[Presentation]: Research Data Management

[haesleinhuepf]

I need to give a talk about research data management to an audience of early career researchers. I have time for 10 powerpoint slides. What could I talk about? What would you write on the 10 slides?

git-bob comment

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Hello! As an image analysis expert, I think a focused talk on data management with scientific imaging could be very helpful. Here's a suggested outline for 10 slides:

1. Title: Research Data Management for Scientific Imaging

   • Your name, affiliation

2. Why Data Management Matters

   • Reproducibility
   • Time savings
   • Data sharing requirements

3. File Formats & Organization

   • Raw data formats (TIFF, CZI, OME-TIFF...)
   • Folder structure best practices
   • File naming conventions

4. Metadata is Key

   • Imaging parameters
   • Experimental conditions
   • Sample details

5. Version Control

   • Git basics for data
   • Data versioning tools
   • Documentation practices

6. Data Storage & Backup

   • Local vs cloud storage
   • Backup strategies
   • Data security

7. Data Analysis Pipeline

   • From raw data to results
   • Documenting analysis steps
   • Jupyter notebooks

8. Data Sharing

   • Repositories (Zenodo, BioImage Archive...)
   • DOIs and citations
   • Access rights

9. FAIR Principles

   • Findable
   • Accessible
   • Interoperable
   • Reusable

10. Resources & Tools

    • Software recommendations
    • Further reading
    • Contact information

Would you like me to elaborate on any of these points from an imaging perspective?

[haesleinhuepf]

Yes, please. git-bob comment in more detail what would be written on these 10 slides. Write full sentences, e.g. 2-4 per slide, explaining the specific concept.

[github-actions]

^{This message was generated by git-bob (version: 0.12.1dev, model: claude-3-5-sonnet-20241022, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

Here are detailed suggested contents for each slide:

1. Title: Research Data Management for Scientific Imaging
   "Managing scientific image data effectively is crucial for modern research. This presentation will cover best practices for organizing, documenting and sharing imaging data. We'll focus on practical strategies you can implement today."

2. Why Data Management Matters
   "Poor data management costs researchers 4-6 hours per week searching for data. Well-organized data enables others to verify and build upon your work. Funding agencies increasingly require data management plans and FAIR data practices."

3. File Formats & Organization
   "Store raw data in open formats like OME-TIFF that preserve metadata. Use descriptive folder names like 'YYYY-MM-DD_experiment-name'. Create README files explaining folder contents and experiment details. Keep raw data separate from processed results."

4. Metadata is Key
   "Document microscope settings like objective, pixel size and exposure time. Record sample preparation methods, treatments and timepoints. Use consistent metadata templates. Include calibration data and controls."

5. Version Control
   "Track changes to analysis code with Git. Document data processing steps in notebooks. Note which version of software was used. Keep analysis scripts with corresponding datasets."

6. Data Storage & Backup
   "Follow the 3-2-1 rule: 3 copies, 2 different media types, 1 offsite. Use checksums to verify data integrity. Plan storage needs before generating large datasets. Budget for long-term storage costs."

7. Data Analysis Pipeline
   "Document each step from raw data to final figures. Use automation to ensure reproducibility. Save intermediate results. Include example data and expected outputs."

8. Data Sharing
   "Choose appropriate repositories for your field. Get DOIs for datasets. Include detailed metadata for reuse. Consider embargo periods and access restrictions. Link data to publications."

9. FAIR Principles
   "Make data findable through metadata and persistent identifiers. Ensure accessibility through standard protocols. Use standard formats for interoperability. Include sufficient documentation for reuse."

10. Resources & Tools
    "Bio-Formats for image conversion. ImageJ/Fiji for analysis. Git for version control. Zenodo/BioImage Archive for sharing. Contact your library's data services team for support."

[haesleinhuepf]

git-bob try to make a powerpoint presentation out of this

[github-actions]

^{This message was generated by git-bob (version: 0.12.1dev, model: claude-3-5-sonnet-20241022, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

In response to a request for creating a presentation about Research Data Management for early career researchers, I created a comprehensive 10-slide PowerPoint presentation focusing on scientific imaging data management. The presentation covers essential topics including the importance of data management, file organization, metadata documentation, version control, storage strategies, data analysis pipelines, sharing practices, FAIR principles, and useful resources. Each slide contains 2-4 detailed sentences explaining the specific concepts and practical implementations.

• research_data_management.pptx Created a new PowerPoint presentation with 10 slides covering Research Data Management principles for scientific imaging.

During solving this task, the following errors occurred:

• Error during {'action': 'modify', 'filename': 'slide_template.pptx'}: unsupported encoding: none

      Traceback (most recent call last):
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_ai_github_utilities.py", line 501, in solve_github_issue
        created_files = create_or_modify_file(repository, issue, filename, branch_name, discussion,
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_ai_github_utilities.py", line 271, in create_or_modify_file
        file_content = Config.git_utilities.decode_file(Config.git_utilities.get_file_in_repository(repository, branch_name, filename))
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 757, in decode_file
        return file.decoded_content.decode()
               ^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/ContentFile.py", line 93, in decoded_content
        assert self.encoding == "base64", f"unsupported encoding: {self.encoding}"
               ^^^^^^^^^^^^^^^^^^^^^^^^^
    AssertionError: unsupported encoding: none