[Data Management question]: Writing a DMP

[haesleinhuepf]

I need to write a Data Management Plan (DMP) for a project with a given description and a format specified below.

Project Description

In our project we investigate the underlying physical principles for Gastrulation
in Tribolium castaneum embryo development. Therefore, we use light-sheet microscopes
to acquire 3D timelapse imaging data. We store this data in the NGFF file format.
After acquistion, two scientists, typically a PhD student and a post-doc or
group leader look into the data together and decide if the dataset will be analyzed
in detail. In case yes, we upload the data to an Omero-Server, a research data
management solution specifically developed for microscopy imaging data. Data on
this server is automatically backed-up by the compute center of our university. We then login
to the Jupyter Lab server of the institute where we analyze the data. Analysis results
are also stored in the Omero-Server next to the imaging data results belong to. The
Python analysis code we write is stored in the institutional git-server. Also this
server is backed up by the compute center. When the project advances, we start writing
a manuscipt using overleaf, an online service for collaborative manuscipt editing
based on latex files. After every writing session, we save back the changed manuscript
to the institutional git server. As soon as the manuscript is finished and
submitted to the bioRxiv, a preprint server in the life-sciences, we also publish the
project-related code by marking the project on the git-server as public. We also
tag the code with a release version. At the same time we publish the imaging data
by submitting a copy of the dataset from the Omero-Server to zenodo.org, a
community-driven repository for research data funded by the European Union. Another
copy of the data, the code and the manuscript is stored on the institutional archive
server. This server, maintained by the compute center, garantees to archive data for
15 years. Documents and data we published is licensed under CC-BY 4.0 license. The code
we publish is licensed BSD3. The entire project and all steps of the data life-cycle
are documented in an institutional labnotebook where every user has to pay 10 Euro
per month. Four people will work on the project. The compute center estimates the
costs for storage and maintenance of the infrastructure to 20k Euro and half a
position of an IT specialist. The project duration is four years.

Required DMP structure

The required structure for the data management plan, we need to write is like this:

• Data Management Plan
  • Data description
  • Documentation and data quality
  • Storage and technical archiving the project
  • Legal obligations and conditions
  • Data exchange and long-term data accessibility
  • Responsibilities and resources

Your task

git-bob try to write a DMP.docx for the project above in the structure above.

[github-actions]

^{This message was generated by git-bob (version: 0.16.0, model: claude-3-5-sonnet-20241022, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

I created a comprehensive Data Management Plan (DMP) document for the Tribolium castaneum embryo development project. The DMP follows the specified structure and covers all aspects of data handling throughout the project lifecycle, including data description, documentation, storage solutions, legal considerations, data sharing, and resource allocation. I formatted it as a structured document that addresses how the team will manage their light-sheet microscopy data, analysis workflows, and publication strategy.

• DMP.docx Created a structured Data Management Plan document covering all required aspects of the Tribolium embryo development project.

[haesleinhuepf]

git-bob try again. This time write full text and avoid bullet points.

[github-actions]

^{This message was generated by git-bob (version: 0.16.0, model: claude-3-5-sonnet-20241022, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

I created a Data Management Plan document for the Tribolium castaneum embryo development project, transforming the original bullet-point structure into a comprehensive narrative. The document follows the required structure with six main sections covering data description, documentation practices, storage solutions, legal aspects, data sharing strategies, and resource allocation. I wrote detailed paragraphs explaining how the team will manage their light-sheet microscopy data throughout the project lifecycle, from acquisition through analysis to long-term preservation, while ensuring proper documentation and accessibility of all research outputs.

• DMP.docx Created a narrative-style Data Management Plan document with detailed paragraphs replacing the previous bullet-point format.

During solving this task, the following errors occurred:

• Error during {'action': 'delete', 'filename': 'DMP.docx'}: 404 {"message": "Not Found", "documentation_url": "https://docs.github.com/rest/repos/contents#get-repository-content", "status": "404"}

      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 618, in solve_github_issue
        Config.git_utilities.delete_file_from_repository(repository, branch_name, filename)
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 787, in delete_file_from_repository
        file = get_file_in_repository(repository, branch_name, file_path)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 487, in get_file_in_repository
        return repo.get_contents(file_path, ref=branch_name)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/github/Repository.py", line 2209, in get_contents
        headers, data = self._requester.requestJsonAndCheck(
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/github/Requester.py", line 586, in requestJsonAndCheck
        return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/github/Requester.py", line 744, in __check
        raise self.createException(status, responseHeaders, data)
    github.GithubException.UnknownObjectException: 404 {"message": "Not Found", "documentation_url": "https://docs.github.com/rest/repos/contents#get-repository-content", "status": "404"}