User Guide

New users need to contact the Diamond User Office to request access to the User Administration System (UAS). After registration you will be issued with a Fed ID and password for access to all Diamond IT systems.

Everyone who wants access to Diamond, on-site or remotely, needs to be registered in the User Administration System (UAS). Each user only needs to register once. If you have used Diamond previously but since changed your affiliation (place of work), you will need to register again.

Please email the Diamond User Office (useroffice@diamond.ac.uk) to register a new user in the UAS.  You will need to provide the following details:

• Title
• Family Name
• Given Name
• Date of birth (dd/mm/yyyy)
• Organisation
• Address
• Telephone
• E-mail 

Following registration, you will be issued with a Fed ID and password. Make sure you keep a note of these as you will need them to access all IT systems at Diamond.

 To enter any Diamond facility, you need to have completed an online safety introduction and test.

You can log in to the UAS (http://uas.diamond.ac.uk) using your Fed ID and password.

Under the “Home” tab there is a box entitled “Diamond Safety Test”. You will need to click on this button to watch a safety video. You will then need to follow the links to complete an online test. Only once you have passed the safety test will you be able to participate in on-site experiments at Diamond.

This is a requirement for on-site visits only.

 Registered users need to be added as investigators to a new proposal in the UAS. Experimental risk assessments (ERAs) for samples need to be submitted and validated before shipping them to Diamond.

1. Log in to the UAS (http://uas.diamond.ac.uk) with your Fed ID and password. If you have signed a new contract with Diamond or have recently renewed your existing contract, you will find your new proposal number in the UAS.
    
2. A Principal Investigator (PI) will be added to the proposal when it is created. The PI is responsible for adding additional investigators to the proposal in the UAS. Go to the proposal “Investigators” tab and click “Add investigator”. An investigator whose role is defined as Alternate Contact (AP) can also edit the proposal and add investigators.
   Further information
    
3. You will need to prepare and submit an Experimental Risk Assessment (ERA) for each sample and experimental method used at Diamond. This can be done in the “ERA” section of your proposal in the UAS. It is the responsibility of the PI to ensure that each ERA is fully and accurately completed at least 2-3 weeks prior to the planned experiment, and is validated by Diamond’s Safety Health and Environment (SHE) group before shipping samples to Diamond.

Further information
 

4. If you plan to continue working on samples with ERAs that have already been submitted and validated within a previous proposal, you can copy these into your new proposal. To do this, go to “ERA/Samples” and select “Copy Samples from a previous Proposal”. You can also copy the Experimental Methods from the previous proposal - for this, go to “ERA/Experimental Methods” and select “Copy Experimental Methods from a previous Proposal”. 

 When an experimental session (visit) has been created, investigators and validated sample ERAs need to be added to the session in the UAS.

1. Log in to the UAS (http://uas.diamond.ac.uk) using your Fed ID and password. Once a new session (visit) has been created you can access it under the “Sessions” tab in your current proposal.

2. The PI or AC needs to add all investigators that require access to the session. To do this, go to the session, and under the“Investigators” tab click “Add investigator”. Select an appropriate team role for the added investigator. Investigators with “leader” and “member” roles refer to those people taking an active part in the experiment, either on-site or remotely. Make sure to tick the “remote” box for remote access. Investigators with “data access only” roles refer to those people not taking an active part in the experiment but who will have access to the data collected. For mail-in sessions, please add all members of the Industrial Liaison MX Team, along with your group, as remote investigators, assigning them “data access only” roles. When all investigators have been added, click “Submit Investigators”. For on-site visits, you can only submit investigators when all investigators listed as on-site users have passed their safety tests.

3. Your already validated sample and experimental method ERAs for this session now need to be added. To do this, go to the session “ERA” tab and select “Samples” or “Experimental methods”. The relevant ERAs can be added from your proposal using the “Add from proposal” or “Add all from proposal” buttons. You also need to indicate whether you require lab access for your session. This is done by selecting an option from the drop-down menu under “Lab access”. If you have specific needs for lab access, please contact the Industrial Liaison MX Team. When all relevant ERAs have been added you should click “Submit session ERA”. 

 
Prepare and mount samples using Diamond compatible pins and containers (pucks)

Samples sent for cryo experiments at Diamond must be mounted on SPINE standard pins placed in Unipucks and shipped in a Shelved Puck Shipping Cane, or a supported crystallisation plate type for in-situ experiments. This is to ensure compatibility with the sample changers on Diamond MX beamlines. Samples in other types of pins, pucks or crystallisation plates cannot be used for data collection.

Further information
 

If you have special requirements for sample holders or shipping containers, please discuss these with the Industrial Liaison MX Team before shipping.

All shipment and sample information needs to be added in ISPyB before
shipping your samples to Diamond.

Diamond uses the Information System for Protein Crystallography Beamlines (ISPyB) to manage sample information, experimental data, and shipments. You can log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password.

1. If you have signed a new contract with Diamond or have recently renewed your existing contract and been issued with a new proposal number, you will need to add your lab contact information into ISPyB. To add a new lab contact, go to “Lab Contacts” in the proposal drop-down menu, and click “Add Home Lab Contacts”. Lab contacts can also be migrated from an old proposal using the “Migrate” page, also accessed from the proposal drop-down menu.
   
   Further information

2. The next step is to register your dewars and containers (pucks) to your proposal. This step needs to be done only once for each dewar or container. Please contact the Industrial Liaison MX Team to register new dewars and containers, or to migrate existing ones from an old proposal. You will need to provide a list of container codes (printed on the container) and dewar facility codes (printed on the Diamond barcode sticker attached to your dewar). If your dewar does not have a Diamond barcode sticker you will need to request one.

3. You can now create a new shipment and complete the necessary shipment details. Go to “Shipments” in the proposal drop-down menu and click “Add Shipment”. On the new shipment page, you will need to name the shipment, select the dewar facility code of the dewar you are sending, and tick the relevant box in the “First experiment / Scheduling” field.

• If you are shipping for a remote or mail-in visit, tick the box for “Responsive Remote / Mail-in”, then complete the required shipment information. When shipping for a remote or mail-in visit you will also need to complete a brief questionnaire in the “Comments” field providing further information. This information will be used for scheduling and adjusted as appropriate to maximise use of the limited beamtime available.

• If you are shipping for a UDC visit, tick the box for “Automated / Imager”, then complete the required shipment information. Please note that for UDC visits additional information is required for the data collection parameters in the container sample information, described below.
  
  Please note that a shipment can only contain samples for either a remote, mail-in or UDC visit. We cannot currently accept samples for different access modes within the same shipment.
  
  Further information

4. You can now add your containers (pucks), with sample information, to your shipment. To add a container, go to your new shipment page and click "Add Container”. On the “Add New Container” page you will need to specify the container type and select a “Registered Container” from the drop-down menu. Please make sure that the “Container Name” matches the registered container code exactly, as differing container names could cause issues with the automatic assignment in the beamline sample changer.
   
   Further information

• If you are shipping samples for a remote or mail-in visit, complete the sample information for each location in the container. The “Protein Acronym” is selected from a drop-down menu that only contains samples with a validated ERA. If the protein acronym is missing, you need to go back to the UAS and make sure the sample ERA for this protein has been validated. A unique “Sample Name” is required for each sample. For mail-in visits the “Comments” field can be used for data collection parameters.

• If you are shipping for a UDC visit, click the button to queue the puck for “Automated Collection”, and complete the sample information for each location in the container. Please note that for UDC visits additional sample information is required for the data collection parameters under the “Unattended (UDC)” tab.
  
  Further information

An alternative to manually creating shipments and adding sample information is to assemble all the information in a csv file and use a Diamond script to upload the data to ISPyB. This is particularly useful if you are shipping a lot of samples and want to save on the time it would take to manually add these in ISPyB.

Further information

Print your Diamond shipment labels, attach these to your dewars and shipment containers,
and arrange the shipment with your courier.

Please note that all shipment and sample information must be added into ISPyB before shipping samples to Diamond. This is to ensure that samples without validated ERAs are not delivered to Diamond, since handling these would be in breach of our safety protocols. Dewars delivered to Diamond with no sample information will not be handled until the information is complete.

1. When your shipment has been created, and all sample information has been added, you must then print the Diamond shipment labels to enable our internal tracking to take place. These can be printed by clicking “Print Shipment Labels” at the top of the new shipment page in ISPyB. Please follow the label instructions on the first page of the ‘shipment labels for attachment to the dewar and shipment case’.

2. You can now arrange the shipment with your courier. The exact procedures for shipment and document requirements depend on your courier and country of origin. Please read the shipping instructions on the Diamond webpage carefully and select the shipment procedures relevant to you.

Further information

Please note that all samples must be shipped to site by a courier service. We cannot accept samples delivered by users in person. When arranging the shipment, please bear in mind that only samples for remote/mail-in visits which arrive by the end of Thursday/Friday morning at the latest will be considered for inclusion in the schedule for the following week. Diamond Goods Handling is open Monday to Thursday 8am - 4pm, and Friday 8am - 3pm, to receive shipments. 

To ensure long-term data storage, it is your responsibility to back up experimental data after your session.

Depending on the proposal type, your data will be stored in the Diamond file system for a limited amount of time. It is therefore important that you back up your experimental data after your session. The recommended way to back up data is by remote download from the Diamond file system.

Further information

In special circumstances, when a remote backup is not possible (e.g. due to limitations in remote access to Diamond file systems) you can request a backup on a hard drive. Diamond does not recommend the use of hard drives for this purpose as we do not consider them as providing an appropriate level of security for your data. However, if you wish to choose this option, you must inform the Industrial Liaison MX Team in advance and provide a hard drive with sufficient free space in your shipment. The hard drive must be clearly labelled and also registered as an item in your shipment in ISPyB.

After your session, you will need to arrange for the return shipment of your samples with your courier and submit a despatch form to Diamond Goods Handling.

When your experiment is finished, and your dewar has been returned to our storage system, you will receive an automated email notification.

You will then be able to arrange the return shipment of samples with your courier. When the shipment pick-up has been scheduled, you will also need to submit a Dewar despatch form to inform Diamond Goods Handling when they should prepare your dewar for despatch. The despatch form can be accessed through the shipment page in ISPyB or through a link in the email notification.

Further information
 

Please do not arrange the return shipment or submit the despatch form before you are notified that your dewar is back in the storage system.

If your courier is either Fedex or DHL, and you want Diamond Goods Handling to schedule the pick-up with your courier you can indicate this in the comments field of the dewar despatch form. All necessary documents for the return shipments need to be included, and you need to provide your courier account number in the form.

Diamond Goods Handling is open to despatch shipments Monday to Thursday 8am - 4pm and Friday 8am- 3pm.