Merge pull request #55 from supernord/main

Adding draft paper content

docs/publications/BioHackrXiv/paper.bib

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+@article{10.1093/nar/gkac247,
+    author = {The Galaxy Community},
+    title = "{The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update}",
+    journal = {Nucleic Acids Research},
+    volume = {50},
+    number = {W1},
+    pages = {W345-W351},
+    year = {2022},
+    month = {04},
+    abstract = "{Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with \\>230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.}",
+    issn = {0305-1048},
+    doi = {10.1093/nar/gkac247},
+    url = {https://doi.org/10.1093/nar/gkac247},
+    eprint = {https://academic.oup.com/nar/article-pdf/50/W1/W345/45189566/gkac247.pdf},
+}
+
+@article{rost2016openms,
+  title={OpenMS: a flexible open-source software platform for mass spectrometry data analysis},
+  author={R{\"o}st, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and others},
+  journal={Nature Methods},
+  doi={10.1038/nmeth.3959},
+  volume={13},
+  number={9},
+  pages={741--748},
+  year={2016},
+  publisher={Nature Publishing Group}
+}
+
+@article{doi:10.1128/AEM.01541-09,
+author = {Patrick D. Schloss and Sarah L. Westcott and Thomas Ryabin and Justine R. Hall and Martin Hartmann and Emily B. Hollister and Ryan A. Lesniewski and Brian B. Oakley and Donovan H. Parks and Courtney J. Robinson and Jason W. Sahl and Blaz Stres and Gerhard G. Thallinger and David J. Van Horn and Carolyn F. Weber},
+title = {Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities},
+journal = {Applied and Environmental Microbiology},
+volume = {75},
+number = {23},
+pages = {7537-7541},
+year = {2009},
+doi = {10.1128/AEM.01541-09},
+URL = {https://journals.asm.org/doi/abs/10.1128/aem.01541-09},
+eprint = {https://journals.asm.org/doi/pdf/10.1128/aem.01541-09},
+abstract = { mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer. }
+}
+
+@article{black2021edam,
+  title={EDAM: The bioscientific data analysis ontology (update 2021)[version 1; not peer reviewed]},
+  author={Black, Melissa and Lamothe, Lucie and Eldakroury, Hager and Kierkegaard, Mads and Priya, Ankita and Machinda, Anne and Singh Khanduja, Uttam and Patoliya, Drashti and Rathi, Rashika and Che Nico, Tawah Peggy and others},
+  year={2022},
+  doi={10.7490/f1000research.1118900.1},
+  journal={F1000Research},
+  publisher={F1000}
+}
+
+@article{biotoolsSchema,
+    author = {Ison, Jon and Ienasescu, Hans and Rydza, Emil and Chmura, Piotr and Rapacki, Kristoffer and Gaignard, Alban and Schwämmle, Veit and van Helden, Jacques and Kala{\v{s}}, Mat{\'u}{\v{s}} and M{\'e}nager, Herv{\'e}},
+    title = "{biotoolsSchema: a formalized schema for bioinformatics software description}",
+    journal = {GigaScience},
+    volume = {10},
+    number = {1},
+    pages = {giaa157},
+    year = {2021},
+    month = {01},
+    issn = {2047-217X},
+    doi = {10.1093/gigascience/giaa157},
+    url = {https://doi.org/10.1093/gigascience/giaa157},
+    eprint = {https://academic.oup.com/gigascience/article-pdf/10/1/giaa157/36126150/giaa157.pdf},
+}
+
+@article{Ison2019,
+  title = {The bio.tools registry of software tools and data resources for the life sciences},
+  volume = {20},
+  ISSN = {1474-760X},
+  url = {http://doi.org/10.1186/s13059-019-1772-6},
+  DOI = {10.1186/s13059-019-1772-6},
+  number = {1},
+  journal = {Genome Biology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Ison,  Jon and Ienasescu,  Hans and Chmura,  Piotr and Rydza,  Emil and M{\'e}nager, Herv{\'e} and Kala{\v{s}}, Mat{\'u}{\v{s}} and Schw\"{a}mmle,  Veit and Gr\"{u}ning,  Bj\"{o}rn and Beard,  Niall and Lopez,  Rodrigo and Duvaud,  Severine and Stockinger,  Heinz and Persson,  Bengt and Vařeková,  Radka Svobodová and Raček,  Tomáš and Vondrášek,  Jiří and Peterson,  Hedi and Salumets,  Ahto and Jonassen,  Inge and Hooft,  Rob and Nyr\"{o}nen,  Tommi and Valencia,  Alfonso and Capella,  Salvador and Gelpí,  Josep and Zambelli,  Federico and Savakis,  Babis and Leskošek,  Brane and Rapacki,  Kristoffer and Blanchet,  Christophe and Jimenez,  Rafael and Oliveira,  Arlindo and Vriend,  Gert and Collin,  Olivier and van Helden,  Jacques and Løngreen,  Peter and Brunak,  Søren},
+  year = {2019},
+  month = aug 
+}
+
+@article {Bray2022.03.13.483965,
+    author = {Simon Bray and Matthias Bernt and Nicola Soranzo and Marius van den Beek and B{\'e}r{\'e}nice Batut and Helena Rasche and Martin {\v C}ech and Peter Cock and Anton Nekrutenko and Bj{\"o}rn Gr{\"u}ning and John Chilton},
+    title = {Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses},
+    elocation-id = {2022.03.13.483965},
+    year = {2022},
+    doi = {10.1101/2022.03.13.483965},
+    publisher = {Cold Spring Harbor Laboratory},
+    abstract = {There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo{\textquoteright}s implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.Competing Interest StatementThe authors have declared no competing interest.},
+    URL = {https://www.biorxiv.org/content/early/2022/03/14/2022.03.13.483965},
+    eprint = {https://www.biorxiv.org/content/early/2022/03/14/2022.03.13.483965.full.pdf},
+    journal = {bioRxiv}
+}
+
+@misc{datatables,
+	title = {{DataTables} {\textbar} {Table} plug-in for {jQuery}},
+	url = {https://datatables.net/},
+	urldate = {2023-11-28},
+}
+
+@misc{conda,
+    title = {Anaconda Software Distribution},
+    url = {https://anaconda.com},
+    urldate = {2016-11-01}
+}
+
+@article{edamBrowser, doi = {10.21105/joss.00698}, url = {https://doi.org/10.21105/joss.00698}, year = {2018}, publisher = {The Open Journal}, volume = {3}, number = {27}, pages = {698}, author = {Bryan Brancotte and Christophe Blanchet and Hervé Ménager}, title = {A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.}, journal = {Journal of Open Source Software} } 
+
+@misc{edamBrowserCode
+  doi = {10.5281/zenodo.5808818},
+  url = {https://zenodo.org/doi/10.5281/zenodo.5808818},
+  author = {Eldakroury,  Hager and Dhamija,  Sakshi and Rathi,  Rashika and Patoliya,  Drashti and Nkwuda,  Sunday Cletus and Singh,  Guneet and Yadav,  Pooja and D'oleo,  Kelly and Cherop,  Marlene and Che Nico,  Tawah Peggy and Kalaš,  Matúš and Ménager,  Hervé and Brancotte,  Bryan},
+  keywords = {Ontology browser,  Biosciences,  Imaging,  Machine learning,  Domain ontology,  EDAM},
+  language = {en},
+  title = {EDAM Browser 2.0.0: Browsing multiple versions of EDAM},
+  publisher = {Zenodo},
+  year = {2021},
+  copyright = {MIT License}
+}
+
+@article{batut_community-driven_2018,
+	title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}},
+	volume = {6},
+	issn = {24054712},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S2405471218302308},
+	doi = {10.1016/j.cels.2018.05.012},
+	language = {en},
+	number = {6},
+	urldate = {2024-02-26},
+	journal = {Cell Systems},
+	author = {Batut, Bérénice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Guéguen, Loraine and Čech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivière, Delphine and Le Corguillé, Gildas and Manke, Thomas and Mareuil, Fabien and Ramírez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Grüning, Björn},
+	month = jun,
+	year = {2018},
+	pages = {752--758.e1},
+}
+
+@Article{elixirBiodiversity,
+AUTHOR = { Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Heil, KF and Hughes, GM and Jermiin, LS and Kala\v{s}, M and Lanfear, J and Pafilis, E and Papageorgiou, AC and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T},
+TITLE = {{The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity [version 1; peer review: 1 approved with reservations, 1 not approved]}},
+JOURNAL = {F1000Research},
+VOLUME = {12},
+YEAR = {2023},
+NUMBER = {499},
+DOI = {10.12688/f1000research.133724.1}
+}
+
+@misc{RSEc,
+  doi = {10.7490/f1000research.1119604.1},
+  url = {https://f1000research.com/slides/12-1044},
+  author = {Ienasescu,  Hans and Capella-Gutiérrez,  Salvador and Coppens,  Frederik and Fernández,  José María and Gaignard,  Alban and Goble,  Carole and Gr\"{u}ning,  Bj\"{o}rn and Gustafsson,  Johan and Gelpi,  Josep Ll and Harrow,  Jennifer and Manos,  Steven and Miura,  Kota and M\"{o}ller,  Steffen and Owen,  Stuart and Paul-Gilloteaux,  Perrine and Peterson,  Hedi and Pitoulias,  Manthos and Tedds,  Jonathan and Repchevsky,  Dmitri and Zambelli,  Federico and Zharkov,  Oleg and Kala\v{s},  Mat\'{u}\v{s} and Ménager,  Hervé},
+  title = {The ELIXIR research software ecosystem: an open software metadata commons (BOSC track) [version 1; not peer reviewed]},
+  publisher = {F1000 Research},
+  year = {2023}
+}
+
+@article{bioimageWorkflows,
+  title = {Bioimage analysis workflows: community resources to navigate through a complex ecosystem},
+  volume = {10},
+  ISSN = {2046-1402},
+  url = {https://doi.org/10.12688/f1000research.52569.1},
+  DOI = {10.12688/f1000research.52569.1},
+  journal = {F1000Research},
+  publisher = {F1000 Research Ltd},
+  author = {Paul-Gilloteaux,  Perrine and Tosi,  Sébastien and Hériché,  Jean-Karim and Gaignard,  Alban and Ménager,  Hervé and Marée,  Raphaël and Baecker,  Volker and Klemm,  Anna and Kalaš,  Matúš and Zhang,  Chong and Miura,  Kota and Colombelli,  Julien},
+  year = {2021},
+  month = apr,
+  pages = {320}
+}