IceBear: Research Data Management
for Structural Biology

Installing IceBear

You will need a computer to act as the IceBear server.

Follow the installation instructions to set it up with Ubuntu Server and install IceBear on it.

Updating IceBear

Recent versions include an updater, which can download the latest version and update your IceBear installation. Log in to IceBear as a user with Administrator privileges, then select Configuration from the main menu (or visit http(s)://your.icebear/config/) and go to the "IceBear Version" tab.

If your older version of IceBear does not have the updater, contact us for help.

Downloads

The IceBear install files can be found below. You probably want to follow the install or update instructions above.

Latest IceBear version: Version 1.9.1

Rigaku image push

Choosing items: "Choose" buttons on the left, beside names, for easier reading and less mouse travel

Minor changes and code quality improvements

Download version 1.9.1
Version 1.9.0     

Shipment page: Summary of all datasets, grouped by protein acronym

Shipment page: Sort the available proposals into a consistent order

Shipment submission: Create protein in proposal if synchrotron supports it (MAX-IV only)

Bugfix: API key restriction by IP address was too restrictive

Bugfix: "Table render error" warning appeared in cells that were supposed to be empty

Other small fixes, refactoring, etc.

Version 1.8.2     

Fixes for issues in 1.8.0 and 1.8.1, including:

  • Plate best scores were not updated correctly
  • Automatically scoring drop when crystals were marked could score, e.g., Micro-crystals instead of Crystals
  • Email address match on Formulatrix user import was case-sensitive
Version 1.8.1     

Fixes for issues in 1.8.0, including:

  • Scoring and unscoring crystals was broken, if the plate was in the default project
  • Setting the protein acronym didn't work
  • Some issues regarding setting protein and construct
  • Plate view didn't refresh after setting a screen (but screen was set correctly)
  • Crystal QuickFish failed under several circumstances
Version 1.8.0     

Dataset, autoprocessing retrieval from EXI synchrotrons

Fix for drop image scores not being carried forward

Fix some bad remote crystal URLs

Changes in advance of automatic scoring support

Begin work on Lightbug support including mapping

Synchrotron records managed by IceBear

Improvements to Rigaku plate importer:

  • Plate and imager name handling
  • Handle late generation of plate XML file (caused earliest inspections to be ignored)
  • delay generating inspection XML (where not done automatically) to allow inspection to finish

Various code quality improvements

Version 1.7.2     

Fixes including:

  • Shipping: Additional SynchWeb parameters needed due to breaking changes at synchrotron
  • When marking a crystal, score the drop as "Crystals" automatically
  • Project owner couldn't update permissions on their project
  • Scores were not carried forward from previous images of the drop
  • Crystal page: "Add dataset" box opened when clicking anywhere in the shipment box
  • Pasting into the header search box didn't work, also select on Enter didn't work
  • Hide dummy pins in header search
  • Device API should accept API key in Authorization: Bearer header, not just X-IceBear-API-Key
Version 1.7.1     

Do not install or update to this version; instead, update directly to v1.8.0.

Version 1.7.0     

After a shipment and data collection, it is now possible to retrieve the data collection and auto-processing metadata. The metadata will be correctly associated with the relevant crystals and datasets.

Standard screens can now be installed in a single click from the Rock Maker XML library curated by Formulatrix. Upload of CSV and XML continues to be supported.

Homepage brick sizes are now configurable (per-user).

The permissions interface has been simplified. Rather than setting individual create/read/update/delete permissions, you now set "no access", "read-only access" or "full access".

Pre-cache drop viewer thumbnails and display them when full image not available, to improve usability.

Hooks allow custom code to be run before/after create/delete, enabling site- or Icebox-specific actions without if/else all over the code.

Bugfixes:

It was not possible to remove an optimization screen once it had been set, or to upload a replacement.

In some cases, clearing checkboxes would cause an error because the client would send "" to the database instead of "0".

Version 1.6.0      Formulatrix image push, API device keys

This release adds a mechanism for issuing API keys that can be used to access supporting code on the IceBear server, and uses this mechanism to support image push to IceBear from a Formulatrix Rock Maker system, enabling HTTP push to cloud-installed IceBear systems.

Separate code must be installed on the Rock Maker server to use this image push. If your IceBear and imager are on the same network, such that the Rock Maker image stores can be mounted on the IceBear server, the existing Formulatrix importer is probably your best bet for now.

Version 1.5.1      Formulatrix importer configuration

This release adds configuration items, allowing you to specify whether images are copied to IceBear's image store or served directly from the Rock Maker image store, and where the Rock Maker stores are mounted on the IceBear server. Previously, copying and /mnt/Formulatrix/ were assumed. Note that images served directly from the Rock Maker store will become unavailable should you purge that store using Rock Maker's image management tools!

Version 1.5.0      Star ratings

Add star ratings to your crystals and datasets. These let you make subjective judgements about the quality of your crystals and data, and then sort them on that basis.

Standard screens

Screens that have been used in a plate can be made unavailable for further use.

Version 1.4.1      Dataset management

Automatically retrieve datasets from MAX-IV and Diamond, and associate them with crystals.

Manual drop images

Add scale information to manually-uploaded drop images.

Version 1.4.0      Dataset management

You can now associate datasets with your crystals, and with PDB depositions.

Shipment data submission to MAX-IV.

Various bugfixes and improvements.

Version 1.3.1      Crystal shipping

Beta of shipment data submission to MAX-IV.

Various bugfixes and improvements.

Version 1.3.0      Crystal shipping

Shipment data submission to SynchWeb synchrotrons. A default shipment handler is provided for non-SynchWeb synchrotrons.

New interface for adding data collection notes and deciding whether to keep or wash the crystal on return.

Shipment return interface for post-shipment container management.

Nudge users to provide protein and screen information, with warning symbols on plate view tabs.

Various bugfixes and improvements.

Version 1.2.4      Crystal shipping beta
Further improvements to shipping beta following testing.
Version 1.2.2      Crystal shipping beta
Beta release of crystal shipping functionality, supporting shipments to Diamond Light Source.
Version 1.2.1      Further bugfixes and minor refactoring.
Version 1.2.0      Test update
Dummy upgrade for testing updater. Some minor improvements to crystal fishing.
Version 1.1.0      Crystal fishing
Added new drag-drop interface for crystal fishing, with support for barcoded pins, pucks and dewars.
Version 1.0.0      First release
Original release of IceBear, containing a crystal drop viewer and integration with Formulatrix imagers.

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