Skip to main content

Launch GNomEx

Launch Seven Bridges

Launch cBioPortal

1. What is happening?

We are moving to the cloud! Existing datasets will be moved to cloud storage and PIs will need to take ownership of their data and manage it in the cloud. Moving forward, sequencing and analysis data will only be retained in our local repository for six months. If you do not want your data in the cloud, you will need to make your own arrangements for long-term storage; otherwise, continue reading for more details on using the Seven Bridges Platform.

2. Why is our data being moved?

Our GNomEx data repository has been growing nearly exponentially over the past 13 years, particularly with improvements to Illumina sequencing technology. While the Bioinformatics Shared Resource has absorbed the costs of this storage, this has become unsustainable, particularly as our storage infrastructure ages. None of our peer institutions provide long-term data storage. After extensive evaluation and vetting by members of the faculty advisory committee for the High-Throughput Genomics and Bioinformatics Shared Resource and in close consultation with the Directors of those shared resources, as well as Research Informatics, we have decided to move data storage from local to cloud using the Seven Bridges platform for data processing and storage management.

3. Why Seven Bridges?

Seven Bridges provides a number of benefits besides just cloud storage:

  • Fast bioinformatics analysis enabled by access to Amazon Web Services compute resources
  • Point-and-click interface to run many common bioinformatics analyses using common workflow language
  • Point-and-click interface to archive data to Amazon Glacier storage to save on storage costs
  • Ability to securely share data with collaborators around the world
  • Access to public datasets from TCGA (cancer genomes), TARGET (cancer therapies), ENCODE (functional and epi-genetics), CCLE (cancer cell lines), SGDP (ethnic whole genomes), CPTAC (proteomics), TCIA (cancer imaging), and dbGaP (genetic variants, with appropriate authentication).

4. What about the other GNomEx instances, including UGP, B2B, and the new Clinical GNomEx?

These are not affected. This only concerns the main research GNomEx.

5. I have Sanger-sequenced DNA through the DNA Sequencing core (directed by Derek Warner). Will that be transferred?

No, this only concerns the sequencing from the High-Throughput Genomics Core (directed by Brian Dalley), as well as Analyses associated with such data. Microarray data from the HTG core prior to 2010 will also be included in the transfer.

6. I am not part of the University of Utah. What about my data?

For external clients of the High-Throughput Sequencing Core and external users of GNomEx, sequencing and analysis data will be maintained for six months. Users will need to make their own arrangements to store their data elsewhere. Data will be deleted from local servers after six months.

7. Is Seven Bridges free?

HCI is paying the licensing fees associated with Seven Bridges for any University of Utah GNomEx user. The storage and compute costs for individual labs or users will be invoiced through Seven Bridges.

8. What happens to the data currently on GNomEx?

Legacy data (projects dated before roughly February 2018) was bulk uploaded to Seven Bridges in anticipation of users claiming it. Data from labs that do not claim their Seven Bridges data by the end of 2019 will lose access to it.

Current and future data files on GNomEx will be stored for about six months. If the lab has an active, paid account in Seven Bridges, then data will first be archived. All data will be removed from GNomEx after about six months.

9. How will our data be moved to Seven Bridges?

We transferred legacy data (projects dated before roughly February 2018) to Amazon cloud storage on your behalf. Transfers were completed in May 2018. Unclaimed data will be removed in 2019.

10. What if we don’t want to pay for our data to be stored in Seven Bridges?

If you would like to keep your data but do not want to use Seven Bridges, within six months you should transfer your data to another cloud data storage provider of your choosing (e.g. DNAnexus, Amazon S3/Glacier, Google Cloud, Microsoft Azure Cloud). Or you can download your data to a local compute facility (e.g. departmental IT).

The CHPC offers file storage to University of Utah researchers at very competitive pricing; typically research groups purchase space as a hardware investment for a period of five years. These include both group space (typical file server space) and object-store archival file storing (similar to Amazon S3). See CHPC Storage Services for more information.

If you insist on storing data in your lab, we strongly urge you to use at least two separate devices, preferably three with one offsite, as consumer devices are notoriously prone to failure.

Regardless of your choice, your data will be deleted from our local servers after six months.

11. Will you help me move my data to another storage facility instead of Seven Bridges?

With over 450 labs, we cannot individually manage transfers to other systems.

12. Is our data safe in the cloud?

Yes, data is encrypted both during transfer and in storage in Seven Bridges. Seven Bridges utilizes the Amazon cloud for data storage. Without authorization, the data cannot be accessed or read. The Seven Bridges platform and Amazon maintain the highest standards of data security possible and are trusted by clinical testing labs, hospitals and pharma companies around the world. The data in the cloud is duplicated in multiple data centers in different locations, in case of catastrophic computer failure or natural disaster (redundancy), and the professional hardware is maintained by world-leading IT experts.

13. Our data is under an (old) IRB protocol that prevents data from leaving the University.

Many IRBs allow you to store the data securely offsite. However, if yours does not, please investigate other storage options. Note that the new Clinical GNomEx is not part of this move.

14. Is GNomEx going away?

No, it is not. All High-Throughput Sequencing requests and billing will continue to go through GNomEx, and the database entry of all existing and past sequencing requests will still be available. Further, a list of the files and their metadata for all past experiments and analyses will be available on GNomEx.

15. What about all future high-throughput sequencing data?

Future sequencing results will be delivered first to the GNomEx repository and then uploaded automatically to your Seven Bridges account. Sequence files will remain locally for a period of six months, and then will be automatically deleted. Six months should be enough time to analyze, download, and archive files if you are not using Seven Bridges.

16. What will be left on GNomEx?

We will keep a manifest file of the files that used to be there and were uploaded to Seven Bridges. For analysis projects, bigWig and tabix-indexed VCF files will also remain as a courtesy for users who use GNomEx as a track distribution hub for IGV or UCSC browsers (the files will be uploaded too, just not deleted locally).

All metadata (experiment descriptions, sample names and information, etc) will never be deleted.

17. If we upload new data files to a GNomEx Analysis project (e.g. A5678) in the future, when will the files be deleted?

If you deposit files into a GNomEx Analysis project, either manually or by using the Pysano #a directive, or by a Bioinformatics Shared Resource Core member doing an analysis for you, the files are still subject to the six month time limit and will be removed after that time frame. If the PI has a Seven Bridges account, it will be first archived under the PI’s account, before being removed.

18. When and how do I sign up for a Seven Bridges account?

Invitations were sent via email in May 2018 to University of Utah investigators who had data in GNomEx as of May 2018. New faculty may also set up an account; please contact the Bioinformatics Core for information. Investigators will need to provide a PO # to Seven Bridges in order to take ownership of their data. Once the Principal Investigator has an account, he or she may send additional invitations to members of their lab to sign up accounts.

19. Will there be training sessions?

Our license agreement with Seven Bridges includes two onsite hands-on training sessions for lab members and administrators. The first training session was held in June 2018; the second will be held in Spring 2019.

20. GNomEx is so easy to use! Will Seven Bridges be harder?

Believe it or not, Seven Bridges will actually be easier to use than GNomEx. The web interface is quite intuitive and simple to use to filter, search, and manipulate files. Files will be easily uploaded, downloaded, or archived for long term storage, using either a point-and-click web interface, or in bulk with command line tools.

21. Can I perform analysis through Seven Bridges?

Yes! You will be able to run standard bioinformatics analyses (alignments, variant calling, gene expression comparisons, etc.) by clicking on "Workflows" on the Seven Bridges website–no programming skills necessary. Seven Bridges uses the Amazon compute cloud to run analyses and returns the results to your Seven Bridges account. Seven Bridges has a number of publicly available workflows immediately available. The Bioinformatics Core will be uploading their pipelines as workflows so that you can run their specialized pipelines also. The compute instances in the Amazon compute cloud are adjusted such that only the necessary compute resources are requested for each job (or program) in a workflow, which minimizes the cost of the analysis. You can also create your own custom workflows by stringing together different programs using a visual interface. Each bioinformatics program is loaded via a Docker instance, keeping resources to a minimum. If you would rather write code than point-and-click, multiple analyses may be strung together into a custom workflow using the Common Workflow Language on the command-line, an open source consortium to standardize bioinformatics workflows.

22. How much will it cost to store data and run analyses on Seven Bridges?

Once a PI takes ownership of the data in the Amazon cloud, they will be responsible for paying for the long-term storage of their data and any bioinformatics costs incurred from analyses performed in the Seven Bridges platform. HCI’s purchase of the Seven Bridges license enables users to take advantage of significant cost savings for cloud-based storage and computing. For example, if you pay $1,100 for one lane of paired end 125bp sequencing through the High-Throughput Genomics Core facility, you generate approximately 50GB of data. If you choose to have the data automatically uploaded to the Amazon cloud through the Seven Bridges platform, it will cost approximately $7.00 to store the 50GB in Amazon S3 for six months while you perform bioinformatics analysis. If you use the Seven Bridges app for exome analysis it will cost approximately $2.00 per sample. When you have completed your analyses, you can use the Seven Bridges platform to archive your data in Amazon Glacier storage and it will cost approximately $3.00 per year to store the 50GB of data. This example serves to illustrate that the cost of data storage and compute is marginal compared to the cost of generating the data, and this system enables you to manage and analyze your data efficiently.

For the vast majority of research labs with a handful of sequencing experiments, yearly costs will likely be no more than $50. This is less than the cost of a tube of enzyme, and cheaper than many departmental file storage costs.

23. Do I have to switch to using Seven Bridges for compute, or can I still use compute resources here locally?

Yes, you may continue to use our resources here if you so desire. We will continue to maintain interactive linux servers at HCI and powerful compute nodes at CHPC.

24. Storage costs on Amazon S3 are expensive! Is there a cheaper alternative?

Yes, you may (and are encouraged!) to archive older analysis and data files to Amazon Glacier, which is a slow-access storage system. This can be done easily through the point-and-click Seven Bridges website. It costs nothing to archive files into Glacier and has a fractional cost for storage compared to S3. However, retrieving files from Glacier for new analyses does incur a per-file cost and works via a queued system, i.e. it may take up to a day or more for the files to be retrieved.

25. Will the legacy GNomEx data be stored in Glacier?

Yes, data being archived from GNomEx are stored in Glacier. To avoid a per-file cost retrieval, small analysis files (Excel, PDF, image, text, etc. files) are zipped into a zip archive prior to depositing into Seven Bridges. A manifest file of what was stored in the zip archive will always remain on GNomEx so that you know what was in there.