diff --git a/jose.00193/10.21105.jose.00193.crossref.xml b/jose.00193/10.21105.jose.00193.crossref.xml new file mode 100644 index 0000000..d777397 --- /dev/null +++ b/jose.00193/10.21105.jose.00193.crossref.xml @@ -0,0 +1,235 @@ + + + + 20241020164424-e4323d3a669767cba07cee49a7b4d7b66422319a + 20241020164424 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Education + JOSE + 2577-3569 + + 10.21105/jose + https://jose.theoj.org + + + + + 10 + 2024 + + + 7 + + 80 + + + + The Argo Online School: An e-learning tool to get +started with Argo + + + + Alberto + González-Santana + https://orcid.org/0000-0001-5781-9330 + + + Pedro + Vélez-Belchí + https://orcid.org/0000-0003-2404-5679 + + + + 10 + 20 + 2024 + + + 193 + + + 10.21105/jose.00193 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.13929139 + + + GitHub review issue + https://github.com/openjournals/jose-reviews/issues/193 + + + + 10.21105/jose.00193 + https://jose.theoj.org/papers/10.21105/jose.00193 + + + https://jose.theoj.org/papers/10.21105/jose.00193.pdf + + + + + + Argo user’s manual + Argo data management Team + 10.13155/29825 + 2022 + Argo data management Team. (2022). +Argo user’s manual (Ifremer, Ed.) [Report]. +https://doi.org/10.13155/29825 + + + An introduction to earth and environmental +data science + Ryan Abernathey + GitHub repository + 2021 + Ryan Abernathey, K. K., & Crone, +T. (2021). An introduction to earth and environmental data science. In +GitHub repository. GitHub. +https://github.com/earth-env-data-science/earth-env-data-science-book + + + An interactive quiz generator for jupyter +notebooks and jupyter book + Smith + GitHub repository + 2021 + Smith, A. M., Thaney, K., & +Hahnel, M. (2021). An interactive quiz generator for jupyter notebooks +and jupyter book. In GitHub repository. GitHub. +https://github.com/jmshea/jupyterquiz + + + Argo float data and metadata from global data +assembly centre (argo GDAC) + Argo + 10.17882/42182 + 2021 + Argo. (2021). Argo float data and +metadata from global data assembly centre (argo GDAC). SEANOE. +https://doi.org/10.17882/42182 + + + Jupyter book + Executable Books Community + 10.5281/zenodo.4539666 + 2020 + Executable Books Community. (2020). +Jupyter book (Version v0.10). Zenodo. +https://doi.org/10.5281/zenodo.4539666 + + + On the Future of Argo: A Global, Full-Depth, +Multi-Disciplinary Array + Roemmich + Frontiers in Marine Science + 6 + 10.3389/fmars.2019.00439 + 2019 + Roemmich, D., Alford, M. H., +Claustre, H., Johnson, K., King, B., Moum, J., Oke, P., Owens, W. B., +Pouliquen, S., Purkey, S., Scanderbeg, M., Suga, T., Wijffels, S., +Zilberman, N., Bakker, D., Baringer, M., Belbeoch, M., Bittig, H. C., +Boss, E., … Yasuda, I. (2019). On the Future of Argo: A Global, +Full-Depth, Multi-Disciplinary Array. Frontiers in Marine Science, 6, +439. https://doi.org/10.3389/fmars.2019.00439 + + + Fifteen years of ocean observations with the +global Argo array + Riser + Nature Clim. Change + 2 + 6 + 10.1038/nclimate2872 + 2016 + Riser, S. C., Freeland, H. J., +Roemmich, D., Wijffels, S., Troisi, A., Belbeoch, M., Gilbert, D., Xu, +J., Pouliquen, S., Thresher, A., Le Traon, P.-Y., Maze, G., Klein, B., +Ravichandran, M., Grant, F., Poulain, P.-M., Suga, T., Lim, B., Sterl, +A., … Jayne, S. R. (2016). Fifteen years of ocean observations with the +global Argo array. Nature Clim. Change, 6(2), 145–153. +https://doi.org/10.1038/nclimate2872 + + + Argo quality control manual for CTD and +trajectory data + Wong Annie + 10.13155/33951 + 2022 + Wong Annie, C. T., Keeley Robert. +(2022). Argo quality control manual for CTD and trajectory data. Argo; +Argo Data Management Team. +https://doi.org/10.13155/33951 + + + Argovis: A web application for fast delivery, +visualization, and analysis of argo data + Tucker + Journal of Atmospheric and Oceanic +Technology + 3 + 37 + 10.1175/JTECH-D-19-0041.1 + 2020 + Tucker, T., Giglio, D., Scanderbeg, +M., & Shen, S. S. P. (2020). Argovis: A web application for fast +delivery, visualization, and analysis of argo data. Journal of +Atmospheric and Oceanic Technology, 37(3), 401–416. +https://doi.org/10.1175/JTECH-D-19-0041.1 + + + Jupyter notebooks – a publishing format for +reproducible computational workflows + Kluyver + 10.3233/978-1-61499-649-1-87 + 2016 + Kluyver, T., Ragan-Kelley, B., Pérez, +F., Granger, B., Bussonnier, M., Frederic, J., Kelley, K., Hamrick, J., +Grout, J., Corlay, S., Ivanov, P., Avila, D., Abdalla, S., & +Willing, C. (2016). Jupyter notebooks – a publishing format for +reproducible computational workflows (F. Loizides & B. Schmidt, +Eds.; pp. 87–90). IOS Press. +https://doi.org/10.3233/978-1-61499-649-1-87 + + + Argopy: A python library for argo ocean data +analysis + Maze + Journal of Open Source +Software + 53 + 5 + 10.21105/joss.02425 + 2020 + Maze, G., & Balem, K. (2020). +Argopy: A python library for argo ocean data analysis. Journal of Open +Source Software, 5(53), 2425. +https://doi.org/10.21105/joss.02425 + + + + + + diff --git a/jose.00193/10.21105.jose.00193.pdf b/jose.00193/10.21105.jose.00193.pdf new file mode 100644 index 0000000..70ef181 Binary files /dev/null and b/jose.00193/10.21105.jose.00193.pdf differ diff --git a/jose.00193/paper.jats/10.21105.jose.00193.jats b/jose.00193/paper.jats/10.21105.jose.00193.jats new file mode 100644 index 0000000..2c6e889 --- /dev/null +++ b/jose.00193/paper.jats/10.21105.jose.00193.jats @@ -0,0 +1,583 @@ + + +
+ + + + +Journal of Open Source Education +JOSE + +2577-3569 + +Open Journals + + + +193 +10.21105/jose.00193 + +The Argo Online School: An e-learning tool to get started +with Argo + + + +https://orcid.org/0000-0001-5781-9330 + +González-Santana +Alberto + + + + +https://orcid.org/0000-0003-2404-5679 + +Vélez-Belchí +Pedro + + + + + +Centro Oceanográfico de Canarias, Instituto Español de +Oceanografía (IEO - CSIC) + + + + +14 +10 +2024 + +7 +80 +193 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Jupyter Notebooks +Oceanography +Operational oceanography +Observing systems +Robotics + + + + + + Summary +

The Argo Online School (AoS) is a collection of + videos, animations and hands-on Python-driven Jupyter notebooks + designed to make the data accessible from more than 4,000 profiling + floats that constitute the Argo program. The Argo program samples, in + near real-time, the upper 2,000 meters of the ocean using a fleet of + floats that drift with the ocean currents. The AoS consists of 28 + chapters about the Argo program and its data, organized into a total + of 3 lessons and 2 self-assessment sections:

+ + +

Lesson 1 is intended to introduce the basics of Argo, its + objectives and key elements, such as the structure of the Argo + floats and their operation in the open ocean.

+
+ +

Lesson 2 focuses on the data coming from the Argo network, from + its organization to its accessibility. Data quality control is + also addressed through its two main modes: Real-Time and + Delayed-Mode.

+
+ +

Lesson 3 is the AoS hands-on component, and it requires basic + knowledge of Python. It provides a set of instructions for + preparing a Python environment in case the user wants to run the + Python Jupyter Notebooks on a local machine. This environment + already includes recommended packages. The walk-through of Lesson + 3 shows how to work with the netCDF format, how to access and + process Argo data, and create visualizations to enhance + understanding of the information derived from Argo data.

+
+
+

The target audience of the AoS is high school, undergraduate or + early graduate students. The programming content in Lesson 3 offers an + ideal opportunity to support students pursuing a technical or science + curriculum. Lessons 1 and 2 form a closed module and can be used + independently by learners who wish to focus solely on Argo. It is + recommended not to skip any lesson in the AoS, as the content is + carefully structured from simpler to more complex concepts, providing + a progressive learning experience. Users have the opportunity to + self-assess their learning progress through the proposed interactive + self-assessments in the AoS.

+

The AoS has been designed to be expanded in the future to follow + the implementation of new features in the Argo program.

+
+ + Statement of need +

Argo + (Riser + et al., 2016; + Roemmich + et al., 2019) is an international program that collects + information from inside the ocean using a fleet of floats that drift + with the ocean currents. The floats move up and down between the + surface and a mid-water level, measuring ocean variables, and spend + almost their entire lifespan below the surface. Since 2012, Argo has + collected over 100,000 oceanographic profiles per year and consists of + approximately 4,000 floats, making it the major component of the + Global + Ocean Observing System.

+

Although data from Argo + (Argo, + 2021) is publicly and freely available, it represents a vast + dataset with thousands of files. The accompanying documentation can be + quite complex, as it must address the various models of floats and + sensors, as well as the traceability of quality control for all + measurements. The Argo community has always recognized the challenges + faced by new users in managing the complex and extensive datasets from + the network. In this context, the Argo Online School meets the need + for effective communication about the Argo program and how its + invaluable dataset can be utilized for various applications.

+

The Argo Online School leverages the potential of e-learning tools + to provide a variety of resources to users, thereby promoting and + enhancing access to and use of Argo data. In this way, the AoS is + defined as an e-learning tool that offers an interactive environment + similar to other established educational platforms. It is a tool with + significant educational potential that aims not only to demonstrate + the basic steps for using Argo data but also to empower users to + tackle future programming scenarios in their academic + and professional careers with confidence.

+

The AoS was presented at the + 2nd + Ocean Observers Workshop on November 20th, 2021 and at the + 22nd + Argo Data Management Team meeting on December 10, 2021.

+
+ + Notes on instructional design +

The AoS aims to teach the fundamental concepts needed to understand + and use Argo data. It does not seek to cover every aspect of the Argo + program, as comprehensive documentation is available from the Argo + Data Management Team + (http://www.argodatamgt.org/Documentation) + Wong Annie + (2022) + for deeper learning. The AoS is also not library or Application + Programming Interface to ease Argo data access, as other initiatives + already fulfill that purpose, among others, Argopy, a + Python library for Argo data beginners and experts + (Maze + & Balem, 2020) or ArgoVis, a web + application for fast delivery, visualization, and analysis of argo + Data + (Tucker + et al., 2020).

+

The AoS is a set of videos and hands-on Python-driven Jupyter + notebooks, designed for high school, undergraduate or graduate + students in any discipline, and it offers:

+ + +

An overview of the Argo program and an assessment of the need + for Argo.

+
+ +

A description of how the Argo data is organized.

+
+ +

A description of how to access the Argo data.

+
+ +

A description of the main characteristics of the Argo data + format: the netCDF.

+
+ +

A review of the main characteristics of the quality controls + used: Real-Time and Delayed-Mode.

+
+ +

Step-by-step instructions on data access, processing, and + product generation, through the execution of commands based on the + programming language Python.

+
+
+

All content is divided into three lessons: 1. The Argo Program, + that describes the basic concepts of this ocean observing network; 2. + The Argo Data, that describes how the data is organized; and 3. Using + the Argo data, that takes the knowledge of the previous sections and + Python-driven Jupyter notebooks to teach how to use the data. Finally, + a quiz section is included for self-assessment.

+

Lessons 1 and 2 are designed for students with knowledge comparable + to that acquired in high school, this is, basic knowledge about the + relationships between the Earth’s processes, weather and climate; and + basic skills in interpreting maps, charts, and tables to organize and + analyze data

+

These lessons are aimed at users with minimal or no knowledge of + the Argo network, and they are a closed module and could be used by a + learner without using Lesson 3, assuming the goal is simply to learn + about Argo. Lessons 1 and 2 contain 32 short videos and 14 chapters + and require about 5 hours to completed. Lesson 3 is intended for + advanced users, as it requires basic programming skills in + Python.However, Lesson 3 follows a step by step approach, to + facilitate the transition of users coming from Lessons 1 and 2. The + basic recommendations and instructions for configuring the hands-on + section of the AoS are also provided, whether the users want to work + online or if they want to work on their local computer. Specific + python libraries and packages are recommended to guarantee the correct + functioning of the AoS. Lesson 3 contains 8 short videos and 14 + chapters and requires about 10 hours to be completed, assuming basic + knowledge of Python.

+

The AoS has been developed using markdown, Python driven Jupyter + notebooks + (Kluyver + et al., 2016) and Jupyter book + (Executable + Books Community, 2020), open source projects that allow editing + control in a clear and easy way, and also permits web-based + interactive development environments that contain code, visualizations + and texts. It is widely used for data science, and inspired by the + course + An + Introduction to Earth and Environmental Data Science + (Ryan + Abernathey & Crone, 2021).

+

The AoS is accessible through the Euro-Argo webpage + https://www.euro-argo.eu/argo-online-school, but all the content that + makes it up is hosted in a public GitHub repository.: + https://github.com/euroargodev/argoonlineschool. + As long as the Argo program continues to grow, the AoS will too. This + first version contains the basic content of Argo; subsequent versions + will showcase the newest aspects of the Argo network, such as + biochemical measurements, deep observations and more. Anyone + interested in helping to further develop the AoS may open an issue on + the public GitHub repository to begin organizing the update.

+

Given the structure of the AoS, it could be used for educational + purposes. For high school students, Lessons 1 and 2 could be a project + to identify scientific questions that ocean observations, like those + from Argo, may help address while developing essential know-how. For + students with a curriculum that includes programming in Python, other + projects could involve finding the seasonal change in surface + temperature at a specific ocean and comparing it with changes at 1,000 + m or 2,000 m, or explaining the trajectory of a given float, which can + be quite challenging. Teachers are welcome to open an issue in the + github repository to get assistance in how to develop new + projects.

+

As part of the Argo community, the AoS follows the same philosophy + regarding data access. To ensure barrier-free learning, the + information and data provided in the AoS is open access to the public + and free of charge and therefore, no subscription is required

+
+ + Acknowledgements +

The AoS has been possible thanks to the collaboration of the + Euro-Argo members, the Argo Steering Team + (https://argo.ucsd.edu) + and has been funded by the European Union’s Horizon 2020 research and + innovation program under grant agreement Euro-Argo RISE 824131 + (https://www.euro-argo.eu/EU-Projects/Euro-Argo-RISE-2019-2022).

+

The audiovisual work has been recorded and edited by Rafael Méndez + Pérez + (http://rafaelmendezp.com/) + while proofreading and english coaching support was provided by + Agustín Prunell-Friend. The self-assessment sections are based on John + M. Shea + (Smith + et al., 2021) software.

+
+ + + + + + + + Argo data management Team + + Argo user’s manual + + Ifremer + + 2022 + https://doi.org/10.13155/29825 + 10.13155/29825 + + + + + + Ryan AbernatheyKerry Key + CroneTim + + An introduction to earth and environmental data science + GitHub repository + GitHub + 2021 + https://github.com/earth-env-data-science/earth-env-data-science-book + + + + + + SmithA. M. + ThaneyK. + HahnelM. + + An interactive quiz generator for jupyter notebooks and jupyter book + GitHub repository + GitHub + 2021 + https://github.com/jmshea/jupyterquiz + + + + + + Argo + + Argo float data and metadata from global data assembly centre (argo GDAC) + SEANOE + 2021 + https://doi.org/10.17882/42182 + 10.17882/42182 + + + + + + Executable Books Community + + Jupyter book + Zenodo + 202002 + https://doi.org/10.5281/zenodo.4539666 + 10.5281/zenodo.4539666 + + + + + + RoemmichDean + AlfordMatthew H. + ClaustreHervé + JohnsonKenneth + KingBrian + MoumJames + OkePeter + OwensW. Brechner + PouliquenSylvie + PurkeySarah + ScanderbegMegan + SugaToshio + WijffelsSusan + ZilbermanNathalie + BakkerDorothee + BaringerMolly + BelbeochMathieu + BittigHenry C. + BossEmmanuel + CalilPaulo + CarseFiona + CarvalThierry + ChaiFei + ConchubhairDiarmuid Ó. + d’ OrtenzioFabrizio + Dall’OlmoGiorgio + DesbruyeresDamien + FennelKatja + FerIlker + FerrariRaffaele + ForgetGael + FreelandHoward + FujikiTetsuichi + GehlenMarion + GreenanBlair + HallbergRobert + HibiyaToshiyuki + HosodaShigeki + JayneSteven + JochumMarkus + JohnsonGregory C. + KangKiRyong + KolodziejczykNicolas + KörtzingerArne + TraonPierre-Yves Le + LennYueng-Djern + MazeGuillaume + MorkKjell Arne + MorrisTamaryn + NagaiTakeyoshi + NashJonathan + GarabatoAlberto Naveira + OlsenAre + PattabhiRama Rao + PrakashSatya + RiserStephen + SchmechtigCatherine + SchmidClaudia + ShroyerEmily + SterlAndreas + SuttonPhilip + TalleyLynne + TanhuaToste + ThierryVirginie + ThomallaSandy + TooleJohn + TroisiAriel + TrullThomas W. + TurtonJon + Velez-BelchiPedro Joaquin + WalczowskiWaldemar + WangHaili + WanninkhofRik + WaterhouseAmy F. + WatermanStephanie + WatsonAndrew + WilsonCara + WongAnnie P. S. + XuJianping + YasudaIchiro + + On the Future of Argo: A Global, Full-Depth, Multi-Disciplinary Array + Frontiers in Marine Science + 2019 + 6 + https://www.frontiersin.org/article/10.3389/fmars.2019.00439 + 10.3389/fmars.2019.00439 + 439 + + + + + + + RiserStephen C. + FreelandHoward J. + RoemmichDean + WijffelsSusan + TroisiAriel + BelbeochMathieu + GilbertDenis + XuJianping + PouliquenSylvie + ThresherAnn + Le TraonPierre-Yves + MazeGuillaume + KleinBirgit + RavichandranM. + GrantFiona + PoulainPierre-Marie + SugaToshio + LimByunghwan + SterlAndreas + SuttonPhilip + MorkKjell-Arne + Velez-BelchiPedro Joaquin + AnsorgeIsabelle + KingBrian + TurtonJon + BaringerMolly + JayneSteven R. + + Fifteen years of ocean observations with the global Argo array + Nature Clim. Change + 201602 + 6 + 2 + http://dx.doi.org/10.1038/nclimate2872 + 10.1038/nclimate2872 + 145 + 153 + + + + + + Wong AnnieCarval ThierryKeeley Robert + + Argo quality control manual for CTD and trajectory data + Argo; Argo Data Management Team + 202201 + https://doi.org/10.13155/33951 + 10.13155/33951 + + + + + + TuckerTyler + GiglioDonata + ScanderbegMegan + ShenSamuel S. P. + + Argovis: A web application for fast delivery, visualization, and analysis of argo data + Journal of Atmospheric and Oceanic Technology + American Meteorological Society + Boston MA, USA + 2020 + 37 + 3 + https://journals.ametsoc.org/view/journals/atot/37/3/JTECH-D-19-0041.1.xml + 10.1175/JTECH-D-19-0041.1 + 401 + 416 + + + + + + KluyverThomas + Ragan-KelleyBenjamin + PérezFernando + GrangerBrian + BussonnierMatthias + FredericJonathan + KelleyKyle + HamrickJessica + GroutJason + CorlaySylvain + IvanovPaul + AvilaDamián + AbdallaSafia + WillingCarol + + Jupyter notebooks – a publishing format for reproducible computational workflows + + LoizidesF. + SchmidtB. + + IOS Press + 2016 + 10.3233/978-1-61499-649-1-87 + 87 + 90 + + + + + + MazeGuillaume + BalemKevin + + Argopy: A python library for argo ocean data analysis + Journal of Open Source Software + The Open Journal + 2020 + 5 + 53 + https://doi.org/10.21105/joss.02425 + 10.21105/joss.02425 + 2425 + + + + + +