From c9d26996db8e0c58c588f074b41fe10ee4b97664 Mon Sep 17 00:00:00 2001
From: Theresa Mieslinger <theresa.mieslinger@gmail.com>
Date: Mon, 8 Jul 2024 00:25:26 +0200
Subject: [PATCH] add content to Respect&Accountability section

---
 lectures/good-practice/slides.qmd | 161 ++++++++++++++++++++++++++----
 1 file changed, 140 insertions(+), 21 deletions(-)

diff --git a/lectures/good-practice/slides.qmd b/lectures/good-practice/slides.qmd
index ffd0c13..76e79ae 100644
--- a/lectures/good-practice/slides.qmd
+++ b/lectures/good-practice/slides.qmd
@@ -193,7 +193,6 @@ See also Python docstring conventions [PEP-257](https://peps.python.org/pep-0257
 :::
 
 ## Beyond FAIR data
-Make it FUN :)
 
 :::: {.columns}
 
@@ -206,41 +205,164 @@ Make it FUN :)
 :::
 
 ::: {.column width="50%"}
-**Make it FUN to work with the data**
+**Make it FUN :)**  
+to work with the data
 
-* design user-friendly datasets
-* make them publicly available
+* openly accessible
+* analysis-ready cloud-optimized data formats ([Abernathey et al., 2021](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9354557))
 :::
 ::::
 
-## Which tools shall we use?
-### Open Source
-decentralized software development model that encourages open collaboration
-relies on goal-oriented yet loosely coordinated participants who cooperate voluntarily to create a product (or service) of economic value, which is made freely available to contributors and noncontributors alike
+::: {.notes}
+* “Cloud-ready”: datasets shall be possible to be opened directly from any other server, e.g. OPeNDAP
+* cloud-optimized (zarr, TileDB, …) 
+:::
+
+## Which tools shall we use? {.leftalign}
+
+:::fragment
+### Open Source / Open Collaboration
+*Open source is a decentralized software development model that encourages open collaboration.*
+:::
+:::fragment
+> [It] relies on **goal-oriented** yet loosely coordinated participants who **cooperate voluntarily** to create a product (or service) of economic value, which is made **freely available** to contributors and noncontributors alike. [Levine and Prietula, 2013](https://pubsonline.informs.org/doi/10.1287/orsc.2013.0872)
+:::
 
-* trustworthy sources, supply chain bug
+## Which tools shall we use? {.leftalign}
+### Trustworthy sources {.leftalign}
+:::fragment
+* open source products
+* software products under active development and maintenance, e.g. according to Git commit history
+* proper documentation
+:::
 
 ::: {.notes}
-* you are responsible for the result
+* you are responsible for the result!
+* try to stay out of supply chain bugs
 :::
-## Summary on Reproducibility
+
+## Summary on Reliability & Reproducibility
 * save the primary data needed to reproduce the argument of your scientific study
+* go beyond FAIR data by creating user-friendly datasets and making them publicly available
+* use trustworthy sources
+* contribute to open source products whenever suitable
 
 # Respect & Accountability
 *What shall we credit and how?*
 
-## Authorship versus Acknowledgment
+## Authorship versus Acknowledgements
+
+:::fragment
+> Authorship provides credit for a researcher's contributions to a study and carries accountability. [-- nature](https://www.nature.com/nature-portfolio/editorial-policies/authorship)
+
+> To protect the integrity of authorship, only persons who have significantly contributed to the research and paper preparation should be listed as authors. [-- ACP](https://publications.copernicus.org/for_authors/obligations_for_authors.html)
+:::
+
+## Authorship
+*Which contributions qualify for authorship?*
+
+:::leftalign
+**Substantial contributions to** 
+
+* the conception or design of the work
+* the acquisition, analysis, or interpretation of data for the work
+* drafting the work or reviewing it critically for important intellectual content
+:::
+
+:::fragment
+**Authorship implies responsibility and accountability for the published work.**
+:::
 
-## Licenses
-CC0 versus CC-BY
+:::notes
+* approval of the published work
+* Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. 
+* includes being accountable for data / code!
+:::
 
-## Intellectual Property (IP)
-Copyright versus Copyleft
+## Acknowledgements
 
-## Using AI
-* you are still responsable for your scientific results
+:::leftalign
+Typically used to acknowledge
+
+* acquisition of funding
+* data sources / providers
+* software
+* general supervision of a research group or general administrative support
+* writing or coding assistance
+:::
+:::notes
+* Institute contributions (for instance through IT or administrative services or even technical help) are to be acknowledged through the author’s affiliation.
+* The provision of data, model output, or the use of a model, that has been published in a previous study does not constitute a basis for authorship.
+:::
+
+## Using and declaring Artificial Intelligence (AI)
+:::leftalign
+The usage of AI needs to be declared in the respective section:
+
+:::smaller
+* if AI was used for writing assistance -> acknowledgment section
+* if AI was used for data collection, analysis, or figure generation -> methods section
+:::
+:::fragment
+**Humans / authors are still responsable for any published material, also if it includes AI-assisted technology**
+:::
+:::
+
+## Does ChatGPT qualify for authorship? {.special}
+
+:::fragment
+*No, because they cannot be responsible for the accuracy, integrity, and originality of the work.*
+:::
+
+:::notes
+ChatGPT's answer: No. [...] AI systems like ChatGPT can provide immense help in information search, organization, and preliminary drafting, they don't possess the capability to understand, interpret, or conceptualize the results of a research study or to take responsibility for it.
+:::
+
+## Intellectual Property (IP) rights
+Two main legal concepts relevant for software:
+
+* **Copyright** gives the creator exclusive rights to use, modify, and share the work. In Germany, copyright arises automatically when the work is created. It cannot be transferred, however, the author can grant others the right to use the work.
+* **Copyleft** is a licensing method that encourages the unrestricted sharing, modification, and utilisation of creative works.
+
+:::notes
+* Any creative work, be it information, literature, art, or software could be replicated if not protected by intellectual property rights.
+* copyright can be granted by public law and depends on the given country/state. In Germany, the German Copyright Act (Urheberrechtsgesetz) regulates copyright.
+* because of Copyright, we need to think of licenses that regulate usage, modification and sharing of software
+* other types of IP rights: patents, trademarks
+:::
+
+## Types of Software Licenses
+* **Public domain licenses** allow others to use, modify, distribute software without any restrictions
+* **Permissive licenses** allow others to use, modify, and distribute the software with minimal requirements (e.g. MIT, Apache 2.0, BSD)
+* **Copyleft / "Share-alike" licenses** ensure that any derivative work of a software adopts the same licensing type, typically an open-source license (e.g. GPL, LGPL)
+* **Proprietary / non-reuse licenses** restricts users from accessing, modifying, and redistributing the software. 
+
+:::notes
+* if you upload code to GitHub without stating a license, in principle, nobody is allowed to use it
+* GNU General Public License (GPL)-licensed code cannot be integrated with proprietary closed-source code. mostly used for Linux software and for ICON! :)
+* GPL, AGPL - require sharing of modified source code; LGPL allows linking with proprietary code
+* changing licenses can be a huge challenge.
+* Unlike proprietary software that places restrictions on usage and distribution, open source software guarantees end users the freedom to use, modify, and share the software.
+* more Info here: https://osssoftware.org/blog/open-source-software-licenses-explained-a-beginners-overview/
+:::
+
+## Creative Commons (CC) Licenses
+*used e.g. for images, videos, documentation, presentations, and conference poster.*
+
+[CC licenses](https://creativecommons.org/share-your-work/cclicenses/) provide a way to grant permission to creative work that is under copyright law.
+
+* **CC0 Public Domain Dedication**: enables creators to give up their copyright
+* **CC BY**: allow others to use, modify, distribute creative work, as long as attribution is given to the creator.
+* Further possible restrictions: **SA** - Share-alike, **NC** - for noncommercial purpose only, **ND** - no derivatives allowed
+
+## Is AI-generated work protected by copyright? {.special}
+:::fragment
+Many countries do not put AI-generated work under copyright. But the status is unclear.
+:::
 
 ## Summary on Authorship and Credit
+* Authors have made substantial contributions to the published work and agree to be accountable for these.
+* Respect intellectual property of others and communicate a suitable license for your own work.
 
 # Good Coding Practice
 
@@ -272,6 +394,3 @@ Good Scientific Practice ensures research integrity and the advancement of knowl
 # Further Reading
 * [European Code of Conduct for Research Integrity](https://allea.org/wp-content/uploads/2023/06/European-Code-of-Conduct-Revised-Edition-2023.pdf)
 * [DFG Guidlines for Safeguarding Good Research Practice. Code of Conduct](https://zenodo.org/records/6472827)
-
-# Slide example
-
-- 
GitLab