From 6252a2c5dbfcfcb367de437aa7bb97916462830d Mon Sep 17 00:00:00 2001 From: Stephan Koenig Date: Thu, 30 Nov 2023 08:41:52 -0800 Subject: [PATCH] Update UDL section & notes on teaching philosophy --- .../01_first-steps/execute-results/html.json | 4 +- slides/01_first-steps.qmd | 75 +++++++++++++------ 2 files changed, 56 insertions(+), 23 deletions(-) diff --git a/_freeze/slides/01_first-steps/execute-results/html.json b/_freeze/slides/01_first-steps/execute-results/html.json index 65d895f..245d83d 100644 --- a/_freeze/slides/01_first-steps/execute-results/html.json +++ b/_freeze/slides/01_first-steps/execute-results/html.json @@ -1,8 +1,8 @@ { - "hash": "1291cbcc8e91c19fa3bb50668e93b131", + "hash": "ce6a59d294bde6e5544187fe8efdf7c1", "result": { "engine": "knitr", - "markdown": "---\ntitle: \"First steps into reproducible bioinformatics\"\nsubtitle: \"Seminar at MBIM, Nov 30, 2023\"\nauthor:\n - name: Stephan König\n orcid: 0000-0002-1597-3628\n email: stephan.koenig@ubc.ca\n affiliations:\n - name: Skylight, University of British Columbia\n department: Computer Science\n \nformat:\n revealjs:\n theme: [default, ../styles/theme.scss]\n chalkboard: true\n controls: true\n footer: \"[bit.ly/td-website](https://bit.ly/td-website)\"\n\nfilters:\n - include-code-files\n - ../filters/new-page-links.lua\n---\n\n::: {.cell}\n\n:::\n\n\n# Mini lesson:
Reproducible reporting of computational analyses {background-color=\"#faa928\"}\n\n## Learning outcomes\n\n- Describe why combining natural language and code enables reproducible analysis and research.\n\n- Discover how symbols and text convey formatting and the structure of a document.\n\n::: notes\n- Explored ways of describing microbial communities using various diversity metrics.\n:::\n\n## Microbiomes at different lake depths\n\n::: center-xy\nSequence barcode marker of each sample\n\n\n{{< fa arrow-down title=\"Down arrow\" >}}\n\n\n\nGroup similar sequences
defining
amplicon sequence variants (ASVs)
ASV ≅ species\n\n\n{{< fa arrow-down title=\"Down arrow\" >}}\n\n\n\nASV counts table\n:::\n\n::: notes\n- Extract DNA from the lake samples and a sequence barcode marker.\n- Group similar sequences into amplicon sequence variants, i.e., ASVs.\n- ASV approximates a species.\n- Record number of sequences in an ASV count table.\n- Simplest way to describe is species richness.\n:::\n\n## Species richness at 10 m depth\n\n::: {layout-ncol=\"3\"}\n\n::: {#tbl-asv-counts .cell tbl-cap='ASV counts'}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n\n\n \n\n\n \n\n\n \n\n\n \n\n\n \n \n \n
namedepth_10_mdepth_20_m
ASV_12814
ASV_2512
ASV_303
ASV_41441
ASV_51828
\n
\n```\n\n:::\n:::\n\n:::\n\n\n::: {.cell output-location='column-fragment'}\n\n```{.r .cell-code}\nasv_counts |> \n select(depth_10_m) |>\n filter(depth_10_m >= 1) |> \n nrow()\n```\n\n::: {.cell-output .cell-output-stdout}\n\n```\n[1] 4\n```\n\n\n:::\n:::\n\n\n::: notes\n- Draw a cross-section of the lake and indicate samples\n- Counts for each ASV by row.\n- Counts for each sample by column.\n- Let's calculate the species richness at 10 m.\n- We select the corresponding column.\n- An ASV is present only if the count is at least 1.\n- Count of the number of rows left.\n:::\n\n## How to report the results? {background-image=\"../images/word.png\" background-size=\"75%\" aria-label=\"An open Word document reads 'The species richness of the sample is 4.'\"}\n\n::: notes\n- At some point you will have to report your results, for example for an assignment.\n- What happens if your analysis changes? How do you keep track that the most up-to-date number is in your report?\n:::\n\n## {{< fa comments >}} Your Turn: Think-pair-share {background-color=\"#447099\"}\n\nHow would ensure the correct reporting of your analysis?\n\n- Think for one minute about possible solutions by yourself.\n- Then discuss with your neighbour your solution.\n\n`
\n
\n02:00\n
`{=html}\n\n## Do you want your grades to be reproducible? {.center .r-fit-text}\n\n::: notes\n- One solution is to mix the analysis with the reporting, i.e., mix code with natural language.\n- Code if often written in plain text.\n- One approach is to write everything in plain text. But how can we format the text?\n:::\n\n## {{< fa file-alt >}} Your Turn: Worksheet {background-color=\"#447099\"}\n\n- Review the report of a fellow student.\n- Discover how symbols and text structure the document.\n\n::: columns\n::: {.column width=\"50%\"}\n### Plain text\n\n``` {include=\"../worksheets/analysis.qmd\" filename=\"analysis.qmd\" start-line=\"1\" end-line=\"20\"}\n```\n:::\n\n::: {.column width=\"50%\"}\n### PDF\n\n\n:::\n:::\n\n::: notes\n- For our worksheet, we will act like we review the analysis of a friend.\n- Your worksheet has three pages.\n- The second one has a plain text file printed on a grey background called `analysis.qmd`.\n- The third contains the PDF output of that file.\n- The first one contains the exercises. We will work on the first 4.\n- Please highlight any difference in text or symbols between the two files.\n- *Demonstrate highlighting*.\n:::\n\n## {{< fa file-alt >}} Your Turn: Worksheet {background-color=\"#447099\"}\n\n- Take about 2 minute to highlight differences between plain text and the PDF output (exercise 1).\n- Compare your results with your neighbour and work with them on exercise 2--4.\n\n`
\n
\n05:00\n
`{=html}\n\n::: notes\n**Wrap up**: *Before proceeding, point out how students could understand some of the structure and formatting by contrasting input and output, even though it might have been challenging. You are constantly practicing a skill you will need for coding all the time: reading and understanding someone's code.\n:::\n\n## {{< fa brands markdown >}} Markdown\n\n::: fragment\n- Simple expressive formatting with symbols and text.\n- Used in many [apps and services](https://www.markdownguide.org/tools/), for example {{< fa brands discord title=\"Discord\" >}} {{< fa brands slack title=\"Slack\" >}} {{< fa brands github title= \"GitHub\" >}}.\n:::\n\n+-------------------------------------+\n| Markdown syntax |\n+=====================================+\n| # \\# Heading 1 |\n+-------------------------------------+\n| ## \\#\\# Heading 2 |\n+-------------------------------------+\n| **\\*\\*strong\\*\\*** |\n+-------------------------------------+\n| *\\*emphasized\\** |\n+-------------------------------------+\n\n## How Quarto works {background-image=\"https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/c2ef45f1-4a68-4c7a-a43f-bdcf0f90e104_rw_3840.png?h=783eba914284e5adfb9feadcf4ba5f1e\" background-size=\"contain\" aria-label=\"A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.\"}\n\n::: footer\nArtwork from \"Hello, Quarto\" keynote by Julia Lowndes and Mine Çetinkaya-Rundel, presented at RStudio Conference 2022.\nIllustrated by Allison Horst.\n:::\n\n::: notes\n- Offers many different output formats, not only PDF.\n- One option is to create HTML including websites.\n- In fact, this entire website was made in Quarto!\n:::\n\n## {#down-the-rabbit-hole-1 data-meny-title=\"Down the rabbit hole\" background-iframe=\"https://stephan-koenig.github.io/teaching-demo/\" background-interactive=\"true\"}\n\n## {#down-the-rabbit-hole-2 .centered data-menu-title=\"Down the rabbit hole\"}\n\n``` {include=\"../index.qmd\" filename=\"index.qmd\" start-line=\"1\" end-line=\"15\"}\n```\n\n::: notes\nDemo MICB: 2XX website as an example of a Quarto project.\n:::\n\n## {{< fa laptop-code >}} Next lab: Create your own website! {background-color=\"#447099\"}\n\n::: incremental\n- Build a professional ePortfolio online.\n- Reflect on and record your growth across the MICB program.\n- Demonstrate your coding and collaboration skills.\n- Showcase your work as a developing microbiologist and immunologist to future employers.\n:::\n\n::: notes\nLearn relevant technologies for web development and reproducible workflows using industry-standard tools.\n:::\n\n# Universal Design for Learning:
Embracing open source {background-color=\"#faa928\"}\n\n::: notes\nUDL strives to provide multiple means for three principles of effective instruction.\n:::\n\n## {#representation data-menu-title=\"Representation\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-recognition-networks.png\"}\n\n::: footer\nCAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Representation\n\n- Open source tools support alt text for images.\n- Easy to provide headings and descriptive hyperlinks.\n- Support for different file formats.\n\n## {#engagement data-menu-title=\"Engagement\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-affective-networks.png\"}\n\n::: footer\nCAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Engagement\n\n- Follow the **mastery learning** model, i.e., frequent practice, assessment and feedback.\n- Use online assessment platform (e.g., [PrairieLearn](https://prairielearn.readthedocs.io/)) to support mastery learning at scale.\n - Academic integrity by randomization.\n - Use questions in practices and exams.\n- Use authentic examples and assessments (for example, ePortfolio)\n- Use relevant, widespread technologies, such as web technologies (HTML, CSS).\n- Model inclusive practices in the way course is run (syllabus) and materials are provided.\n\n## {#prairielearn data-menu-title=\"PrairieLearn\" background-iframe=\"https://www.prairielearn.com/\" background-interactive=\"true\"}\n\n## {#action-and-expression data-menu-title=\"Action and expression\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-strategic-networks.png\"}\n\n::: footer\nCAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Action and expression\n\n- Alternative ways of participating, e.g., discussion section on course website.\n- Increased expression and communication (Quarto offers a lot of flexibility).\n- Accommodations supported by PrairieLearn.\n\n## Open education resources\n\n- Affordability is an accessibility issue.\n- Uses open source material makes material more accessible.\n- Cloud computing for accessibility.\n- Support for desktop and mobile.\n- Collect feedback on the relevant pages.\n- [UBC OER Fund](https://oerfund.open.ubc.ca/)\n\n## {#comments-1 data-meny-title=\"Comments\" background-iframe=\"https://stephan-koenig.github.io/teaching-demo/posts/welcome/\" background-interactive=\"true\"}\n\n## {data-meny-title=\"Comments\" background-iframe=\"https://github.com/stephan-koenig/teaching-demo/discussions/5\" background-interactive=\"true\"}\n\n## We are not alone: UDL community of practice {.center}\n\n[Universal design for learning fellows program](https://tlef.ubc.ca/application/special-call/universal-design-for-learning-fellows-program/)---2024 cohort.\n\n::: notes\nThere is always more to learn from our colleagues.\n:::\n\n# Teaching philosphy: Practicing expert behaviour {background-color=\"#faa928\"}\n", + "markdown": "---\ntitle: \"First steps into reproducible bioinformatics\"\nsubtitle: \"Seminar at MBIM, Nov 30, 2023\"\nauthor:\n - name: Stephan König\n orcid: 0000-0002-1597-3628\n email: stephan.koenig@ubc.ca\n affiliations:\n - name: Skylight, University of British Columbia\n department: Computer Science\n \nformat:\n revealjs:\n theme: [default, ../styles/theme.scss]\n chalkboard: true\n controls: true\n footer: \"[bit.ly/td-website](https://bit.ly/td-website)\"\n\nfilters:\n - include-code-files\n - ../filters/new-page-links.lua\n---\n\n::: {.cell}\n\n:::\n\n\n# Mini lesson:
Reproducible reporting of computational analyses {background-color=\"#faa928\"}\n\n## Learning outcomes\n\n- Describe why combining natural language and code enables reproducible analysis and research.\n\n- Discover how symbols and text convey formatting and the structure of a document.\n\n::: notes\n- Explored ways of describing microbial communities using various diversity metrics.\n:::\n\n## Microbiomes at different lake depths\n\n::: center-xy\nSequence barcode marker of each sample\n\n\n{{< fa arrow-down title=\"Down arrow\" >}}\n\n\n\nGroup similar sequences
defining
amplicon sequence variants (ASVs)
ASV ≅ species\n\n\n{{< fa arrow-down title=\"Down arrow\" >}}\n\n\n\nASV counts table\n:::\n\n::: notes\n- Extract DNA from the lake samples and a sequence barcode marker.\n- Group similar sequences into amplicon sequence variants, i.e., ASVs.\n- ASV approximates a species.\n- Record number of sequences in an ASV count table.\n- Simplest way to describe is species richness.\n:::\n\n## Species richness at 10 m depth\n\n::: {layout-ncol=\"3\"}\n\n::: {#tbl-asv-counts .cell tbl-cap='ASV counts'}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n\n\n \n\n\n \n\n\n \n\n\n \n\n\n \n \n \n
namedepth_10_mdepth_20_m
ASV_12814
ASV_2512
ASV_303
ASV_41441
ASV_51828
\n
\n```\n\n:::\n:::\n\n:::\n\n\n::: {.cell output-location='column-fragment'}\n\n```{.r .cell-code}\nasv_counts |> \n select(depth_10_m) |>\n filter(depth_10_m >= 1) |> \n nrow()\n```\n\n::: {.cell-output .cell-output-stdout}\n\n```\n[1] 4\n```\n\n\n:::\n:::\n\n\n::: notes\n- Draw a cross-section of the lake and indicate samples\n- Counts for each ASV by row.\n- Counts for each sample by column.\n- Let's calculate the species richness at 10 m.\n- We select the corresponding column.\n- An ASV is present only if the count is at least 1.\n- Count of the number of rows left.\n:::\n\n## How to report the results? {background-image=\"../images/word.png\" background-size=\"75%\" aria-label=\"An open Word document reads 'The species richness of the sample is 4.'\"}\n\n::: notes\n- At some point you will have to report your results, for example for an assignment.\n- What happens if your analysis changes? How do you keep track that the most up-to-date number is in your report?\n:::\n\n## {{< fa comments >}} Your Turn: Think-pair-share {background-color=\"#447099\"}\n\nHow would ensure the correct reporting of your analysis?\n\n- Think for one minute about possible solutions by yourself.\n- Then discuss with your neighbour your solution.\n\n`
\n
\n02:00\n
`{=html}\n\n## Do you want your grades to be reproducible? {.center .r-fit-text}\n\n::: notes\n- One solution is to mix the analysis with the reporting, i.e., mix code with natural language.\n- Code if often written in plain text.\n- One approach is to write everything in plain text. But how can we format the text?\n:::\n\n## {{< fa file-alt >}} Your Turn: Worksheet {background-color=\"#447099\"}\n\n- Review the report of a fellow student.\n- Discover how symbols and text structure the document.\n\n::: columns\n::: {.column width=\"50%\"}\n### Plain text\n\n``` {include=\"../worksheets/analysis.qmd\" filename=\"analysis.qmd\" start-line=\"1\" end-line=\"20\"}\n```\n:::\n\n::: {.column width=\"50%\"}\n### PDF\n\n\n:::\n:::\n\n::: notes\n- For our worksheet, we will act like we review the analysis of a friend.\n- Your worksheet has three pages.\n- The second one has a plain text file printed on a grey background called `analysis.qmd`.\n- The third contains the PDF output of that file.\n- The first one contains the exercises. We will work on the first 4.\n- Please highlight any difference in text or symbols between the two files.\n- *Demonstrate highlighting*.\n:::\n\n## {{< fa file-alt >}} Your Turn: Worksheet {background-color=\"#447099\"}\n\n- Take about 2 minute to highlight differences between plain text and the PDF output (exercise 1).\n- Compare your results with your neighbour and work with them on exercise 2--4.\n\n`
\n
\n05:00\n
`{=html}\n\n::: notes\n**Wrap up**: \\*Before proceeding, point out how students could understand some of the structure and formatting by contrasting input and output, even though it might have been challenging.\nYou are constantly practicing a skill you will need for coding all the time: reading and understanding someone's code.\n:::\n\n## {{< fa brands markdown >}} Markdown\n\n::: fragment\n- Simple expressive formatting with symbols and text.\n- Used in many [apps and services](https://www.markdownguide.org/tools/), for example {{< fa brands discord title=\"Discord\" >}} {{< fa brands slack title=\"Slack\" >}} {{< fa brands github title= \"GitHub\" >}}.\n:::\n\n+-------------------------------------+\n| Markdown syntax |\n+=====================================+\n| # \\# Heading 1 |\n+-------------------------------------+\n| ## \\## Heading 2 |\n+-------------------------------------+\n| **\\*\\*strong\\*\\*** |\n+-------------------------------------+\n| *\\*emphasized\\** |\n+-------------------------------------+\n\n## How Quarto works {background-image=\"https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/c2ef45f1-4a68-4c7a-a43f-bdcf0f90e104_rw_3840.png?h=783eba914284e5adfb9feadcf4ba5f1e\" background-size=\"contain\" aria-label=\"A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.\"}\n\n::: footer\nArtwork from \"Hello, Quarto\" keynote by Julia Lowndes and Mine Çetinkaya-Rundel, presented at RStudio Conference 2022.\nIllustrated by Allison Horst.\n:::\n\n::: notes\n- Offers many different output formats, not only PDF.\n- One option is to create HTML including websites.\n- In fact, this entire website was made in Quarto!\n:::\n\n## {#down-the-rabbit-hole-1 data-menu-title=\"Down the rabbit hole\" background-iframe=\"https://stephan-koenig.github.io/teaching-demo/\" background-interactive=\"true\"}\n\n## {#down-the-rabbit-hole-2 .centered data-menu-title=\"Down the rabbit hole\"}\n\n``` {include=\"../index.qmd\" filename=\"index.qmd\" start-line=\"1\" end-line=\"15\"}\n```\n\n::: notes\nDemo MICB: 2XX website as an example of a Quarto project.\n:::\n\n## {{< fa laptop-code >}} Next lab: Create your own website! {background-color=\"#447099\"}\n\n::: incremental\n- Build a professional ePortfolio online.\n- Reflect on and record your growth across the MICB program.\n- Demonstrate your coding and collaboration skills.\n- Showcase your work as a developing microbiologist and immunologist to future employers.\n:::\n\n::: notes\nLearn relevant technologies for web development and reproducible workflows using industry-standard tools.\n:::\n\n# Universal Design for Learning:
Embracing open source {background-color=\"#faa928\"}\n\n::: notes\nUDL strives to provide multiple means for three principles of effective instruction.\n:::\n\n## {#representation data-menu-title=\"Representation\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-recognition-networks.png\" background-size=\"contain\" aria-label=\"A diagram of a brain from the side highlighting brain regions involved in recognition.\"}\n\n::: footer\nCAST (2018).\n[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Representation\n\n::: incremental\n- Open source tools support alt text for images.\n- Easy to provide headings and descriptive hyperlinks.\n- Support for different file formats and integrating other media.\n:::\n\n## {#comments-1 data-menu-title=\"Comments\" background-iframe=\"https://stephan-koenig.github.io/teaching-demo/labs/02_create-website.html\" background-interactive=\"true\"}\n\n## {#engagement data-menu-title=\"Engagement\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-affective-networks.png\" background-size=\"contain\" aria-label=\"A diagram of a brain from the side highlighting brain regions involved in motivation\"}\n\n::: footer\nCAST (2018).\n[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Engagement\n\n::: incremental\n- Follow the **mastery learning** model, i.e., frequent practice, assessment and feedback.\n- Use online assessment platform (e.g., [PrairieLearn](https://prairielearn.readthedocs.io/)) to support mastery learning at scale.\n - Academic integrity by randomization.\n - Use questions in practices and exams.\n:::\n\n## {#prairielearn data-menu-title=\"PrairieLearn\" background-iframe=\"https://www.prairielearn.com/\" background-interactive=\"true\"}\n\n## Engagement\n\n::: incremental\n- Use authentic examples and assessments (for example, ePortfolio).\n- Use relevant, widespread technologies and industry standards, such as HTML, CSS, Git and GitHub, in a framework that can be adapted to any bioinformatics pipeline.\n- Model inclusive practices in the way course is run and materials are provided.\n:::\n\n## {#action-and-expression data-menu-title=\"Action and expression\" background-image=\"https://www.cast.org/binaries/content/gallery/castm/our-work/brain-strategic-networks.png\" background-size=\"contain\" aria-label=\"A diagram of a brain from the side highlighting brain regions involved in strategizing.\"}\n\n::: footer\nCAST (2018).\n[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org)\n:::\n\n## Action and expression\n\n::: incremental\n- Alternative ways of participating, e.g., discussion section on course website.\n- Increased expression and communication (open source platforms offer a lot of flexibility).\n- Accommodations supported by online assessment platforms.\n:::\n\n::: notes\n- Affordability is an accessibility issue.\n- Uses open source material makes material more accessible.\n- Cloud computing for accessibility.\n- Support for desktop and mobile.\n- Collect feedback on the relevant pages.\n- [UBC OER Fund](https://oerfund.open.ubc.ca/)\n:::\n\n## {#comments data-menu-title=\"Comments\" background-iframe=\"https://stephan-koenig.github.io/teaching-demo/posts/welcome/\" background-interactive=\"true\"}\n\n## We are not alone: UDL community of practice {.center}\n\n[Universal design for learning fellows program](https://tlef.ubc.ca/application/special-call/universal-design-for-learning-fellows-program/)---2024 cohort.\n\n::: notes\nThere is always more to learn from our colleagues.\n:::\n\n# Teaching philosphy: Lifelong learner {background-color=\"#faa928\"}\n\n::: notes\n- Constructivist, thus learner centered.\n- Near-limitless ability to learn.\n- Raise students awareness.\n- Perfectionist.\n- Learning as an iterative process resembles coding to me.\n- Assess students' prior knowledge.\n- Mastery learning.\n- Normalizing struggle. Live coding.\n- Monitor classroom climate.\n:::\n\n## Acknowlegements\n\n- Tracy Kion and the search committee\n- Hannah Wong\n- Karen Smith\n", "supporting": [ "01_first-steps_files" ], diff --git a/slides/01_first-steps.qmd b/slides/01_first-steps.qmd index 1c79ccb..f24264c 100644 --- a/slides/01_first-steps.qmd +++ b/slides/01_first-steps.qmd @@ -166,7 +166,8 @@ How would ensure the correct reporting of your analysis? `r countdown(minutes = 5)` ::: notes -**Wrap up**: *Before proceeding, point out how students could understand some of the structure and formatting by contrasting input and output, even though it might have been challenging. You are constantly practicing a skill you will need for coding all the time: reading and understanding someone's code. +**Wrap up**: \*Before proceeding, point out how students could understand some of the structure and formatting by contrasting input and output, even though it might have been challenging. +You are constantly practicing a skill you will need for coding all the time: reading and understanding someone's code. ::: ## {{< fa brands markdown >}} Markdown @@ -181,7 +182,7 @@ How would ensure the correct reporting of your analysis? +=====================================+ | # \# Heading 1 | +-------------------------------------+ -| ## \#\# Heading 2 | +| ## \## Heading 2 | +-------------------------------------+ | **\*\*strong\*\*** | +-------------------------------------+ @@ -201,7 +202,7 @@ Illustrated by Allison Horst. - In fact, this entire website was made in Quarto! ::: -## {#down-the-rabbit-hole-1 data-meny-title="Down the rabbit hole" background-iframe="https://stephan-koenig.github.io/teaching-demo/" background-interactive="true"} +## {#down-the-rabbit-hole-1 data-menu-title="Down the rabbit hole" background-iframe="https://stephan-koenig.github.io/teaching-demo/" background-interactive="true"} ## {#down-the-rabbit-hole-2 .centered data-menu-title="Down the rabbit hole"} @@ -231,60 +232,74 @@ Learn relevant technologies for web development and reproducible workflows using UDL strives to provide multiple means for three principles of effective instruction. ::: -## {#representation data-menu-title="Representation" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-recognition-networks.png"} +## {#representation data-menu-title="Representation" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-recognition-networks.png" background-size="contain" aria-label="A diagram of a brain from the side highlighting brain regions involved in recognition."} ::: footer -CAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) +CAST (2018). +[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) ::: ## Representation +::: incremental - Open source tools support alt text for images. - Easy to provide headings and descriptive hyperlinks. -- Support for different file formats. +- Support for different file formats and integrating other media. +::: + +## {#comments-1 data-menu-title="Comments" background-iframe="https://stephan-koenig.github.io/teaching-demo/labs/02_create-website.html" background-interactive="true"} -## {#engagement data-menu-title="Engagement" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-affective-networks.png"} +## {#engagement data-menu-title="Engagement" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-affective-networks.png" background-size="contain" aria-label="A diagram of a brain from the side highlighting brain regions involved in motivation"} ::: footer -CAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) +CAST (2018). +[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) ::: ## Engagement +::: incremental - Follow the **mastery learning** model, i.e., frequent practice, assessment and feedback. - Use online assessment platform (e.g., [PrairieLearn](https://prairielearn.readthedocs.io/)) to support mastery learning at scale. - Academic integrity by randomization. - Use questions in practices and exams. -- Use authentic examples and assessments (for example, ePortfolio) -- Use relevant, widespread technologies, such as web technologies (HTML, CSS). -- Model inclusive practices in the way course is run (syllabus) and materials are provided. +::: ## {#prairielearn data-menu-title="PrairieLearn" background-iframe="https://www.prairielearn.com/" background-interactive="true"} -## {#action-and-expression data-menu-title="Action and expression" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-strategic-networks.png"} +## Engagement + +::: incremental +- Use authentic examples and assessments (for example, ePortfolio). +- Use relevant, widespread technologies and industry standards, such as HTML, CSS, Git and GitHub, in a framework that can be adapted to any bioinformatics pipeline. +- Model inclusive practices in the way course is run and materials are provided. +::: + +## {#action-and-expression data-menu-title="Action and expression" background-image="https://www.cast.org/binaries/content/gallery/castm/our-work/brain-strategic-networks.png" background-size="contain" aria-label="A diagram of a brain from the side highlighting brain regions involved in strategizing."} ::: footer -CAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) +CAST (2018). +[Universal Design for Learning Guidelines version 2.2](http://udlguidelines.cast.org) ::: ## Action and expression +::: incremental - Alternative ways of participating, e.g., discussion section on course website. -- Increased expression and communication (Quarto offers a lot of flexibility). -- Accommodations supported by PrairieLearn. - -## Open education resources +- Increased expression and communication (open source platforms offer a lot of flexibility). +- Accommodations supported by online assessment platforms. +::: +::: notes - Affordability is an accessibility issue. - Uses open source material makes material more accessible. - Cloud computing for accessibility. - Support for desktop and mobile. - Collect feedback on the relevant pages. - [UBC OER Fund](https://oerfund.open.ubc.ca/) +::: -## {#comments-1 data-meny-title="Comments" background-iframe="https://stephan-koenig.github.io/teaching-demo/posts/welcome/" background-interactive="true"} - -## {data-meny-title="Comments" background-iframe="https://github.com/stephan-koenig/teaching-demo/discussions/5" background-interactive="true"} +## {#comments data-menu-title="Comments" background-iframe="https://stephan-koenig.github.io/teaching-demo/posts/welcome/" background-interactive="true"} ## We are not alone: UDL community of practice {.center} @@ -294,4 +309,22 @@ CAST (2018). [Universal Design for Learning Guidelines version 2.2](http://udlgu There is always more to learn from our colleagues. ::: -# Teaching philosphy: Practicing expert behaviour {background-color="#faa928"} +# Teaching philosphy: Lifelong learner {background-color="#faa928"} + +::: notes +- Constructivist, thus learner centered. +- Near-limitless ability to learn. +- Raise students awareness. +- Perfectionist. +- Learning as an iterative process resembles coding to me. +- Assess students' prior knowledge. +- Mastery learning. +- Normalizing struggle. Live coding. +- Monitor classroom climate. +::: + +## Acknowlegements + +- Tracy Kion and the search committee +- Hannah Wong +- Karen Smith