some content
Note, this will also center all images on the slide (including those in the footer)!
E.g. a figure coming from what used to be a slide with header/footer
Dominik Brilhaus, Martin Kuhl, DataPLANT, CEPLAS, +
Dominik Brilhaus, Martin Kuhl, DataPLANT, CEPLAS, 2022-10-24 ✏️ Edit me
Martin Kuhl, DataPLANT, +
Martin Kuhl, DataPLANT, 2022-10-25 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, +
Dominik Brilhaus, DataPLANT, CEPLAS, 2023-03-16 ✏️ Edit me
Cristina Martins Rodrigues, DataPLANT, +
Cristina Martins Rodrigues, DataPLANT, 2023-02-17 ✏️ Edit me
Dominik Brilhaus, Martin Kuhl, DataPLANT, CEPLAS, 2023-03-07 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, 2022-11-10 ✏️ Edit me
Martin Kuhl, DataPLANT, 2023-03-16 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, 2022-10-11 ✏️ Edit me
Cristina Martins Rodrigues, DataPLANT, 2023-03-24 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, 2023-02-02 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, 2023-04-13 ✏️ Edit me
Dominik Brilhaus, DataPLANT, CEPLAS, 2023-03-29 ✏️ Edit me
Martin Kuhl, Dominik Brilhaus, DataPLANT, CEPLAS, +
Martin Kuhl, Dominik Brilhaus, DataPLANT, CEPLAS, 2023-03-16 ✏️ Edit me
FAIR research in your hands
Title slide to class
Source to slide(s)
../custom/bricks/ceplas-title-01.md
../custom/bricks/ceplas-dataplant-collab.md
../../bricks/ARC_DataCentricIntegration.md
../../bricks/ARC_Structure_DataPLANT-1Folder_Structure.md
../../bricks/ARC_Structure_DataPLANT-2Folder_Structure_ExperimentalData.md
../../bricks/ARC_Structure_DataPLANT-3Folder_Structure_ExperimentalData_Images.md
../../bricks/ARC_Structure_DataPLANT-4Folder_Structure_DataAnalysis-Computation.md
../../bricks/ARC_Structure_DataPLANT-5Folder_Structure_DataAnalysis-Computation_Images.md
../../bricks/ARC_Structure_DataPLANT-6Folder_Structure_MetadataAnnotation.md
../../../units/lesson_022_ARC_structure_DataPLANT/lesson_022_ARC_structure_DataPLANT.md
Here you could address the general problems of the user. FAIRData_ActivationEnergy and FAIRData_ActivationEnergy_withDataPLANT would also be appropriate.
../../bricks/User_Challenges.md
Here one could elaborate on the ARC structure as deeply as desired. In addition, Swate incl. ontology could be discussed here.
../../bricks/FAIR-using-ARC.md
../../bricks/BigPicture_ARC_DataPLANT-1Storage-and-BackUp.md
../../bricks/BigPicture_ARC_DataPLANT-2Versioning.md
../../bricks/BigPicture_ARC_DataPLANT-3CollaborationAndAccessManagement.md
Here one could address repositories in general, but also ROC, Galaxy or Invenio.
../../bricks/BigPicture_ARC_DataPLANT-4MultipleContribution.md
../../bricks/BigPicture_ARC_DataPLANT-5ReferenceAndReuse.md
../../bricks/BigPicture_ARC_DataPLANT-6Publish.md
../../bricks/BigPicture_ARC_DataPLANT.md
../../../units/lesson_030_BigPicture_ARC_DataPLANT/lesson_030_BigPicture_ARC_DataPLANT.md
## Tutor prep: diff --git a/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-05-17_CEPLAS-Session02-prep/2023-05-17_CEPLAS-Session02-prep.html b/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-05-17_CEPLAS-Session02-prep/2023-05-17_CEPLAS-Session02-prep.html index c31a2066a..49747ab70 100644 --- a/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-05-17_CEPLAS-Session02-prep/2023-05-17_CEPLAS-Session02-prep.html +++ b/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-05-17_CEPLAS-Session02-prep/2023-05-17_CEPLAS-Session02-prep.html @@ -26,7 +26,7 @@
Dominik Brilhaus – CEPLAS Data Science
Please follow the next slides to register with DataPLANT and install some helper tools on your computer
If you do not have a DataPLANT account, please register at the DataPLANT website.
Please add your Project/consortium (e.g. CEPLAS, SFB, TRR) and choose the role Guest
Project/consortium
Guest
Find the command-line interface (CLI) on your system.
Please install the latest version of the ARC Commander and dependencies for your operating system according to the manual's setup instructions.
Check if the ARC Commander is functional by displaying the ARC Commander version and help menu:
arc --version
In the hands-on session, we would like to start creating an ARC together. To do so, please bring some data!
This can be data of your current research project or an already published manuscript with supplemental data. Anything that you feel familiar with.
@@ -87,7 +87,7 @@ https://git.nfdi4plants.org GitHub: https://github.com/nfdi4plants
../custom/bricks/ceplas-title-02.md
- Install ARCitect on your computer :white_check_mark:
../../../bricks/checklist_ARC_hands-on.md
../../../bricks/datahub_registration.md
../custom/bricks/ceplas-datahub-registration.md
../../../bricks/tutorial_IntroCLI-The_command_line.md
../../../bricks/tutorial_arc_installation.md
../../../bricks/arc-hands-on-byod.md
../custom/bricks/links-resources.md
## Open the online notepad diff --git a/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-01_CEPLAS-Session03-prep/2023-06-01_CEPLAS-Session03-prep.html b/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-01_CEPLAS-Session03-prep/2023-06-01_CEPLAS-Session03-prep.html index 93e60c700..bee766b17 100644 --- a/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-01_CEPLAS-Session03-prep/2023-06-01_CEPLAS-Session03-prep.html +++ b/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-01_CEPLAS-Session03-prep/2023-06-01_CEPLAS-Session03-prep.html @@ -26,25 +26,25 @@
Dominik Brilhaus - CEPLAS Data Science
Please follow these instructions to install the latest version of Swate.
mkdir -p ~/Desktop/workshop-arcs/my-arc cd ~/Desktop/workshop-arcs/my-arc
Initialize your ARC by executing
arc init
In order to connect your local ARC with a remote ARC, you can specify the remote address with the flag -r followed by the URL of the remote ARC
-r
arc sync -r https://git.nfdi4plants.org/<username>/my-arc
Check if the upload was successful by visiting your ARC at the respective URL in your browser.
Before you can fill your ARC, let's revise your data.
It might help to have this info ready in a text file. In particular, try to think about useful identifiers for investigation, study and assay.
The ISA investigation (-i) workbook allows you to record administrative metadata of your project. Add the isa.investigation.xlsx workbook including an identifier to your ARC with
-i
arc investigation create --identifier <YourInvestigationID>
Avoid using spaces in the identifier. Use underscores and capital letters instead.
The ISA study (s) and ISA assay (a) workbooks allow you to annotate your experimental data.
s
a
Add a study folder with the isa.study.xlsx workbook including an identifier to your ARC with
arc s add --studyidentifier <YourStudyID>
Add an assay folder with the isa.assay.xlsx workbook including an identifier to your ARC with
arc assay add --studyidentifier <YourStudyID> --assayidentifier <YourAssayID>
An assay must be linked to a study. If a study does not exist, it will be created automatically in this step.
The ARC Commander adds subdirectories to the studies and assays folders. Your ARC should, look similar to this now:
These steps can be repeated to add as many studies and assays as needed. Accordingly, more subdirectories will be added
To save the changes, sync the ARC to the DataHUB including a message (-m).
-m
arc sync -m "initiate arc structure"
Check your ARC in the DataHUB.
Try to place your resources, datasets and protocols for each study and assay in the respective folders.
@@ -155,53 +155,53 @@ Start adding your data to the ARCSometimes you might not immediately find a suitable position for your data
Guest Have the least rights. This is recommended for people you ask for consultancy.
Maintainers Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well.
A detailed list of all permissions for the individual roles can be found here
Slides presented here include contributions by
../../bricks/datahub_invite-collaborators.md
../../bricks/datahub_choose-collaborator-role.md
../../bricks/datahub_congrats-for-sharing.md
../../bricks/ARC_ISA-tab.md
../../bricks/ARC_ISAmodel.md
../../bricks/ARC_ISAxlsx01.md
../../bricks/ARC_ISAxlsx02.md
../../bricks/ARC_ISAxlsx03.md
../../bricks/ARC_ISAxlsx04.md
