diff --git a/01-OS-and-FAIR.html b/01-OS-and-FAIR.html index dd0e204..07e0ba4 100644 --- a/01-OS-and-FAIR.html +++ b/01-OS-and-FAIR.html @@ -885,10 +885,219 @@

Reusable
  • for data Creative Commons Attribution (CC BY) license,
  • for code a permissive open source license such as the MIT, BSD, or Apache license.
    • - + --> diff --git a/aio.html b/aio.html index bea3837..4e44fb8 100644 --- a/aio.html +++ b/aio.html @@ -978,12 +978,241 @@

    Reusable license,
  • for code a permissive open source license such as the MIT, BSD, or Apache license.
    • + +
    +
    + +
    +
    +

    Challenge +

    +
    +

    ## Exercise 4: Example of FAIR data (4 min)

    +

    Zenodo is general data repository. Have a look at the dataset record +with COVID-19 data: https://doi.org/10.5281/zenodo.6339631

    +

    Identify how each of F.A.I.R principles has been met.
    Hint: navigate to linked github record to easily access the README +file

    +
    +
    +
    +
    +
    + +
    +
    +
      +
      • +
      1. The dataset is identified by a PID (doi). It can be found by its ID. +It human accessible description and keywords, both suitable for +discovery.
        2. +
      • +
      • +
      1. Data can be downloaded using standard browser.
        2. +
      • +
      • +
      1. Dataset entries are in common formats: csv, R, jpg
        2. +
      • +
      • +
      1. Dataset is linked to publication, github record and project +website
        2. +
      • +
      • +
      1. The record contains rich metadata in README file, including files +structure and the detailed tables formats.
        2. +
      • +
      • +
      1. Data are released under open Creative Commons Attribution +Licence
        2. +
      • +
    +
    +
    +
    +
    + + +
    +

    FAIR and You (3 min) +

    +

    The FAIR acronym is sometimes accompanied with the following labels: +* Findable - Citable * Accessible - Trackable and countable * +Interoperable - Intelligible * Reusable - Reproducible

    +

    ## Solution

    + +
    +
    +

    FAIR vs Open Science (3 min teaching) +

    +

    FAIR does not mean Open. Actually, FAIR guideline +only requires that the metadata record is always accessible. For +example, the existence of the data can be known (their metadata), the +data can have easy to use PID to reference them, but the actual data +files can only be downloaded after the login and authorization.

    +

    However, if data are already in the FAIR form, i.e. accessible over +the internet, in interoperable format and well documented, then it is +almost effortless to “open” the dataset and make it available to the +whole public. The data owner can do it any time when he no longer +perceives oppening as a risk.

    +

    At the same time, Open data which does not follow FAIR guidelines +have little value. If they are not well described, not in open formats +then they are not going to be re-used even if they were made “open” by +posting them on some website.

    +
    +

    Where to next +

    +
    +

    SH +

    +
     Further reading/links:
+ - [Challenges & benefits of OS](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000246)
+ - [Centre for Open Science](https://www.cos.io/)
+ - [Ted talk supporting OS](https://www.youtube.com/watch?v=c-bemNZ-IqA)
    +
    +
    +
    + +
    +
    +

    Open Science and FAIR Quiz (5 min + runs over +break) +

    +
    +

    Which of the following statements about the OS movement are +true/false?

    +
      +
    • Open Science relies strongly on the Internet
      • +
    • Open Access eliminates publishing costs
      • +
    • Open Data facilitates re-use
      • +
    • Open Data can increases confidence in research findings
      • +
    • In Open Peer Review, readers vote on publication acceptance
      +
      • +
    • Open Access permits the whole society to benefit from scientific +findings
      • +
    • Citizen Science engages the public in the research process
      • +
    • Release of public datasets is important for career progression
      • +
    • F in FAIR stands for free.
      • +
    • Only figures presenting results of statistical analysis need +underlying numerical data.
      • +
    • Sharing numerical data as a .pdf in Zenodo is FAIR.
      • +
    • Sharing numerical data as an Excel file via Github is not FAIR.
      • +
    • Group website is a good place to share your data.
      • +
    • Data should always be converted to Excel or .csv files in order to +be FAIR.
      • +
    • A DOI of a dataset helps in getting credit.
      • +
    • FAIR data are peer reviewed.
      • +
    • FAIR data accompany a publication.
      • +
    +
    +
    +
    +
    +
    + +
    +
    +
      +
    • Open Science relies strongly on the Internet T
      • +
    • Open Access eliminates publishing costs F
      • +
    • Open Data facilitates re-use T
      • +
    • Open Data increases confidence in research findings T
      • +
    • In Open Peer Review, readers vote on publication acceptance F
      • +
    • Open Access permits the whole society to benefit from scientific +findings T
      • +
    • Citizen Science engages the public in the research process T
      • +
    • Release of public datasets is important for career progression +T
      • +
    • F in FAIR stands for free. F
      • +
    • Only figures presenting results of statistical analysis need +underlying numerical data. F
      • +
    • Sharing numerical data as a .pdf in Zenodo is FAIR. F
      • +
    • Sharing numerical data as an Excel file via Github is not FAIR. +F
      • +
    • Group website is a good place to share your data. F
      • +
    • Data should always be converted to Excel or .csv files in order to +be FAIR. F
      • +
    • A DOI of a dataset helps in getting credit. T
      • +
    • FAIR data are peer reviewed. F
      • +
    • FAIR data accompany a publication. F
      • +
    +
    +
    +
    +
    +
    +
    +
    +

    Attribution +

    +
    +

    SH +

    +
     Content of this episode was adapted from:
+ * Wiki [Open Science](https://en.wikipedia.org/wiki/Open_science)
+ * [European Open Science Cloud](https://www.eosc-hub.eu/open-science-info)
+ * [Science is necessarily collaborative - The Biochemist article](https://portlandpress.com/biochemist/article/42/3/58/225220/Science-is-necessarily-collaborative).
    +
    +
    +
    + +
    +
    +

    Key Points +

    +
    +
      +
    • Open Science increases transparency in research
      • +
    • Publicly funded science should be publicly available
      • +
    • FAIR stands for Findable Accessible Interoperable Reusable
      • +
    • FAIR assures easy reuse of data underlying scientific findings
      • +
    +
    +
    +
    -

    Content from Using Markdown

    Last updated on 2024-02-24 | diff --git a/instructor/01-OS-and-FAIR.html b/instructor/01-OS-and-FAIR.html index a59af2d..49053d0 100644 --- a/instructor/01-OS-and-FAIR.html +++ b/instructor/01-OS-and-FAIR.html @@ -887,10 +887,219 @@

    Reusable
  • for data Creative Commons Attribution (CC BY) license,
  • for code a permissive open source license such as the MIT, BSD, or Apache license.
    • - + --> diff --git a/instructor/aio.html b/instructor/aio.html index 598d91e..10fb4c6 100644 --- a/instructor/aio.html +++ b/instructor/aio.html @@ -981,12 +981,241 @@

    Reusable license,
  • for code a permissive open source license such as the MIT, BSD, or Apache license.
    • + +
    +
    + +
    +
    +

    Challenge +

    +
    +

    ## Exercise 4: Example of FAIR data (4 min)

    +

    Zenodo is general data repository. Have a look at the dataset record +with COVID-19 data: https://doi.org/10.5281/zenodo.6339631

    +

    Identify how each of F.A.I.R principles has been met.
    Hint: navigate to linked github record to easily access the README +file

    +
    +
    +
    +
    +
    + +
    +
    +
      +
      • +
      1. The dataset is identified by a PID (doi). It can be found by its ID. +It human accessible description and keywords, both suitable for +discovery.
        2. +
      • +
      • +
      1. Data can be downloaded using standard browser.
        2. +
      • +
      • +
      1. Dataset entries are in common formats: csv, R, jpg
        2. +
      • +
      • +
      1. Dataset is linked to publication, github record and project +website
        2. +
      • +
      • +
      1. The record contains rich metadata in README file, including files +structure and the detailed tables formats.
        2. +
      • +
      • +
      1. Data are released under open Creative Commons Attribution +Licence
        2. +
      • +
    +
    +
    +
    +
    + + +
    +

    FAIR and You (3 min) +

    +

    The FAIR acronym is sometimes accompanied with the following labels: +* Findable - Citable * Accessible - Trackable and countable * +Interoperable - Intelligible * Reusable - Reproducible

    +

    ## Solution

    +
      +
    • Findable data have their own identity, so they can be easily cited +and secure the credits to the authors
      • +
    • Data accessibility over the Internet using standard protocols can be +easily monitored (for example using Google analytics). This results in +metrics on data popularity or even geo-locations of data users.
      • +
    • Interoperable data can benefit the future you, for example you will +be able to still read your data even when you no longer have access to +the specialized, vendor specific software with which you worked with +them before. Also the future you may not remember abreviations and +ad-hoc conventions you used before (Intelligible).
      • +
    • Well documented data should contain all the details necessary to +reproduce the experiments, helping the future you or someone taking over +from you in the laboratory.
      • +
    • Saves time and money.
      • +
    +
    +
    +

    FAIR vs Open Science (3 min teaching) +

    +

    FAIR does not mean Open. Actually, FAIR guideline +only requires that the metadata record is always accessible. For +example, the existence of the data can be known (their metadata), the +data can have easy to use PID to reference them, but the actual data +files can only be downloaded after the login and authorization.

    +

    However, if data are already in the FAIR form, i.e. accessible over +the internet, in interoperable format and well documented, then it is +almost effortless to “open” the dataset and make it available to the +whole public. The data owner can do it any time when he no longer +perceives oppening as a risk.

    +

    At the same time, Open data which does not follow FAIR guidelines +have little value. If they are not well described, not in open formats +then they are not going to be re-used even if they were made “open” by +posting them on some website.

    +
    +

    Where to next +

    +
    +

    SH +

    +
     Further reading/links:
+ - [Challenges & benefits of OS](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000246)
+ - [Centre for Open Science](https://www.cos.io/)
+ - [Ted talk supporting OS](https://www.youtube.com/watch?v=c-bemNZ-IqA)
    +
    +
    +
    + +
    +
    +

    Open Science and FAIR Quiz (5 min + runs over +break) +

    +
    +

    Which of the following statements about the OS movement are +true/false?

    +
      +
    • Open Science relies strongly on the Internet
      • +
    • Open Access eliminates publishing costs
      • +
    • Open Data facilitates re-use
      • +
    • Open Data can increases confidence in research findings
      • +
    • In Open Peer Review, readers vote on publication acceptance
      +
      • +
    • Open Access permits the whole society to benefit from scientific +findings
      • +
    • Citizen Science engages the public in the research process
      • +
    • Release of public datasets is important for career progression
      • +
    • F in FAIR stands for free.
      • +
    • Only figures presenting results of statistical analysis need +underlying numerical data.
      • +
    • Sharing numerical data as a .pdf in Zenodo is FAIR.
      • +
    • Sharing numerical data as an Excel file via Github is not FAIR.
      • +
    • Group website is a good place to share your data.
      • +
    • Data should always be converted to Excel or .csv files in order to +be FAIR.
      • +
    • A DOI of a dataset helps in getting credit.
      • +
    • FAIR data are peer reviewed.
      • +
    • FAIR data accompany a publication.
      • +
    +
    +
    +
    +
    +
    + +
    +
    +
      +
    • Open Science relies strongly on the Internet T
      • +
    • Open Access eliminates publishing costs F
      • +
    • Open Data facilitates re-use T
      • +
    • Open Data increases confidence in research findings T
      • +
    • In Open Peer Review, readers vote on publication acceptance F
      • +
    • Open Access permits the whole society to benefit from scientific +findings T
      • +
    • Citizen Science engages the public in the research process T
      • +
    • Release of public datasets is important for career progression +T
      • +
    • F in FAIR stands for free. F
      • +
    • Only figures presenting results of statistical analysis need +underlying numerical data. F
      • +
    • Sharing numerical data as a .pdf in Zenodo is FAIR. F
      • +
    • Sharing numerical data as an Excel file via Github is not FAIR. +F
      • +
    • Group website is a good place to share your data. F
      • +
    • Data should always be converted to Excel or .csv files in order to +be FAIR. F
      • +
    • A DOI of a dataset helps in getting credit. T
      • +
    • FAIR data are peer reviewed. F
      • +
    • FAIR data accompany a publication. F
      • +
    +
    +
    +
    +
    +
    +
    +
    +

    Attribution +

    +
    +

    SH +

    +
     Content of this episode was adapted from:
+ * Wiki [Open Science](https://en.wikipedia.org/wiki/Open_science)
+ * [European Open Science Cloud](https://www.eosc-hub.eu/open-science-info)
+ * [Science is necessarily collaborative - The Biochemist article](https://portlandpress.com/biochemist/article/42/3/58/225220/Science-is-necessarily-collaborative).
    +
    +
    +
    + +
    +
    +

    Key Points +

    +
    +
      +
    • Open Science increases transparency in research
      • +
    • Publicly funded science should be publicly available
      • +
    • FAIR stands for Findable Accessible Interoperable Reusable
      • +
    • FAIR assures easy reuse of data underlying scientific findings
      • +
    +
    +
    +
    -

    Content from Using Markdown

    Last updated on 2024-02-24 | diff --git a/instructor/key-points.html b/instructor/key-points.html index c989351..094487c 100644 --- a/instructor/key-points.html +++ b/instructor/key-points.html @@ -259,7 +259,13 @@

    Introduction to Open Science and FAIR principlesBeing FAIR

    -

    Using Markdown

    +
    +
      +
    • Open Science increases transparency in research
      • +
    • Publicly funded science should be publicly available
      • +
    • FAIR stands for Findable Accessible Interoperable Reusable
      • +
    • FAIR assures easy reuse of data underlying scientific findings
      • +

    Using Markdown

    • Use .md files for episodes when you want static diff --git a/key-points.html b/key-points.html index 259d0ae..abbe8dc 100644 --- a/key-points.html +++ b/key-points.html @@ -257,7 +257,13 @@

      Introduction to Open Science and FAIR principlesBeing FAIR

      -

      Using Markdown

      +
      +
        +
      • Open Science increases transparency in research
        • +
      • Publicly funded science should be publicly available
        • +
      • FAIR stands for Findable Accessible Interoperable Reusable
        • +
      • FAIR assures easy reuse of data underlying scientific findings
        • +

      Using Markdown

      • Use .md files for episodes when you want static diff --git a/md5sum.txt b/md5sum.txt index 7e02c6c..f410972 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -4,7 +4,7 @@ "config.yaml" "78527fcaaab88132938042a98642abe4" "site/built/config.yaml" "2024-02-23" "index.md" "4e900476217a21b1af6c5ef17c813b22" "site/built/index.md" "2024-02-24" "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2022-04-22" -"episodes/01-OS-and-FAIR.md" "6b03c2c0786b43527d7ebe6aa2ec8c5a" "site/built/01-OS-and-FAIR.md" "2024-02-25" +"episodes/01-OS-and-FAIR.md" "2eaeb21d1d2adb284d5279b9f6556bf5" "site/built/01-OS-and-FAIR.md" "2024-02-25" "episodes/xTemplate.md" "6c55d31b41d322729fb3276f8d4371fc" "site/built/xTemplate.md" "2024-02-24" "instructors/instructor-notes.md" "63eca1767f6b7a73a86bb27da69bf71b" "site/built/instructor-notes.md" "2024-02-23" "learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2023-03-16" diff --git a/pkgdown.yml b/pkgdown.yml index f9a6262..ccc34db 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,5 +2,5 @@ pandoc: 2.19.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2024-02-25T00:11Z +last_built: 2024-02-25T00:15Z