[ome-users] Set-up information

[Jason Swedlow]

Hi Gareth-

Thanks for your email.

On 24 Jul 2008, at 10:38, Gareth Howell wrote:
> Dear all
>
> I have a few hardware questions regarding the OME.
>
Happy to help.  The answers below pertain to OMERO, the data  
management system released by the OME Consortium.  For more info on  
OMERO, see the screencast videos at

http://www.openmicroscopy.org/site/videos

However, the comments below also pertain to the OME Server.

> We are thinking of applying for support to set up a server to store  
> images collected within our bioimaging facility, but unfortunately  
> have no experience of how to select servers. What servers do people  
> use? Are they lab based or do you use them to collect and store  
> data from a whole facility? What sort  of memory capacity would you  
> suggest (we have a Delta Vision, and two LSM510 systems)?
>
The way to think about this is to consider the number of users, and  
the amount of data collected.  Those numbers roughly translate into  
the kind of server you should buy and the kind and amount of storage  
you should try to purchase.

For our production server, we are using a Dell PowerEdge 2970:

http://www.dell.com/content/products/productdetails.aspx/ 
pedge_2970_rack?c=us&l=en&s=biz&cs=555

config'd as dual quad-core, with 8 GB RAM (I think).  (We have no  
affiliation with Dell, we also have IBM, Sun, and Compaq boxes-- we  
just buy what is best value at the time we need to buy).

That covers about 40 users, and about 10 concurrent users, quite  
easily, and was quite reasonably priced.

For storage, you really need to consider how much data you generate  
and store, so you need to spend a few mins thinking about your next 5  
years (also remember, for example BBSRC's data of holding all data  
for 10 years).

Make a reasonable estimate of the amount   of data you will store,  
and how that scales for the next few years.  Then decide what kind of  
backup you'll want-- you can trawl around the web abit to find all  
sorts of opinions on what you'll need (it's one of those areas where  
everyone is an expert).  Most importantly, develop some strategy for  
storing the data semi-resiliently (i.e, RAID) and include a provision  
for backup (we like having a fully off-line back-up on tape, others  
will tell you that is not necessary).

Then decide how the costs you can consider match what is available.   
If you have a good IT person at Leeds, talk to them-- they can help  
you with all the terminology.  If at all possible, enlist their  
interest and support early-- ideally, you'll need power, space, and  
cooling for all this stuff and they can help.

However, a lab's needs could easily be solved by a reasonably powered  
desktop server, an attached disk, and some low level backup.  Anyone  
on the list have a low level solution like this working?
> Finally, if you were applying for grant support to set this up what  
> 'bases' would you try and cover (I guess that is quite a big  
> question! Sorry!!)
>
Not sure, but all of the major UK funding bodies now ask specifically  
for a sound, articulated data management strategy.

OMERO doesn't do anything specifically about storage-- that is a  
disk's job.  OMERO provides data management-- visualization,  
analysis, tagging, annotation, linking, etc.  I guess you want to hit  
those buttons.
> I'm clearly missing some vital information so any help would be  
> much appreciated!
>
I'm happy to discuss off-line if you want.  I'm away from office a  
wee while-- email me and we can set up a time to chat.
>
> Apologies in advance for my ignorance!
>
Not at all-- this stuff is tricky.

Cheers,

Jason

**************************
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: jason at lifesci.dundee.ac.uk

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Open Microscopy Environment: http://openmicroscopy.org
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