IceBear integrates with the ISPyB system at some synchrotrons to submit your shipment data automatically. The only thing you have to type is your synchrotron username and password.
The shipment page not only lets you assemble and send the shipment, but also gives you a convenient place to record notes during data collection and to manage the returned containers.
To create a shipment, select New shipment from the main menu.
You can also create a shipment from the Crystal Fishing page. Once you have fished your crystals and packaged them into dewars, click the "Ship this dewar" or "Ship these dewars" link in the bottom right of the page.
You will see the shipment creation form.
Give the shipment a name, and set the destination synchrotron, then click Create.
Typically, you will need to be in the Shippers or Administrators usergroup to create and send shipments.
The shipment view contains a details tab, plus one tab for every dewar in the shipment. If you created the shipment from the Crystal Fishing page, you will see your dewars here immediately after creating the shipment.
Click in the "Scan a barcode" box and scan your dewar barcode. (IceBear works best if your barcode scanner is configured to send Enter after a successful scan. See your scanner's user manual for details.) If it doesn't have a barcode, type a name (which must be unique within the shipment) and press Enter.
Your dewar will appear as a new tab. Click the tab to view and edit the dewar contents.
Scan a puck barcode into the Add a puck box at the top of the tab to add a puck to this dewar. If IceBear knows about the contents of the puck, these will be shown.
Scan a pin barcode into the box at the relevant puck position. The contents of the pin will appear in the table.
You can move a pin to a different puck position. Simply scan or type its barcode into the new position. The pin will be removed from the old position and put into the new position.
Click the X beside a pin's barcode to remove it from the shipment. This does not unlink the crystal from the pin, so you can put the pin into a storage dewar and scan it into a later shipment.
Click the Remove puck button to remove a puck from the dewar and the shipment. IceBear remembers the contents of the puck, so you can add the whole puck to a later shipment.
Click the Remove dewar button to remove a dewar from the shipment. As with pucks, IceBear remembers the contents of the dewar, so you can easily add the dewar to a later shipment.
IceBear will attempt to submit the shipment automatically where this is possible, but you must be aware of the synchrotron's requirements. For example, in ISPyB systems it's typical that each sample must be identified by a "protein acronym" that is already defined in the proposal and approved by the synchrotron. If any samples in the shipment don't have a protein acronym, or have one that isn't on the proposal, the shipment will not submit.
When you are happy with the contents of the shipment, click the Send shipment... button on the Shipment tab to begin.
From here, the process varies slightly depending on where you are sending the shipment.
For synchrotrons where IceBear can't submit the data automatically, the shipment status is simply updated; you will need to submit the shipment data to the synchrotron yourself.
Where IceBear can submit the data, there are some variations, but typically the process will look something like this (submitting to Diamond Light Source):
Provide your synchrotron username and password. This is needed to authenticate you at the synchrotron. IceBear does not store your credentials.
After authenticating, you will see all the proposals to which you have access. Click to open the right proposal. You will see a list of sessions (or visits) on that proposal. Click "Use this visit" to select the session.
Next choose the lab contact for this shipment. Note that the lab contact must already be defined in the synchrotron's ISPyB system.
Next choose the safety level for this shipment.
Finally, review the shipment details. When you are happy, click Send shipment to submit the details to the synchrotron. Click OK to confirm.
You will see the shipment being submitted to the synchrotron, hopefully without errors. If there are errors, you will need to fix these before re-submitting.
After submitting the data, you will need to arrange for the dewars to be collected by the courier.
The shipping page now has a link to the shipment record in the synchrotron's systems. Click this link to be taken to the synchrotron's shipment record, where you can arrange for dewar collection and print labels, etc.
Once the shipment has been submitted, there is a new Data collection tab on the shipping page:
The Data collection tab lets you take notes, and decide whether to wash the pin on return or retain the crystal for a later shipment.
There is a large button for each puck. As the puck is loaded onto the sample changer, click its button to open a set of tabs, one for each position in the puck.
You can type notes, which will be attached to the crystal. The "Quick notes" buttons let you add commonly-written notes with a single click.
Select "Wash the pin" or "Keep the crystal" as appropriate.
Click Save. IceBear will automatically advance to the next tab, so you can make notes on the next pin. Tabs for pins where you have already made notes will be highlighted with a green checkmark, as will completed pucks.
If you prefer to make hand-written notes and transcribe them later, you might find IceBear's printable shipment manifest helpful. It has space to write notes for every sample in the shipment. A link to this can be found on the Shipment tab. Note that the Data collection tab will disappear when the shipment is marked Returned, so don't wait too long to transcribe your notes. You can always add notes to the individual crystals, but the Data collection tab puts all those notes boxes in the same place.
When your dewars come back to the lab, you'll need to unpack them, wash some pins, put others into storage... and tell IceBear what you did, so the pins, pucks, and dewars are correct for next time.
On the Shipment tab, click Return shipment to begin. The Data collection tab will be replaced with a Shipment return tab:
Each dewar in the shipment is shown as a heading bar, along with the number of pucks remaining inside it. Click on the dewar to open it and see the pucks inside.
Each dewar in the puck is shown as a heading bar, with a summary of the actions needed on the pins inside it. These are "Keep crystal", "Wash pin", or in the case where the pin owner has not specified an action, "Check with owner".
Click the puck header to see a list of all puck positions, along with the pins in them.
For each pin, you will see its barcode, crystal name, protein, and what the pin owner wants to happen to it ("Keep crystal" or "Wash pin"). If the pin owner did not make a choice, "Check with owner" is shown.
Clicking Keep crystal will remove the pin from the puck, but will keep the association between pin and crystal. You can then add the crystal to a future shipment by scanning the pin barcode. "Keep crystal" is not available if a non-barcoded pin was used.
Clicking Wash pin will remove the pin from the puck, and will break the association between pin and crystal. In the case of a barcoded pin, this makes it available for use with another crystal in a future shipment.
Click the Remove puck from dewar button on the puck header to remove it from the dewar and make it available for future shipments.
Note that removing the puck does not empty the pins from inside it! IceBear will assume that you are putting the whole puck back into a storage dewar with all its pins and crystals still inside. If this isn't what you're doing, remove the pins from the puck first.