Joint Research Activity 1
User Infrastructure Platform in Europe
for Protein Crystallography
The generic nature of the experiments performed means that users can (and do) apply to more than one site for a particular project.
This may be because specific beam-lines are more suitable to some aspects of the experiment, may simply reflect the immediacy of demand, the difficulty of the project, travel and budgetary considerations.
The provision of a common application platform would enhance the efficiency of the application procedure for the users, and, if correctly implemented, might lead to a Europe-wide clearing-house for applications in this area in the mid-term future.
The goal of WP1 is the development of this common application platform.
In order to reach this goal the Vitual Unified Office (VUO) application (https://vuo.elettra.trieste.it) will be transformed in an open-source project taking into account any requirement from the participating partners. This will allow the facilities which does not have this kind of application to have one ready to customize and use.
There is a very low possibility that a facility with an already operating VUO like application will use the open version of the VUO.
In order to overcome this problem we decided to use the open-VUO as a reference platform and to use webservices technology to integrate the facilities with an already existing and operating VUO like system.
After having defined a common XML schema to capture all the required information for a beamtime application an open source version of the VUO was developed.
Using the open-VUO (https://vuo.elettra.trieste.it) the user can now
- prepare a beamtime application using a from based wizard
- save locally and XML file compliant with the defined schema
- speed up the propoal process by uploading the XML file
We will then install the open-VUO software at MAX-Lab and connect together ELETTRA and MAX-lab open-VUOs creating in this way a Virtual Organisation (VO) of 2 laboratories. A web transfer implementation will allow the exchange via software of application proposals between the members of the VO.
After this step other functionalities of the VUO will be gradually ported to the open-VUO and deployed in the VO.
The Europe-wide clearing house could be then implemented with further development steps. If we define a simplified beamline descriptions in terms of a limited number of parameter, an open-VUO can fetch a restricted list of suitable beamlines in the VO and present it to the user. The decision of which to apply to is up to the user. The webservices already in place in the VO will allow proposal submission to the required facility.
WP2 aims at developing a standard transport system to allow users to send their protein crystals to European synchrotrons which are equipped with a different sample mounting robots. A proposal for a standard transport dewar equipped with a data logger to monitor the temperature has been produced. The diverse sample holders for different sample mounting robots (see below) means that it is not possible to standardise on these. However it is proposed that all sample holders should be bar coded for identification.
One user group might send several hundred samples for each visit and the number of user groups is in to the hundreds and still increasing. Safety requirements mean that transporting these samples across national boundaries is a significant issue and a survey of suitable couriers will be carried out. Once the samples arrive at the synchrotron, they will need to be transferred to storage dewars, for long term storage. A set of samples might be examined on several beamlines during several visits by the group or during service mode data collection. Tracking the location of the sample holders is therefore a significant issue and we will examine the requirements for a database to carry out this task.
Robotics for transferring sample pins between one sort of cassette and another.
• Where possible to reduce the number of sample pucks/cassettes in use to allow users to be able to ship to all synchrotrons without repackaging.
• To be able to transfer SPINE standard pins between pucks used by the various sample changers in use at the synchrotron sites (see above).
• Transfer system between EMBL/ESRF and Rigaku ACTOR system pucks using a commercial robot has been built. It involves a specially designed gripper and a rotation stage activated by the robotic arm.
• The sample workbench has been mounted in a Dewar and the system also functions under liquid nitrogen.
• A simple front end GUI controls all functions.
• Development of calibration/ transformation system to allow highest reproducibility and recovery from crashes.
• Involvement of robotics in unloading cassettes from the transport Dewar.
• Improvement of user interface and integration with sample tracking database(s).
Standardized Data-Backup System for Protein Crystallography (PX-DBS)
• Within the European PX-synchrotron community accepted backup system with consistent look-and-feel in order to reduce training effort beamline users
• Common set of a wide range supported backup devices
• Future requirements for beamline operators to provide fast and high-performance means for data backup in the near future
• Evaluation of high-performance backup technologies in order to support the storage of very large PX datasets
• Implementation of 1st stage prototype system has been finished
• 1st stage prototype system is as the standard backup device for all BESSY operated PX beamlines
• Evaluation of recent backup technologies with respect to performance, compatibility and stability issues
• Implementation of 2nd stage prototype system at BESSY and SLS (see below)
• Specification and implementation of user-friendly software interface
Contact: Paul Tucker, EMBL, Tel. +49 40 89902 129