ynic-users

ynic-users@ynic.york.ac.uk

1 participants
2786 discussions

Stimuli scripts after YNiC systems upgrade
by Richard Aveyard 21 Sep '23

21 Sep '23

Hi All, I am writing to remind everyone that, following our recent operating system upgrade,* it is important to check that your stimuli scripts are running as intended before resuming scanning*. There are testing PCs available in YNiC for this purpose, and in many cases we can help to resolve issues you might have difficulties with. *Psychopy users* Our testing has highlighted that *some psychopy scripts will be susceptible to inaccurate timing* issues with the new psychopy version (2023.2.0). We now strongly recommend that when initialising your visual window you set waitBlanking=False, or that you ensure your script runs at 120 Hz, and the monitor is adjusted accordingly using the Applications>>Settings>>Display menu. In addition, the event.getkeys() function is deprecated, an example update to fix this can be found here: https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html#psychopy Please remember that it is your responsibility to thoroughly test your stimuli scripts and ensure that everything is working as intended. Cheers, Rich -- Dr Richard Aveyard Senior Technical Specialist York NeuroImaging Centre University of York, UK

1 0

This Week at YNiC
by Jennifer Ashton 20 Sep '23

20 Sep '23

Hello, Please find details about Open Plan availability and the next inductions and training sessions. *Open Plan Availability* MSc inductions will be taking place at YNiC this *Friday (22nd of September) 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Friday the 13th of October, at 13:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Friday the 20th of October, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

1 0

Important information for everyone using YNIC
by Fiona McNab 15 Sep '23

15 Sep '23

Dear All, As you know, most of the imaging data we collect at YNIC is potentially biometric. As well as making sure we have appropriate consent from participants, we have to abide by certain legislative requirements relating to collecting, storing and sharing personal data. We've put in place some procedures to make things easier. What you need to know is summarised below and there's a diagram attached (it contains the same information but with boxes and arrows!) Any questions, please ask. Please also be aware that we have a new page for YNIC forms <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>, where you will find new versions of the participant information sheet and study-specific consent form (we're now on version 9 for both). Best wishes, Fiona and Andre *Collecting data at YNIC and keeping it at YNIC* - Before submitting your ethics application, you need to check whether your study needs a separate *Data Protection Impact Assessment (DPIA)*, or whether it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> (found on the new YNIC forms webpage <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>). If it is not covered by DPIA_183 v2, there's a DPIA screening tool here <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> . - If it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>, make sure you follow the procedures outlined in that document. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Bringing into YNIC data that were collected elsewhere* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - If there are any agreements to sign, you will need to get HOD approval before signing. *Transferring data collected at YNIC to external collaborators* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - You will also need an external collaborator agreement. We have had one approved already. Andre can provide a template and let you know the procedure for obtaining approval from the HOD and the contracts office. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Transferring data collected at YNIC to former staff or students* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. (It's the same template as used for sharing data with external collaborators). - You will also need a data sharing agreement. This is not the same as the one used for external collaborators. We'll have a template soon, which Andre will be able to provide. The procedure for obtaining approval from the HOD and the contracts office will be the same. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Making data collected at YNIC publicly available* (many thanks to Angela for this) - Make sure that this is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> and you abide by the procedures outlined in that document. This includes making sure you use version 9 of the information sheet <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>and version 9 of the consent form <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>. There is a guidance document here <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/Open_Data_Sharin…> . - If it is not covered by DPIA_183 v2, you will need to complete and submit your own DPIA <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> .

1 0

This Week at YNiC
by Jennifer Ashton 13 Sep '23

13 Sep '23

Hello, Please find details about Open Plan availability, the next inductions and training sessions and an upcoming workshop. *Open Plan Availability* MSc inductions will be taking place at YNiC on *Friday the 22nd of September, 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Thursday the 21st of September, at 10:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Tuesday the 19th of September, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. *Upcoming Workshops* The first *Environmental Impacts of Computing in Health & Life Sciences Research workshop <https://www.eicworkshop.info/> *will be taking place on November 7th in London, and online. This will be a great opportunity to learn about the carbon footprint of high-performance computing, in neuroimaging research and beyond. Find more information on the workshop website <https://www.eicworkshop.info/>, and register for attendance here <https://www.tickettailor.com/events/universityofsussex/986909>. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

1 0

YNiC Cluster: now available
by Joe Lyons 13 Sep '23

13 Sep '23

Good Morning The cluster is now back up and online. The upgrade has now been completed. There are a few small changes to some software packages so please check the upgrade notes wiki page if you have any queries. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html Any other issues not covered in the wiki page, please email support(a)ynic.york.ac.uk. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

1 0

Update: Remote Desktops are now up
by Joe Lyons 11 Sep '23

11 Sep '23

The remote desktops are now stable. We're still waiting on a few jobs running on the cluster before it's available for use. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

1 0

Update: YNiC partially open after systems maintenance
by Joe Lyons 11 Sep '23

11 Sep '23

Good Morning. We're still having some issues from the upgrade last week. The desktops in Openplan are up and running. The cluster is currently down as we're debugging an issue with the new OS. The remote desktops are also down as we're seeing problems with some of the nodes. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

1 0

Reminder: YNiC Closed for systems maintenance
by Joe Lyons 05 Sep '23

05 Sep '23

YNiC is closed for the week while we perform some essential systems maintenance. All remote desktops and cluster services will be down. We'll update you once services are back up and running. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

1 0

Test your stimuli on new PC in YNiC
by Rebecca Lowndes 30 Aug '23

30 Aug '23

Hi all Just reminding you all that there is a new stim PC with new software available in OpenPlan to test scripts/stimuli. All the desktops will move over to this software when we are closed next week Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

1 0

YNiC Desktop Upgrades
by Joe Lyons 23 Aug '23

23 Aug '23

Hello As mentioned in the "This Week at YNiC" email, we'll be doing our annual software upgrades on the YNiC desktops w/c 4th September. The centre will be closed while we undertake the upgrades. A wiki page has been setup with details of the changes. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html A desktop with the new software is available in OpenPlan to test scripts/stimuli. Please email support if you have any questions. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

1 0

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users