Running NBLAST against FlyCircuit neurons

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Shruthi Ravindranath

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Jun 18, 2019, 4:37:48 PM6/18/19
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Hello, 

I had a question about running NBLAST against the database of FlyCircuit neurons.

I use the following few lines of code to try and run NBLAST with a query against the FlyCircuit database:
devtools::source_gist("bbaf5d53353b3944c090", filename="FlyCircuitStartupNat.R") # This creates a neuronlistfh called dps
nblast(query, target = dps)


However, this produces the following error which terminates the execution of the code above

InternetOpenUrl failed: 'The operation timed out'Error in download.file(url = paste0(attr(fh, "remote"), missing[i]), destfile = file.path(objDir,  : 



However, since these references only use the kcs20 dataset as an example, I was wondering if I'm missing something in how to use the FlyCircuit database as my target instead?

Many thanks, 
Shruthi

Gregory Jefferis

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Jun 18, 2019, 5:01:06 PM6/18/19
to Shruthi Ravindranath, nat-user
Dear Shruthi,

What happens if you try to access that url directly in your web browser? It works ok from here. 

However, this produces the following error which terminates the execution of the code above

InternetOpenUrl failed: 'The operation timed out'Error in download.file(url = paste0(attr(fh, "remote"), missing[i]), destfile = file.path(objDir,  : 



The gist page (listed below) suggests doing this the first time you download these data:
dps<-read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/dpscanon.rds",
    localdir=getOption('flycircuit.datadir'))
remotesync(dps,download.missing = TRUE) 
Did you try that yet?

Best,

Greg. 



However, since these references only use the kcs20 dataset as an example, I was wondering if I'm missing something in how to use the FlyCircuit database as my target instead?

Many thanks, 
Shruthi

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Shruthi Ravindranath

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Jun 18, 2019, 5:34:17 PM6/18/19
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Thank you for your response. When I try to access the URL directly from my browser, I have no troubles and a file is downloaded. 

I am now downloading the data as suggested by the gist. Are these the dps files of the FlyCircuit neurons? Once the download is complete, would it be sufficient to say the following to read in the dps and run NBLAST?
flyCircuit_db = read.neurons('path/to/flycircuit.datadir')

nblast(query, flyCircuit_db)


Best, 
Shruthi


On Tuesday, June 18, 2019 at 5:01:06 PM UTC-4, Gregory Jefferis wrote:
Dear Shruthi,

What happens if you try to access that url directly in your web browser? It works ok from here. 

However, this produces the following error which terminates the execution of the code above

InternetOpenUrl failed: 'The operation timed out'Error in download.file(url = paste0(attr(fh, "remote"), missing[i]), destfile = file.path(objDir,  : 



The gist page (listed below) suggests doing this the first time you download these data:
dps<-read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/dpscanon.rds",
    localdir=getOption('flycircuit.datadir'))
remotesync(dps,download.missing = TRUE) 
Did you try that yet?

Best,

Greg. 


However, since these references only use the kcs20 dataset as an example, I was wondering if I'm missing something in how to use the FlyCircuit database as my target instead?

Many thanks, 
Shruthi

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Greg Jefferis

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Jun 21, 2019, 5:39:58 AM6/21/19
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Dear Shruthi,

When you are finished, you can just run the original command:

devtools::source_gist("bbaf5d53353b3944c090", filename="FlyCircuitStartupNat.R") # This creates a neuronlistfh called dps 
nblast(query, target = dps)
Or you can do:
dps<-read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/dpscanon.rds",	localdir=getOption('flycircuit.datadir'))
nblast(query, target = dps)
(which is basically just copying the first line from in the gist)

Best,

Greg.

Gregory Jefferis

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Jun 21, 2019, 7:34:13 AM6/21/19
to Shruthi Ravindranath, nat-...@googlegroups.com
Dear Shruthi, I missed this query previously but essentially the same command that I detailed in my last message would read the dps object into R or trigger the download of the individual flycircuit neurons for the first time. Best, Greg.

Sent from my iPhone

> On 19 Jun 2019, at 14:47, Shruthi Ravindranath <shruthi.rav...@gmail.com> wrote:
>
> Just following up on this - I now have all the files saved to disk. I was wondering if there is a function packaged with nat that helps me read in these dps to R so they can be used as the NBLAST target.

Shruthi Ravindranath

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Jun 26, 2019, 3:30:12 PM6/26/19
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Thank you, that works great!
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