Stuart Fisher
This year has seen a significant upgrade to the ISPyB Laboratory Information Management System (LIMS) deployed to the Macromolecular Crystallography (MX) user community, bringing improvements for remote and local users, as well as new tools for staff members. ISPyB1 was initially developed as a collaboration between the UK, through e-HTTPx, and the ESRF, designed to deal with the large amount of information that needs to be recorded at high throughput MX beamlines.
ISPyB records information about data collection parameters, sample details, and provides access to results from automatic processing pipelines. A new interface to this database has been developed called SynchWeb, with the driving factors being the need to improve the existing workflows and make the presentation of harvested data more efficient and interactive. This new interface was deployed to the user community in March 2014. Since then around 99% of Diamond’s MX users have switched over, which equates to roughly 800-1,000 logins per week. A significant amount of positive feedback has been received both directly from users and through the user committee.
SynchWeb provides a fast and efficient interface guiding users all the way from sample preparation and shipping, through to experiment design and optimisation, and finally experiment evaluation and structure solution. SynchWeb makes use of responsive design to allow the interface to work on all sizes of devices from smart phones to tablets, to desktop computers. SynchWeb includes all of the functionality of the original ISPyB interface; allowing users to search proposals and visits, register shipments, containers, and samples, as well as contact details. In the new implementation, most pages aim to be self-explanatory, with embedded help and visual hints. A number of pages have had significant redesigns - key improvements include reworking of the sample registration workflow, making it significantly easier to register samples. The new projects workflow allows users to easily organise data collections and samples into a single location. The data collections page has been reworked to include all types of data collections and robot actions (Fig. 1). The new interface adds an integrated diffraction image viewer (Fig. 2) with features similar to ADXV2 but accessible directly within the browser. Remote users can directly monitor the beamline through embedded webcams. Key machine and beamline parameters and their status are clearly displayed. It has also been extended to include results from Diamond’s downstream processing pipelines3 such as experimental phasing, difference map generation, and automated molecular replacement. Importantly, these results can be directly inspected in the browser using an integrated map and model viewer (Fig. 3)4. For lab managers and facility staff, SynchWeb also provides statistics for proposals and visits, giving the breakdown of time used, number of samples evaluated, and any issues that occurred.
Prior to Experiment
Sample registration has been significantly overhauled; all samples in a container can now be registered simultaneously from a single page. This follows the same layout as is present in the beamline control software (MX-GDA). Proteins can be automatically created from this page and samples can be cloned to speed up the filling of containers. For protein registration, users can now provide a sequence and PDB file which will be automatically used for Diamond’s difference map and molecular replacement pipelines. The experimental hutches of I02, I03, and I04 feature a touchscreen computer through which sample containers can be directly allocated to the beamline control software as they are physically loaded into the sample changer (Fig. 4). This is especially useful on I03, which can now handle 23 containers.
Figure 2: Interactive browser based diffraction image viewer.
During an Experiment
The data collection page provides a live view of all actions for the current visit, which includes screenings, data collections, absorption edge scans, and fluorescence spectra, as well other sample actions. If the visit is ongoing, this page will update in real time without the need to be refreshed. Data is retrieved asynchronously and is polled regularly, making this an ideal way to remotely monitor an experiment. Data collections are paginated, filterable by type (e.g. fluorescence scans, absorption edge scans), and easily searched. This page also provides access to all of Diamond’s automated pipeline results including automated indexing and integration, as well as downstream pipelines such as difference map calculation, and experimental phasing. Diffraction images can be inspected directly in the browser and a plot of image quality is displayed5. The sample changer view shows at a glance the current status of all of the samples in the sample changer.
Figure 3: Built in map and model viewer for downstream processing pipelines such as Diamond’s automated difference map pipeline (DIMPLE) and experimental phasing (Fast EP).
For ongoing visits, users are able to view the webcams for the beamline as well as the status of a number of synchrotron and beamline parameters. The collation of this data into SynchWeb is extremely useful for remote users as it provides all essential information on the current status of the beamline and the storage ring in a web based application in real-time.
Post Experiment Analysis
SynchWeb implements a project workflow which allows users to group together proteins, samples, and data collections into a single location. This is especially useful for Block Allocation Groups (BAGs), which often contain not only multiple research groups, but also multiple universities. When users regularly collect hundreds of datasets per visit it can become difficult to find information from datasets that actually contain good data, or keep track of a particular project.
SynchWeb provides, for the first time, tools to allow both staff and users to evaluate how successful their beamtime was. This is especially useful for lab managers and BAG organisers, who need to understand how their allocated time is being used. Statistics are calculated for each visit, showing what percentage of time was used for different types of data collections, how much time the robot used, and how much time was remaining at the end of the visit
Figure 4: Touchscreen sample changer allocation in the experimental hutches of I02, I03 and I04.
Future Perspectives
As the productivity of the MX beamlines continues to increase, thanks to advancements in instrumentation (faster detectors, improved sample changers, and automation pipelines), the amount of information that needs to be stored continues to soar. SynchWeb provides a modern interface to the ISPyB database allowing users to manage metadata and processing results associated with their data collections.
References:
1. Delagenière, S. et al. ISPyB: an Information Management System for Synchrotron Macromolecular Crystallography. Bioinformatics 27(22): p. 3186-3192 (2011).
2. Arvai, A. ADXV – a program to display X-ray diffraction images. http://www.scripps.edu/~arvai/adxv.html (2012).
3. Winter, G. and McAuley K.E. Automated data collection for macromolecular crystallography. Methods 55(1): p. 81-93 (2011).
4. Nakane, T. GLmol: http://webglmol.sourceforge.jp/index-en.html (2014).
5. Zhang, Z. et al. Automated diffraction image analysis and spot searching for high-throughput crystal screening. Journal of Applied Crystallography 39(1): p. 112-119 (2006).
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