Please take a look at the User Manual

 

Please contact the ISPyB team if you are lost within ISPYB.

 

  Rapid access to the paragraphs of that web page:
  ISPYB Access
  How-to's demos
  New ! Manual creation of a shipping form : step by step
  Modified ! Upload of shipment form to ISPYB : guidelines
  Frequently asked questions
  Some icons in ISPYB

 

Access

  • from any browser at ISPyB Login / password required are the ESRF proposal account number and your ESRF site associated password (LDAP) = what you use for NICE disks log-in

 

  • Logoff buttom appears on the top right of your ISPYB window when you succesfully logged-in - To be pressed when you have finished working on it before killing your web browser interface.

 

Demos on video support demo on video support

  • Click on the link and after charging, the video will play by itself in your browser.

 

Creation of a shipment form

This allows you to use the NEW dewar tracking options AND describe the samples you ship to ESRF

Click here to open a step-by-step guide or follow these instructions:

  • In the Shipment tab
  • A shipment consist of a set of Dewars which is sent from your home lab to the synchrotron. Each Dewar contains a set of Containers (Baskets or canes). Each of these containers holds a series of Sample
  • Fill in the Lab-Contact and the experiment details so your shipment is tracked to the ESRF. The lab contact will receive an email when the dewar arrives at the ESRF. The location of the dewar at the ESRF can then be monitored through ISPyB.
  • Step-by-step guide to creating a shipment
  1. In the Create menu (on the left) select Shipment
  2. Fill-in the description of this shipment :Shipment label (which has a meaning for you - remember it corresponds to one sending and maybe composed of several dewars) ; Number of dewars, Other components ( e.g. tool boxes), Beamline/Expt (there should be a list of experiment dates and beamlines - select the one relevant to this shipment. Comments.

  3. Lab-Contacts - if you have already completed the lab contact information simply selecting the lab contact is sufficient. Please make sure that Courier name and account number is provided as it is important for the safe return of your dewar. SAVE !
  4. After saving you will automatically get to the View shipments menu where you can access this latest shipment. You can either add components to this shipment or upload sample information via an excel form upload at this point.
  5. From this page you can: a) print dewar labels (click on 'Comp. labels'), b) Modify dewar information, c) Add sample information
  6. When the shipment is sent to the ESRF - click on 'Send shipment to the ESRF' this will inform ESRF staff that a shipment is on route to the ESRF, it will also lock this shipment so no further samples can be added. However, it will still be possible to modify Lab-contact information and Beamline/Expt.


Upload a shipment form in ISPYB : guidelines

You can look at the above video to see how to upload a shipment form in ISPYB and read the following guidelines which will help you prepare that file step-by-step prior to upload it.

 

Frequently Asked Questions:

 

  • What happened to the upload excel file in the create shipment tab.

Since the Dewar Tracking release of ISPyB, the upload excel file is no longer available in the Create Shipment tab. To upload a file, you have first to create a shipment (with the appropriate number of dewars). Then, on the shipment, just after the shipment creation or by selecting your shipment in the shipment list, you will have an "Upload Shipment from Excel file" link. It will allow you to download a template and to upload a file in the current shipment.

 

  • I can't see my image thumbnails in ISPYB

Check on this webpage the status of the JpegServer which is used. Each beamline has its own JpegServer and if it is in bad state you should contact your Local contact to get helped from BLISS to restart it.

 

  • I have created a shipment, I want to see my samples from the beamline datacollection software MXcube or DNA

In ISPYB, go to the 'Prepare experiment' TAB and select the shipment(s) you are working on and save. if you are working on 'stand-alone' samples, you can select them from the left menu of that page.

If you have entered your bar codes for each sample in ISPYB you can then 'get the sample changer content' from DNA or 'scan sample changer' in MXcube to get a list of your samples with the information retrieved from ISPYB.

If you have no bar code in ISPYB, you will have to mention where you have put the baskets in the sample changer. For that you will need to click on the link 'fill the sample changer' at the top of the 'prepare experiment' page.

 

  • What does this headband at the top of my pages stands for?
  • Why some names are underlined?

Clicking on them will lead to a 'view action'. i.e. click on dewar label will provide you with a list of containers in this particular dewar, click on sample name will provide you with all information attached to that sample ( protein information, crystal information, shiping information...)

 

  • Why can't I modify a shipment I previously entered?

Because it is in 'processing state' : meaning accessible from the beamline data collection software.

In order to make it editable again, you have to go in the 'Prepare experiment' TAB, deselect it from the 'select for experiment' column and Save it. You'll see that you Shipment goes from processing to opened in the 'shipment status' column.

 

Some usefull icons found in ISPyB:

 
To have a full description of the icons used, go to icons in ISPyB document.

Add dewar: Add a new dewar to your shipment

View_Dewar : View all the dewars belonging to a shipment

View_containers : View Containers (within a shipment or a dewar if selected respectively from the shipment table or the dewar table)

View_samples : View samples (within a shipment, a dewar or a container if selected respectively in the shipment table, the dewar table or the container table)

Edit: Edit

Delete: Delete

remove_sample: Remove sample from container

Sort: Sort by alphabetical/date order ascending or descending

Up: Go one level up - is usually followed by an explanation on what level you go to

Calendar : Calendar for shipment date