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Repository for the NeMO Analytics project.
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Upload and test 40k single cell RNAseq data set "CtxDevoMidGestGesch40k" #92

Closed carlocolantuoni closed 3 years ago

carlocolantuoni commented 4 years ago

i just put this data in: /autofs/encrypted/NEMO/incoming/brain/other/grant/development/Geschwind/CtxDevoMidGestGesch40k

apaala commented 4 years ago

@carlocolantuoni @jorvis

Upon replacing "" with "NA" in the metadata file, I was able to upload these to the bucket.

carlocolantuoni commented 4 years ago

Great, ill see if they are visualized efficiently in the NeMO Neocortical Development environment. Thanks, Carlo

On Mon, Mar 2, 2020, 15:26 apaala notifications@github.com wrote:

@carlocolantuoni https://github.com/carlocolantuoni @jorvis https://github.com/jorvis

Upon replacing "" with "NA" in the metadata file, I was able to upload these to the bucket.

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carlocolantuoni commented 4 years ago

hey guys - i saw the other new data sets in there, but not this big one - has it been processed yet?

apaala commented 4 years ago

@carlocolantuoni the uid c96c6990-55b9-48a0-b7f1-08157487a7af is CtxDevoMidGestGesch40k... It should be in the bucket...

carlocolantuoni commented 4 years ago

ok thanks - will try to find it

On Fri, Mar 20, 2020 at 12:35 PM apaala notifications@github.com wrote:

@carlocolantuoni https://github.com/carlocolantuoni the uid c96c6990-55b9-48a0-b7f1-08157487a7af is CtxDevoMidGestGesch40k... It should be in the bucket...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nemoarchive/analytics/issues/92#issuecomment-601795359, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH7KC7VO63RMJWRNOJG3WT3RIOLNLANCNFSM4KQUJCUQ .

-- Carlo

carlocolantuoni commented 4 years ago

i am in the data set manager and cant get it to come up in a search with text elements that i know are in the experiment meta data. how would i find it in the data set manager? carlo

On Fri, Mar 20, 2020 at 2:57 PM Carlo Colantuoni colantuonicarlo@gmail.com wrote:

ok thanks - will try to find it

On Fri, Mar 20, 2020 at 12:35 PM apaala notifications@github.com wrote:

@carlocolantuoni https://github.com/carlocolantuoni the uid c96c6990-55b9-48a0-b7f1-08157487a7af is CtxDevoMidGestGesch40k... It should be in the bucket...

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-- Carlo

-- Carlo

carlocolantuoni commented 4 years ago

@jorvis - this is the dataset that i cant find but that apaala said was in there.

jorvis commented 4 years ago

Carlo - Can you send the original path on the filesystem for these files? I want to check the logs.

carlocolantuoni commented 4 years ago

/autofs/encrypted/NEMO/incoming/brain/other/grant/development/Geschwind/CtxDevoMidGestGesch40k/

On Wed, Mar 25, 2020 at 4:49 PM Joshua Orvis notifications@github.com wrote:

Carlo - Can you send the original path on the filesystem for these files? I want to check the logs.

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-- Carlo

jorvis commented 4 years ago

Carlo -

I just got it converted and uploaded into Analytics. I have done zero testing so far but will check on it later. Wanted you to at least know it was there.

jorvis commented 4 years ago

Up next is testing and performance tuning so it is usable.

carlocolantuoni commented 4 years ago

Can i giv it a shot, or do u want to? Im happy to tinker and make views.

On Thu, Mar 26, 2020, 17:16 Joshua Orvis notifications@github.com wrote:

Up next is testing and performance tuning so it is usable.

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jorvis commented 4 years ago

You can certainly try, yes. I just mean there are some performance ideas I want to try that should help here.

On Thu, Mar 26, 2020, 4:55 PM Carlo Colantuoni notifications@github.com wrote:

Can i giv it a shot, or do u want to? Im happy to tinker and make views.

On Thu, Mar 26, 2020, 17:16 Joshua Orvis notifications@github.com wrote:

Up next is testing and performance tuning so it is usable.

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carlocolantuoni commented 4 years ago

oh - cool - im trying to curate a view for this right now - took a long time to load the 1st pull down menu for "display type" ... maybe 1 min. waited >20 min for gene pull down menu, but menu never activated. guessing it pulls in the data to chk available gene names?

btw - why does the user need to enter a gene name? the user does this for any gene from the front page after setting up the view, right? isnt the gene name unrelated to the display itself?

carlo

On Thu, Mar 26, 2020 at 6:11 PM Joshua Orvis notifications@github.com wrote:

You can certainly try, yes. I just mean there are some performance ideas I want to try that should help here.

On Thu, Mar 26, 2020, 4:55 PM Carlo Colantuoni notifications@github.com wrote:

Can i giv it a shot, or do u want to? Im happy to tinker and make views.

On Thu, Mar 26, 2020, 17:16 Joshua Orvis notifications@github.com wrote:

Up next is testing and performance tuning so it is usable.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

https://github.com/nemoarchive/analytics/issues/92#issuecomment-604690991

, or unsubscribe <

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-- Carlo

carlocolantuoni commented 4 years ago

This data set does not load, so it looks like this will be a problem for any large dataset - is this true? Do we not have any other datasets working on this scale, i.e. 40k cells?