IceBear crystal tracking software

The IceBear (Integrated Crystal-data-tracking Enhancing Biochemistry Education And Research) software, developed and installed at FBMM, is designed to help the FBMM researchers to follow the results of their crystallization experiments from their desk (or from outside the workplace, anywhere in the world). It is also possible to annotate these results.


Figure 1: Viewing crystals in IceBear.

IceBear will enable tracking of crystal data from crystallization to PDB deposition of co-ordinates. It aims not only to support home-lab crystallization work but also to integrate seamlessly with synchrotrons and other X-ray sources via standardized data exchange protocols.

So far, IceBear supports:

  • Plate and image import from Formulatrix/Rock Maker and Rigaku imagers, as well as manual plate creation and image upload where automatic imaging systems are not available;
  • Hands-off viewing of drop images, including full imaging history for a given drop (which can be filtered to show only visible or UV images);
  • Scoring of drop images and measuring of interesting features (with scale information imported from Formulatrix imaging systems);
  • Marking and annotation of interesting crystals for onward processing, including attaching files
  • Attachment of screen information to plates, via simple selection of standard screens or file upload for optimizations;
  • Recording of protein and DNA sequences, including complexes, which can then be associated with plates;
  • Highly flexible access control via a project-usergroup mechanism;
  • Individually-configurable start pages to suit each user’s work;
  • Per-user task lists, prompting users to provide missing plate information, remove expired plates from imagers, etc.;

Administrative and technical support is aided by:

  • (Formulatrix imagers only) Imager loading overview and contents list with inspections remaining and last inspection due date/time, with bar graph overview providing at-a-glance imager status;
  • Identification and flagging of “zombie plates” (where the host imaging system fails to identify a plate as expired), enabling rescue of lost imaging capacity;
  • Overview of disk space on both the IceBear server and imaging systems’ file stores.

An interface to support crystal harvesting and shipment assembly is currently in development. This builds on experience from previous LIMS software to minimise the user interaction required during crystal harvesting; the various containers’ barcodes are scanned in advance, then a simple drag-drop operation records the fishing of the crystal into a pin and storage in a puck for shipping. A touch screen installed at the crystal harvesting workbench will further enhance usability of this feature.


Figure 2: Drag-drop interface for recording crystal harvesting on barcoded and non-barcoded pins.

Future developments will include:

  • Seamless one-click submission of crystal shipments to ISPyB at synchrotrons;
  • Provision of per-plate “task lists” of crystal crosshair XYs to a home-lab X-ray plate scanner;
  • Retrieval of X-ray diffraction data;
  • Reporting on imager and other resource usage (plates per year, etc.) for monitoring, internal billing, etc., and to provide statistics for funding bodies;
  • Viewing of imager usage over time (already logged), to highlight capacity loss due to expired plates, inform future purchasing decisions, and allow trends to be identified.

The FBMM IceBear server can be reached at https://icebear.oulu.fi/. There is a demo account, username and password both demo. Note that the demo account is read-only and has very limited access; you will need a personal IceBear account to view your own plates and to use all the available functionality.

Further information on the use and setting up an individual account can be provided by Ed Daniel.

Should you wish to install IceBear in your own lab, it is available under an MIT license. Please get in touch to discuss your requirements.

IceBear user guide.

Contact person:

Ed Daniel, Software developer
Faculty of Biochemistry and Molecular Medicine F202C
University of Oulu
PO Box 5400, 90014 University of Oulu, Finland
tel. +358-(0)465 218511
email: edward.daniel (at) oulu.fi

 

Last updated: 1.3.2018