Re: [ccp4bb] Database for submitting unprocessed diffraction data

[JEROME JOHNSON]

Hey All,

Thank you kindly for the feedback. I will go ahead to sift through these
options, I'll let you all know what we do in the end!

Best,
Jerome

On Thu, Oct 19, 2023 at 3:39 PM Mirek Gilski  wrote:

> Dear Graeme ,
>
> Our repository is hosted by one of the biggest computer center in Poland
> - Interdisciplinary Center for Mathematical and Computational Modelling
> of University of Warsaw (ICM UW), and as I was assured that their disk
> resources would be sufficient even for very demanding users. You are
> welcome to test this pledge.
>
> Best,
> Mirek
>
> On 19.10.2023 14:19, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
> > Dear Mirek
> >
> > Scraping metadata from the image headers is a very nice idea
> >
> > I wonder, how sustainable is your system? For example would I be thanked
> or cursed for uploading substantial interesting data sets?
> >
> > One of the advantages of Zenodo, as much publicised and also highlighted
> by Loes, is the sustainability element - CERN are well equipped to curate
> vast amounts of data, and the Zenodo organisation is explicitly funded to
> support this
> >
> > Best wishes Graeme
> >
> >> On 19 Oct 2023, at 13:10, Mirek Gilski  wrote:
> >>
> >> Dear Jerome,
> >>
> >> You can consider a Macromolecular Xtallography Raw Data Repository
> (MX-RDR), which is a dedicated archive of raw diffraction data collected
> for macromolecular crystals. It includes tools for creating sets of
> crystallographic metadata by combining information extracted directly from
> diffraction image headers and obtained from the PDB deposit and/or user
> input.
> >> The MX-RDR repository is located at https://mxrdr.icm.edu.pl/
> >>
> >> All the best,
> >> Mirek Gilski
> >>
> >>
> >> ---
> >> -
> >> Prof. UAM dr hab. Mirosław Gilski
> >> Crystallography Department
> >> Faculty of Chemistry AMU
> >> Poznan, Poland
> >> mi...@amu.edu.pl
> >> -
> >>
> >> On 18.10.2023 18:23, JEROME JOHNSON wrote:
> >>> Hello all,
> >>>
> >>> As the subject says, I am looking for an open online database to store
> unprocessed diffraction data.  Does such a database exist? Essentially we
> would like our diffracted data to be freely available online while also
> outsourcing some of our data management.
> >>>
> >>> Any advice would be wonderful!
> >>>
> >>> Best,
> >>> Jerome
> >>>
> >>>
> 
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
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> >> 
> >>
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Mirek Gilski]

Dear Graeme ,

Our repository is hosted by one of the biggest computer center in Poland 
- Interdisciplinary Center for Mathematical and Computational Modelling 
of University of Warsaw (ICM UW), and as I was assured that their disk 
resources would be sufficient even for very demanding users. You are 
welcome to test this pledge.


Best,
Mirek

On 19.10.2023 14:19, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:

Dear Mirek

Scraping metadata from the image headers is a very nice idea

I wonder, how sustainable is your system? For example would I be thanked or 
cursed for uploading substantial interesting data sets?

One of the advantages of Zenodo, as much publicised and also highlighted by 
Loes, is the sustainability element - CERN are well equipped to curate vast 
amounts of data, and the Zenodo organisation is explicitly funded to support 
this

Best wishes Graeme


On 19 Oct 2023, at 13:10, Mirek Gilski  wrote:

Dear Jerome,

You can consider a Macromolecular Xtallography Raw Data Repository (MX-RDR), 
which is a dedicated archive of raw diffraction data collected for 
macromolecular crystals. It includes tools for creating sets of 
crystallographic metadata by combining information extracted directly from 
diffraction image headers and obtained from the PDB deposit and/or user input.
The MX-RDR repository is located at https://mxrdr.icm.edu.pl/

All the best,
Mirek Gilski


---
-
Prof. UAM dr hab. Mirosław Gilski
Crystallography Department
Faculty of Chemistry AMU
Poznan, Poland
mi...@amu.edu.pl
-

On 18.10.2023 18:23, JEROME JOHNSON wrote:

Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear Mirek

Scraping metadata from the image headers is a very nice idea

I wonder, how sustainable is your system? For example would I be thanked or 
cursed for uploading substantial interesting data sets?

One of the advantages of Zenodo, as much publicised and also highlighted by 
Loes, is the sustainability element - CERN are well equipped to curate vast 
amounts of data, and the Zenodo organisation is explicitly funded to support 
this

Best wishes Graeme

> On 19 Oct 2023, at 13:10, Mirek Gilski  wrote:
>
> Dear Jerome,
>
> You can consider a Macromolecular Xtallography Raw Data Repository (MX-RDR), 
> which is a dedicated archive of raw diffraction data collected for 
> macromolecular crystals. It includes tools for creating sets of 
> crystallographic metadata by combining information extracted directly from 
> diffraction image headers and obtained from the PDB deposit and/or user input.
> The MX-RDR repository is located at https://mxrdr.icm.edu.pl/
>
> All the best,
> Mirek Gilski
>
>
> ---
> -
> Prof. UAM dr hab. Mirosław Gilski
> Crystallography Department
> Faculty of Chemistry AMU
> Poznan, Poland
> mi...@amu.edu.pl
> -
>
> On 18.10.2023 18:23, JEROME JOHNSON wrote:
>> Hello all,
>>
>> As the subject says, I am looking for an open online database to store 
>> unprocessed diffraction data.  Does such a database exist? Essentially we 
>> would like our diffracted data to be freely available online while also 
>> outsourcing some of our data management.
>>
>> Any advice would be wonderful!
>>
>> Best,
>> Jerome
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
>> 
>>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Mirek Gilski]

Dear Jerome,

You can consider a Macromolecular Xtallography Raw Data Repository 
(MX-RDR), which is a dedicated archive of raw diffraction data collected 
for macromolecular crystals. It includes tools for creating sets of 
crystallographic metadata by combining information extracted directly 
from diffraction image headers and obtained from the PDB deposit and/or 
user input.

The MX-RDR repository is located at https://mxrdr.icm.edu.pl

All the best,
Mirek Gilski


---
-
Prof. UAM dr hab. Mirosław Gilski
Crystallography Department
Faculty of Chemistry AMU
Poznan, Poland
mi...@amu.edu.pl
-

On 18.10.2023 18:23, JEROME JOHNSON wrote:

Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? 
Essentially we would like our diffracted data to be freely available 
online while also outsourcing some of our data management.


Any advice would be wonderful!

Best,
Jerome



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Kroon-Batenburg, L.M.J. (Loes)]

Dear Jerome,

Zenodo (zenodo.org) is a sustainable solution for archiving raw data. Within 
Zenodo datasets can be grouped in communities. One such community is 
Macromolecular Crystallography. I would like to point you to my recent paper in 
Acta Cryst F. : https://doi.org/10.1107/S2053230X23007987. It explains how and 
why to deposit datasets on Zenodo.

Good luck!
Best wishes,
Loes


___

Dr. Loes Kroon-Batenburg

Structural Biochemistry
Bijvoet Centre for Biomolecular Research
Utrecht University
Universiteitsweg 99, 3584 CG Utrecht
The Netherlands

E-mail : l.m.j.kroon-batenb...@uu.nl
phone  : +31-30-2532865


Van: CCP4 bulletin board  namens JEROME JOHNSON 
<b0fa085259cb-dmarc-requ...@jiscmail.ac.uk>
Verzonden: woensdag 18 oktober 2023 18:23
Aan: CCP4BB@JISCMAIL.AC.UK 
Onderwerp: [ccp4bb] Database for submitting unprocessed diffraction data


CAUTION: This email originated from outside of Utrecht University. Do not click 
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Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Mark J. van Raaij]

This months publication in Acta Cryst F by Loes Kroon-Batenburg may be of 
interest:
https://journals.iucr.org/f/issues/2023/10/00/va5053/index.html 



Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> On 18 Oct 2023, at 18:23, JEROME JOHNSON 
>  wrote:
> 
> Hello all,
> 
> As the subject says, I am looking for an open online database to store 
> unprocessed diffraction data.  Does such a database exist? Essentially we 
> would like our diffracted data to be freely available online while also 
> outsourcing some of our data management.
> 
> Any advice would be wonderful!
> 
> Best,
> Jerome
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Kroon-Batenburg, L.M.J. (Loes)]

Van: CCP4 bulletin board  namens JEROME JOHNSON 
<b0fa085259cb-dmarc-requ...@jiscmail.ac.uk>
Verzonden: woensdag 18 oktober 2023 18:23
Aan: CCP4BB@JISCMAIL.AC.UK 
Onderwerp: [ccp4bb] Database for submitting unprocessed diffraction data


CAUTION: This email originated from outside of Utrecht University. Do not click 
links or open attachments unless you recognize the sender and know the content 
is safe.


Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Keitaro Yamashita]

Hi,

XRDa https://xrda.pdbj.org/ archives raw crystallography datasets for
both PDB and non-PDB entries (e.g. https://xrda.pdbj.org/entry/93), as
well as MicroED datasets (e.g. https://xrda.pdbj.org/entry/140).

Best regards,
Keitaro

On Thu, 19 Oct 2023 at 05:48, Kay Diederichs
 wrote:
>
> There is one more - https://mxrdr.icm.edu.pl/
>
> HTH,
> Kay
>
> On Wed, 18 Oct 2023 19:23:06 +0300, JEROME JOHNSON  
> wrote:
>
> >Hello all,
> >
> >As the subject says, I am looking for an open online database to store
> >unprocessed diffraction data.  Does such a database exist? Essentially we
> >would like our diffracted data to be freely available online while also
> >outsourcing some of our data management.
> >
> >Any advice would be wonderful!
> >
> >Best,
> >Jerome
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> >list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> >https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
> 
>
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Kay Diederichs]

There is one more - https://mxrdr.icm.edu.pl/

HTH,
Kay

On Wed, 18 Oct 2023 19:23:06 +0300, JEROME JOHNSON  wrote:

>Hello all,
>
>As the subject says, I am looking for an open online database to store
>unprocessed diffraction data.  Does such a database exist? Essentially we
>would like our diffracted data to be freely available online while also
>outsourcing some of our data management.
>
>Any advice would be wonderful!
>
>Best,
>Jerome
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Filipe Maia]

Hi,

There's proteindiffraction.org although I'm not sure if it requires a
deposited PDB.
If that fails, you can deposit it at cxidb.org, a repository focused on
data acquired at XFELs which I started, but which also hosts other data
(e.g. https://cxidb.org/id-42.html).

Cheers,
Filipe

On Wed, 18 Oct 2023 at 18:33, JEROME JOHNSON <
b0fa085259cb-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello all,
>
> As the subject says, I am looking for an open online database to store
> unprocessed diffraction data.  Does such a database exist? Essentially we
> would like our diffracted data to be freely available online while also
> outsourcing some of our data management.
>
> Any advice would be wonderful!
>
> Best,
> Jerome
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Tanner, John J.]

You could try https://www.proteindiffraction.org/


From: CCP4 bulletin board  on behalf of JEROME JOHNSON 
<b0fa085259cb-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, October 18, 2023 at 11:33 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Database for submitting unprocessed diffraction data
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Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Green, Todd Jason]

Two other choices:

https://data.sbgrid.org/

https://proteindiffraction.org/

Best-
Todd


From: CCP4 bulletin board  on behalf of JEROME JOHNSON 
<b0fa085259cb-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, October 18, 2023 11:23 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Database for submitting unprocessed diffraction data

Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Database for submitting unprocessed diffraction data

[Patrick Loll]

We’ve used Zenodo. It’s not dedicated solely to diffraction data, but it does 
check the “freely available” box. 

> On Oct 18, 2023, at 12:23 PM, JEROME JOHNSON 
>  wrote:
> 
> Hello all,
> 
> As the subject says, I am looking for an open online database to store 
> unprocessed diffraction data.  Does such a database exist? Essentially we 
> would like our diffracted data to be freely available online while also 
> outsourcing some of our data management.
> 
> Any advice would be wonderful!
> 
> Best,
> Jerome
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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[ccp4bb] Database for submitting unprocessed diffraction data

[JEROME JOHNSON]

Hello all,

As the subject says, I am looking for an open online database to store
unprocessed diffraction data.  Does such a database exist? Essentially we
would like our diffracted data to be freely available online while also
outsourcing some of our data management.

Any advice would be wonderful!

Best,
Jerome



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