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Bio Image data retention

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Chris Guerin

Bio Image data retention

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Hello everyone:

Can anyone let me know if you have an official institutional policy on the
archiving/retention of bio imaging data? I'm particularly interested in an
policies defining whose responsibility it is to retain unchanged raw data
and for how long such data must be kept. Feel free to contact me off list if
you prefer.

Many thanks,

Chris Guérin

Kurt Thorn

Re: Bio Image data retention

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I'm not sure what the official policy is here, but the imaging center I
run does not do any long term data archiving. We leave this up to the
labs as we neither have the resources nor the expertise to provide long
term data storage for the many terabytes of data generated here.

We allow users to keep data on the microscope workstations for 30 days.
We maintain an 8 TB file server for data transfer and temporary storage
that we allow users to keep data on for 1 year. If we let users keep
data on there much longer it gets full so it seems like users generate
data at at least 6 TB/yr, which is a fair amount of data to store.

Kurt

On 4/16/2013 3:30 AM, Christopher Guerin wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello everyone:
>
> Can anyone let me know if you have an official institutional policy on the
> archiving/retention of bio imaging data? I'm particularly interested in an
> policies defining whose responsibility it is to retain unchanged raw data
> and for how long such data must be kept. Feel free to contact me off list if
> you prefer.
>
> Many thanks,
>
> Chris Guérin
>
>

Wiegraebe, Winfried-2

Re: Bio Image data retention

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At the Stowers Institute, at this moment users are responsible for their original data. We recently introduced a policy that members of the institute have to post all original data for their publications at our Original Data Repository http://odr.stowers.org/websimr/. To help them to organize the data, we are setting up an OMERO server (http://www.openmicroscopy.org/). We will automatically copy all data acquired at the Microscopy Center into the OMERO database. Our IT department and the Microscopy Center will maintain the server.
Winfried

Winfried Wiegraebe
Head of Microscopy
Stowers Institute for Medical Research

[hidden email]
(816) 926-4415
http://research.stowers.org/microscopy/
http://www.stowers.org/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Kurt Thorn
Sent: Tuesday, April 16, 2013 11:41 AM
To: [hidden email]
Subject: Re: Bio Image data retention

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

I'm not sure what the official policy is here, but the imaging center I run does not do any long term data archiving. We leave this up to the labs as we neither have the resources nor the expertise to provide long term data storage for the many terabytes of data generated here.

We allow users to keep data on the microscope workstations for 30 days.
We maintain an 8 TB file server for data transfer and temporary storage that we allow users to keep data on for 1 year. If we let users keep data on there much longer it gets full so it seems like users generate data at at least 6 TB/yr, which is a fair amount of data to store.

Kurt

On 4/16/2013 3:30 AM, Christopher Guerin wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello everyone:
>
> Can anyone let me know if you have an official institutional policy on
> the archiving/retention of bio imaging data? I'm particularly
> interested in an policies defining whose responsibility it is to
> retain unchanged raw data and for how long such data must be kept.
> Feel free to contact me off list if you prefer.
>
> Many thanks,
>
> Chris Guérin
>
>

Jason Swedlow-2

Re: Bio Image data retention

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To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi,

As many of you might guess, at the University of Dundee, we use OME's OMERO
(we contribute to OMERO development, as a participant in the Open
Microscopy Environment Consortium; http://openmicroscopy.org) to manage,
share, analyse and now publish our image data. We hope to have examples of
the latter soon-- it means integration with Drupal, which is a bit fussy.
The OMERO instance is accessed by a separate system where we run Matlab
analysis tools for spot finding and measurements-- pretty simple stuff, but
very helpful to automate and manage. All the analyses are stored alongside
with the original files, etc. All data is backed up on redundant tape
libraries.

The production OMERO instance is backed with a size-limited filesystem, so
only high value data is moved there and analysed. We also have a separate
hierachical filesystem, with about 270 TB of available on-line storage, and
redundant 2 PB LTO4 tape arrays. The whole thing is run by Tivoli. Most
of the images we ever collect are somewhere in this system, but we know
from over 10 years use of this system that 95% of recorded data are never
touched after 3 months have passed from collection. That is why we use
tape-- it's cheap, reliable, space efficient and doesn't require power.

We're looking at a tape-based archiving solution for our OMERO instance.
This will take a few months, but we'll hopefully know whether this approach
works and will obviously pass that info on, once we have it.

So much of our work is funded by the Wellcome Trust, CRUK, BBSRC or MRC, we
have to follow their data retention and provenance policies.

HTH,

Cheers,

Jason

On Tue, Apr 16, 2013 at 9:58 PM, Wiegraebe, Winfried <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> At the Stowers Institute, at this moment users are responsible for their
> original data. We recently introduced a policy that members of the
> institute have to post all original data for their publications at our
> Original Data Repository http://odr.stowers.org/websimr/. To help them to
> organize the data, we are setting up an OMERO server (
> http://www.openmicroscopy.org/). We will automatically copy all data
> acquired at the Microscopy Center into the OMERO database. Our IT
> department and the Microscopy Center will maintain the server.
> Winfried
>
>
> Winfried Wiegraebe
> Head of Microscopy
> Stowers Institute for Medical Research
>
> [hidden email]
> (816) 926-4415
> http://research.stowers.org/microscopy/
> http://www.stowers.org/
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Kurt Thorn
> Sent: Tuesday, April 16, 2013 11:41 AM
> To: [hidden email]
> Subject: Re: Bio Image data retention
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I'm not sure what the official policy is here, but the imaging center I
> run does not do any long term data archiving. We leave this up to the labs
> as we neither have the resources nor the expertise to provide long term
> data storage for the many terabytes of data generated here.
>
> We allow users to keep data on the microscope workstations for 30 days.
> We maintain an 8 TB file server for data transfer and temporary storage
> that we allow users to keep data on for 1 year. If we let users keep data
> on there much longer it gets full so it seems like users generate data at
> at least 6 TB/yr, which is a fair amount of data to store.
>
> Kurt
>
> On 4/16/2013 3:30 AM, Christopher Guerin wrote:
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Hello everyone:
> >
> > Can anyone let me know if you have an official institutional policy on
> > the archiving/retention of bio imaging data? I'm particularly
> > interested in an policies defining whose responsibility it is to
> > retain unchanged raw data and for how long such data must be kept.
> > Feel free to contact me off list if you prefer.
> >
> > Many thanks,
> >
> > Chris Guérin
> >
> >
>

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone: 44 1382 385819
FAX (01382) 388072
email: [hidden email]

Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org
**************************

Kirsten Miles-2

Re: Bio Image data retention

In reply to this post by Wiegraebe, Winfried-2

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This is a wonderful and very forward thinking policy, and you are fortunate
to have the resources to fund it, Winifried. I advise students and
faculty to always design a way to retain original data into their
proposals, and am continually asked how to gain resources to do so. This
and data sharing are the primary reasons for some of our federal grant
requirements for a data plan to be included with grant submission. Just
having the conversation to consider it is important!!

Kirsten

Kirsten Miles
P.I. Outcomes
www.scienceimageintegrity.org
434-960-5193

On Tue, Apr 16, 2013 at 4:58 PM, Wiegraebe, Winfried <[hidden email]>wrote:

Liz Williams

Re: Bio Image data retention

In reply to this post by Chris Guerin

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

The emphasis here is on institutional image data retention, and I don’t want
to sidetrack that important conversation. It is worth mentioning, however,
that The Journal of Cell Biology, in collaboration with Glencoe Software,
developed the JCB DataViewer, which is a browser-based application based on
OMERO for presentation and sharing of image data associated with papers
published in the journal. We offer this as a mechanism for authors to
present and archive their published image data in its original format
(either in the absence of or in addition to institutional resources) and
hope to see this resource expanded to other journals soon.

Liz Williams, PhD
Executive Editor, The Journal of Cell Biology
The Rockefeller University Press

mcammer

Re: Bio Image data retention

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*****

In 2011-12 I went to a number of meetings of IT personnel and faculty/staff from the medical center to establish a method for the institution to provide a universal solution to keep accessible all digital data in a cost effective, for the researchers, manner. However, Hurricane Sandy changed the equation, at least temporarily. Parts of the center are still closed and the servers that were in the basement just went back online in the last two months. Last week I moved 2 TB of data to the server (now I have a total of 6 TB there). The increased traffic flagged my account and I was emailed that the fee was now $50/month/TB. So essentially it's each lab for itself. With 4TB internal drives now available for $50/TB, I'm proposing we buy our own.

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208 Cell: (914) 309-3270

________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Liz Williams [[hidden email]]
Sent: Thursday, April 18, 2013 2:33 PM
To: [hidden email]
Subject: Re: Bio Image data retention

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

The emphasis here is on institutional image data retention, and I don’t want
to sidetrack that important conversation. It is worth mentioning, however,
that The Journal of Cell Biology, in collaboration with Glencoe Software,
developed the JCB DataViewer, which is a browser-based application based on
OMERO for presentation and sharing of image data associated with papers
published in the journal. We offer this as a mechanism for authors to
present and archive their published image data in its original format
(either in the absence of or in addition to institutional resources) and
hope to see this resource expanded to other journals soon.

Liz Williams, PhD
Executive Editor, The Journal of Cell Biology
The Rockefeller University Press