http://confocal-microscopy-list.275.s1.nabble.com/IT-infrastructure-tp7590206p7590270.html
Yes we have been running Imaris on a virtual desktop infrastructure since the summer. We love it! This is a clear improvement for everyone.
You need a floating licence manager. Another facility at KI had one but had no VDI so we are merging our licences. We have 14 Imaris licences at KI! In the long run it would be really great if we could merge all or most of them.
Bitplane is quite pleased with the process as far as I know and they are very helpful. The first challenge was to manage to get in contact with all the licence owners.
Many of these licences have not been updated for ages. Grouping all licences gives great (up to 70 or 80%) discount on upgrades and service contracts so on top of the great advantage of having a super infrastructure accessible to users from anywhere and maintained by the university IT people, there is money to be saved. Also in our case all modules are pulled together instead of being associated with one licence so this add flexibility. But I know that there are many ways to run university-wide licences. Each licence could be instead associated with one group of users. We see a great advantage is pulling everything.
For Bitplane there is a clear advantage that old licences are upgraded and start being used again. The more researchers use Imaris under good conditions the more Imaris will develop when researchers move to another lab.
The second challenge is to find a way to balance the cost models: At our facility, those who have paid the (usually yearly) membership have access to Imaris for free. The other facility makes people pay per hour. This is what we are discussing right now but there is a strong will to find common ground so I am sure we will find a way.
I think that once you have migrated to a virtual infrastructure of high quality, there is no turning back. :)
> On Behalf Of Holly L. AARON
We are looking into setting up a virtual machine to run Imaris. You mention you are doing this now and so I am wondering how the licensing works for this? Do you have a campus-wide license or just a single license for Imaris? Thank you! I have reached out to them but have not heard back about whether or not it is possible to do this.
*Holly L. Aaron, **Director*
*Misspellings and typos* are all mine. * **Who am I kidding, it's either auto-correct or poor spelling. Mostly poor spelling. I am a terrible speller. Don't tell my mom! *
> *****
> To join, leave or search the confocal microscopy listserv, go to:
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> *****
>
> My experience is that many cloud infrastructures do not allow to
> upload files that are larger than 4 GB.
> Not sure if it is true for all of them.
> On top of that, there is of course the problem of speed to upload and
> need to download again to analyse the data.
> With a local infrastructure, you skip this time which is considerable
> if one has a light sheet system.
>
> Med vänlig hälsning / Best regards
>
> Sylvie
>
> @@@@@@@@@@@@@@@@@@@@@@@@
> Sylvie Le Guyader, PhD
> Live Cell Imaging Facility Manager
> Karolinska Institutet- Bionut Dpt
> Blickagången 16,
> Room 7362 (lab)/7840 (office)
> 14157 Huddinge, Sweden
> mobile: +46 (0) 73 733 5008
> LCI website
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>
> -----Original Message-----
> From: Confocal Microscopy List <
[hidden email]> On
> Behalf Of Feinstein, Timothy N
> Sent: 22 November 2019 17:01
> To:
[hidden email]
> Subject: Re: IT infrastructure
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
>
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> Post images on
>
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> and include the link in your posting.
> *****
>
> My current institution mostly uses cloud solutions, due to
> University-wide agreements with cloud providers. As pointed out this
> isn't great for lab-wide aggregating and archiving. My previous
> institution also had a centralized PB-scale Isilon server for
> rapid-access needs, plus an offline tape backup service for long term
> archiving. This has a great economy of scale - and it made it very
> easy for us to implement OMERO, which is a fantastic image data
> management package! However not many institutions can support that kind of centralized data handling.
>
>
> T
>
> On 11/22/19, 8:40 AM, "Confocal Microscopy List on behalf of Gary
> Laevsky" <
[hidden email] on behalf of
>
[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
>
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787410149&sdata=FZ654QbTR873n%2FRKi3zjmojPVBwk1r5o2AFmjI3OsNc%3D&reserved=0> Post images on
>
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> and include the link in your posting.
> *****
>
> Hi Matthieu,
>
> We just purchased 5 PB and migrated to an Isilon.
>
> We do run some applications on the server, but time there is at a
> premium.
>
> We also have a few fairly beefy PCs to crunch data locally.
>
> Right now, this is our short-medium-long-term solution. Not sure if we
> will migrate to something like Glacier for long-term eventually.
>
> We are collecting cryo and light-sheet, so the numbers are getting up
> there. We are also updating applicable systems to 10GB fiber for
> transfer.
>
> Interested to hear other solutions as well.
>
> Big Data is always a favorite topic at our NAMS meetings, and it's
> also the
> name of our light-sheet workshop next summer as well (plug intended!)!
>
> On Fri, Nov 22, 2019 at 7:54 AM George McNamara <
>
[hidden email]>
> wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> >
>
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>
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> 50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111
> 061787410149&sdata=vxNUs%2FA9xL4yX8dj%2B0cVjLBAmx3F7dwbf1LgMHTJExM
> %3D&reserved=0
> and include the link in your posting.
> > *****
> >
> > Hi Matthieu,
> >
> > 20 TB WD My Book Duo USB 3.1 are $700 ... orWD 20TB My Cloud EX2
> Ultra
> > Network Attached Storage $999 ...
> > <
> >
>
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
> amazon.com%2FCloud-Ultra-Network-Attached-Storage%2Fdp%2FB07179ZYH2%2F
> ref%3Dsr_1_3%3Fcrid%3D3ILUXD0SCQ70Z%26keywords%3Dwd%2B20tb%2Bmy%2Bbook
> %2Bduo%26qid%3D1574426442%26sprefix%3Dwd%2B20%2Btb%252Caps%252C129%26s
> r%3D8-3&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a5
> 0b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C6371110
> 61787410149&sdata=OU%2B1lZIUlacJ0tvJufCOA2dn9NSGhyaVlnOTqrnST8Q%3D
> &reserved=0
> >you
> >
> > may want to have one or more in your facility for backup (move
> month old
> > data) AND encourage P.I.'s to have in for their labs (and most PI's
> > think about their research, not about I.T. and need for data
> backups).
> >
> > In a previous thread I posted about what we have ... some 10 Gbe
> > computers, 10 Gbe server (40 Tb HDD RAID array), and a switch 10 Gbe
> > Ethernet (CAT7 copper wire, others pointed out SFP+ fiber optic
> is less
> > expensive ... future: connect our image core rooms to the fiber optic
> > switch room), some PCs with ASUS Hyper M.2 PCIe card with 4 Silicon
> > Power 2 Tb NVMe SSDs, ~$1050 for 8Tb fast local storage (PCIe
> x16 slot,
> > BIOS configure the slot as x4x4x4x4) ... goal is fast local
> acquisition
> > saving --> fast network --> best wishes.
> >
> > JHU now provides 5 Terabytes Microsoft OneDrive cloud storage per
> > employee/student ... and in principle could call I.T. and get more.
> So
> > far, not easily "aggregated" by lab ... I hope this gets changed
> so a PI
> > of a 20 person lab gets 100 Tb to start with, organized by user
> (say
> 1
> > Tb private to that user, visible to the PI) and mostly organized by
> > projects.
> >
> > enjoy,
> >
> > George
> >
> > On 11/22/2019 6:43 AM, VERMEREN Matthieu wrote:
> > > *****
> > > To join, leave or search the confocal microscopy listserv, go to:
> > >
>
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787410149&sdata=FZ654QbTR873n%2FRKi3zjmojPVBwk1r5o2AFmjI3OsNc%3D&reserved=0> > > Post images on
>
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> %3D&reserved=0
> and include the link in your
> > posting.
> > > *****
> > >
> > > Dear all,
> > >
> > > We are producing massive amount of data that legally needs to
> be stored
> > for up to ten years. This data also needs to be analysed fairly
> quickly
> > -hence storage on local servers. Furthermore, some software
> companies
> > (Huygens, Imaris...) are now offering server-based applications
> for image
> > analysis -all the hard work is done on the server and your
> computer is just
> > a terminal.
> > >
> > >
> > > Currently, we tell users to transfer their data to NAS
> immediately after
> > imaging, so the microscope computers are not clogged. Image
> files found on
> > these computers are fair game after a month. We expect users to
> then back
> > up their files from the NAS to cloud. All our image analysis is
> done on
> > fairly beefy workstations and not server based.
> > >
> > > As I'd like to future proof our IT, it would be great to know what
> > servers/storage space do you have as part of your
> facilities/institutes?
> > What solutions do you have for long term storage vs short to
> medium terms?
> > Do you have server based applications?
> > >
> > > Matthieu
> > > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
>
>
> --
> Best,
>
> Gary Laevsky, Ph.D.
> Director, Confocal Imaging Facility
> Nikon Center of Excellence
> Co-Founder, North Atlantic Microscopy Society (NAMS)
>
>
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnamsmicroscopy.com%2F&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787410149&sdata=4xzdzvdKxu1M1HrX1GRvuOVHvDjeEAtQ6a%2F8mGqPrug%3D&reserved=0> Dept. of Molecular Biology
> Washington Rd.
> Princeton University
> Princeton, New Jersey, 08544-1014
> (O) 609 258 5432
> (C) 508 507 1310
>
> North Atlantic Microscopy Society Spring Meeting at UPENN, April
> 23, 2020.
>
>
>
>
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