover the reasons for following on GitHub and a complementary quantitative analysis of the activity of GitHub users to examine influence. Our quantitative analysis studied ... a new type of leadership is emerging through GitHub’s following feature and popularity can be more ...
Tópico(s): Software Engineering Techniques and Practices
2015 - Elsevier BV | Information and Software Technology
... projects that utilize the Git revision control system. Github is hugely popular in industry and many companies use programmers' GitHub portfolios as a basis for hiring. The only downside to using a site like GitHub is it emphasizes social coding, meaning individuals can ... assignments, where students need to keep projects private. GitHub has realized this problem, and offers university students ... of the questions I asked myself before using GitHub in the classroom, were: 1) Is version control ... a hands on approach to learning Git and GitHub.
Tópico(s): Software Engineering Research
2013 - Consortium for Computing Sciences in Colleges | Journal of computing sciences in colleges
Alexandre Decan, Tom Mens, Hassan Onsori Delicheh,
GitHub Actions was introduced as a way to automate CI/CD workflows in GitHub, the largest social coding platform. Thanks to its deep integration into GitHub, GitHub Actions can be used to automate a wide ... provide quantitative empirical evidence that reusing Actions in GitHub workflows is common practice, even if this reuse ...
Tópico(s): Scientific Computing and Data Management
2023 - Elsevier BV | Journal of Systems and Software
... rivals of well-known AlphaFold2, including ESMFold (https://github.com/facebookresearch/esm) developed by the Meta AI ... from bacteria, viruses, and other microorganisms; RoseTTAFold (https://github.com/RosettaCommons/RoseTTAFold) developed by David Baker, which ... 1998 and great academic reputation; Uni-Fold (https://github.com/dptech-corp/Uni-Fold) developed by DP ... 5281/zenodo.4533424. RoseTTAFold Diffusion (RF Diffusion, https://github.com/RosettaCommons/RFdiffusion) developed by David Baker proposes ... novel ones with the same shapes. Progen (https://github.com/salesforce/progen) developed by Salesforce Research is ...
Tópico(s): Protein Structure and Dynamics
2023 - Elsevier BV | The Innovation
Pedro Henrique Pereira Braga, Katherine Hébert, Emma J. Hudgins, Eric R. Scott, Brandon P.M. Edwards, Luna L. Sánchez‐Reyes, Matthew Grainger, Vivienne Foroughirad, Friederike Hillemann, Allison D. Binley, Cole B. Brookson, Kaitlyn M. Gaynor, Saeed Shafiei Sabet, Ali Güncan, Helen Weierbach, Dylan Gomes, Robert Crystal‐Ornelas,
... code as well as document research is fundamental. GitHub is an online, cloud‐based service that can ... and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To ... in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 ... responsibilities, we describe how the optimal use of GitHub features may vary among members of a research ... ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries ...
Tópico(s): Species Distribution and Climate Change
2023 - Wiley | Methods in Ecology and Evolution
Wubin Ding, David Goldberg, Wanding Zhou,
... essential Python libraries, including matplotlib [12], pandas (https://github.com/pandas-dev/pandas), scipy [13], and numpy [ ... the help of the open-source community on Github, it can be enhanced further. For more examples, please refer to the documentation site: https://dingwb.github.io/PyComplexHeatmap. As single-cell sequencing sample sizes ... these two packages can be found at https://github.com/DingWB/PyComplexHeatmap/tree/main/comparison. While PyComplexHeatmap ... The PyComplexHeatmap package and documentation are available on Github: https://github.com/DingWB/PyComplexHeatmap. Supplementary materials (figures, ...
Tópico(s): Gene expression and cancer classification
2023 - Wiley | iMeta
Siti N. Yaakub, Tristan A. White, Eric Kerfoot, Lennart Verhagen, Alexander Hammers, Elsa Fouragnan,
... transcranial ultrasound stimulation (TUS) studies in humans (https://github.com/sitiny/mr-to-pct). Our validated open- ... open-source MR to pseudo-CT toolbox (https://github.com/sitiny/mr-to-pct) and code to ... temperature as described in the Supplementary Methods (https://github.com/sitiny/BRIC_TUS_Simulation_Tools). Since its ... as described in this work are available on GitHub: https://github.com/sitiny/mr-to-pct and https://github.com/sitiny/BRIC_TUS_Simulation_Tools. The pre- ...
Tópico(s): Ultrasound Imaging and Elastography
2023 - Elsevier BV | Brain stimulation