Merge pull request #83 from matuskalas/patch-3

Cite QIIME 2 instead of mothur?

docs/publications/BioHackrXiv/paper.bib

@@ -206,3 +206,18 @@ @misc{dev_tool_annotation
 	url = {https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-annotation/tutorial.html},
 	note = {Online; accessed Thu Mar 14 2024}
 }
+
+@article{Bolyen2019,
+  title = {Reproducible,  interactive,  scalable and extensible microbiome data science using QIIME 2},
+  volume = {37},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-019-0209-9},
+  DOI = {10.1038/s41587-019-0209-9},
+  number = {8},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Bolyen,  Evan and Rideout,  Jai Ram and Dillon,  Matthew R. and Bokulich,  Nicholas A. and Abnet,  Christian C. and Al-Ghalith,  Gabriel A. and Alexander,  Harriet and Alm,  Eric J. and Arumugam,  Manimozhiyan and Asnicar,  Francesco and Bai,  Yang and Bisanz,  Jordan E. and Bittinger,  Kyle and Brejnrod,  Asker and Brislawn,  Colin J. and Brown,  C. Titus and Callahan,  Benjamin J. and Caraballo-Rodríguez,  Andrés Mauricio and Chase,  John and Cope,  Emily K. and Da Silva,  Ricardo and Diener,  Christian and Dorrestein,  Pieter C. and Douglas,  Gavin M. and Durall,  Daniel M. and Duvallet,  Claire and Edwardson,  Christian F. and Ernst,  Madeleine and Estaki,  Mehrbod and Fouquier,  Jennifer and Gauglitz,  Julia M. and Gibbons,  Sean M. and Gibson,  Deanna L. and Gonzalez,  Antonio and Gorlick,  Kestrel and Guo,  Jiarong and Hillmann,  Benjamin and Holmes,  Susan and Holste,  Hannes and Huttenhower,  Curtis and Huttley,  Gavin A. and Janssen,  Stefan and Jarmusch,  Alan K. and Jiang,  Lingjing and Kaehler,  Benjamin D. and Kang,  Kyo Bin and Keefe,  Christopher R. and Keim,  Paul and Kelley,  Scott T. and Knights,  Dan and Koester,  Irina and Kosciolek,  Tomasz and Kreps,  Jorden and Langille,  Morgan G. I. and Lee,  Joslynn and Ley,  Ruth and Liu,  Yong-Xin and Loftfield,  Erikka and Lozupone,  Catherine and Maher,  Massoud and Marotz,  Clarisse and Martin,  Bryan D. and McDonald,  Daniel and McIver,  Lauren J. and Melnik,  Alexey V. and Metcalf,  Jessica L. and Morgan,  Sydney C. and Morton,  Jamie T. and Naimey,  Ahmad Turan and Navas-Molina,  Jose A. and Nothias,  Louis Felix and Orchanian,  Stephanie B. and Pearson,  Talima and Peoples,  Samuel L. and Petras,  Daniel and Preuss,  Mary Lai and Pruesse,  Elmar and Rasmussen,  Lasse Buur and Rivers,  Adam and Robeson,  Michael S. and Rosenthal,  Patrick and Segata,  Nicola and Shaffer,  Michael and Shiffer,  Arron and Sinha,  Rashmi and Song,  Se Jin and Spear,  John R. and Swafford,  Austin D. and Thompson,  Luke R. and Torres,  Pedro J. and Trinh,  Pauline and Tripathi,  Anupriya and Turnbaugh,  Peter J. and Ul-Hasan,  Sabah and van der Hooft,  Justin J. J. and Vargas,  Fernando and Vázquez-Baeza,  Yoshiki and Vogtmann,  Emily and von Hippel,  Max and Walters,  William and Wan,  Yunhu and Wang,  Mingxun and Warren,  Jonathan and Weber,  Kyle C. and Williamson,  Charles H. D. and Willis,  Amy D. and Xu,  Zhenjiang Zech and Zaneveld,  Jesse R. and Zhang,  Yilong and Zhu,  Qiyun and Knight,  Rob and Caporaso,  J. Gregory},
+  year = {2019},
+  month = jul,
+  pages = {852–857}
+}

docs/publications/BioHackrXiv/paper.md

@@ -64,7 +64,7 @@ authors_short: Paul Zierep, Bérénice Batut, \emph{et al.}
 Galaxy [@citesAsAuthority:10.1093/nar/gkac247] is a web-based analysis platform offering almost 10,000 different tools, which are developed in various GitHub repositories.  
 Furthermore, the Galaxy community embraces granular implementation of software tools as sub-modules. 
 In practice, this means that tool suites are separated into sets of Galaxy tools, also known as Galaxy wrappers, that contain functionality of a corresponding sub-component.
-Some key examples of tool suites include [Mothur](https://bio.tools/mothur) [@citesAsAuthority:10.1128/AEM.01541-09] and [OpenMS](https://bio.tools/openms) [@citesAsAuthority:rost2016openms], which translate to tens and even hundreds of Galaxy tools. 
+Some key examples of tool suites include [QIIME 2](https://bio.tools/qiime2) [@citesAsAuthority:Bolyen2019] and [OpenMS](https://bio.tools/openms) [@citesAsAuthority:rost2016openms], which translate to tens and even hundreds of Galaxy tools. 
 While granularity supports the composability of tools into diverse purpose-specific workflows, this decentralised development and modular architecture can make it difficult for Galaxy users to find and use tools. 
 It may also result in Galaxy tool-wrapper developers duplicating efforts by simultaneously wrapping the same software. 
 This is further complicated by the scarcity of tool metadata, which prevents filtering of tools as relevant for a specific scientific community or domain, and makes it impossible to employ advanced filtering by ontology terms like the ones from EDAM [@citesAsAuthority:black2021edam].