JOSS manuscript #265
JOSS manuscript #265
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Hi all, happy New Year! As a reminder, please do give your approval to this PR when you're happy for me to submit to JOSS ✅ |
ammedd
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ammedd
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Whoops, went ahead and pushed some changes I should have written as comments. Just compare and keep what you like. Looks good!
No worries - the changes look good, thanks! I have changed @surgura's affiliation back to FI though as I believe they paid for his work, according to @erikvansebille's previous comment. |
Indeed, @surgura was paid through the FI as far as I know |
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Hi, it's on my todo list for this week. Sorry for not finishing sooner. |
iuryt
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I have made few comments, but I approve this version. Please, let me know if I can be of any help.
docs/paper/paper.md
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| # Functionality | ||
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| `VirtualShip` simulates the deployment of virtual instruments commonly used in oceanographic fieldwork, with emphasis on realism in how users plan and execute expeditions. For example, users must consider ship speed and instrument deployment/recovery times to ensure their expedition is feasible within given time constraints. Possible instrument selections include surface `Drifter` [@Lumpkin2017], `CTD` (Conductivity-Temperature-Depth; @Johnson2007), `Argo float` [@Jayne2017], `XBT` (Expendable Bathythermograph; @Goni2019), underway `ADCP` (Acoustic Doppler Current Profiler; @Kostaschuk2005), and underway `Underwater_temperature/salinity` [@Gordon2014] probes. More detail on each instrument is available in the [documentation](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#Measurement-Options). |
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Underwater_temperature/salinity is the variable name?
underway Underwater_temperature/salinity seems like a pleonasm. Maybe it would be better to say
", and underway temperature/salinity [@gordon2014] probes"
docs/paper/paper.md
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| The software can simulate complex multidisciplinary expeditions. One example is a virtual expedition across the Agulhas Current and the South Eastern Atlantic that deploys a suite of instruments to sample physical and biogeochemical properties (\autoref{fig:fig1}). Key circulation features appear early in the expedition track, with enhanced ADCP speeds marking the strong Agulhas Current (\autoref{fig:fig1}b) and drifters that turn back toward the Indian Ocean indicating the Agulhas Retroflection (\autoref{fig:fig1}c). The CTD profiles capture the vertical structure of temperature and oxygen along the route, including the warmer surface waters of the Agulhas region (\autoref{fig:fig1}d, early waypoints) and the Oxygen Minimum Zone in the South Eastern Atlantic (\autoref{fig:fig1}e, final waypoints). | ||
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Maybe move this figure below. There is a big blank space in page 2 of the PDF.
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| Under the hood, `VirtualShip` is modular and extensible. The workflows are designed around `Instrument` base classes and instrument-specific subclasses and methods. This means the platform can be easily extended to add new instrument types. Instrument behaviours are coded as `Parcels` kernels, which allows for extensive customisability. For example, a `Drifter` advects passively with ocean currents, a `CTD` performs vertical profiling in the water column and an `ArgoFloat` cycles between ascent, descent and drift phases, all whilst sampling physical and/or biogeochemical fields at their respective locations and times. | ||
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| Moreover, the data ingestion system relies on Analysis-Ready and Cloud-Optimized data (ARCO; @Stern2022, @Abernathey2021) streamed directly from the Copernicus Marine Data Store, via the [`copernicusmarine`](https://github.com/mercator-ocean/copernicus-marine-toolbox) Python toolbox. This means users can simulate expeditions anywhere in the global ocean without downloading large datasets by default. Leveraging the suite of [physics and biogeochemical products](https://virtualship.readthedocs.io/en/latest/user-guide/documentation/copernicus_products.html) available on the Copernicus plaform, expeditions are possible from 1993 to present and forecasted two weeks into the future. There is also an [option](https://virtualship.readthedocs.io/en/latest/user-guide/documentation/pre_download_data.html) for the user to specify local `NetCDF` files for data ingestion, if preferred. |
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In general for clean scientific writing, you want one set of parentheses only in this situation. So, I think this should be
"(ARCO; Stern et al. 2022; Abernathey et al. 2021)"
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Unfortunately this is a result of the pandoc-style citations used, and I haven't been able to find a way to hack around it
docs/paper/paper.md
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| `VirtualShip` has already been extensvely applied in Master's teaching settings at Utrecht University as part of the [VirtualShip Classroom](https://www.uu.nl/en/research/sustainability/sustainable-ocean/education/virtual-ship) initiative. Educational assignments and tutorials have been developed alongside to integrate the tool into coursework, including projects where students design their own research question(s) and execute their fieldwork and analysis using `VirtualShip`. Its application has been shown to be successful, with students reporting increased self-efficacy and knowledge in executing oceanographic fieldwork [@Daniels2025]. | ||
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| The package opens space for many other research applications. It can support real-life expedition planning by letting users test sampling routes before going to sea. It also provides tooling to explore real-time adaptive strategies in which sampling plans shift as forecasts or observations update. The same workflow can also be used to investigate sampling efficiency, for example, examining how waypoint number or spacing shapes the ability to capture features of interest. Moreover, the software is well-suited for developing Observation System Simulation Experiments (OSSEs; e.g. @Errico2013) to test and optimise observational strategies in a cost- and time-efficient manner. |
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I think this citation would be better as
"(OSSEs; e.g. Errico et al., 2013)"
Co-authored-by: Iury Simoes-Sousa <iuryt@pm.me>
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Thank you everyone for your help - it's ready for submission now! Next stop JOSS |
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Hi all (@erikvansebille @ammedd @VeckoTheGecko @iuryt @surgura), Unfortunately there will be a small delay with submission to JOSS, I need to update the formatting in line with the very recently announced changes to the JOSS scope requirements, see here. With this change comes an updated set of manuscript requirements, some of which are not in the current version of the manuscript, but hopefully won't take long to implement. I'll make a new PR soon with the changes. |
This PR is for visibility of a draft of the VirtualShip JOSS manuscript, and for the review as co-authors to be organised here.
Feel free to add comments and commits to this PR, or branch off as new PRs for suggested changes.
@VeckoTheGecko @iuryt @surgura you have all made substantial contributions to the code. I have listed you as co-authors, alongside @ammedd and @erikvansebille. In the first place, are you happy to be involved with the manuscript? If so, please also let me know what kind of timeline I can expect to get your feedback!