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Ecosystems in GitHub and a Method for Ecosystem Identification Using Reference Coupling

Kelly Blincoe, Francis Harrison, Daniela Damian
2015 2015 IEEE/ACM 12th Working Conference on Mining Software Repositories  
In this paper, we propose a new method, known as reference coupling, for detecting technical dependencies between projects.  ...  We use our method to identify ecosystems in GitHubhosted projects, and we identify several characteristics of the identified ecosystems.  ...  We used this reference coupling method to identify ecosystems in GitHub-hosted projects by using an existing community detection algorithm to identify densely connected clusters of projects.  ... 
doi:10.1109/msr.2015.26 dblp:conf/msr/BlincoeHD15 fatcat:fbvyxbh3jbc3db65oautfew44a

Identification-Method Research for Open-Source Software Ecosystems

Zhifang Liao, Ningwei Wang, Shengzong Liu, Yan Zhang, Hui Liu, Qi Zhang
2019 Symmetry  
Therefore, how to extract useful information in GitHub and identify software ecosystems is particularly important, and it is also a research area in symmetry.  ...  A variety of open-source software ecosystems have emerged, for instance, GitHub, StackOverflow, and SourceForge.  ...  Acknowledgments: We would like to thank the referees for their valuable comments and suggestions. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/sym11020182 fatcat:ustevvmw2bb57mesjxxi75g22e

Socio-technical evolution of the Ruby ecosystem in GitHub

Eleni Constantinou, Tom Mens
2017 2017 IEEE 24th International Conference on Software Analysis, Evolution and Reengineering (SANER)  
We study the Ruby ecosystem in GitHub over a nine-year period by carrying out a socio-technical analysis of the co-evolution of a large number of base projects and their forks.  ...  We present an empirical study of the magnitude and effect of permanent modifications in both the social and technical parts of a software ecosystem.  ...  We express our gratitude to Philippe Grosjean and the anonymous reviewers for the very useful feedback on an earlier version of this article.  ... 
doi:10.1109/saner.2017.7884607 dblp:conf/wcre/ConstantinouM17 fatcat:ucs3bzi5hvglnfzji4bffqjlzy

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

Johannes Rainer, Andrea Vicini, Liesa Salzer, Jan Stanstrup, Josep M. Badia, Steffen Neumann, Michael A. Stravs, Vinicius Verri Hernandes, Laurent Gatto, Sebastian Gibb, Michael Witting
2022 Metabolites  
We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics  ...  Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference  ...  provide a comprehensive infrastructure for the annotation and identification of features from untargeted LC-MS and LC-MS/MS experiments using established methods.  ... 
doi:10.3390/metabo12020173 pmid:35208247 pmcid:PMC8878271 fatcat:ieu6n25kqzgpzeddfckdm7dqka

World of Code: Enabling a Research Workflow for Mining and Analyzing the Universe of Open Source VCS data [article]

Yuxing Ma, Tapajit Dey, Chris Bogart, Sadika Amreen, Marat Valiev, Adam Tutko, David Kennard, Russell Zaretzki, Audris Mockus
2020 arXiv   pre-print
To answer such questions we: a) create a very large and frequently updated collection of version control data in the entire FLOSS ecosystems named World of Code (WoC), that can completely cross-reference  ...  To evaluate its research potential and to create vignettes for its usage, we employ WoC in conducting several research tasks.  ...  Acknowledgment This work was supported by the National Science Foundation NSF Awards 1633437, 1901102, and 1925615.  ... 
arXiv:2010.16196v1 fatcat:wonvbkuqtncttja2us5uiidvdy

Mining file histories: should we consider branches?

Vladimir Kovalenko, Fabio Palomba, Alberto Bacchelli
2018 Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering - ASE 2018  
We analyze over 1,400 Git repositories of four open source ecosystems and compute modification histories for over two million files, using two different algorithms.  ...  We show that the two algorithms consistently deliver different results, but the scale of the difference varies across projects and ecosystems.  ...  The numbers of commits in the repositories within each ecosystem greatly vary. A median number of commits in a repository ranges from 172 for Github to 1,039 for OpenStack.  ... 
doi:10.1145/3238147.3238169 dblp:conf/kbse/KovalenkoPB18 fatcat:bgdujvsczfgm3bdy7ly6nvd43i

A Web API ecosystem through feature-based reuse [article]

Ruben Verborgh, Michel Dumontier
2018 arXiv   pre-print
Applying these principles enables a granular reuse of client and server code, documentation, and tools.  ...  We discuss a vision for developing Web APIs based on reuse of interface parts called features.  ...  should not depend on methods they do not use.  ... 
arXiv:1609.07108v3 fatcat:a64d5nxcvnfv3or6potmsewkjm

A Data Ecosystem to Support Machine Learning in Materials Science [article]

Ben Blaiszik, Logan Ward, Marcus Schwarting, Jonathon Gaff, Ryan Chard, Daniel Pike, Kyle Chard, Ian Foster
2019 arXiv   pre-print
Here, we present two projects, the Materials Data Facility (MDF) and the Data and Learning Hub for Science (DLHub), that address these needs.  ...  We use examples to show how MDF and DLHub capabilities can be leveraged to link data with machine learning models and how users can access those capabilities through web and programmatic interfaces.  ...  as searching by dataset name, author names, or elemental composition, and that then use Globus methods to retrieve data records identifed by such searches.  ... 
arXiv:1904.10423v1 fatcat:gibssrxzxbaqxdjsfa4ld4gd2a

A Web API Ecosystem through Feature-Based Reuse

Ruben Verborgh, Michel Dumontier
2018 IEEE Internet Computing  
Case in point: whereas Facebook and Twitter show a near-identical user interface for updating a status (a light-colored textbox with an encouraging question and a camera icon), the corresponding interactions  ...  For example, the user interfaces to update a status message on Facebook, Twitter, and Instagram are all highly similar.  ...  depend on methods they do not use.  ... 
doi:10.1109/mic.2018.032501515 fatcat:6pq27lfbr5dyvcxbgwuxlwhpei

Key Questions for Next-Generation Biomonitoring

Andreas Makiola, Zacchaeus G. Compson, Donald J. Baird, Matthew A. Barnes, Sam P. Boerlijst, Agnès Bouchez, Georgina Brennan, Alex Bush, Elsa Canard, Tristan Cordier, Simon Creer, R. Allen Curry (+33 others)
2020 Frontiers in Environmental Science  
Questions for Next-Generation Biomonitoring not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field  ...  Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems.  ...  ABo, FK, VV, MK, JP, and TC would like to acknowledge fruitful discussions in the framework of the COST action DNAqua-Net (CA15219).  ... 
doi:10.3389/fenvs.2019.00197 fatcat:garu26qrbzgbldzsc5n6fi2avy

The three major axes of terrestrial ecosystem function

Mirco Migliavacca, Talie Musavi, Miguel D. Mahecha, Jacob A. Nelson, Jürgen Knauer, Dennis D. Baldocchi, Oscar Perez-Priego, Rune Christiansen, Jonas Peters, Karen Anderson, Michael Bahn, T. Andrew Black (+55 others)
2021 Nature  
The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure.  ...  The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate.  ...  The overly tight coupling of ecosystem functions by models indicates a lack of flexibility in ecosystem responses to environmental drivers, such as adaptive carbon and water couplings.  ... 
doi:10.1038/s41586-021-03939-9 pmid:34552242 pmcid:PMC8528706 fatcat:4i4qbwx6gnerhjdhruaa4i2pjq

Hydraulic diversity of forests regulates ecosystem resilience during drought

William R. L. Anderegg, Alexandra G. Konings, Anna T. Trugman, Kailiang Yu, David R. Bowling, Robert Gabbitas, Daniel S. Karp, Stephen Pacala, John S. Sperry, Benjamin N. Sulman, Nicole Zenes
2018 Nature  
in a changing climate.  ...  Our results demonstrate that diversity in the hydraulic traits of trees mediates ecosystem resilience to drought and is likely to have an important role in future ecosystem-atmosphere feedback effects  ...  We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.  ... 
doi:10.1038/s41586-018-0539-7 pmid:30232452 fatcat:sgr3gq3jcfbodmy5p4bcw6yecu

Next-generation ensemble projections reveal higher climate risks for marine ecosystems

Derek P. Tittensor, Camilla Novaglio, Cheryl S. Harrison, Ryan F. Heneghan, Nicolas Barrier, Daniele Bianchi, Laurent Bopp, Andrea Bryndum-Buchholz, Gregory L. Britten, Matthias Büchner, William W. L. Cheung, Villy Christensen (+24 others)
2021 Nature Climate Change  
Compared with the previous generation CMIP5-forced Fish-MIP ensemble, the new ensemble ecosystem simulations show a greater decline in mean global ocean animal biomass under both strong-mitigation and  ...  Regional shifts in the direction of biomass changes highlight the continued and urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change to help support adaptation  ...  Acknowledgements We thank ISIMIP for assistance with processing ESM inputs and outputs and the ESM community for enabling these impact analyses.  ... 
doi:10.1038/s41558-021-01173-9 pmid:34745348 pmcid:PMC8556156 fatcat:kkjn7zmdqfc33efhu3m4tbbfbu

A Quantitative EEG Toolbox for the MNI Neuroinformatics Ecosystem: Normative SPM of EEG Source Spectra

Jorge Bosch-Bayard, Eduardo Aubert-Vazquez, Shawn T. Brown, Christine Rogers, Gregory Kiar, Tristan Glatard, Lalet Scaria, Lidice Galan-Garcia, Maria L. Bringas-Vega, Trinidad Virues-Alba, Armin Taheri, Samir Das (+6 others)
2020 Frontiers in Neuroinformatics  
An updated precis of the methods is provided in Appendix I as a reference for the toolbox. qEEGt/CBRAIN is the first installment of instruments developed by the neuroinformatic platform of the Cuba-Canada-China  ...  Openly releasing this software in the CBRAIN platform will facilitate the use of standardized qEEGt methods in different research and clinical settings.  ...  ACKNOWLEDGMENTS We want to acknowledge the effort of a group of persons that have been carrying out the qEEGt project at the Cuban neuroscience Center since the early 90's.  ... 
doi:10.3389/fninf.2020.00033 pmid:32848689 pmcid:PMC7427620 fatcat:oqmum373evfsndmirffvr3alk4

Bug Characteristics in Quantum Software Ecosystem [article]

Mohamed Raed El aoun, Heng Li, Foutse Khomh, Lionel Tidjon
2022 arXiv   pre-print
Quantum programming is different from classical programming, for example, the state of a quantum program is probabilistic in nature, and a quantum computer is error-prone due to the instability of quantum  ...  With the advance in quantum computing in recent years, quantum software becomes vital for exploring the full potential of quantum computing systems.  ...  To select representative projects from the quantum ecosystem, we searched through the GitHub search API. We used two ways to search for quantum software projects.  ... 
arXiv:2204.11965v1 fatcat:o2hg5jpipnfgxnaskgcjrxxjuq
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