Frequently Asked Questions
This page contains the frequently asked questions regarding Hartwig Medical Foundation Data Access Requests. Please note that this page is not exhaustive and that you should consult your License Agreement regarding the exact agreements that were made between Hartwig Medical Foundation and your institute.
Where can I find information about the procedure for Hartwig Medical Foundation's Data Access Requests?
You can find all details regarding the Data Access Procedure at our website.
Is it possible to collaborate while using your data?
Collaboration is possible on the following grounds:
- The person(s) you are collaborating with will not have access to the raw Hartwig Medical Foundation data that is shared with you through GCP. Only the people that are mentioned in your Data Access Request and registered 'Download Contacts' are allowed to access the raw Hartwig Medical Foundation data. You are allowed to share the results of your analysis.
- If you need your collaborator to have access to the raw data as well, please add him/her as a 'Download contact'. For a collaborator to be added as a 'Download contact', he/she needs to be appointed within the same 'Legal Entity' or institution. See instructions on this page, section 'New User procedure'.
- If your collaborator does not work at the same institute (or 'Legal Entity'), you need to put in a new Data Access Request and add your collaborator in the 'Consortium request' part of the application. A License Agreement will be drafted that allows people from multiple institutions to collaborate on analysing the raw data.
- It is not possible to request data as a consortium, as this is no official 'Legal Entity'.
How is the data processed / Can I use your tools?
An overview of the methods for data collection is available, as well as a guide that describes the data that we make available.
All our tools and code is publicly available on our GitHub.
Google Cloud Platform Questions
Can you help us with setting up a GCP account?
We are not able to set the GCP account up for you, but we do have a preferred Google Partner that can help you out. To get the onboarding proces started with our preferred Google Partner, please visit this webpage. General instructions on getting a GCP account can be found in our Getting a Google account instructions. If the instructions are somehow not working for you, please contact us.
Why can't I sign up with my Gmail account?
As you may know, the data included in the database of Hartwig Medical Foudation is very sensitive information and concerns health and genetic data of patients. In view hereof, Hartwig Medical Foundation must ensure that the data that it makes available for research is only used for the purposes for which the data is made available and by the persons authorized to access it. Further, it wishes to safeguard as much as possible that the data are duly processed and protected, once made available for research. It is in view hereof that Hartwig Medical Foundation makes available the data to legal entities (such as the institution you are working for), why the data access request is submitted on behalf of your institution and why the license agreement covering the use of data is entered into by your institution. It is your institution that is responsible for compliance with the terms of the license agreement. By requiring you to use your institution email address, we can ensure that you are indeed working for the institution that was granted access to the data and that you will no longer have access to the data once you no longer work for the institution (and are no longer authorized to access the data). Further, your institution’s email account is often better secured than a private email account. So in brief, we require you to use your institution email address to access the data from Hartwig Medical Foundation in order to protect the data.
Why do we make the data available through the Google Cloud Platform?
Advantages for you as researcher:
- No duplications of public resources
- You will have access to data analysed with our latest-greatest toolset
- You can use our data in a state-of-the-art compute environment that gives you a lot of flexibility, you only pay for what you use, and the GCP compute is generally cheap (see our cost example in the 'Billing questions' section below).
- You don’t have to pay for storage as you can use the files from within our infrastructure (also see our cost example in the 'Billing questions' section below)
- There is a good backup procedure in place for our data set
- Data is encrypted with our own key See for more details on why Hartwig chose for GCP as our Cloud provider below.
Are there any privacy concerns related to using Google Cloud Platform for genomics data?
We sometimes receive feedback from external parties asking if we’re not afraid of data misuse by handing it over to Google. We don’t hand over any data to Google! We have a contract with Google to use their Google Cloud Platform (GCP) service. The data that we upload to GCP is encrypted using our own key-pair and as a result is not accessible by Google.
Are there any ethical concerns related to using Google Cloud Platform?
We have received feedback from external parties whether it is ethical to ‘make Google rich’ by using their platform to make data available to the public. GCP is in fact one of the cheapest cloud vendors available on the market. There are also private cloud providers on the market, but they are more expensive than our current solution. Either way, any ‘cloud provider’ will render revenue with deploying their compute and storage services. We have made an extensive analysis of all relevant providers. In our opinion we chose a good, solid and relatively cheap solution by moving our business to GCP.
Why did Hartwig Medical Foundation decide to move to GCP?
Hartwig Medical Foundation decided to move to Google Cloud Platform as it's infrastructure provider for multiple reasons:
- We are managing ~ 1 Petabyte of aligned read data, that we could not (easily) make available for scientific research from our own hardware infrastructure due to the constraints of the data set size.
- We can now make the raw CRAM files available to external researchers, while this was previously limited to analysis files.
- GCP makes it possible to rerun tools and improved analysis pipelines on our entire database in one go.
- We never have to wait for availability of or buying additional hardware resources, this holds for both storage and compute.
- We can do production and development in parallel on the same infrastructure.
- Multiple storage tiers.
- Broad range of VM types.
- Ready made 'Products' that we could benefit from in our workflow, for example BigQuery and Kubernetes engine.
- Using different tiers of storage reduced our infrastructure cost considerably.
- Running VMs only when needed, instead of always-on.
- Application of pre-emptibles resulted in even bigger cost reduction.
- Back-ups at different locations possible in the European Economic Region.
- Encryption of data.
- Less copies of the data (we can also manage informed consent requirements in this way).
- Data privacy
- Compliance with GDPR, AVG, UAVG.
- ISO27001 compliance.
- DPIA on transition to GCP.
- DPIA on Contract with GCP.
- Future proof considering all above points
Of course, we also considered the downside of moving to GCP (or any other public/non-public cloud provider):
- Vendor lock-in; data requesters would have to go through GCP to get access to the data. There will always be some kind of lock in by choosing 1 provider.
- Privacy concerns; Our solution: this is managed by performing our own encryption, putting additional security measures in place and implementing GDPR-compliant legal terms with Google.
- Egress costs for downloading data out of GCP; this item has two sides:
- Hartwig was paying for egress costs in our previous set-up, but after the move to GCP this will be 'requester pays', allowing us to redirect the egress costs to development.
- Users do not have to download the data as for the GCP solution, in contrast to our previous solution, computational resources are available. In the case of 1 Petabyte of data, we do not consider it beneficial to download the data, but want researchers to bring compute to the data (instead of the other way around).This also circumvents the need to arrange local storage, which turns out to become an increasing challenge for many data users.
We also considered hybrid alternatives, for example by moving some of our data to EGA. At this point in time however, EGA would mean a duplication of our database, as we also still need the data readily available to keep the data that we provide for data access requests on our latest-greatest version of tools.
Is it possible to have an admin email address in my GCP project?
No, we can only allow personal institutional email addresses as GCP accounts to release the data to. When releasing data to a service account, an admin account may be added to the project, but can't have the rights to access the service account that the data is linked to. Please see the question right above this one for the specific explanation why we can't allow this.
What can I do with a service account on GCP?
A service account allows you to process the data that you can access through the ACL in a more efficient way, as you're able to automatise. With a service account, you can spin up multiple VMs simultaniously in one go, whereas with your personal GCP account, you'd have to do this for each sample seperately.
Why do you need to audit my service account?
We need to audit your project IAM settings when you want to use a service account for data access, as we want to make sure only the registered 'Download contacts' have access to the data (through restricted access to the service account), as agreed upon in the License Agreement. The audit is performed like this:
- You will need to add one of the Hartwig employees to your project with the role 'Viewer', so he/she is able to see the users with access to your project via IAM.
- Our Hartwig employee will take a look at the users within your project and register the accounts and roles with access.
- Then Hartwig will check if the users with priviledged access are also registered 'Download contacts' on the data access request documentation. We only allow the following scenarios:
- Only the download contact has an account in the project (and multiple service accounts are allowed)
- The download contact has an account in the project, and is the only one that can work with the service account. This means that there are other users allowed, but their roles should not be one of the following (the below roles give a user access to all service accounts within a project):
- Service Account User
- When this is all in order, you will be notified by us and the data collection is started.
I can't seem to set up a GCP account with my institutional email address?
Please follow the instructions in our Getting a Google account documentation. In short, go to the Google Account creation page, click 'Use my current email address instead' and follow the prompts. Please note that we need multi-factor authentication enabled for all accounts we share our data with.
Will I be billed for accessing your data?
Hartwig won't bill you for accessing our data, but accessing the data through Google Cloud Platform does come with costs. Basically, there are two ways to approach the data:
- Download the data onto your own servers. This will result in egress costs (data that is pulled over the network will be charged per GB, see Google's Network Pricing page for more details.
- Analyse the data on GCP itself. This will results in storage and compute costs. More information can be found on Google's Cloud Storage pricing page and Google's VM Instances pricing page. If you analyse the data in the same region as it is stored, you won't be charged egress costs.
What option to choose depends on your use case and specific requirements.
How much will I get billed for my download?
A resource that might help you in estimating costs is the Google Pricing calculator. Another factor that you need to include when estimating cost, is the cost for egress.
Could you give a cost example for a use case on GCP?
Utilising the Google Cloud Platform could also work in your benefit, compare the following scenarios that could occur when your data access request is approved for 100 samples:
- Spin up 100 VMs to run a different aligner on the CRAM files. This would result in ~€5 analysis costs per sample. You only store the resulting VCFs (~50 Mb each) for one year, as you can always reuse the CRAMs that are in Hartwigs buckets without having to pay for it's storage.
- €0 egress costs (egress to VM in same storage region is free)
- €5 VM compute costs * 100 samples = €500
- €0,09 for 1 year storage (Standard, region europe-west4) of resulting VCF files (~€0,0179 * ~5 Gb)
- Total cost: €500,09
- Download all 100 CRAM files to your local server, do the same analysis and then store the resulting VCFs and CRAM files for one year on your local server.
- €857 egress costs (100 * ~120 Gb * ~€0.0714)
- €0 compute costs (assuming your department pays for compute resources, this is in most cases not 'free' but invisible to the end-user)
- €1 for 1 year storage of resulting VCF files (~5 Gb), assuming the costs of storing 1Tb of data on a HPC hot storage costs ~€200 (amount is taken from more some of our collaborators)
- Total cost: €858 (but please note: you’d probably have to store the CRAM files as well, adding 100 * 120 Gb = 12 Tb -> €2400 to your bill each year)
I'm worried about incurring costs on GCP, how can I make sure I stay within budget?
There is no hard cap to cut off costs at a certain point, but there are several options to monitor your budget within GCP:
- Set budgets and budget alerts in GCP. This option does not let you cap the budget, but allows you to monitor everything and set reminders at appropriate amounts of money spend.
- Examples of automated cost control responses. Here you can find examples on shutting down VMs when the bill reaches a certain amount within a project.