Comments on: Bio-Mirrors: To be, or not to be

By: abhishektiwari

abhishektiwari — Mon, 02 Mar 2009 23:55:08 +0000

thanks Eric, whole comment is self-explanatory I guess nothing left to say

By: Eric Jain

Eric Jain — Mon, 02 Mar 2009 22:54:42 +0000

Looking up http://www.uniprot.org simply returns multiple A records (i.e. one for each mirror) in a round-robin manner. So if one of the sites is unreachable, browsers (or other HTTP clients) should automatically try another mirror. Also, all sites are behind reverse proxies, so if a site is down e.g. because it is being updated, requests are proxied to another mirror. But there’s no geo-affinity. That was tried for a while and it sort of worked, but at the cost of the failover. In either case having three mirrors (two of them in Europe) rather than two is useless and even a bit counterproductive, from a technical point of view.

By: abhishektiwari

abhishektiwari — Mon, 02 Mar 2009 00:22:19 +0000

Yes, that’s very true life sciences informatics in learning mode is better

By: mndoci

mndoci — Sun, 01 Mar 2009 23:39:53 +0000

Abhishek,

As mentioned, the UniProt architecture is a class “no single point of failure” design, and serves to provide fast response to requests.

The life sciences can learn a lot from the web in general where people are serving up information globally. Different use cases, but many lessons there

By: abhishektiwari

abhishektiwari — Sat, 28 Feb 2009 19:05:58 +0000

Nicholas, thanks for comment and information, we need well established mirrors with timely synchronization and good inter connectivity, just by copying the whole website at difference locations does not make sense (except there are funding and political issues) particularly for big databases such as PDB. UniProt as you mentioned is perfect example how we should establish biological mirror and I was not really aware about that. I hope BioModels will make similar kind of arrangements .

By: abhishektiwari

abhishektiwari — Sat, 28 Feb 2009 19:05:18 +0000

I guess i am mentioning (dragging) BioModels a lot in my posts !!!!!!!

By: Nicolas Le Novere

Nicolas Le Novere — Sat, 28 Feb 2009 03:44:39 +0000

Abhishek, I think you are mainly right, but the situation you describe is not general in life sciences. A good example is UniProt. If you are in the US, you are redirected to UniProt@PIR, in Germany to UniProt@SIB and in the UK in UniProt@EBI. It is very much our purpose to move toward a similar systems for the EBI. But these mirrors play another role. If the central domain is down, you still need to be able to access independently the other resources. Over the last few years, there were half a dozen times when the EBI had to shut down, between 1 hour and 3 days. Because we had no data replication, BioModels DB was effectively unavailable.

And just FYI, the 3.5 MB tarball is not the whole of BioModels Database, but only the export of the models. multiply that by 3000 to get the current size at the EBI
(for instance with all the metadata, used to search the models, and all the versions of the models.)

By: Abhishek Tiwari

Abhishek Tiwari — Fri, 27 Feb 2009 11:49:07 +0000

Bio-Mirrors: To be, or not to be: Yesterday I got email from SBML mailing list about release of BioModels Databa.. http://tinyurl.com/ddkrzy

By: abhishektiwari

abhishektiwari — Fri, 27 Feb 2009 11:49:07 +0000

Bio-Mirrors: To be, or not to be: Yesterday I got email from SBML mailing list about release of BioModels Databa.. http://tinyurl.com/ddkrzy