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NA-MIC Project Weeks

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Girder and SlicerCLIs in the Cloud

Girder is a web based data management platform, capable of running SlicerCLIs. I’ll demonstrate this along with some info about deployment as part of the Medical and Scientific software in the cloud breakout session, Tuesday Jan 9, 1-2 pm.

Key Investigators

Project Description

My expertise is in Girder and scalable cloud based processing. I will give a ~15 min talk on web/cloud tech, where I’ll demo Girder in AWS on Tuesday Jan 9, 1-2 pm. I am going to be at Project Week on Monday and Tuesday. Please reach out if you want to chat!

Discussion Topics

Using commercial cloud services in scientific research projects

General thoughts

Commercial cloud services are good for experimentation without long term commitment, and are useful when you need to have dynamic and elastic scaling. The providers are constantly rolling out new services, and there is a large amount of expertise encoded into these services (e.g. compare the cost of using AWS Elastic Load Balancer versus the time to gain the expertise of knowing how to run a load balancer), but the accounting model may have a mismatch with grant funded research (e.g. it may be easier to pay for an hour of someone’s time to build a service versus paying for an hour of a cloud based service, even though the cloud based service is much cheaper in this comparison).

To realize the full power of the cloud, a different mindset is in order compared to purchased hardware and software. Think about using extremely powerful and expensive cloud resources for a very short period of time, or using many more resources in the short term than you would otherwise.



Using a private cloud based on OpenStack gives you many advantages of commercial cloud services (elasticity, APIs) without some of the drawbacks, but it does require specialized expertise and HW purchases. Where does an approach like Massachusets Open Cloud fit in?

Use a hybrid approach, where most of your resources are on premises, but you use cloud services for marginal needs. E.g., have an expensive GPU in your lab, and add in additional cloud based GPUs for load spikes. This also lets you try new and expensive HW without paying the full purchase price.

DevOps and Infrastructure as Code (IaC)

Using IaC is key to achieving scale in the cloud (of machine resources and to scale the number of projects you can take on with a fixed number of people) and for repeatable development.

The IaC approach relies on keeping your infrastructure in source control so there is a shared document and understanding between development and operations (sys admin teams). When a problem is discovered in one instance, the fix is encoded into IaC. This also depends on having API access to scale the number of projects – it doesn’t work nearly as well when every site you interact with has a different process and setup, and your API is email. Another example of time vs money tradeoff with cloud infrastructure.

Kitware has had good luck with

We use these technologies for our project deployments, and have built reusable tooling on top of them for Girder and Resonant tools.

Girder and SlicerCLIs

Resonant tools and what problems they solve


Girder Worker

At the end of a large refactor as of January 2018. Documentation is the last step to completing the refactor!

SlicerCLIs and Docker (item_tasks)


SlicerCLITask Listing a SlicerCLI as a task after ingestion.

ExecuteTask Task execution UI.

TaskJob Task Job record after execution.