[Bioperl-l] [Fwd: Enquiry about Remoteblast.pm]

Robert Bradbury robert.bradbury at gmail.com
Fri Mar 5 08:20:36 EST 2010

On Fri, Mar 5, 2010 at 5:05 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

> My apologies for jumping the gun on the email thing — that won't take
> effect until June 1.
> See full details here:
> http://groups.google.com/group/bioperl-l/browse_thread/thread/979a35fb9e22e45d/e7c88e7f087ff42d
> Looks like the problems with RemoteBlast (as Chris reported elsewhere in
> this thread) is at NCBI's servers (and is probably temporary).
I would not be at all surprised if any problems involving RemoteBlast were
related to the recent changeovers to a Javascript requirement for all
interfaces to NCBI databases (this took place around mid-February and I
complained about this in a previous email to the BioPerl list).

I received a response back from Dr. Eric Sayers at NCBI on Feb. 26 that
indicated that they were aware of the problem (involving a Javascript
requirement) and indicated that NCBI developers were "investigating" ways to
mitigate the problem.

I've looked briefly at the new Javascript code that one is required to run
when using PubMed, etc. and it looks like they may have completely changed
the external interfaces to NCBI databases -- so I'm not surprised if that
broke some or all other external interfaces used by BioPerl (RemoteBlast,
Eutils, etc.).  I'd suggest that you try to document the problems as best
you can and submit them to the NCBI help desk (or info at ncbi.nlm.nih.gov).
It may be worth noting that it took ~3 weeks for me to receive any response
to my reports.

Also note, that (a) to the best of my knowledge there has been no public
discussion regarding these recent changes at NCBI; and (b) under the Jan.
21, 2009 Memorandum on Transparency and Open Government, and under the Dec
8, 2009 Open Government Directive, NCBI *should* be doing a better job
working with its end users (and the taxpayers) -- and at least thus far,
while NIH seems to be making an effort that doesn't seem to have filtered
down to NCBI.

(For example, no open/public discussion regarding the email requirement for
remote blasts...).

It is also worth noting that it should be possible to file FOI requests with
NIH/NCBI to find out exactly what they are doing and why they are doing it.
I haven't taken such steps yet but I have given consideration to doing so.


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