Re: Inquiry regarding NBLAST on-the-fly

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Dr Gregory Jefferis

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Jan 31, 2021, 5:34:04 PM1/31/21
to 大橋 拓朗, sup...@virtualflybrain.org, nat-user
Dear Takuro,

Thank you for your message and interest in NBLAST. I am sorry for the
trouble you have been experiencing. The NBLAST server is now run by the
virtual fly brain project. Rob Court, the lead developer, recently had
to do some work on some of the underlying infrastructure and it seems
likely to me that this may be the source of the problem with the server.
Rob, can you provide any insight? I can confirm that I cannot maintain a
stable connection to the server.

As for the desktop install instructions:

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/nblast_desktop/

although they have not been updated for some time, I think they should
work. Have you run into a specific problem? If so, could you please send
a message describing the code that you have run and the error messages
that you observed to:

https://groups.google.com/g/nat-user

The only variation that I would make to the install procedure is for the
flycircuit package itself, where I would now recommend:

install.packages('natmanager')
natmanager::install(pkgs = 'flycircuit')

Although the original instructions should still be fine and the next
steps remain the same:

if(!require("devtools")) install.packages("devtools")
devtools::source_gist("bbaf5d53353b3944c090")
remotesync(dps,download.missing = TRUE)

With best wishes,

Greg.

On 31 Jan 2021, at 2:15, 大橋 拓朗 wrote:

> Hello,
>
> I am Takuro Ohashi, a PhD student in the lab of Prof Azusa Kamikouchi
> at Nagoya University.
>
> My research is focused on comparing the neural circuitry of two
> closely-related Drosophila species, D. melanogaster and D. simulans.
> As part of my project, I wanted to utilize your NBLAST online
> community tool
> (http://nblast.virtualflybrain.org:8080/NBLAST_on-the-fly/);
> however when I tried to access the server, it seems to be already
> down.
> Furthermore, when I attempted to build a local installation, the
> tutorial video appears to refer to a previous version of the
> installation rather than the most up-to-date version.
> Could you please help me to access the online version, or provide me
> with an updated tutorial for local installation?
>
> Thank you very much for your help, I look forward to reading your
> response.
>
> Sincerely,
> Takuro Ohashi
>
> --
> Takuro Ohashi
>
> Graduate School of Science
> Nagoya University
> Furo, Chikusa, Nagoya 464-8602
> Japan
>
> E-mail: oohashi...@f.mbox.nagoya-u.ac.jp


--
Gregory Jefferis, PhD Tel: +44 1223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 0QH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/research/groups/connectomics

大橋 拓朗

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Feb 1, 2021, 10:35:21 PM2/1/21
to Dr Gregory Jefferis, sup...@virtualflybrain.org, Kamikouchi Azusa
Dear Dr Jefferis,

Thank you for your email and advice, they are very much appreciated.
I hope that the NBLAST server becomes available again in the future,
but for now I was able to successfully install the software locally with
your additional guidance and the weblinks you provided.

Many thanks again,

Takuro


2021-02-01 07:33 に Dr Gregory Jefferis さんは書きました:

Rob Court

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Feb 2, 2021, 11:38:08 AM2/2/21
to Dr Gregory Jefferis, 大橋 拓朗, sup...@virtualflybrain.org, nat-user
The NBLAST on-the-fly server is now back in service.

Thanks for letting us know and sorry for any inconvenience,

Robert Court
VirtualFlyBrain.org

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Dr Gregory Jefferis

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Feb 2, 2021, 11:45:40 AM2/2/21
to Rob Court, 大橋 拓朗, sup...@virtualflybrain.org, nat-user
Thank you very much, Rob. That's great.

Just a note for any future readers that Takuro also confirmed that he
was able to run the local version of NBLAST on his own machine using the
instructions referred to in this thread.

Best,

Greg.
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