[BioPython] Fwd: NCBI Abuse Activity with BioPython

[Chris Fields]

No, not just threading.  The requests could be made by a simple script/ 
program of any kind with no timeout implemented; the IPs of those  
abusing the timeout will likely be blocked.

The idea is not to spam their server (let alone any server which  
provides a free service) with tons of requests of any kind, be it  
eutils or BLAST submission requests, BLAST report retrieval requests  
using RID, etc.  Any tools using these services should implement the  
minimum recommended delay between them.  Alternatively, set up a local  
BLAST service as Peter recommends.

chris

On Jun 27, 2008, at 11:18 AM, Frederico Arnoldi wrote:

>
> Right, thanks for the answers.
> If I understood, the problem is threading the requests. If I am not  
> threading my requests I am not abusing NCBI server, so don't thread  
> them.
> Thanks again,
> Fred
>>>> 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
>>
>> The above appears to submit a single job at a time and wait 3 sec.
>> between polling the server until the current job is finished.  I  
>> don't
>> think that is the problem indicated in the link above.  The 3 sec. is
>> for submitting new BLAST jobs, for instance if you want to submit one
>> BLAST request after another (gathering the RIDs), then grab all the
>> reports at once, or if you are threading 50 submission requests all  
>> at
>> once.
>>
>> chris
>
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