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). If you have used Diamond previously but since changed your affiliation (place of work), you will need to register again.

 

PLEASE NOTE! Do not register in the UAS yourself. Registration of industrial users is handled by the User Office.

 

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

 

• Title
• Family Name
• Given Name
• Gender
• 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.

 

In order to perform data collection and access collected data, 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.

 

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.

 

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 can also edit the proposal and add investigators. Please see the UAS for a complete list of investigator roles. Further information

 

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, giving enough time for it to be validated by Diamond’s Safety Health and Environment (SHE) group before shipping samples to Diamond. Further information

 

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 a previous proposal - for this, go to “ERA/Experimental Methods” and select “Copy Experimental Methods from a previous Proposal”.

 

 

 

Lab contact information and registration of dewars and containers in ISPyB needs to be done before you can use these for shipments to Diamond

 

Diamond uses the Information System for Protein Crystallography Beamlines (ISPyB) and its web interface SynchWeb 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.

 

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

 

The next step is to register your dewars and containers (pucks) to your proposal. This needs to be done so you can add these to a shipment in ISPyB. 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 (as 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 from the Industrial Liaison MX Team. Further information

 

PLEASE NOTE! Registration of dewars and containers is essential for our internal sample tracking. You cannot send dewars or containers to Diamond if they are not registered in ISPyB.

 

 

 

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. Further information
 

 

PLEASE NOTE! Samples in pins, pucks or crystallisation plates that do not conform to our standards will not be accepted for data collection at Diamond.

 

If you have specific 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) and its web interface SynchWeb to manage sample information, experimental data, and shipments. Log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password.

 

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 facility dewar code of the dewar you are sending (If you do not see your dewar facility code in the drop-down menu, please contact the Industrial Liaison MX Team, and tick the relevant box in the “First experiment / Scheduling” field. Further information

 

• If you are shipping for a remote, on-site or mail-in visit, tick the box for “Responsive Remote / Mail-in”, then complete the required shipment information.

 

• If you are shipping for an Unattended data collection (UDC) visit, tick the box for “Automated / Imager”, then complete the required shipment information.
   

PLEASE NOTE! 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. 

 

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. If you do not see your container in the drop-down menu, please contact the Industrial Liaison Team. Further information.

 

• If you are shipping samples for a remote, on-site 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 time compared to manually adding them in ISPyB. It could also be used to integrate with your laboratory information management system. Further information

 

 

Print your Diamond shipment labels, attach these to your dewar and shipping container,
and arrange the shipment with your courier.

 

PLEASE NOTE! 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 in ISPyB will not be accepted.

 

When your shipment has been created, and all sample information has been added in ISPyB, you must then print the Diamond shipping labels by clicking “Print Shipment Labels” at the top of the new shipment page in ISPyB. Please follow the instructions on the first page of the shipment labels for how to attach them to the dewar and shipment case. The Diamond shipping labels are essential for our internal sample tracking system and if not correctly attached will result in shipment and data collection delays.

 

Please include a printed copy of the return airway bill in the shipment case.

 

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.

 

Shipping Address:

Diamond Light Source
Goods Handling
Synchrotron Zone 8
Harwell Science & Innovation Campus
Didcot
OX11 0DE

 

Specify Diamond contact details as: goodshandling@diamond.ac.uk and +44 1235 395381.

 

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

 

PLEASE NOTE! Samples must be shipped to site by a courier service. We cannot accept samples delivered by users in person.

 

Here are some additional instructions regarding shipments. These are general advice and should be confirmed with your courier.

 

The carriage of Dewars is likely subject to dangerous good provisions. Typically, road and air transport require these declarations: 

 

• Not restricted ADR A346 as per packing instruction 203. 
• Dry shipper - not restricted as per IATA special provision A152. 

 

Shipments from abroad should be arranged under Delivered Duty Paid Incoterms, subject to VAT and duty tax. Please include the printed customs invoice for the return shipment in the shipment case.
 

 

 

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

 

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

 

PLEASE NOTE! This is only required for remote, on-site and mail-in visits. Unattended data collection (UDC) visits are created, and session ERAs submitted automatically, when the samples are loaded on the beamline. 

 

The Principal Investigator or Alternate Contact 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, where data is collected for you, please add all members of the Industrial Liaison MX Team as remote investigators, along with members of your organisation assigned with “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, available under the “Home” tab in UAS..

 

Your already validated sample and experimental method ERAs now need to be added to the session. 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”.

 

 

 

For interactive visits where users will be collecting data themselves, remote users need to connect to the beamline workstation using the software NoMachine. Both remote and on-site users will collect data using Diamonds GDA (Generic Data Acquisition) software. Collected data and results from our autoprocessing pipelines can be monitored in SynchWeb/ISPyB.

 

Prior to a scheduled visit, you should receive an email notification with contact information for your local contact at Diamond. The local contact is your point of contact regarding any questions you may have before or after your visit, or if you need support during your visit. If you need support during a visit scheduled outside our office hours (weekdays 9am – 5pm) you should contact the Experimental Hall Coordinator (EHC) on tel. +44 (0)1235 778787.

 

Remote users need to download and set up the latest version of the software “NoMachine” in order to connect to Diamond and the MX beamline workstations. In order to connect, please use “nx.diamond.ac.uk, port 4000” and your FedID and password. This remote connection can also be used to manually analyse and process data after your visit. Further information

 

PLEASE NOTE! The remote connection should be set up and tested before the scheduled visit to leave enough time to fix any connection issues.

 

You can connect to the beamline workstation shortly before your scheduled visit is about to start (please remember the visit start time will be in UK time). If you have been added as a remote investigator to the session (see previous section Prepare your experimental session in the UAS) the two workstations for the beamline you are scheduled on should be available for you. Connect to “[Beamline] workstation 1” as your first option, but “workstation 2” can also be used if needed. If you want to access your home directory to manually analyse and process data already collected, use the “Automatically select a node” option.

 

Experiments at Diamond are controlled through the software “GDA” (Generic Data Acquisition). Once you have connected to the beamline workstation, start GDA through the icon in the system tray (top right screen corner), or through the link in the “[beamline]_launchers” folder on the Desktop. You can also open a terminal window and use the command “gdaclient” to start GDA.

 

PLEASE NOTE! You need to familiarise yourself with GDA and data collection procedures at Diamond before your visit. Please read the GDA manual and contact the Industrial Liaison MX team to schedule a test visit (a training session for new and returning users) if needed.

 

We recommend that you monitor your data collections, the incoming results from our autoprocessing pipelines, and the beamline webcams in SynchWeb/ISPyB. This should be done in a local browser, and not on the remote beamline workstation, to reduce the data transfer load which might slow down your remote connection. Log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password. Go to “Visits” in the proposal drop-down menu and select your current visit. Webcams can be viewed by clicking the “[Beamline] Webcams & Beamline Status” banner on the top of the page. Further information.

 

 

 

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

 

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

 

PLEASE NOTE! Data collected under IN type of proposal will be deleted 2 weeks after collection.

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 to back up your data on a hard drive. Diamond does not recommend the use of hard drives for this purpose as we do not consider them to provide an appropriate level of security for your data. If you still need to use this backup option, please inform the Industrial Liaison MX Team in advance and provide a hard drive with sufficiently free space in your shipment. The hard drive must be clearly labelled and 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 the storage area, the lab contact listed in ISPyB 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 NOTE! Do not arrange the return shipment or submit the despatch form before you have been notified that your dewar is back in storage.

 

If your courier is either Fedex or DHL, and you want Diamond Goods Handling to schedule the return shipment 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.