[BioPython] Fwd: NCBI Abuse Activity with BioPython

[Peter]

On Fri, Jun 27, 2008 at 2:19 PM, Frederico Arnoldi <fredgca at hotmail.com> wrote:
>
> Guys (sorry the informality),
>
> I have followed the discussion about "NCBI Abuse Activity with BioPython". I
> have to confess that followed it superficially, since I am not able to understand
> everything you said. So, I am going to make some questions about it:
>
> 1)I believe that using BLAST with NCBIWWW.qblast is included in "Abuse Activity". Right?

I'm not aware that abuse of BLAST was singled out, only Entrez / E-utils.

> I am asking because sometimes I use it. The recommendation of NCBI is
> "Make no more than one request every 3 seconds.".

True, http://www.ncbi.nlm.nih.gov/blast/Doc/node60.html

> Biopython code does not assure it with the following  code in NCBIWWW.py,
> line 779:
> [code]
> limiter = RequestLimiter(3)
> while 1:
>    limiter.wait()
> [/code]

I believe that bit of code is polling the server for results every
three seconds.  Perhaps we should insert an additional enforced three
second delay between submission of queries as well.

> 2)Do you have any recommendation for using it that it is not included in the
> tutorial? Maybe listing some recommendations here would help.

I would recommend running your own local BLAST server for any large
jobs - either the standalone blast tools, or if you have a machine on
the network that many people could share, run the WWW version locally.

Peter