Bioinformatics

Cloud computing: a new standard platform?


Cloud computing is becoming a technology mature enough for its use in genome research experiments. The use of large datasets, its highly demanding algorithms and the need for sudden computational resources, make large-scale sequencing experiments an attractive test-case for cloud computing. So far I have seen cloud computing demonstrated using R (1). However, it remains to be seen a rigorous comparison of its performance using a BLAST (2) search and its ability to cope with ever-increasing databases and open source frameworks such as bioperl (3) or bioconductor (4).

Cloud computing claims to be a resource where IT power is delivered over the Internet as you need it, rather than drawn from a desktop computer (5), in a fashion seemingly similar to having your own virtual servers available over the Internet (6). Some of the most important aspects of cloud computing are:

* Software as a Service (SaaS): where you buy a software license for a determined period of time.
* Utility Computing: storage and virtual servers that IT can access on demand.
* Web Services.

My first exposure to cloud computing came of an email from Matt Wood (7), a newly established group leader at the Sanger Institute (8), announcing the Cloud Computing Group (9) in Cambridge, UK. At that point I had no idea of what it meant. When I attended the meeting at Cambridge University’s Centre for Mathematical Sciences (10), to my surprise I found there a very select audience, ranging from the director of IT at Sanger, Phil Butcher (11), one of the Ensembl (12) software coordinators, Glenn Proctor (13), and quite a few local start-up companies.

Among the presenters, we had Simone Brunozzi, from Amazon’s Cloud Computing (14). I think he had an interesting story to tell: how Amazon, a well known company, is now involved in the business of cloud computing and selling it. Apparently, this technology they sell was developed for Amazon’s own business. Among their main challenges was to be able to address the capricious shopping habits of customers, with orders peaking around Christmas and quite flat the rest of the year. These trends required rapid adaptability of computational resources. The idea of cloud computing fitted well with their business model of e-commerce: you don’t need to care about where your computation is done, the only thing you care about is that you have the needed resources and do not have to pay for them when you don’t need them. One of the things that stroke me about Amazon’s presentation was that they would not tell us the number of processors they had at their disposal.

When it comes to using cloud computing for genomics research, prices may be quite expensive when they add up. The bioinformatics field, greatly influenced by the open-source movement, is not likely to rush to join Amazon’s cloud. Private efforts trying to make money out of human genome technology have remained rather unsuccessful to date: think of Celera Genomics or Lion Bioscience. I am skeptical of the bioinformatics community adopting cloud computing unless open source ideals are embraced: i) allowing people to develop and contribute to the technology if and when they want to, ii) allowing total openness in terms of its achievements and pitfalls and iii) making it free to use for everyone. I do not think that making it free does not mean there is no margin for profit. Think of the profitability of free-to-use technologies such as java (15) or MySQL (16), both components of SUN Microsystems’ (17) business.

Despite the promise of potential benefits for the bioinformatics community, the way the cloud is being portrayed does not conform the ideals of free access and openness. Unless these ideals are implemented to some extent, I see it difficult for the cloud to take root in the bioinformatics field and become a new standard platform for genome research.

References

1. http://www.r-project.org/
2. http://blast.ncbi.nlm.nih.gov/Blast.cgi
3. http://www.bioperl.org/wiki/Main_Page
4. http://www.bioconductor.org/
5. http://www.guardian.co.uk/technology/2008/sep/29/cloud.computing.richard.stallman
6. http://www.infoworld.com/article/08/04/07/15FE-cloud-computing-reality_1.html
7. http://www.sanger.ac.uk/Users/mw4/
8. http://www.sanger.ac.uk/
9. http://cloudcamb.org/
10. http://www.cms.cam.ac.uk/site/
11. http://www.yourgenome.org/people/phil_butcher.shtml
12. http://www.ensembl.org/index.html
13. http://www.ebi.ac.uk/Information/Staff/person_maintx.php?s_person_id=299
14. http://aws.amazon.com/ec2/
15. http://www.java.com/en/
16 http://www.mysql.com/
17. http://www.sun.com/

1 reply »

  1. Just ran into this article — I’m also interested in the impact cloud computing will have on bioinformatics, but if anything, I can’t help thinking that it both relies on and encourages open-source principles. The main reason being, no-one can make efficient use of a cloud if they are using commercial software with per-processor licensing. Open-source software is naturally finding a niche in the cloud while commercial vendors struggle to work out new pricing models.

    If you mean you’d like to see Amazon’s own cloud management software made open-source, well, I can’t really see there being much demand for it. It’s probably quite specific to Amazon’s own network topology and server farm layout. And there are already perfectly good free platforms like Grid Engine for running your own local ‘cloud’ or ‘grid’.

    Like

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