How to apply for a virtual machine (VM) in the de.NBI cloud Tübingen

The de.NBI landing page gives a general overview of the steps required to apply for computing resources in the de.NBI cloud. This manual adds TRR356 PlantMicrobe-specific details.

The application to de.NBI services is centralized. However, the de.NBI cloud is distributed over several compute centres in Germany, all of which differ somewhat in their procedures and services. TRR356 PlantMicrobe projects are handled through de.NBI Tübingen; the de.NBI Wiki supplies Site-specific information.

If you have further questions or find mistakes in this manual, pleas contact PlantMicrobe support.

For whom is this guide intended?

You are member of the TRR356*
You do not know where to run your analysis
Your PI supports your application

*Non-TR356 members can also apply, but application details differ.

What does de.NBI Tübingen offer?

Cloud resources free of charge (for members of German research institutions).
Time limited VMs: re-application every 3-6 months.
Initially smallish VM (and disc space) that can be extended if needed.
VM with ubuntu server operating system:
- All command line.
- Very few pre-installed applications.
- Applications are normally processed within a few days.
- If there is demand, we may consider offering machines with some often-needed software pre-installed.

How to get access the de.NBI cloud

Register with de.NBI

Go to https://cloud.denbi.de/get-started/. The system uses the same login as the TRR356 PlantMicrobe DataHUB. You can skip the registration step with LifeScience RI and proceed to step 2:

Fig. 1

Click the Portal button and use the same login details you are using for the TRR356 DataHUB. When using the de.NBI Portal for the first time (and sometimes in between) you may be asked for consent to share your information from the authentication service (LifeScience RI) with de.NBI. Please consent.

Consent granted, the information that LifeScience RI shared with de.NBI will be displayed.

Fig. 2

Applying for computing resources

Initial steps

Login to de.NBI with the Login you set up for de.NBI. This can be done, for example, from the de.NBI landing page page, by using the portal button.

Fig. 3.

On the user info page that opens automatically, select + New Project from the left-hand panel.

Fig. 4.

Selecting the project type

The project type overview page offers a number of option. de.NBI Tübingen only offers Openstack options. Select New Openstack Application.

Fig. 5.

Filling in the application form

In the application form, the ? symbol after each item offers context.

If you leave out filling in obligatory fields, the frames will turn red.

Fig. 8.

Project description

For the Project Description, a smallish number of lines of text is expected. Please bear in mind that the more information you supply on your research, the easier it will be to assess the compute requirements adequately.

Fig. 9.

Desired lifetime

Periods of up to six months are possible to select initially. Once a project is running, extension can be asked for easily.

Fig. 10

Amount of resources

The Standard Flavors window with the different options for resources can be opened with the ^ caret symbol. Go for the de.NBI small VM.

The amount of resources requested here is not definite. Additional resources can be requested any time after the approval of the project.

Fig. 11.

Volume space

Initial suggested volume space is, under Number of storage volumes, one volume with, under Volume Storage Total Limit 1000 GB. As above, additional volume space can be added later as required.

Fig. 12.

Important for quick handling of your application. Under Comment, state

“TRR356 - will be handled by de.NBI Tübingen. In doubt, please refer to Jens Krüger.”
Mention that you will be using GitLab.
State the name of your PI.
Add any questions you may have.

Fig. 13.

Additional information on research

The Research Topics includes a dropdown list. Several items can be selected. As with the general information on your research, please bear in mind that the more information you supply, the easier it will be to assess the required resources adequately.

The tick boxes underneath Research Topics refers to research on humans.

Fig. 14.

Project information

The full name of the TRR356 PlantMicrobe project is “TRR356 PlantMicrobe Genetic Diversity Shaping Biotic Interactions of Plants” and is financed by the DFG.

Make sure to enter the correct email address for your Principal Investigator (PI)!

Fig. 15.

Re-check all entries and submit your application.

Behind the scenes

As explained on the de.NBI landing page,

The application is reviewed by the cloud committee.
You will get notified as soon as your application is approved.
The requested resources are now allocated in the de.NBI cloud. The resources can be accessed through the de.NBI portal
If you are TRR356 AND your proposal was declined, something went wrong in the communication - please get in touch with PlantMicrobe support.
If your project was allocated fewer resources than expected, you are welcome to ask for the reason.

de.NBI Tübingen-specific help files

TRR356 projects are handled through de.NBI Tübingen. To find de.NBI Tübingen-specific information go to the Wiki menu item in the left-hand panel of the user information page.

Fig. 3.

On the Cloud Wiki page that opens you find a list of the compute centres with links to their specific information pages in the panel on the left under Compute Center Specific. Here is the direct link to the Compute Center Tübingen.

Fig. 4.