eBIC User Guide

What are facilities like at eBIC?

eBIC is housed in a modern, purpose built facility, with microscopes located on the ground floor, with the exception of Titan Krios 1 which is a short walk away in Diamond's synchrotron building.

Samples are clipped in the laboratory space on the ground floor and loaded onto microscopes, then data collection is managed remotely from the control room (located on the 1st floor of the I14 building).

eBIC users who visit site have use of break-out areas and a kitchen (with tea, coffee, water cooler, and the use of a fridge and microwave). A short stroll across the road is the on-site restaurant, where meals and snacks can be purchased.

Accommodation for eBIC visitors is normally booked at the on-site guest house, which is within easy walking distance of the eBIC facility. The Diamond User Office organise accommodation bookings for rooms, with breakfast included. More information is available at Experiment at Diamond.

What needs to be organised ahead of microscope sessions?

Before commencing a session eBIC users need to be aware of and take these actions:

• good quality samples are required for the first day of a session
  (more information on grids and samples)

• register samples and ship the dewar to eBIC using Diamond systems
  SCAUP sample shipping (specifically for cryo-EM workflows at eBIC)
  ISPyB sample shipping

• eBIC recommend users consider the imaging conditions and detector
  they wish to use, prior to visiting

• users are welcome to contact eBIC staff with specific questions prior to the visit

• liaise with the Diamond User Office to make arrangements for visiting eBIC

Information to be aware of:

• BAG Krios sessions may be longer than 48-hours
  eBIC recommends no more than 4 grids are loaded per 48-hour session
  the maximum number of grids which can be loaded at once is 11 grids

• all samples will be loaded on the first day of a BAG Krios session
  a second load maybe possible for sessions which are longer than 4-days

• guidance instructions for user sessions are available:
  User guide instructions

Note: cryoFIB sessions run differently - for more details contact: james.gilchrist@diamond.ac.uk

Information to be aware of:

• rapid proposals will be reviewed and allocated session time as soon as practically possible
   
• please email eBIC to let us know when a rapid proposal has been submitted (ebicadmin@diamond.ac.uk or eBIC PBS)
   
• eBIC expect to have reviewed rapid proposals within 4 - 6 weeks of submission
   
• typically a session will be allocated within 90-days
   
• rapid proposals are usually 48-hours
   
• successful rapid proposals are allocated a 48-hour slot during weekdays and either
  48 or 72-hour slots at weekends starting on Fridays
   
• rapid proposals are only scheduled during Diamond run time of which 10% is dedicated to rapid sessions
   
• please see machine operation calendar for run dates:
  Quick Links - Operations Calendar
   
• guides for user sessions are available:
  User guide instructions

Note: cryoFIB sessions run differently - for more details contact:
james.gilchrist@diamond.ac.uk

Remote visits (Krios sessions)

Users will be contacted by local contacts prior to the start of a session, asking for data collection parameters. On the day of the session, users should check they can log on remotely after 09:00 am (UK) and be ready to take over control of the microscope around 11:00 am (UK). More information on essential user actions and advice is available here: Remote Sessions 

Onsite visits (Krios sessions)

Local contacts will meet users at the I14 entrance and take them to the control room. Local contacts will then load samples and set up the microscope with the aim that users can take control of the microscope at around 11:00 am. More information on essential user actions and data collection set up is available here: On-site sessions

Users are expected to provide samples suitable for continuous automated data collection and have enough samples to actively use the whoe of the allocated time.
 

Note: cryoFIB sessions run differently - for more details contact: 
james.gilchrist@diamond.ac.uk

What needs to be organised after microscope sessions?

eBIC users organise the return of dewars to their home institute by completing a Diamond dewar dispatch form. Dewars can be sent using Diamond's shipping agents. Diamond pay for sample shipping for UK users using Diamond shipping agents, 2 dewars per shift. Follow this link for details about returning a dewar.

Experimental report

Diamond require users to promptly submit an experimental report through the User Administration System UAS upon returning to the home establishment. Follow this link for more details on the experimental report.

Users publishing work containing data from eBIC should ensure to:
 

More information on publishing work is available here:
Publications acknowledgement
After you Leave - publications

How is data stored?

eBIC users need to be aware of the following:

• all raw data are permanently archived by Diamond to tape media - but data remains accessible on spinning disk for 40-days

• HDD backup support has been phased out - users should copy their data via high bandwidth file tansfer systems such as Globus or SFTP 
  Remote access and analysis: User guide

• Data backup - eBIC users are responsible for backing up data to transfer to local systems and provide long term data storage 
  Diamond data back up

Who is responsible for monitoring an ongoing data collection?

Responsibility resides with the user for monitoring an ongoing data collection session - instructions on how to monitor can be found here: Remote access and analysis: User guide

What if there is a problem with ongoing data collection?

If a user observes an issue with ongoing data collection, eBIC request that the user informs the Experimental Hall Coordinators (EHC) on +44 (0) 1235 778787.
The EHC will communicate the issue to a local contact as required.