Uppsala Multidisciplinary Center for Advanced Computational Science

Applying for projects

This page guides you through the process of applying for projects at UPPMAX. 

Click here to go to the actual instructions and skip over the background information. 


UPPMAX is a supercomputing facility hosted by Uppsala University and is a part of the Swedish National Infrastructure for Computing (SNIC). As a SNIC center, we provide computational resources for a wide variety of researchers all over Sweden. Access to our resources is granted through the SNIC project application portal, SUPR.

In order to do any kind of sequence analysis, you need two resources:

  1. Computations. It takes time for a CPU to run programs. Computational resources are measured in core-hours. Allocations are granted in core-hours per month
    • For example, if you have a hundred samples and it takes a single core a week run a pipeline on one sample, then the total core-hours needed is 100 samples * 7 days/week * 24 hours/week * 1 core/hour = 16800 core-hours. If you're planning to do this analysis over the course of 6 months then you'll need a project that provides about 16800/6 = 2800 core-hours/month. 
    • Our current SNIC-funded compute cluster is called Rackham.​
    • If a project exceeds its allocation of CPU time, you can keep working but at a lower priority in the queue. We call this the bonus queue.
  2. Data storage. It takes disk space to store sequences and related data. Space is usually measured in GB.
    • The sequencing facility should be able to tell you roughly how much space the raw sample will take. When you're working with the data, it usually expands by a factor ranging between 50%-300%, and you will need to account for this when you apply for a storage project.
    • The storage system attached to Rackham is named Crex.
    • If a project exceeds its storage quota, no one can write any more data to its directory.

On Rackham, we have divided projects into two types: Compute Projects and Storage Projects. On our secure cluster, Bianca, projects include both compute and storage resources.

Compute Projects: SNIC SMALL, SNIC MEDIUM, SNIC LARGE. These are called "SNAC" projects while in the proposal phase. They also come with 128 GB of storage, which is enough for many.

  • SMALL: Anyone can apply. Default limit of 2000 core-hours/month, can go up to 5000 upon request.
  • MEDIUM: PI must be permanently employed researcher. Up to 100 kch/m. Subject to a technical evaluation.
  • LARGE: For very large projects involving large groups or multiple groups. Proposals are accepted twice per year. 

Storage Projects: You should use the round UPPMAX Storage to apply for storage projects. 

Sensitive Data Projects: These use the Bianca compute cluster in SNIC SENS.

Course Projects: Small projects for education purposes. 

Getting your projects

Below are links to step-by-step instructions for getting a project for data-intensive life science research.

Read this page first if you work with human dataIt is very important that sensitive personal data is handled lawfully.

Instructions for applying for a project involving sensitive personal data

As described above, you'll need a compute project and probably a storage project. It is best to submit both proposals at once.

Instructions for applying for a compute project

Instructions for applying for a storage project

This page has more information about course projects

After having submitted BOTH proposals, a decision will be made by the end of the month. Feel free to contact support@uppmax.uu.se with questions.