Applying for a SNIC SENS project
SNIC SENS provides a secure cluster environment for the analysis of sensitive personal data, mainly from large-scale molecular experiments. The compute cluster is called Bianca, and the storage systems are called Castor and Cygnus.
If you are uncertain whether Bianca is the right system for you, read this FAQ page.
A SNIC SENS project includes both compute (Bianca) resources and storage (Castor/Cygnus) resources. Please make sure to add both types of resource to your proposal before submitting.
SNIC SENS, like all SNIC projects, are open for applications from researchers affiliated with Swedish institutions of higher education. International collaborators may become members of a project.
Important note: data stored in a SENS project on Bianca is only visible when logged in to that project. Data that will be analysed together must be placed into a single project. Separate your datasets when you need to, but only then.
Expiration of SENS projects: One month before a project is due to expire, an email reminder is sent to the PI (and proxy, if applicable). Projects can be extended by contacting UPPMAX support. Describe the need and motivate the requested resources in a similar fashion as in a new proposal.
Evaluation of SENS projects and project extensions: Project proposals and requests for extensions must be submitted before the 23rd of each month. See the evaluation section below.
NGI data deliveries: If you have engaged NGI (National Genomics Infrastructure) for sequencing and want to import data to your SENS project easily, you must make sure that the PI of the sequencing project and the PI of your SENS project are identical. See the Delivery user guide for more information.
User accounts created for Bianca project also work for Rackham. This feature can be used to access the Bianca-like Linux environment (but with Internet access!) on Rackham to build a workflow for your project on Bianca.
More information about proper handling of sensitive personal data can be found on our FAQ.
Submitting a SNIC SENS proposal
- Estimate how much raw data you're expecting to need to store during the upcoming year, in GB.
- If you're going to work from existing databases, this is relatively straightforward.
- If an NGS platform is producing data for you, they can provide an estimate.
- Estimate the "expansion factor", i.e. how much additional data you'll produce when analyzing the raw data. This number is usually 1.5x-3x, sometimes more.
- Calculate a final estimate of your total storage needs. This is "GB of raw data" times "expansion factor".
- Figure out how much computation time you will need, in core-hours per month.
- If your usage history doesn't reflect the future you expect, try to make an estimate — a rule of thumb is that you consume on average 1000 core-hours per month for every 2 TB of data (1 TB = 1000 GB) in your project.
- Note that this value is a monthly allocation.
- Go to SUPR. Log in.
- Go to the SNIC SENS Small round (< 20 TB total, < 10 kch/month) or the SNIC SENS Medium round (> 20 TB total, > 10 kch/month). Create a new proposal.
- Complete the proposal and submit.
- Project Title should be the topic of your activity.
- Edit Basic Information.
- Abstract should summarise your research plan
- Resource usage should summarise the compute and storage resources your project will need. Describe the software you will use and how you will use it.
- Data management plan should contain an abbreviated data management plan. Answer the questions included in the instructions. If you have an online DMP, you may link to it. Clearly state whether the data in this project is sensitive personal data.
- Add co-investigators (if any).
- If someone other than the PI needs control over the project, assign a co-investigator the role of proxy.
- Add resources to your proposal:
- Add the Castor /proj resource and set the Requested Capacity to your amount of raw data. You may ignore the other fields.
- Add the Castor /proj/nobackup resource and set the Requested Capacity to your estimated total minus your raw data. You may ignore the other fields.
- Add the Bianca resource and set the Requested Capacity to the thousands of core-hours/month you estimated
- Submit the Proposal.
Proposal evaluation (new for summer 2021)
Due to the growing amount of data on Castor, the storage system attached to Bianca, we cannot always approve all projects.
Our goal is to ensure that as many researchers as possible can continue to work without being affected by a lack of space on Castor. The bottom line is that we will have to deny allocations to projects if users continue to store inactive data on the system. Additionally, we need to encourage responsible and correct use of the system, as well as promote high-quality research.
Allocations are made on a monthly basis. Each month, we grant allocations that sum up to the amount of space that was freed on the system. The available space will be announced in the UPPMAX Newsletter for that month. Requests will be accepted until the 23rd of each month, and decisions will be made by the 30th. Requests that come after the 23rd will be decided upon in the following month.
In the event that we have to deny projects due to a lack of available space, we will rank all Small and Medium storage requests (new projects, continuation projects, and allocation increases) according to the following factors:
- Motivation (detailed itemisation of the data that covers the entire allocation of the project, and reasoning that motivates why described data needs to be present concurrently)
- Track record (previous history as a SNIC user)
- Scientific productivity (from Activity Reports, if applicable)
- Data formats, e.g. proper compression
- Use of nobackup (describe what needs backup etc)
- Use of central reference databases in /sw/data (https://www.uppmax.uu.se/resources/databases/)
- Time plan
- Plan for data after analysis, including a destination for it
- Whether you follow the recommendation of keeping your own copy of the data elsewhere
When applying for a new project, a continuation project, or emailing us about storage quota increase, please include as much of the above information as possible.
We understand that the reality of scientific research does not always coincide with a strict monthly schedule and a formal grading rubric. We therefore reserve the right to be flexible and will endeavour to work with you in special circumstances.