Wiki source code of Extended ISPyB (EXI)

Last modified by hakanj on 2025-11-24 09:34

version	line-number	content
10.1	1	{{toc/}}
	2
	3
40.1	4	EXI can be used for creating a shipment to and from P11. After shipment creation, the sample information can be uploaded as a csv-file for synchronization with MXCuBE during beamtime. Note: Even if you are bringing the dewar to DESY yourself, the shipment creation is necessary for the sample information upload.
1.7	5
1.6	6	= Logging in to EXI =
	7
31.1	8	Users with Door credentials can log in to [[EXI>>https://exi.desy.de/exi/mx/#/welcome]] and create shipments for their already scheduled P11 experiments.
2.1	9
37.1	10	* Go to the DESY EXI website ([[https:~~/~~/exi.desy.de/exi/mx/#/welcome>>https://exi.desy.de/exi/mx/#/welcome]] ).
38.1	11	* Log in with your DOOR user portal credentials.
52.4	12	* In Home/Sessions tab, select the period of time for the experiments you'd like to view (Fig. 1). List of your upcoming beamtimes appear. Click on the proposal identifier to specify which proposal you'd like to work with, even if you are only part of one proposal. Please note that if you are not the proposer or co-proposer and the participant list of the beamtime has not been filled in yet by the PI, you might not see the beamtime in Door.
31.21	13	* If your proposal is not listed and you need help, please contact the beamline staff with p11beamline@desy.de
2.4	14
11.2	15	[[image:Proposal.png\|\|height="263" width="600"]]
10.4	16
11.2	17	Figure 1.
10.4	18
3.2	19	= Create a shipment =
	20
52.4	21	In the shipment tab you can manage the shipping addresses and modify the shipping address card. If the tab appears unaccessible (greyed out), you have not specified under which proposal you are working by clicking the proposal number in Session tab (see above). Please do check that the information given in the shipping address cards is correct.
3.2	22
52.4	23	To create a shipment:
	24
18.4	25	* From the Shipment drop down menu, select Shipments and Add new (Fig. 2).
32.1	26	* Fill in the shipment form.
53.2	27	The name** field entry will appear in the list of created shipments and the ID labels. Names easily linking to sessions (e.g. July_2025) are recommended.
33.11	28	The session** dropdown menu connects the shipment to a specific beamtime.
34.1	29	Select from the From** drop down the name of your shipping address card and verify that information in it is correct. This can be seen in Shipment tab/Manage Shipping Addresses.
59.3	30	Add to Comments any additional information e.g. if you will transport the dewar yourself, or the tracking code for already booked transports**.
36.1	31	Specify the return address and Save** the entered information.
50.1	32	If you wish to view or edit the information after saving the form, select List under Shipments** in the Shipment dropdown menu. That will show a list of your shipments in the left side of the window with latest on top (you might need to refresh the page to show the newly created shipment). Clicking on specific shipment in the list will open the shipment information.
35.1	33	* Add the contents of the shipment as explained in the following section
4.2	34
17.1	35	[[image:CreateShipment.png\|\|height="204" width="700"]]
	36
18.3	37	Figure 2.
17.1	38
18.3	39
38.4	40	= Create new samples and provide a sample list =
3.2	41
38.19	42	This section describes the pragmatic and tested order of assigning sample information, following this order of events is recommended. Please note that creating a shipment is necessary to be able to synchronize the sample names from EXI to MXCuBE.
38.4	43
38.20	44	== Creating samples ==
4.2	45
53.3	46	Protein names and acronyms are not carried over from the user portal as listing the sample acronyms is currently not demanded in Door. To create a protein, follow these steps (once you have created the protein it will be available in the future experiments) and repeat for each protein in your shipment:
4.2	47
18.4	48	* Click on Proteins and Crystals in the upper menu bar (Fig. 3).
51.1	49	* Select Add new protein. You can also display the List to check if the protein is already present.
38.30	50	* Enter the protein name and acronym and click Save. Acronym will be used by the software.
38.37	51	* In Proteins and Crystals, List you find all your added proteins (you might need to refresh the page). Here it is also possible to add crystal forms, however, our MXCuBE is currently not able to use this information yet.
4.2	52
18.2	53	[[image:CreateSample.png\|\|height="188" width="700"]]
	54
18.3	55	Figure 3.
18.2	56
18.3	57
6.1	58	== Fill the sample information in a CSV file ==
4.2	59
38.40	60	* After you have added all your proteins to EXI, return to your shipment by selecting List in the Shipment dropdown menu. In the list of your shipments on the left side of the window (you might need to refresh the page to show the newly created shipment) you find your shipments with the most recently created on top. Click on the shipment card you wish to work on, to open the shipment information.
55.2	61	* While it is possible to insert all the information manually (see next chapter), the most pragmatic way is to upload a CSV file, which you can create from an excel-sheet. In EXI you find an example of how the file should be formatted.
59.1	62	* The upload menu is accessed by clicking the Import from CSV button in the shipment card (Fig. 4). You can add multiple parcels, which are usually dewars or dry shippers, they can hold various number of containers (unipucks, if you are shipping something else, please contact the staff) and samples, which are identified after the protein acronyms you gave in the previous section. Note that the protein + sample name should be unique for the shipment. Errors will be marked red and this disables saving. If you run into trouble, please contact the staff.
18.6	63	* After saving the sample list, you can edit the information by going to the shipment page, clicking on the containers and selecting Edit. That will display the sample list for that container. You can also make corrections to the CSV file, then delete the parcel by clicking on the “Edit” icon to the right of the parcel pane and clicking on Remove, and finally reload the corrected CSV again.
59.4	64	* You can also view the filled up parcel in the shipment page. Once the shipment is complete and you are ready to ship, use the icon to the right to print the shipping labels. Pressing the button next 'Send shipment to the facility' notifies the beamline staff by email about incoming shipment. Please note, that you still have to order the courier yourself. The tracking code can be added e.g. to the comments field in EXI.
4.2	65
22.1	66	[[image:FillSamples.png\|\|height="287" width="700"]]
4.2	67
22.2	68	(% class="wikigeneratedid" %)
	69	Figure 4.
	70
	71
52.1	72	== Fill the sample information manually online (without csv-file) ==
4.2	73
42.2	74	* To add containers and sample information go back to your shipment by selecting List in the Shipment dropdown menu. That will show a list of your shipments in the left side of the window in inverse order of creation (you might need to refresh the page to show the newly created shipment). Click on the shipment card to open the shipment information.
22.2	75	* Click the Add parcel button (Fig. 4).
42.3	76	* Fill in the parcel name (must be unique within the shipment) and select the type (usually “dry shipper”). Then, click Save.
	77	* Click on the Add container link to the right of the page (Fig. 4).
42.2	78	* Enter the name of the container. This must be the name engraved in the Unipuck, and it must be unique within the shipment. Then select Unipuck as the type; this is the only type of container supported at P11. If shipping something else, please contact the staff and agree on this. When you save, an image of the Unipuck will be displayed in the parcel card (Fig. 5).
25.2	79	* Click on the Unipuck and select Edit This will direct to the spreadsheet form where you can list the samples in the container (Fig. 6).
42.6	80	Select the protein from the drop down menu. If it is not there, create a new sample as either from the Proteins and Crystals menu as described above or by clicking on the Add Protein** button in the container sample list spreadsheet form. You might need to refresh the page for the newly added protein to appear in the list.
12.13	81	** Enter a sample name. It must be unique for each sample of each protein.
42.7	82	** After filling up the sample information, save the changes and return to shipment.
4.2	83
24.3	84	[[image:Unipuck.png\|\|height="99" width="400"]]
24.2	85
24.3	86	Figure 5.
24.2	87
25.2	88	[[image:Screenshot 2024-12-09 at 14.38.08.png\|\|data-xwiki-image-style-border="true" height="283" width="700"]]
24.2	89
25.2	90	Figure 6.
	91
	92
59.2	93	= Send the shipment to DESY =
3.5	94
59.2	95	* Click on the Print labels icon (Fig. 7) to the right of each parcel to generate a PDF file with the shipping address and return address. Make sure that the information on the labels is correct. If not, go to the “Shipping addresses” list and correct the information.
	96	* If everything is correct, print the labels. Please attach the dewar label and the shipping label on your dewars, and enclose the return label within the dewar box with other return forms (courier waybill or invoice).
	97	* If you are sending to and from outside EU and need customs declarations:
	98	** You need to fill in a Proforma invoice to send along with the shipment.
	99	** Be sure to use a proper description of the content of the shipment, as an example: “Dry shipper containing small frozen protein crystals for scientific experiments. Crystals are non-hazardous. Dewar contains non-flammable gas (liquid N2).”
62.3	100	* The button Send Shipment to the facility (Fig. 7) will activate once you print the labels (you need to update the page for this, you will be prompted about this). Pressing the button will send an e-mail to [[p11beamline@desy.de>>mailto:p11beamline@desy.de]] to notify the staff of incoming dewar. Please note that you still need to order the courier yourself, this is not possible via EXI currently. You can paste the tracking code and information if the dewar can be let to warm up after the experiments to the comments of the shipment. Should you have forgotten to include some information or something changes in the shipment plans, you can inform the staff by email (p11beamline@desy.de) or if you need to add additional pucks or information, you can still edit the shipment.
60.1	101	* When the dewar arrives at DESY, staff will scan it and you can follow the location status of the dewar in 'transport history' tab of this shipment page, upper right hand corner.
59.2	102	* After your dewar has arrived to DESY and it is the time for your experiment the local contact will insert the pucks in the sample changer dewar and assign the actual Unipuck position in to the Prepare experiment tab for synchronizing the information to MXCuBE.
3.5	103
26.2	104	[[image:Print&Send.png\|\|height="289" width="700"]]
	105
	106	Figure 7.
	107
	108
3.7	109	= Arrange the return of dewar(s) =
3.5	110
62.1	111	* Please order the return shipment after the beamtime allowing sufficient time for the staff to take out your pucks, e.g. for beamtimes ending in the morning, order the courier earlier at noon for the same day.
46.2	112	* Should the schedule of the beamtime alter for any reason, this will be taken into account and we will by default keep the samples cold until return shipment. If your dewar may be let warmed up after the experiments, please let your LC know.
60.1	113	* Inform the beamline and the user office about expected pick-up date and time by email to the p11beamline@desy.de at least a day in advance.
15.1	114	* If you are sending to and from outside EU please enclose the Proforma invoice.
5.1	115
3.1	116

Wiki source code of Extended ISPyB (EXI)

Applications

Navigation