Blast - The Amazon version

December 19, 2007

It’s my fault. I take full responsibility. For months, I’ve been meaning to harass Michael Cariaso about building bioinformatics apps on EC2. (a) I am about 6 months behind in my efforts to start running NAMD actively on EC2 (b) that I haven’t talked about RunBlast tatamounts to criminal negligence.

RunBlast is going to be available as a download soon, and will allow you to run Blast and other apps on a virtual EC2 cluster. Oh, by the way, RunBlast uses the Amazon payment system. Wait, isn’t Blast free? Why should I pay for it? Well if you run Blast once a year, perhaps you shouldn’t be using RunBlast, but if you’re a regular user, and do some serious crunchching, this beats buying a cluster anyday.

Note that a lot of this is possible because of getting MPICH2 working with EC2

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Posted by Deepak Singh | Filed Under Computing, Informatics, Software & Internet 

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    It most certainly is. And if you want to see part 3 of the series it will be delivered at PyCon 2008 Chicago by

    Peter Skomoroch
    http://us.pycon.org/2008/profile/0773dc/

    for his talk
    http://us.pycon.org/2008/conference/talks/?filt...


    131. MPI Cluster Programming with Python and Amazon EC2

    Amazon EC2 may offer the possibility of high performance computing to programmers on a budget. Instead of building and maintaining a permanent Beowulf cluster, we can launch a cluster on-demand using Python and EC2. This talk will cover the basics involved in getting your own cluster running using Python, demonstrate how to run some large parallel computations using Python MPI wrappers, and show some initial results on cluster performance.









    RunBlast is going to be available as a download soon, and will allow you to run Blast and other apps on a virtual EC2 cluster. Oh, by the way, RunBlast uses the Amazon payment system. Wait, isn’t Blast free? Why should I pay for it? Well if you run Blast once a year, perhaps you shouldn’t be using RunBlast, but if you’re a regular user, and do some serious crunchching, this beats buying a cluster anyday.



    People who mainly use the NCBI service will do well to continue doing so. This is really targeted at groups who have a small cluster inhouse which is mainly used to run blast.


    When your needs have outgrown the NCBI webserver, RunBlast allows you to have that cluster without the big upfront purchase, or the hassles of maintaining latest versions of major tools and databases.

    I actually use it to run bioperl, emboss, and MrBayes. NAMD has been on my todo list but hearing its of interest should bump it up. I'll drop a line when its available.

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