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Frequently Asked Questions (FAQ)

Annotated Research Context

Section titled Annotated Research Context
Where should the metadata annotation be made. In the same documents containing the data?

No. The metadata describing the data is collected in separate xlsx-files – called isa.assay.xlsx – that resides in the parent folder of the dataset.

Is it necessary to fill in the empty fields in the investigation-file manually?

No. Although it is possible to fill out the workbook manually, we recommend using ARC Commander or ARCitect to add this metadata.

Where in the ARC can I store "external" data?

Research projects rarely start out of the blue. Rather every project builds on previous findings and published datasets. To properly re-use and reference such a dataset, we recommend to add a study to your ARC. Every study by default comes with four parts:

└── <StudyName>
    ├── README.md
    ├── isa.study.xlsx
    ├── protocols
    └── resources
  • In the resources directory you can add the data (e.g. supplemental data files)
  • In the protocols directory you can add notes on how you retrieved the data and from where.
  • The study is registered in your ARC’s isa.investigation.xlsx, which includes a section “STUDY PUBLICATIONS” for every study. Here, you can add publication details (author, DOI, etc.) about the external data source.

ARC Commander

Section titled ARC Commander
Are there any recommendations for titles or identifiers?

Avoid using spaces in the identifier. Use underscores and capital letters instead. There are no specific restrictions regarding the title. Although it is possible to fill in the workbook manually, we recommend using ARC Commander to add this metadata.

How often should I sync my ARC?

We would not want to recommend a fixed time interval (once every hour / day / week) for how often you ideally sync the ARC. In general, the more you work with your ARC, the more you add or update, annotate or analyze data, the more you will want to make sure these changes are saved. Consider the syncing as a way to backup your project’s progress as well as an “undo button”.

Why do I get the error `'arc' is not recognized as an internal or external command, operable program or batch file.`?

Your machine cannot find your ARC commander executable. Possible reasons are that you have not yet installed the ARC commander or that the arc executable was not added to your path.

Please carefully retry the ARC Commander setup.

If this does not do the trick, please follow these steps towards debugging (on Windows):

  1. Open the command prompt (cmd) or powershell in the folder (e.g. C:\Programs\ArcCommander) where you stored the ARC Commander program (e.g. arc.exe). If arc --version shows the version, the executable is intact.
  2. Next, execute path to check wether the folder (e.g. C:\Programs\ArcCommander) appears in your path.
  3. Adapt the user’s path (not admin)

:bulb: If you do not have admin rights on the computer, please open the settings “Edit environment variables for your account” and follow steps described in the ARC Commander setup.

ARCitect

Section titled ARCitect
I already committed my changes, but they are still displayed in the ARCitect and are not uploaded to the DataHUB.

Sometimes, the ARCitect does not “accept” a commit or when writing a commit message and hitting the “commit” button the changes are still displayed. You can try the following:

  1. Close all windows (e.g. windows explorer) and files (in particular Excel workbooks) related to the ARC
  2. Try to commit again.
What does the "Credential Helper Selector" mean?

During ARCitect login, Windows asks you wether you want to use a “Credential Helper”. This can be used to store your DataHUB credentials. You do not need this for ARCitect to work. You can choose “no helper” or “manager” and tick the check box “always use this from now on” to avoid the popup in the future.

Metadata annotation (Swate, ISA)

Section titled Metadata annotation (Swate, ISA)
Do I have to fill in all columns when using a template?

No. However, if you want to submit your data to a public data repository, these will require specific metadata. For this purpose we provide the corresponding templates helping you to annotate your data accordingly.

DataHUB

Section titled DataHUB
Why do I see banners about "SSH Key", "SAML", "Personal Access Tokens" when logging into the DataHUB?

After login to the DataHUB you see the following banners

If you use DataPLANT tools (ARCitect or ARC commander) to sync your ARC with the DataHUB, you can safely ignore them and click “Don’t show again”.