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Task #2976

closed

Upload public dataset to EMPIAR

Added by Neil Voss about 10 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Sargis Dallakyan
Category:
-
Target version:
-
Start date:
11/11/2014
Due date:
% Done:

0%

Estimated time:

Description

I think we should upload our important data sets to EMPIAR to avoid any catastrophes like losing the 06jul12a GroEL dataset.

http://www.ebi.ac.uk/pdbe/emdb/empiar/

"EMPIAR, the Electron Microscopy Pilot Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload, and download and reprocess the thousands of raw, 2D images used to build a 3D structure."

NRAMM public datasets, http://nramm.scripps.edu/public-datasets/

You may know more about the issue, but I think it is good idea.

Related issues 1 (1 open — 0 closed)

Related to Appion - Bug #2939: Appion Developers Conference Call NotesNew09/24/2014

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 #1

Updated by Neil Voss about 10 years ago

  • Related to Bug #2939: Appion Developers Conference Call Notes added
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 #2

Updated by Sargis Dallakyan about 10 years ago

  • Assignee set to Sargis Dallakyan

I'll do this. It is good idea indeed. I'll be making another copy of this dataset that will be shipped to NYC separate from the rest of the servers.

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 #3

Updated by Neil Voss almost 10 years ago

  • Status changed from New to Assigned
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 #4

Updated by Neil Voss almost 10 years ago

Dear Ardan,

Thank you for the quick response. Please find enclosed these additional details:

1) Pixel size in A on the micrographs - 1.63 Å
2) Pixel type (eg 32 float) for micrographs - 32bit float
3) Pixel size in A on the picked particles - 1.63 Å
4)Pixel type (eg 32 float) for picked particles - 32bit float
5) List of authors - Stagg SM1, Lander GC, Pulokas J, Fellmann D, Cheng A, Quispe JD, Mallick SP, Avila RM, Carragher B, Potter CS.
6) Related EMDB entry (or entries) - http://www.ebi.ac.uk/pdbe/entry/EMD-5336
7) Related publication (if any) - http://www.ncbi.nlm.nih.gov/pubmed/16762565

Many thanks and best wishes,
Sargis

On 11/17/2014 01:28 PM, Ardan Patwardhan wrote:
Dear Sargis

I have created a token code for your upload: XXXXXXXXXXXXXXX

The password is: XXXXXXXXXXXXXXX

I had a look at the link, you could upload both the micrographs and picked particles (and any auxiliary files) to this directory. Most of the info I need I can get off the web-page but I was wondering if you could give me these additional details (or clarifications):
1) Pixel size in A on the micrographs
2) Pixel type (eg 32 float) for micrographs
3) Pixel size in A on the picked particles
4)Pixel type (eg 32 float) for picked particles
5) List of authors
6) Related EMDB entry (or entries)
7) Related publication (if any)

Many thanks and best wishes

On 17 Nov 2014, at 21:06, Sargis Dallakyan <> wrote:

Greetings,

I would like to deposit the following data to EMPIAR:

https://emg.nysbc.org/projects/ami/wiki/06jul12a_GroEL_dataset

Please let me know if you have questions or need more information.

Thank you,
Sargis

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 #5

Updated by Sargis Dallakyan almost 10 years ago

  • Status changed from Assigned to Closed

06jul12a dataset is now published at http://pdbe.org/empiar as EMPIAR-10018.

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 #6

Updated by Neil Voss almost 10 years ago

Hi Sargis, the data set you uploaded was 05may19a not 06jul12a; 06jul12a was lost. But the reference is correct.

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 #7

Updated by Sargis Dallakyan almost 10 years ago

Hi Neil, thanks for the update. I also made copy of the following public datasets onto external drive:

appion:
total 0
drwx------ 1 sargis carragher 0 Apr 22 2011 .
drwx------ 1 sargis carragher 0 Sep 17 2010 ..
drwx------ 1 sargis carragher 0 Mar 23 2011 05may19a
drwx------ 1 sargis carragher 0 Jul 16 2007 05nov11a
drwx------ 1 sargis carragher 0 Jul 3 2007 05oct20a
drwx------ 1 sargis carragher 0 Jul 3 2007 05oct27b
drwx------ 1 sargis carragher 0 May 1 2007 06mar09a
drwx------ 1 sargis carragher 0 Jan 31 2011 07jul25b
drwx------ 1 sargis carragher 0 Aug 5 2009 09apr14b
drwx------ 1 sargis carragher 0 May 11 2009 09feb12b
drwx------ 1 sargis carragher 0 Jun 11 2009 09feb18c
drwx------ 1 sargis carragher 0 May 5 2009 09mar04b

leginon:
total 0
drwx------ 1 sargis carragher 0 Nov 18 10:39 .
drwx------ 1 sargis carragher 0 Sep 17 2010 ..
drwx------ 1 sargis carragher 0 Jul 3 2007 05may19a
drwx------ 1 sargis carragher 0 Nov 21 2006 05nov11a
drwx------ 1 sargis carragher 0 Nov 21 2006 05oct20a
drwx------ 1 sargis carragher 0 Nov 21 2006 05oct27b
drwx------ 1 sargis carragher 0 Jul 4 2007 06apr27c
drwx------ 1 sargis carragher 0 Nov 19 13:10 06jul12a
drwx------ 1 sargis carragher 0 Aug 2 2010 06mar09a
drwx------ 1 sargis carragher 0 Jul 25 2007 07jul25b
drwx------ 1 sargis carragher 0 Apr 14 2009 09apr14b
drwx------ 1 sargis carragher 0 Mar 16 2009 09feb12b
drwx------ 1 sargis carragher 0 Apr 16 2009 09feb18c
drwx------ 1 sargis carragher 0 Mar 4 2009 09mar04b

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