Merge pull request #11 from ScaDS/final-exercises

Finalized exersices

docs/links.md

@@ -4,6 +4,11 @@
 - Policies
   - [Statement by the Executive Committee of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) on the Influence of Generative Models of Text and Image Creation onScience and the Humanities and on the DFG’s Funding Activities](https://www.dfg.de/resource/blob/289676/89c03e7a7a8a024093602995974832f9/230921-statement-executive-committee-ki-ai-data.pdf)
   - [Helmholtz Recommendations on the Use of Artificial Intelligence](https://www.helmholtz.de/assets/helmholtz_gemeinschaft/Downloads/Helmholtz_Recommendations_on_use_of_AI_Version_1.0.pdf)
+  - [Research Ethics in the Age of AI: Embracing Openness as a Path Forward](https://doi.org/10.48440/os.helmholtz.080)
 - Resources
   - [AI for students](https://aivoorstudenten.be/en/courses/ai-voor-studenten/)
-  - [UFZ RDM Guidelines: AI for science](https://rdm.pages.ufz.de/guidelines/AI-for-science/)
+  - [UFZ RDM Guidelines: AI for science](https://rdm.pages.ufz.de/guidelines/AI-for-science/)
+  - Some relevant, highly topical Talks at 38C3 on AI:
+    - [Klimaschädlich by Design – die ökologischen Kosten des KI-Hypes](https://fahrplan.events.ccc.de/congress/2024/fahrplan/talk/LVVRLL/)
+    - [Hacking Life: How to decode and manipulate biological cells with AI ](https://fahrplan.events.ccc.de/congress/2024/fahrplan/talk/UBWU9D/)
+    - [Let's build dodos! How generative AI is upturning the world of synthetic biology and hopelessly overwhelming traditional governance instruments. ](https://fahrplan.events.ccc.de/congress/2024/fahrplan/talk/GNZG8R/)

docs/session3/exercise.md

@@ -4,7 +4,8 @@ For each of the following exercises, pls. evaluate the service in regard to the
 suitability for your individual research and for science in general. Also,
 provide a brief summary of your experience in general.
 
-We prepared a [collaborative document for this exercise]() where you can share
+We prepared a [collaborative document for this
+exercise](https://notes.desy.de/-n-DggKjRyiDOXfkvcANcQ?edit) where you can share
 your experience with the others.
 
 Feel free to also try out other tools mentioned in [our overview](introduction.md)
@@ -15,7 +16,7 @@ and other tasks as well.
 This prompt can help you get past so-called writer’s block by offering you some
 ideas that can inspire you to start your assignment:
 
-```
+```markdown
 Take on the role of an expert in brainstorming. I want you to help me
 brainstorm on the theme [insert theme]. Take the role of a brainstorming expert
 in this area. Ask me what task I want to brainstorm about and what goal I want
@@ -28,18 +29,37 @@ to expand on any of the ideas.
 1. Try it out with a GenAI of your choice
 2. Try it out with several GenAIs and compare results and the process to get there
 
-(Source: https://aivoorstudenten.be/en/courses/ai-voor-studenten/lessons/brainstormen-2/)
+(Source: <https://aivoorstudenten.be/en/courses/ai-voor-studenten/lessons/brainstormen-2/>)
 
 ## Mindmap from PDFs with Claude.AI
 
 0. Register at <https://claude.ai/>
-1. Upload the PDF downloaded from https://doi.org/10.1080/02602938.2024.2386662 to Claude.
+1. Upload the PDF downloaded from <https://doi.org/10.1080/02602938.2024.2386662> to Claude.
 2. create a Mermaid code visual based on the themes addressed in the attached article.
-3. Copy the resulting code to https://mermaid.live/edit
+3. Copy the resulting code to <https://mermaid.live/edit>
 
 (Based on <https://aivoorstudenten.be/en/courses/ai-voor-studenten/lessons/visualiseren/>)
 
-## Literature search with Consensus
+## Literature exploration/search with Consensus / SCISPACE / Undermind / ORKG
+
+0. Optional: Register at the mentioned service (for Undermind it is necessary)
+1. Ask a research question of your choice or choose one of the suggested
+   questions (e.g. how does climate change impact biodiversity?)
+2. Evaluate and (in case) compare the services
+3. If and how would you incorporate the tool into your research routine?
+
+## Explore an article and related work with LitMaps / ConnectedPapers
+
+0. Optional: Register at the mentioned service
+1. Explore an article of your choice and its related work (example from above: <https://doi.org/10.1080/02602938.2024.2386662>)
+2. Evaluate and (in case) compare the services
+3. If and how would you incorporate the tool into your research routine?
+
+## Summarize a Paper using Scholarcy / Elicit
 
-0. Optional: Register at <https://consensus.ai/>
-1. Ask a research question of your choice or choose one of the suggested questions
+0. Optional: Register at the mentioned service
+1. Summarize an article of your choice (e.g. example from above: <https://doi.org/10.1080/02602938.2024.2386662>)
+   (Scholarcy: More -> Article Summarizer -> Add Paper)
+   (Elicit: Extract Data from PDFs)
+2. Evaluate and (in case) compare the services
+3. If and how would you incorporate the tool into your research routine?

docs/session3/introduction.md

@@ -1,14 +1,50 @@
 # Tools for the everydays research routine
 
-In this session, we will explore a variety of AI-powered tools that can be used in the everyday research routine. These tools can help researchers to discover relevant research papers, analyze and summarize scientific literature, and visualize complex data. By leveraging AI technology, researchers can gain new insights, identify key trends, and make more informed decisions in their research.
+In this session, we will explore a variety of AI-powered tools that can be used
+in the everyday research routine. These tools can help researchers to discover
+relevant research papers, analyze and summarize scientific literature, and
+visualize complex data. By leveraging AI technology, researchers can gain new
+insights, identify key trends, and make more informed decisions in their
+research.
 
 (generated with GitHub Copilot)
 
+## Open Research Knowledge Graph (ORKG) Summary
+
+The Open Research Knowledge Graph (ORKG) enables
+researchers to create, share, and reuse research knowledge in a structured and
+machine-readable format. ORKG allows researchers to describe their research
+contributions, such as papers, datasets, and methods, using a standardized
+vocabulary and ontology. This enables the creation of a knowledge graph that can
+be queried and analyzed to identify relationships and patterns in research
+outputs. ORKG aims to facilitate collaboration, reproducibility, and
+transparency in research by providing a common framework for representing and
+sharing research knowledge. The platform is designed to be domain-agnostic and
+can be used across various disciplines.
+
+* Input and Output Formats
+  * Input Formats:
+  * RDF (Resource Description Framework)
+  * JSON-LD (JavaScript Object Notation for Linked Data)
+  * CSV (Comma Separated Values)
+  * BibTeX (for bibliographic data)
+* Output Formats:
+  * RDF (Resource Description Framework)
+  * JSON-LD (JavaScript Object Notation for Linked Data)
+  * CSV (Comma Separated Values)
+  * HTML (for human-readable representations)
+  * SPARQL (for querying the knowledge graph)
+
 ## Perplexity
 
 [Perplexity](https://perplexity.ai/)
 
-Perplexity is a platform that uses AI to provide answers to complex questions. In the context of science, Perplexity can be used to find relevant information and insights from a vast amount of scientific literature. It can help researchers and students to quickly grasp the core concepts and findings of a research area. Additionally, Perplexity can assist in identifying gaps in current knowledge and suggesting new research directions.
+Perplexity is a platform that uses AI to provide answers to complex questions.
+In the context of science, Perplexity can be used to find relevant information
+and insights from a vast amount of scientific literature. It can help
+researchers and students to quickly grasp the core concepts and findings of a
+research area. Additionally, Perplexity can assist in identifying gaps in
+current knowledge and suggesting new research directions.
 
 * Input formats
   * Natural language queries
@@ -166,7 +202,7 @@ Litmaps is a platform that uses AI to create interactive maps of research papers
 
 ## Petal
 
-[Petal](https://petal.io/)
+[Petal](https://petal.org/)
 
 Petal is an AI-powered platform for discovering and analyzing research papers. For scientists, Petal can be used to quickly find relevant papers and authors, and to understand the relationships between different studies. Petal's algorithms can identify key themes and trends in a research area and provide insights into the current state of knowledge. Additionally, Petal can assist in identifying gaps in current knowledge and suggesting new research directions.