diff --git a/README.md b/README.md index 951626ee..b30e566e 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ -VirtualShipParcels is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including: +VirtualShip is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including: - ADCP (currents) - CTD (conductivity and temperature + biogeochemical variables) diff --git a/docs/conf.py b/docs/conf.py index 19f44777..ceb8c01a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -2,7 +2,7 @@ import importlib.metadata -project = "Virtual Ship Parcels" +project = "VirtualShip Parcels" copyright = "2024, Emma Daniëls" author = "Emma Daniëls" version = release = importlib.metadata.version("virtualship") diff --git a/docs/index.md b/docs/index.md index 72718866..0bdf1002 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,4 @@ -# Virtual Ship Parcels +# VirtualShip ```{toctree} :maxdepth: 1 diff --git a/docs/user-guide/assignments/Code_of_conduct.ipynb b/docs/user-guide/assignments/Code_of_conduct.ipynb index 4c791b69..bf209157 100644 --- a/docs/user-guide/assignments/Code_of_conduct.ipynb +++ b/docs/user-guide/assignments/Code_of_conduct.ipynb @@ -5,39 +5,41 @@ "metadata": {}, "source": [ "## Code of conduct\n", - "_As used during the Dynamical Oceanography 2024/25 course at Utrecht University_" + "_As used during the Dynamical Oceanography 2025/26 course at Utrecht University_" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "_Please read this code of conduct, fill out the [parts between brackets] after consultation with your group, remove these italic sections, and then all individually upload a copy._ \n", + "_Please read this code of conduct, fill out the [parts between brackets] after consultation with your group, remove these italic sections, and then all individually upload a copy to Brightspace before Wednesday 18 February 13:00._ \n", "\n", - "_Note that the Code of Conduct applies to the actual collaboration within your group in the Virtual Ship Assignment; so is not about how you would work on the ship._" + "**Note that the Code of Conduct applies to the actual collaboration within your group in the VirtualShip Assignment; so is not about how you would work on the ship.**\n", + "\n", + "---" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "This code of conduct has been decided by [NAMES] for their group project during the Virtual Ship Classroom and is enacted from [DD-MM-YYYY]. The procedure is based an exercise by Aurelia Moser.\n", + "This code of conduct has been decided by [NAMES] for their group project during the Virtual Ship Classroom and is enacted from [DD-MM-YYYY]. The procedure is based on [this exercise by Aurelia Moser](http://aureliamoser.com/aaas-guides/conduct/index.html).\n", "\n", "Everyone taking part in the course and group discussions (mentors, helpers, coordinators, and learners) is required to conform to the following Code of Conduct. Coordinators will oversee adherence to this code throughout the course.\n", "\n", - "Characteristics we value: [FILL IN]\n", - "\n", - "Behaviors we encourage: [FILL IN]\n", + "**Characteristics we value**: [FILL IN]\n", "\n", - "Behaviors we discourage: [FILL IN]\n", + "**Behaviours we encourage**: [FILL IN]\n", + " \n", + "**Behaviours we discourage**: [FILL IN]\n", "\n", - "The way we redistribute the grade: [FILL IN]\n", + "**The way we redistribute the grade**: [FILL IN]\n", "\n", - "Choose for example “Everyone in the team gets the same grade”, “Everyone can propose a bonus point to one other person, which is then subtracted from other team member’s grades”, “We decide as a group who gets up to x bonus/penalty points”, or any other way to redistribute the grade, as long as the average of the group is not affected. \n", + "_Choose for example “Everyone in the team gets the same grade”, “Everyone can propose a bonus point to one other person, which is then subtracted from other team member’s grades”, “We decide as a group who gets up to x bonus/penalty points”, or any other way to redistribute the grade, as long as the average of the group is not affected._\n", "\n", - "We make each others feel safe and supported by: [FILL IN]\n", + "**We make each others feel safe and supported by**: [FILL IN]\n", "\n", - "How to report an issue, should someone violate the code?\n", + "**How to report an issue, should someone violate the code?**\n", "1.\tContact the course instructor by private message, or in person. All communication will be treated as confidential.\n", "2.\tIf for any reason you don’t want to do 1, you can contact the university Academic Integrity Counsellor." ] @@ -54,11 +56,12 @@ "metadata": {}, "source": [ "Apart from the code of conduct, all participants in this course must follow these general guidelines.\n", - "Participation \n", "\n", - "When participating in Dynamical Oceanography, respect the Utrecht University guideline for academic and scientific integrity and code of conduct. These guidelines cover our behaviour as participants, mentors, experts, staff, volunteers, and anyone else involved in making this course possible.\n", + "**Participation Guidelines**\n", + "\n", + "When participating in Dynamical Oceanography, respect the Utrecht University guideline for [academic and scientific integrity](https://www.uu.nl/sites/default/files/code_of_conduct_for_scrupulous_academic_conduct_and_integrity_-_en_def_0.pdf) and [code of conduct](https://www.universiteitenvannederland.nl/files/publications/Netherlands%20Code%20of%20Conduct%20for%20Research%20Integrity%202018.pdf). These guidelines cover our behaviour as participants, mentors, experts, staff, volunteers, and anyone else involved in making this course possible.\n", "\n", - "How to treat each other\n", + "**How to treat each other**\n", "\n", "To create a collaborative and inviting learning environment, we also emphasise certain values in how we treat each other:\n", "*\tBe respectful and value each other’s ideas, styles and viewpoints.\n", @@ -77,13 +80,13 @@ "\n", "### Inclusion and Diversity\n", "\n", - "We welcome contributions from everyone as long as they interact constructively with our community, including, but not limited to people of varied age, culture, ethnicity, gender, gender-identity, language, race, sexual orientation, geographical location and religious views.\n", + "We welcome contributions from everyone as long as they interact constructively with our community, including, but not limited to people of varied age, culture, ethnicity, gender, gender-identity, language, race, sexual orientation, geographical location and religious views. \n", "\n", - "Raising Issues\n", + "**Raising Issues**\n", "\n", "If you believe you‘re experiencing practices which don‘t meet the above policies, or if you feel you are being harassed in any way, please immediately contact the course coordinator, or the university Academic Integrity Counsellor.\n", "\n", - "The course coordinator reserves the right to refuse admission to anyone violating these policies, and/or take further action including reporting to the responsible figure for academic integrity at the department.\n" + "The course coordinator reserves the right to refuse admission to anyone violating these policies, and/or take further action including reporting to the responsible figure for academic integrity at the department." ] } ], diff --git a/docs/user-guide/assignments/Sail_the_ship.ipynb b/docs/user-guide/assignments/Sail_the_ship.ipynb index dc71b8e0..2a2d8577 100644 --- a/docs/user-guide/assignments/Sail_the_ship.ipynb +++ b/docs/user-guide/assignments/Sail_the_ship.ipynb @@ -113,10 +113,10 @@ "### Upload the coordinates to your virtual machine\n", "\n", "
\n", - "**IMPORTANT**: _If you have not done so already_, make sure you create a folder for your group's expedition data in the persistent storage on SURF RC (i.e. the `data/storage-osl/` folder). You can do so by running `mkdir /data/storage-osl/{your-group-name}` in Terminal, replacing `{your-group-name}` with your actual group name, or by using the \"New Folder\" button in the JupyterLab file explorer panel.\n", + "**IMPORTANT**: _If you have not done so already_, make sure you create a folder for your group's expedition data in the persistent storage on SURF RC (i.e. the `data/storage/` folder). You can do so by running `mkdir /data/storage/{your-group-name}` in Terminal, replacing `{your-group-name}` with your actual group name, or by using the \"New Folder\" button in the JupyterLab file explorer panel.\n", "
\n", "\n", - "Back in the SURF RC JupyterLab interface, use the **file explorer** on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage-osl/{your-group-name}`). \n", + "Back in the SURF RC JupyterLab interface, use the **file explorer** on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage/{your-group-name}`). \n", "\n", "Then upload the exported .xlsx file (it will be called something like \"Coordinates-20251125T1403.xlsx\") by either dragging and dropping it from your laptop's Downloads into the file explorer, or by using the \"Upload Files\" button (the icon with an upward arrow) at the top of the file explorer panel." ] @@ -130,7 +130,7 @@ "Open a Terminal window if you do not already have one open. Remember, this can be done from the Launcher tab by clicking on \"Terminal\" button under the \"Other\" section, or by going to the \"File\" menu --> \"New\" --> \"Terminal\".\n", "\n", "
\n", - "**IMPORTANT**: Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine. You can do so by `cd /data/storage-osl/{your-group-name}`, replacing `{your-group-name}` with your actual group name. This is where you will be working from for the rest of the session.\n", + "**IMPORTANT**: Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine. You can do so by `cd /data/storage/{your-group-name}`, replacing `{your-group-name}` with your actual group name. This is where you will be working from for the rest of the session.\n", "
\n", "\n", "Now enter the following command in the Terminal (changing `EXPEDITION_NAME` to something more meaningful for your group's expedition):\n", @@ -246,9 +246,9 @@ "\n", "From here you can carry on your analysis. In general, we encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments. Use these to help you get started!\n", "\n", - "If you are using VirtualShip in class, the same tutorial notebooks will be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage-osl/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n", + "If you are using VirtualShip in class, the same tutorial notebooks will be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n", "\n", - "To run these notebooks with your own data, you will need to copy the them over to your expedition working directory (i.e. `data/storage-osl/{your-group-name}`). This can be done by either 1) using the file explorer panel in JupyterLab to copy the relevant files or the via the command line in Terminal. In the terminal, running `cp -r /data/storage-osl/tutorials/* /data/storage-osl/{your-group-name}/` would copy __all__ the tutorial notebooks to your group's directory, so if you only want to copy specific ones, make sure to adjust the command accordingly." + "To run these notebooks with your own data, you will need to copy the them over to your expedition working directory (i.e. `data/storage/{your-group-name}`). This can be done by either 1) using the file explorer panel in JupyterLab to copy the relevant files or the via the command line in Terminal. In the terminal, running `cp -r /data/storage/tutorials/* /data/storage/{your-group-name}/` would copy __all__ the tutorial notebooks to your group's directory, so if you only want to copy specific ones, make sure to adjust the command accordingly." ] }, { diff --git a/docs/user-guide/assignments/index.md b/docs/user-guide/assignments/index.md index e488222c..20a271cd 100644 --- a/docs/user-guide/assignments/index.md +++ b/docs/user-guide/assignments/index.md @@ -5,9 +5,8 @@ maxdepth: 1 caption: Assignments --- -Virtualship_research_proposal.ipynb Research_proposal_intro.ipynb -Research_Proposal_only.ipynb +Virtualship_research_proposal.ipynb sciencecommunication_assignment.ipynb Code_of_conduct.ipynb case_studies_virtualship.ipynb diff --git a/docs/user-guide/assignments/sciencecommunication_assignment.ipynb b/docs/user-guide/assignments/sciencecommunication_assignment.ipynb index 29f090ad..a9ef2a8d 100644 --- a/docs/user-guide/assignments/sciencecommunication_assignment.ipynb +++ b/docs/user-guide/assignments/sciencecommunication_assignment.ipynb @@ -6,7 +6,7 @@ "source": [ "## Science Communication Assignment\n", "\n", - "_As used during the Dynamical Oceanography 2023/24 course at Utrecht University_" + "_As used during the Dynamical Oceanography 2025/26 course at Utrecht University_" ] }, { @@ -17,16 +17,15 @@ "\n", "- You will write a popular scientific article about the virtual expedition. \n", " - This is an individual assignment.\n", - " - The length of the article should be between 400 and 700 words. \n", + " - The length of the article should be between 700 and 1000 words. \n", " - The audience of your science communication article are Physics BSc students.\n", - " - You need to include and refer to the findings/results of at least two scientific articles as background.\n", - "\n", - " - For examples of the style you could use, check out [this article](https://physicsworld.com/a/20000-pings-under-the-sea/) (although at almost 3,000 words that article is way longer than expected here), or [this article](https://blogs.scientificamerican.com/expeditions/to-hades-and-back-exploring-the-deepest-part-of-the-ocean/).\n", - " - You are allowed to use Generative AI to create photos of the expedition (but only for photos; no other uses of Generative AI are allowed!) \n", - "- Submit a first draft of the article to Blackboard by 27 March 17:00. \n", - "- Every student will provide formative feedback for two other articles. Deadline is 2 April 17:00. This formative feedback will be graded and will count 25% of the mark for this assignment. \n", - "- You will incorporate the formative feedback where appropriate into a final version of the article and submit that as a pdf on Blackboard by 5 April.\n", - "- The articles will be graded by the lecturer and the Teaching Assistants\n" + " - You need to include and refer to the findings/results of at least two recent scientific articles on physical oceanography (published after 2020) as background. \n", + " - For an example of the style you could use, check out [this article](https://physicsworld.com/a/20000-pings-under-the-sea/) (although at almost 3,000 words that article is way longer than expected here), or [this article](https://blogs.scientificamerican.com/expeditions/to-hades-and-back-exploring-the-deepest-part-of-the-ocean/). \n", + " - For this assignment, you can use AI for editing and feedback (AI level 3) for the text, and AI is fully permitted (level 5) to create photos of the expedition. You must include an AI disclosure statement (what tools are used and why) and it is required to keep a record of AI prompts used in the assignment. Oral examinations can be conducted on suspicion of non-permitted use of Generative AI. \n", + "- Submit a first draft of the article to Blackboard by 18 March 13:00. \n", + "- Every student will provide formative feedback for three other articles. Deadline is Monday 30 March 17:00. This formative feedback will be graded and will count 25% of the mark for this assignment. \n", + "- You will incorporate the formative feedback where appropriate into a final version of the article and submit that as a pdf on Blackboard by 2 April 17:00. \n", + "- The articles will be graded by the lecturer and the Teaching Assistants.\n" ] }, { @@ -37,18 +36,24 @@ "\n", "|Rubric|What is extra?|Sufficient|What is missing?|\n", "| --- | --- | --- | --- |\n", - "|Introduction to the region | | The physical oceanography of the region is clearly explained. | |\n", + "|Physical oceanography of the region | | The physical oceanography of the region is clearly explained. | |\n", "|Research motivation | | The motivation to do an expedition in this region is clearly articulated. | |\t\n", - "|Explanation of scientific papers | | The results of two scientific papers are described and incorporated in the text.| |\n", - "|Factual correctness | | The scientific claims and information presented are accurate and supported by evidence. | |\n", - "|Effect | | The goal/aim of the text is clear. The article contributes meaningfully to the reader's understanding of the topic. | |\n", + "|Explanation of scientific papers | | The results of two recent scientific papers on physical oceanography are described and incorporated in the text. | |\n", "|Use of visuals | | At least one visual (image, graph, or diagram) is present. It is used effectively to enhance understanding and engagement. | |\n", - "|Emotion/ personalization | | The text has a clear main character and includes reference to (personal) emotions. | |\n", + "|Emotion/personalization | | The text has a clear main character and includes reference to (personal) emotions. | |\n", "|Narrative structure | | The narrative structure is such that readers are enticed to read to the end of the text. | |\n", - "|Suitability for the audience | | The text is understandable for the audience, while also not being too simplistic. | |\t\n", - "|Writing style | | The text is within the word limits, and has few spelling and grammatical errors. | |\n", + "|Writing style | | The text is within the word limits, and has few spelling and grammatical errors. | |\t\n", + "|AI disclosure statement | | The article has a clear and concise AI disclosure statement. | |\n", + "\n", + "Target grade when all aspects are sufficient is a 8.0 \n", + "\n", + "For an example of the style you could use, check out: \n", + "\n", + "1. https://physicsworld.com/a/20000-pings-under-the-sea/ (although at almost 3,000 words that article is much longer than expected here) \n", + "\n", + "2. https://blogs.scientificamerican.com/expeditions/to-hades-and-back-exploring-the-deepest-part-of-the-ocean/ \n", "\n", - "\n" + "3. https://archives.whoi.edu/expeditions/irminger_sea/page.do@pid=27262.html " ] }, { @@ -57,29 +62,19 @@ "source": [ "### Marking Rubric for the peer feedback\n", "\n", + "Student name: ________________________\n", + "\n", "| Rubric | What is extra? | Sufficient | What is missing? |\n", "| --- | --- | --- | --- |\n", - "| Constructive criticism | \t| The peer feedback includes some critical reflections, and these are constructively phrased| |\n", - "|Focused on the content\t| |\tThe peer feedback focuses on the writing, not the writer | |\n", - "Specific | |The peer feedback points to specific places where the draft can be improved\t | |\n", - "Prioritized comments | | The peer feedback is an ordered list with the most important comments at the top | |\n", - "Considerate and thoughtful | | The peer feedback is kind and does not jeopardize social safety (i.e. not ‘ad hominin’) | |\n" + "|Constructive criticism | \t| The peer feedback includes some critical reflections, and these are constructively phrased| |\n", + "|Focused on the content\t| |\tThe peer feedback focuses on the writing, not the writer | \n", + "|Specific | |The peer feedback points to specific places where the draft can be improved\t | \n", + "|Prioritized comments | | The peer feedback is an ordered list with the most important comments at the top | \n", + "|Considerate and thoughtful | | The peer feedback is kind and does not jeopardize social safety (i.e. not ‘ad hominin’) | \n", + "|Writing | | The peer feedback is well-written and presented, with no or few grammar and spelling errors | |\n", + "\n", + "Grade: __ / 10 " ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] } ], "metadata": { diff --git a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb index 64c78d8d..ae28870d 100644 --- a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb +++ b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb @@ -46,7 +46,7 @@ "└── scratch\n", "```\n", "\n", - "__Note__: the persistent storage folder may be called something slightly different in your instance, for example it may have a name specific to the course you are enrolled on, such as `data/storage-1-sept`.\n", + "__Note__: the persistent storage folder may be called something slightly different in your instance, for example it may have a name specific to the course you are enrolled on, such as `data/storage-dyoc` or `data/storage-1-sept`.\n", "\n", "In the Jupyter launcher, you can open a Terminal session by clicking on \"Terminal\" button under the \"Other\" section, or by going to the \"File\" menu --> \"New\" --> \"Terminal\". From here you can navigate the workspace directory structure and run commands.\n", "\n",