IT infrastructure
Locked
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com 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. |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com 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://www.amazon.com/Cloud-Ultra-Network-Attached-Storage/dp/B07179ZYH2/ref=sr_1_3?crid=3ILUXD0SCQ70Z&keywords=wd+20tb+my+book+duo&qid=1574426442&sprefix=wd+20+tb%2Caps%2C129&sr=8-3>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: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com 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. |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com 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: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com 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://www.amazon.com/Cloud-Ultra-Network-Attached-Storage/dp/B07179ZYH2/ref=sr_1_3?crid=3ILUXD0SCQ70Z&keywords=wd+20tb+my+book+duo&qid=1574426442&sprefix=wd+20+tb%2Caps%2C129&sr=8-3>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: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com 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://namsmicroscopy.com/ 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. |
|
|
In reply to this post by VERMEREN Matthieu
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Matthieu We are lucky enough to benefit from a new infrastructure that the university recently set up. This is a central server in the basement of our building (mirrored on the second campus) which is expandable to zetabytes I was told, and can be expanded in increments of 10TB plug and play modules added when needed. Our microscopes are directly connected to the server via a 1Gb/sec fiber. That is Gbit/sec, not GB which is GByte and is 8 times more. So 10 Gb/sec transfers around 120 MBytes/sec. This will likely be upgraded to 10 Gb/sec switch (which will allow us to transfer over 1.2GB/sec). The data is acquired locally on the microscope computer. Our users must transfer all their data to the server and empty the local drive before they turn off the system. Any data found on the local drive is immediately deleted. On top of that, we have a Virtual Desktop Infrastructure (VDI) consisting of 2 powerful Remote Desktop Servers machines (256GB RAM, 2 Graphic cards with 16 GB RAM each) that are maintained by the university and are locate in the server room. These are also expandable/upgradable and we are not in charge of them so we only enjoy using them! :D These machines as well as the server are accessible remotely via a software called VMWare. This allows us to log in to the VDI from any computer (even a mobile phone). Logging to the VDI creates a virtual Windows desktop on which we have Fiji, Cell Profiler, Imaris, NIS elements, Matlab... Several users can log to each RDS at the same time. They share the resources. Having an infrastructure that is maintained centrally has simply changed our (my) microscopy life! :) 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 Follow our microscopy blog! -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of VERMEREN Matthieu Sent: 22 November 2019 12:43 To: [hidden email] Subject: IT infrastructure ***** 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%7C06e3f01041d94c3cbeb708d76f4675af%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100220759179895&sdata=rAmtch7Fqfe%2BZJ1GukSwF9M%2B%2F3JMBmVmQWRrlo5XwlE%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%7C06e3f01041d94c3cbeb708d76f4675af%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100220759179895&sdata=Z9y8IesHqse6PY93QOh4%2Fmt5PAUXcoKklNYsqH258o8%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. När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
|
|
In reply to this post by Gary Laevsky
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com 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://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406551897&sdata=Ui58BD9VsUq9f219WyuDqNGJMCaW%2B4D%2BUgqB%2FVFPTmk%3D&reserved=0 Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406551897&sdata=0HxMKe7jQ0AHoGhVeALA9L0Dq5ZNuFylvz0NSQZrlto%3D&reserved=0 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: > https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406551897&sdata=Ui58BD9VsUq9f219WyuDqNGJMCaW%2B4D%2BUgqB%2FVFPTmk%3D&reserved=0 > Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406551897&sdata=0HxMKe7jQ0AHoGhVeALA9L0Dq5ZNuFylvz0NSQZrlto%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://nam05.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%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406551897&sdata=gyNiT3wyYWNHkHBVM2ycpqcq%2FNSMscMoDGuBwKzB738%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://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406561897&sdata=8tTNITwteT1C9JBM6%2FhdVYhH21VbrtmH68RpHgoIADk%3D&reserved=0 > > Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406561897&sdata=ReyneAM52XTqxVrkVI2QpZfMCAC7z3YXj5PbuNRFxJM%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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnamsmicroscopy.com%2F&data=02%7C01%7Ctnf8%40PITT.EDU%7Ced2724d9240449c1994c08d76f518ed0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637100268406561897&sdata=u3k3zxX7jGw4uCtHfiJd1sJWYsqdKrjFWJeJeqSiY6k%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. |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy 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 Follow our microscopy blog! -----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: 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. ***** 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%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, 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) https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnamsmicroscopy.com%2F&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821342994&sdata=xSlx6AxMMoHUEqLLM%2Fex2nR7kh2dHDnwdjnH1AUexOI%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. När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** 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 *Announcing:* *17th Annual Advanced Imaging Methods Workshop <https://crl.berkeley.edu/molecular-imaging-center/meetings-and-short-courses/advanced-imaging-methods-workshop-2020/>* *January 29 - 31, 2020* *Register Now: **https://aim2020.eventbrite.com* <https://aim2020.eventbrite.com> *Holly L. Aaron, **Director* *CRL Molecular Imaging Center* *251 Life Sciences Addition #2751* *Berkeley, CA 94720* http://imaging.berkeley.edu *[hidden email]* <[hidden email]> *Also:* *306 Barker Hall* *Berkeley, CA 94720* *Click here if you want to use the MIC microscopes <http://crl.berkeley.edu/molecular-imaging-center/faq-training-mic/>* Follow the MIC on Twitter <https://twitter.com/BerkeleyMIC> Follow OpenMIC on Twitter <https://twitter.com/OpenMICBerkeley> *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! * On Fri, Nov 22, 2019 at 8:13 AM Sylvie Le Guyader <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > 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 > Follow our microscopy blog! > > -----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: > > 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. > ***** > > 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%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, > > 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) > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnamsmicroscopy.com%2F&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C72b07d3b21974b1c317a08d76f653775%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637100352821342994&sdata=xSlx6AxMMoHUEqLLM%2Fex2nR7kh2dHDnwdjnH1AUexOI%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. > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI > kommer att behandla dina personuppgifter. Här finns information om hur KI > behandlar personuppgifter< > https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data. You can read more about KI’s processing of personal > data here<https://ki.se/en/staff/data-protection-policy>. > |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Aaron 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. :) 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 Follow our microscopy blog! -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Holly L. AARON Sent: 05 December 2019 02:25 To: [hidden email] Subject: Re: IT infrastructure ***** 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%7C637111061787400209&sdata=xkDg71oFayw3KWYHzIzEAH1nGgYdr%2Fd7g4OQ02vEvRc%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%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=ZbSb0708Cg5BCRI0sq4ACf%2BMCtGopOyV2%2FKuJwGqWj8%3D&reserved=0 and include the link in your posting. ***** 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 *Announcing:* *17th Annual Advanced Imaging Methods Workshop <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcrl.berkeley.edu%2Fmolecular-imaging-center%2Fmeetings-and-short-courses%2Fadvanced-imaging-methods-workshop-2020%2F&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=Z1qKunzHjbXTRUcG5E%2FbrOVZskPaD1Eeic1BX6%2FQ%2FGQ%3D&reserved=0>* *January 29 - 31, 2020* *Register Now: **https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Faim2020.eventbrite.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=VBhtpBxt2oaIqgLyy%2FjgsjbAaw8927fD7MNb1g4puwk%3D&reserved=0* <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Faim2020.eventbrite.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=VBhtpBxt2oaIqgLyy%2FjgsjbAaw8927fD7MNb1g4puwk%3D&reserved=0> *Holly L. Aaron, **Director* *CRL Molecular Imaging Center* *251 Life Sciences Addition #2751* *Berkeley, CA 94720* https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimaging.berkeley.edu&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=fK4uquLZE92V%2F4TCp5mbM%2BXUSKsJm04UwMRj5Pi22qA%3D&reserved=0 *[hidden email]* <[hidden email]> *Also:* *306 Barker Hall* *Berkeley, CA 94720* *Click here if you want to use the MIC microscopes <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcrl.berkeley.edu%2Fmolecular-imaging-center%2Ffaq-training-mic%2F&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=LRYOeDqFFcmEC9nYoTi9PpaLheCubfZ9p5mZXCcER8E%3D&reserved=0>* Follow the MIC on Twitter <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FBerkeleyMIC&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=DSFPA1iop5HBc%2BAAI%2BQucz3Fk46%2BgqXy8LfbiEAyVGY%3D&reserved=0> Follow OpenMIC on Twitter <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FOpenMICBerkeley&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=1GtiX5IxUfu5IiKdPtASU5MM7l5snvo%2Fr45lmFI0%2FOw%3D&reserved=0> *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! * On Fri, Nov 22, 2019 at 8:13 AM Sylvie Le Guyader <[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%7Cs > ylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1 > cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=xkDg71 > oFayw3KWYHzIzEAH1nGgYdr%2Fd7g4OQ02vEvRc%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%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=ZbSb0708Cg5BCRI0sq4ACf%2BMCtGopOyV2%2FKuJwGqWj8%3D&reserved=0 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 > Follow our microscopy blog! > > -----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: > > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists > .umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Cs > ylvie.le.guyader%40KI.SE%7C3df0af341cbf4a50b49508d7792296a6%7Cbff7eef1 > cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111061787400209&sdata=xkDg71 > oFayw3KWYHzIzEAH1nGgYdr%2Fd7g4OQ02vEvRc%3D&reserved=0 > Post images on > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > mgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a > 50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111 > 061787410149&sdata=vxNUs%2FA9xL4yX8dj%2B0cVjLBAmx3F7dwbf1LgMHTJExM > %3D&reserved=0 > 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 > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > mgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a > 50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111 > 061787410149&sdata=vxNUs%2FA9xL4yX8dj%2B0cVjLBAmx3F7dwbf1LgMHTJExM > %3D&reserved=0 > 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: > > > 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 > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > mgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a > 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 > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > mgur.com&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C3df0af341cbf4a > 50b49508d7792296a6%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637111 > 061787410149&sdata=vxNUs%2FA9xL4yX8dj%2B0cVjLBAmx3F7dwbf1LgMHTJExM > %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. > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta > att KI kommer att behandla dina personuppgifter. Här finns information > om hur KI behandlar personuppgifter< > https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI > processing your personal data. You can read more about KI’s processing > of personal data here<https://ki.se/en/staff/data-protection-policy>. > |
«
Return to Confocal Microscopy List
|
1 view|%1 views
| Free forum by Nabble | Edit this page |