Confocal Microscopy List

Re: IT infrastructure

Posted by Holly L. AARON on
URL: http://confocal-microscopy-list.275.s1.nabble.com/IT-infrastructure-tp7590206p7590269.html

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Hi, Sylvie -

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.

Thanks,
Holly

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On Fri, Nov 22, 2019 at 8:13 AM Sylvie Le Guyader <[hidden email]>
wrote:

> *****
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> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> 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
>
> *****
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> *****
>
> 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:
>
> *****
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> *****
>
> 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:
> >
> 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%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821333002&sdata=1zwM2QnH%2BG%2FZxpFUIyIjAu2cB%2FOR3a3EQs1xjMpfAfw%3D&reserved=0
> > Post images on
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821333002&sdata=%2BFmGOVWZjVg8TKAeHDQYE8m6fBUXw0kv9wJ2zivKpqE%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%2Fref%3Dsr_1_3%3Fcrid%3D3ILUXD0SCQ70Z%26keywords%3Dwd%2B20tb%2Bmy%2Bbook%2Bduo%26qid%3D1574426442%26sprefix%3Dwd%2B20%2Btb%252Caps%252C129%26sr%3D8-3&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821333002&sdata=82rqObMNv1MAOuQMw46Txk7ZXI%2B%2FnUGXizCjzh89OEw%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%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821342994&sdata=vGYVviElhyn989IOKopV0pxFmgergEsCPkEiVMtC4aw%3D&reserved=0
> > > Post images on
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821342994&sdata=xx1yWO%2FXv7JOXdqaVIyzwUnwdoAU6F4YwRckbQl6XDo%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)
>
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>
>
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