Cloud Computing Real Implication On Bioinformatics

Question

[Thaman]

Hi,

There has been a little talk about cloud computing on Bioinformatics at the BioStar group. Question Bot and Khadeer question about it earlier. But I want to be more specific on the area like:

1. Infrastructure-as-a-Service (IaaS)

• Data-as-a-Service(DaaS) is a subset of IaaS

2. Platform-as-a-Service (PaaS)

3. Software-as-a-Service (SaaS)

I have found enough information about companies working with cloud computing and their services through website . Most prominent examples can be :http://aws.amazon.com and Google Apps which covers IaaS, PaaS, SaaS?

Can anyone suggest me any work done in Bioinformatics covering:- IaaS, PaaS, SaaS?

If yes, I would be please to know what cloud computing service they have been covering currently in Bioinformatics.

Thank you

Answer 1

[Khader Shameer]

In addition to resources mentioned by Mary, I would suggest you may take a look at the latest publications from Atul Butte's group: In silico research in the era of cloud computing and Translational bioinformatics in the cloud: an affordable alternative.

Deepak Singh / @mndoci's blog / articles about AWS/cloud computing will be a good resource. This includes a list of AMI's focussed on bioinformatics applications.

For SaaS you may check the efforts by companies like EdgeBio, DNA Nexus etc.

AFAIK, many of us are using cloud computing for various applications in bioinformatics (at the moment mostly focused on ngs related analysis, as the scale of genome data increases soon we will see every routine bioinformatics pipelines on the cloud): it's alive, up and running.

[Mndoci]

Khader, I should really move that deepaksingh.net domain over. The latest set of resources are maintained on github

• https://github.com/mndoci/mndoci.github.com/wiki/Computing-in-the-Cloud
• https://github.com/mndoci/mndoci.github.com/wiki/Life-Science-Apps-on-AWS

[Mndoci]

And since it's a git repo, I welcome forking and pull requests

[Thaman]

Thanks mndoci :)

Answer 2

[Mary]

Well, I had a rant recently on Bioinformatics in the Cloud: End users and the cloud in bioinformatics. But for more provider-side and super-user type discussion also see Lincoln Stein's paper on that: The case for cloud computing in genome informatics. Chris Dadigian gave a really nice talk at Beyond the Genome and made his slides available here: Commercial Clouds for Bioinformatics. Mostly I'm hearing about Amazon, but also at Beyond the Genome I heard about the effort by a not-for-profit group and this Bionumbus cloud work. See also the Open Cloud Consortium.

[Roman Valls Guimerà]

There's also CloudBioLinux out there, have a look:

http://cloudbiolinux.com/

[Thaman]

@ Roman Valls- Thanks for the CloudBioLinux link and contributing to this project :)

Answer 3

[Ketil]

Galaxy is also distributed as an Amazon instance, providing a relatively simple way to get it up and running on sufficient hardwarde, and they have an extensive documentation. See e.g. http://usegalaxy.org/cloud

BTW, you could also consider web services as "Library as a Service", since it provides an API in the cloud.

Answer 4

[Larry_Parnell]

To provide an update to this question as it remains relevant today:

There is a new paper in PLoS Comp Biol on this subject. The aims of that paper are:

1. introduce biomedical cloud computing
2. provide a concrete methodology detailing how projects are developed on the cloud
3. demonstrate cloud computing costs

[Thaman]

Thanks, will definitely go through.

[Larry_Parnell]

Thanks as well, for taking a look at my "late" response. When I can, I try to add a new link to a new paper to the relevant question. This keeps BioStar "fresher."

[Mndoci]

I am now also tracking life science-related publications on AWS; https://github.com/mndoci/mndoci.github.com/wiki/AWS-related-Life-Science-publications

[Larry_Parnell]

That sounds good. You may also want to add a few analysis portals, like Galaxy, which promote use of cloud resources.