Hi Franco, We are using Hadoop for next-gen sequence alignment. Earlier we had a classic programming model solution, but currently we are upgrading our software services to M/R modell based on Hadoop. We transferred most of our classic algorithms to Hadoop and I can say that everything is getting more manageable.
We are going with Hadoop on the cloud and/or on datacenter. Another challenge, especially with cloud, how you are transferring the data, because in bioinformatics the amount of data are usually very high. Currently i am working on an open-source version of Amazon multipart upload which will be available in the next release of JClouds<http://code.google.com/p/jclouds/wiki/BlobStore>, here are the starting ideas<http://www.slideshare.net/jclouds/big-data-in-real-life-a-study-on-s3-multipart-uploads>and also a sample client app<https://github.com/jclouds/jclouds-examples/tree/master/blobstore-largeblob> . If you want to follow new results on twitter<http://twitter.com/#%21/tiborkisstibor>, you are invited. I plan to release a paper with results of the data transfer operations based on this open-source approach. Also, soon we are releasing the version of our cloud based service stack which is fully based on Hadoop. Tibor On Mon, Mar 28, 2011 at 4:51 AM, Franco Nazareno <franco.nazar...@gmail.com>wrote: > Good day everyone! > > > > First, I want to congratulate the group for this wonderful project. It did > open up new ideas and solutions in computing and technology-wise. I'm > excited to learn more about it and discover possibilities using Hadoop and > its components. > > > > Well I just want to ask this with regards to my study. Currently I'm > studying my PhD course in Bioinformatics, and my question is that can you > give me a (rough) idea if it's possible to use Hadoop cluster in achieving > a > DNA sequence alignment? My basic idea for this goes something like a string > search out of a huge data files stored in HDFS, and the application uses > MapReduce in searching and computing. As the Hadoop paradigm impies, it > doesn't serve well in interactive applications, and I think this kind of > searching is a "write-once, read-many" application. > > > > I hope you don't mind my question. And it'll be great hearing your comments > or suggestions about this. > > > > Thanks and more power! > > Franco > >
