The following is a list of abstracts submitted and accepted for NOBUGS 2006, presented in order of submission (that is, oldest first). The list is final; no more abstracts may be submitted.
| Organization: | CLRC Daresbury Laboratory |
| Author(s): | M.C Miller |
| Session: | Facility Reports (Wednesday afternoon) |
| Title: | SRS operation to 2008 - making the most of what we've got |
A summary of the current situation of UK Synchrotrons is provided with particular reference to the impending closure of the world's 1st X-ray Synchrotron (Daresbury SRS). A business life cycle model is presented as part of an illustration of the current financial and manpower resourcing at the SRS, which still needs to maintain a research programme until the end of 2008. A number of approaches are discussed, with examples, that are believed to help specifically with data acquisition and computing provision when resources are dwindling. Lessons being learned at the SRS are probably applicable to other large scale facilities, whatever life cycle stage they may be in. |
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| Organization: | Argonne National Laboratory |
| Author(s): | Jan Ilavsky |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | “Nika” & “Irena” packages - SAS data reduction and analysis packages for user support |
Two software packages – “Irena” and “Nika” - were developed during the last 5 years at the Advanced Photon Source to address needs for software support of USAXS and SAXS users. Some scientists using other SAXS and SANS instruments also found these macros useful. Over time number of complementary tools was added while the user community grew. Currently there are over 60 registered users. The packages are downloaded about 30 – 40 per month. The philosophy of these tools is to make complicated tools as convenient and simple to use as reasonably possible while preserving the scientific correctness. The development was motivated by the need to render the tools into a GUI so that users/scientists who are not computer software-proficient can apply the implemented scientific concepts to their data without becoming bogged down in command-line syntax. This broadens the SAS community and resulted in improved quality and quantity of publications from APS beamlines. The “Nika” package provides set of tools to reduce 2-D (area detectors) SAXS/SANS data into 1-D profiles (line profiles). The “Irena” package combines number of tools to import, correct, modify, and graph 1-D profiles – generated either by the “Nika” package or from any other source (e.g., USAXS). The data can be evaluated with selected methods commonly used in materials science, chemistry, physics, and biology –different methods of size distribution calculations, Unifed fit model, fractal model, and Debye-Bueche model useful mostly for gels. Scattering contrast calculator for both X-rays and neutrons, including Cromer-Liberman code for anomalous X-ray effects, is included. User can generate publication quality graphs and export ASCII data for further use. The packages are using version 5 of Igor Pro (Wavemetrics Inc.) software. Igor Pro platform provides necessary components - flexible data management, accommodating GUI capabilities, high level powerful scripting language, and excellent graphing capabilities. Igor scripting language enables both easy GUI programming as well as fast and convenient calculations with large library of functions. Extension to use compiled user C-programs is available. The use of high level scripting language results in convenient coding, while the penalty in processing speed is relatively small. Igor Pro has also excellent user support from both the company as well as user community from around the World. Users required that the support is provided on both Windows and Mac platforms, which is uniquely well satisfied by Igor Pro, which is running on both platforms with the same scripts and relatively modest hardware requirements. These packages (complemented by USAXS data reduction package “Indra”) provide complex data processing system – covering most needed areas of data reduction, data modification, analysis, and graphing. All of this is done using similar GUI system and within one environment, providing improved scientific efficiency for the users. The presentation will cover the packages capabilities overview, details of coding philosophy, including the GUI and data management rules. Plans for future developments will be discussed. |
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| Organization: | ESRF – European Synchrotron Radiation Facility |
| Author(s): | Romeu A. Pieritz, Olof Svensson and Claudio Ferrero |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | Using The Asynchronous Action Library Project at the ESRF |
The project is a Framework based on Pure Object Oriented Concepts to develop asynchronous communication between threads (thread safety) and external process, allowing the development of complete applications in different programming languages and platforms for heterogeneous developers. The current version has been developed using Python in the basic layer, designed to be natively translated to Java and C++. The framework has been tested and validated on Linux, WinXP and UNIX. The main features: i) programming language library dependence and system platform specific code are encapsulated in the basic layer; ii) the basic application framework implements the application resources handling management (thread safety); the automatic asynchronous multithread and inter-process core management, the inter-process basic communication, the system parameters management and iii) an asynchronous plugin architecture to implement evolutive software (thread safety). Projects using the library and the framework are: i) DRank: Crystal Data Ranking Module in the DNA Package – BioXHIT EU Project ii) BeamFocus: BeamLine Assisted Focusing Application and iii) EDFExplorer: ESRF Data Format converter to HDF5 File container. |
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| Organization: | FLNP of JINR |
| Author(s): | Kirilov A.S. |
| Session: | Poster (Tuesday evening) |
| Title: | The approach to incorporate the Python scripting language into an instrument control software |
The Python is a well-known scripting language, which is widely used for task description, programming GUI, etc., in instrument control systems/1/. The Python interpreter named “Pi” takes the important place in the Sonix+ control software at IBR-2 reactor instruments (FLNP of JINR, Dubna, Russia)/2/. The key features of “Pi” are
After analyzing one year of operating experience with the Sonix+ software, as well as user comments, we concluded that the initial approach requires corrections. Some of the implemented features, e.g., viewing of Python variables are not accepted by the user. The script generally consists of device operations and some data calculations (data transformations, preliminary analyses, etc.). Interpretation of some parts of a script with large array calculations in debugger mode is significantly slower than interpretation in the standard mode of Python. For some instruments this is significant restriction. The presentation is devoted to the new approach overcoming the disadvantages of the “Pi” interpreter. We decided to refuse the debugger concept and replace it by the concept of “control points” – points of user influence on the process of script interpretation – which, nevertheless, preserves the debugger mode functionality. The presentation will also touch problems concerning manual device handling by means of Python, and automated continuation the current measurement after unexpected restart of the operating system. /1/ NOBUGS 2002 http://webster.ncnr.nist.gov/events/nobugs2002#general /2/ http://lns00.psi.ch/nobugs2004/papers/paper00020.pdf |
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| Organization: | FLNP of JINR |
| Author(s): | Kirilov A.S., Murashkevich S.M., Petukhova T.B. |
| Session: | Poster (Tuesday evening) |
| Title: | Software complexes Sonix and Sonix+: eleven years of exploitation |
The presentation is devoted to the history, main features and future prospects of software complexes Sonix and Sonix+, developed for instrument control. The first installation of the Sonix was made in 1995 at the Neutron Spectrometer with High Resolution at the IBR-2 reactor (FLNP, JINR, Dubna). Since that time 14 installations (together with its successor Sonix+) were made at neutron and x-rays instruments in Dubna and Ekaterinburg. |
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(this entry has been cancelled) |
| Organization: | ANSTO |
| Author(s): | Tony Lam, Nick Hauser, Paul Hathaway, Darren Kelly, Ferdi Franceschini |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | The NeXus Reloaded |
The computing team from ANSTO is currently building a new software infrastructure to support seven neutron instruments for the OPAL reactor. Those instruments, which are due to operate at 2007, will base on a NeXus data driven client-server system that provides integration across instrument control, data access, visualisation, online and offline data analysis. Within each experimental lifecycle, scientists are guaranteed to perform data acquisition and data analysis under the same scientific domain, ensuring data integrity across the whole scientific workflow. From the software engineering perspective, the use of the model driven approach provides the maximum reusability for constructing complex e-Research system. This paper discusses the detail implementation and design philosophy behind this novel system. Keywords: NeXus, GumTree, Control System, Data Analysis, OPAL Reactor, eResearch |
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| Organization: | LBNL |
| Author(s): | P. Naulleau and P. Denham |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | Vacuum-compatible nano-positioning systems: hardware and software |
In vacuum nanopositioning is crucial to numerous applications in Synchrotron science. Here we describe nanopositioning sytems based on picomoters and LVDT feedback as well as laser-based sample height sensing. Both hardware and software components of the systems are presented. |
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| Organization: | ESRF |
| Author(s): | L.Claustre, G.Berruyer, A.Homs, A.Sole, M.Perez, E.Papillon,A.Beteva,M.Dominguez |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | BLISS software strategies at ESRF |
( NOTE for conference organizers: This talk has two different parts which could be presented, depending on the final program, separately. For example: one as a talk on its own, and the second one as a poster) First part: Data acquisition at ESRF beamlines: performance and strategies. One of the most delicate tasks on beamline control software is to define acquisition strategies that allow for optimal performance of experiments. This article presents the strategies developed by the BLISS group in this field. Results are presented for 0-D detection fast scanning experiments to 2-D detectors experiments involving massive amounts of data. Second part: BLISS management of software distribution to ESRF beamlines The BlissInstaller is a software suite developed at the ESRF for the distribution of software to beamlines. At the ESRF we have now 40 operating beamlines and a large number of laboratories and other internal facilities. The tools have allowed us to have a simple and powerful way of administering software installation, versioning and inspection. The package includes today applications to create packages (blissbuilder), install them (blissinstaller) and search/report/inspect software status (blisswatcher). This strategy has shown extremely useful in the distribution of our software to collaborating institutes. Four other institutes use today this software suite: Anka and Bessy (Germany), Maxlab (Sweden) and LNLS (Brazil). |
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(this entry has been cancelled) |
| Organization: | Lawrence Berkeley National Lab |
| Author(s): | N. Sauter, A. Deacon, A. Gonzalez, R. Grosse-Kunstleve, P. Moorhead, G. Snell, J. Taylor, Z. Zhang, and P. Adams |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | Real-time data analysis at the BCSB |
To enable real-time experimental decision-making at automated macromolecular crystallography beamlines, the Berkeley Center for Structural Biology has deployed a number of software packages developed at LBNL and SSRL. The program DISTL provides a quick analysis of the Bragg spots present on the X-ray diffraction image, and gives important measures of crystal sample quality, including the limiting resolution of diffraction, and the presence of diffraction artifacts such as ice rings. LABELIT removes the need for graphical interaction during the indexing process, with the crystal lattice being determined automatically for both routine experiments and special cases, such as those involving very large unit cell dimensions. The program also has advanced features to analyze the Laue symmetry of the diffraction pattern. Web-Ice gives a platform for organizing the screening of multiple crystals, allowing the investigator to select the best samples for further study. Concurrent data processing also permits the data collection parameters to be optimized so that the impact of radiation damage is minimized. Future work will emphasize the continued integration of data processing results into data collection protocols. |
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| Organization: | Argonne National Laboratory |
| Author(s): | Tom Worlton, Dennis Mikkelson, Ruth Mikkelson, Julian Tao, John Hammonds |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | Data Visualization and Analysis with ISAW |
The Integrated Spectral Analysis Software project (ISAW) is a collaboration between Argonne and the University of Wisconsin-Stout, started in 1999. ISAW is a Java-based package used to visualize neutron scattering data and do data reduction and analysis. Java works very well for scientific software. It is free, easy to install, and portable to different operating systems without recompilation. ISAW is in use on eight instruments at IPNS and four instruments at LANSCE. ISAW includes a GUI, a scripting language, and wizards. Scripts provide an easy way for scientific users to customize an application and automate processes. A combination of a GUI and scripting language is an ideal combination of ease of use and ease of customization. The ISAW GUI allows reading, viewing, transforming, and saving data intuitively. ISAW scripts allow customizing repetitive processes. Input parameters specified in a script automatically generate a GUI containing appropriate widgets for each data type. Scripts and wizards make use of specially packaged procedures called operators. DataSet operators furnished with ISAW appear in the “Operations” menu. Contributed operators and scripts in specified directories are found and included in the “Macros” menu when ISAW starts. An operator is a Java routine or wrapped C routine which meets certain requirements for documentation and interface. The ISAW operator generator can be used to turn a Java or C function into an operator. Operators can be invoked from scripts or interactively through menu selections. A “Category” item can be included in a script to specify the menu item name and location. A “ToolTip” which specifies the source file for each operator or script is displayed when the cursor hovers over that item in the Macros menu. Even “Wizards” can be constructed from a set of scripts using a “Wizard Generator”. Early ISAW development was restricted to a small team of software developers. ISAW development is now guided through feedback from users. I will show examples of ISAW visualization and data reduction and analysis. |
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| Organization: | High Energy Accelerator Research Organization |
| Author(s): | Jiro Suzuki, Ryoichi Kajimoto, Takashi Ohara, Masao Yonemura, Tetsuo Aoyamgi, Atsushi Manabe, Ken Nakatani, Toshiya Otomo, Setsuya Kawabata |
| Session: | Poster (Tuesday evening) |
| Title: | Object-Oriented Analysis Environment for Neutron Scattering |
Materials and Life Science Facility (MLF) of Japan Proton Accelerator Research Complex (J-Parc) will provide one of the highest intensity pulsed beams of neutron and muon. The construction will be finished in 2008. Our basic concept is to provide a framework software which has common and generic analysis functionalities for the neutron scattering experiments. The name of the analysis framework is "Manyo-Lib". Manyo-Lib is composed C++ and Python class libraries. Standard data containers, distributed data analysis environment, NeXus API and templates for analysis operators were designed and developed in C++, and they can be utilized in Python. |
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| Organization: | ESRF |
| Author(s): | Matias Guijarro |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | mxCuBE : software & hardware progress of crystalography beamlines at ESRF |
The mxCuBE (Macromolecular Xtalography CUstomized Beamline Environment) project started two years ago at ESRF. The goals of the project are :
To achieve these goals, the idea was to rely on standard BLISS group tools and know-how :
The first version of mxCuBE was deployed on all MX beamlines at ESRF on last december. Since then, new versions were released in a regularly basis. Two other institutes are using a stripped down version of mxCuBE, adapted to their needs : Maxlab in Sweden and Bessy in Germany. The presentation will focus on the key elements to mxCuBE success, and present an overview of the hardware and software developments. |
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| Organization: | Argonne National Laboratory |
| Author(s): | O.Makarov, S.Devarapalli, and S.Stepanov |
| Session: | Poster (Tuesday evening) |
| Title: | EPICS-based software for the ALS-style sample mounting robot at the GM / CA CAT |
A macromolecular crystallographic facility[1] developed by GM/CA-CAT is operational at the Advanced Photon Source (APS). The facility consists of three beamlines: two lines are based on the two canted undulators and one is based on bending magnet. ALS-style sample mounting robots[2] are being installed for an automated mounting of cryo-protected macromolecular crystals. Each automounter provides access to 72 or 96 samples residing in six Rigaku MSC ACTOR magazines or ALS-style pucks respectively which are residing in a dewar filled with liquid nitrogen. Mounting of a crystal takes approximately 10 seconds, during which the crystal temperature is maintained below 120 K. The control system consists of four DC servo motors and six pneumatic stages connected to the Delta Tau Turbo PMAC2 VME UltraLite motion controller and operational under EPICS-based control software[3]. Low level EPICS server for the automounter is written in the state notation language[4] and accepts two commands for sample loading and unloading via string-type EPICS process variable. The load command has the parameters of puck style, puck number and pin location in the puck. In the state when a sample is already mounted and load command is received, control program in the first action unloads the mounted sample and in the second action it mounts the requested sample. A graphical user interface to sample automounter is implemented as a tab in the BLU-ICE data acquisition software ported into EPICS[5]. On this tab user can select a protein crystal and send a request for mounting it. Information about samples and their positions can be imported into BLU-ICE from a user-supplied file in the Microsoft Excel format. Sample mounting robot is an important milestone for the goal of high-throughput data collection for macromolecular crystallography and automated sample screening. [1] R.F. Fischetti, S. Stepanov, S. Xu, O. Makarov, A. Urakhchin, R. Sanishvili, W.W. Smith, D. Yoder, R. Benn, S. Corcoran, S. Devarapalli, W. Diete, M. Schwoerer-Boehing, R. Signorato, L.E. Berman, and J.L. Smith. “GM/CA canted undulator beamlines for protein crystallography.” Acta Crystallogr. A, v.61, p.C139, 2005. [2] C.W.Cork, E.Cornell, R.Nordmeyer, D.Yegian, G.P.Snell, G.Meigs, T.Borders, C.Bryant, A.Dauz, J.Dickert, J.Jin, and T.Earnest. “Status of the BCSB automated sample mounting and alignment system for macromolecular crystallography at the Advanced Light Source.” SRI-2003, San-Francisco, CA, USA, August 25-29, 2003. [3] O.Makarov and S.Stepanov. “EPICS software for Turbo PMAC2 motion controller: Provisions for much faster beamline.” NOBUGS 2004 Conference, New Opportunities for Better User Group Software, PSI, Switzerland, October, 18-20, 2004. [4] http://www.slac.stanford.edu/comp/unix/package/epics/sequencer/ [5] O.Makarov, A.Urakhchin, S.Devarapalli, and S.Stepanov. “BLU-ICE implementation at GM/CA CAT.” 2006 Users' Meeting for the Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA, May 1-5, 2006. |
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| Organization: | Argonne National Laboratory |
| Author(s): | S.Stepanov, O.Makarov, A.Urakhchin, S.Devarapalli, D.Yoder and R.Fischetti |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | GM/CA CAT beamline control system for protein crystallography at the APS |
The GM/CA CAT has been established by the National Institutes of Health's National Institute of General Medical Sciences and National Cancer Institute to build and operate a national user facility for protein crystallography at the Advanced Photon Source. The facility provides two insertion device beamlines based on a canted undulator design and a bending magnet line. With the two ID lines fully operational and the BM line already installed, most of the pieces of the control system have been put in place, tested by users and refined. This presentation gives an overview of what has been implemented and outlines further plans. The GM/CA CAT deploys EPICS for the low-level controls including two VME IOCs per beamline, an embedded IOC for bimorph focusing mirrors and several Linux-based EPICS IOCs interfacing MAR CCD, beamline equipment protection system, and etc. An essential highlight of the system is the deployment of the Delta Tau Turbo PMAC Ultralite motion controllers that we made available in EPICS. The extended functionality of PMACs is used to implement coordinated motions at the beamline and synchronize motions with digital I/O: for example, goniometry with a fast X-ray shutter. On top of EPICS, we have built a collection of beamline optimization tools based on on-the-fly scanning algorithms and data acquisition software for which we implemented an EPICS port of BLU-ICE by SSRL. The latter was reduced to a regular EPICS client similar to MEDM being assisted by multiple state-notation-type EPICS servers, such as a frame processing engine, fluorescence scan engine, sample centering server, frame audit server, and etc. For automatic sample centering we have interfaced the packages C3D by Lavault Bernard at ESRF and XREC by Viktor Lamzin’s group at DESY. For automated sample mounting, we have installed the ALS-style robots and developed EPICS controls for them. The computing infrastructure has been designed as a combination of Linux and Windows workstations with central password management based on patched OpenLDAP. All workstations are linked to fast SAN with 2Gb fiber connectivity and 8 to 12 terabytes of FC disk space per beamline. Data storage deploys GFS that is exported to all workstation via NFS and Samba. Remote access to the facility is in the nearest plans. Access Grid software developed at Argonne National Laboratory is currently considered as the most attractive framework for it. Other plans include automated optimization of beam focus at the sample position deploying the inverse matrix algorithm in the control of bimorph mirrors. This will be essential for the plans to use the ID lines for small crystals about 10um in size. Also, automated sample screening tab is planned to be implemented in BLU-ICE as soon as the robots testing and refinements are complete. |
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| Organization: | Argonne National Laboratory |
| Author(s): | S.Stepanov, O.Makarov, E.Kondrashkina, B.Deriy, D.Yoder, S.Devarapalli, S.Corcoran, and R.Fischetti |
| Session: | Poster (Tuesday evening) |
| Title: | Hardware-synchronized on-the-fly scans at GM/CA CAT beamlines |
Increasing efficiency of the synchrotron radiation beamlines is an important task. Since a considerable share of beamtime is consumed by various alignment and data acquisition scans, the efficiently can be raised tenfold by using on-the-fly scanning algorithms. As an additional benefit for biological studies, fast scans help reducing radiation damage to samples. At the GM/CA CAT we have developed hardware and software for on-the-fly scans using advanced features of the Turbo-PMAC motion controllers in combination with Struck multichannel scalers. The software reprograms the PMAC controller before each scan, so that for a given motion the pulse and direction signals are fed into the Struck multichannel scaler via a converter producing up and down pulses while other inputs of the scaler count the X-ray intensity signal. As a result, the scaler accumulates arrays of X-ray intensities vs. axis position. Importantly, scan axes can combine motions of several motors. With our system we have done scans with 1ms time resolution and the hardware limit is ~5Žµs. The software exists as a GUI implementing multidimensional scans and a scripting library written in Perl. It also supports fast scans with fluorescence detector for protein crystallography. In that case the detector signal is discriminated by triple channel analyzer to select the region of interest and then is fed into the scaler. |
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| Organization: | Argonne National Laboratory |
| Author(s): | S.Stepanov |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | Transformation of X-ray Server into WWW-based library with simple API |
X-ray Server [1,2] is a public project launched in 1997 with the goals to explore Internet technology for more efficient sharing of personal research results with scientific community, establishing collaborations, and refining X-ray scattering models and scientific software. The Server provides Web-based access to a collection of programs implementing author's models in the field of X-ray diffraction and scattering. The software operates directly on the Server available for use without downloading. This has proven to be the most efficient technology for having feedback from users and thus refining the software and extending the models. The advantages on users' side are also essential as confirmed by the project success: more than 133,000 job requests from 5,500 sites have been served with a base of about 1,500 regular users who performed 10 or more calculations. At present the Server includes 7 programs that provide calculations of X-ray Bragg diffraction from strained crystals and multilayers for any Bragg-case geometry including grazing incidence and/or exit and with scans around arbitrary axes; calculations of X-ray specular reflection from multilayers with interface roughness using a recursive algorithm converging faster than the Parratt recursion; calculations of X-ray resonant specular reflection from magnetic multilayers with magnetic interface roughness; calculations of X-ray diffuse scattering from correlated interface roughness in multilayers; calculations of multiple Bragg diffraction with new algorithm applicable to grazing incidence and/or exit; interpolation of X-ray dispersion corrections from discrete sets with an algorithm derived from X-ray physics. About 55% server applications are the simulations of X-ray curves and the rest are the requests for databases interpolations and related services for planning X-ray experiments. This report describes recently developed software wrappers and mechanisms addressing numerous requests to expand the Server access beyond plain web browser sessions and facilitate batch processing, remote fitting and integration of Server programs into users' data analysis software. References: [1] X-ray server: http://x-server.gmca.aps.anl.gov [2] S.Stepanov, Proceedings SPIE, 5536, 16-26 (2004) |
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| Organization: | Paul Scherrer Institut, PSI |
| Author(s): | Gerd Theidel, Mark Koennecke |
| Session: | Poster (Tuesday evening) |
| Title: | Histogram Memory Computer with Linux/RTAI and integrated Web-Server |
The detected neutron events by various instruments at the Swiss Spallation Neutron Source SINQ are summed into multidimensional arrays of bins by histogram memory computers. This poster shows the new realization of such a histogram memory using a VME single board computer with Linux as operating system and RTAI as real-time extension. An integrated web-server provides a standard HTML interface for communication with the instrument server, for debugging purposes and as status display. The configuration of the numerous possible histogram types, dimensions and binning options is described using a simple XML file format. |
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| Organization: | SPring-8/JASRI, RIKEN SPring-8 Center |
| Author(s): | N. Okazaki, K. Hasegawa, G. Ueno, H. Murakami, H. Sakai, M. Yamamoto |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | Mail-in data collection at SPring-8 protein crystallography beamlines |
The mail-in data collection system at SPring-8 makes it possible that distant users collect diffraction data without visiting SPring-8. The mail-in users only send samples to SPring-8 via home-delivery services as the first step. Then they can request measurement conditions and check results at their laboratory on the Web. The data collection for delivered samples are carried out with the automated beamline operation system using sample auto-changer SPACE [1] and beamline control software BSS [2]. For smooth communication with distant users via the Internet, we have newly developed the data management system D-Cha (Database for Crystallography with Home-lab Arrangements) which mediates between the users and SPring-8 beamlines. D-Cha provides the GUI for users to deposit the experimental conditions for samples and to browse / download the collected data on web browser. The mail-in system has been developed and operated for Structural Genomics Project at RIKEN Structural Genomics II (BL26B2) since September 2005. Then the system has been presented for public users at Structural Biology III (BL38B1) since December 2005. In addition, the commercial mail-in service has just started in July 2006, as the joint project among JASRI, RIKEN and analysis service companies. The mail-in data collection is our first step of remote beamline access at SPring-8. The next step is to achieve the fully remote control data collection based on the mail-in system. [1] Ueno G, Hirose R, Ida K, Kumasaka T, Yamamoto M, "Sample management system for a vast amount of frozen crystals at SPring-8" J Appl. Cryst. 2004 Dec;37(Pt 6):867-873 [2] Ueno G, Kanda H, Kumasaka T, Yamamoto M, "Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8" J Synchrotron Radiat. 2005 May;12(Pt 3):380-4 |
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| Organization: | CCLRC Daresbury Laboratory |
| Author(s): | Graeme Winter, representing the the DNA Development Team and the e-HTPX Development Team |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | Recent Developments in the DNA & e-HTPX Projects |
The DNA collaboration aims to provide automation of protein crystallography data collection at the beamline. The e-HTPX project aims to provide a remote user interface to all steps of the protein crystallography pipeline, from crystallisation to structure deposition. This includes protein crystallisation, data collection & processing and structure solution. DNA is a key part of e-HTPX. DNA 1.1 includes functionality to link into the experiment database (e.g. ISPyB), screen and rank a set of samples, provide lightweight experimental requirements and collect & analyse data. The screening & ranking is implemented with a flexible ranking system where a large number of possible ranking schemes, from “resolution” to “minimise exposure in data collection” are available. From here it is possible to rank the samples, then collect data on a selection automatically, according to a strategy computed by BEST. The experimental requirements may be either input by the interface, or imported from e-HTPX via the Diffraction Plan. The requirements include the desired and minimum resolution, the multiplicity and completeness of the data and whether to collect anomalous pairs. Once the data are collected and integrated they may be summarised by the “quick scale” button. This performs a very rapid scaling using Scala to produce the summary table, to give confidence that the experimental requirements provided have been satisfied. Acknowledgements The DNA collaboration is primarily funded by collaborating institutions and projects including e-HTPX, with substantial contributions from BioXHIT. A full list of collaborators can be found at http://www.dna.ac.uk The e-HTPX project is funded by the BBSRC and UK DTI, with contributions from CCLRC, ESRF, OPPF, York University Structural Biology, CCP4 and Diamond Light Source. |
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| Organization: | Centro AtŽómico Bariloche, Argentina |
| Author(s): | J. Dawidowski, F. J. Bermejo, M. L. Ristig, and S. M. Bennington |
| Session: | Poster (Tuesday evening) |
| Title: | Experimental corrections and data-analysis in the study of momentum distributions with time-of-flight inelastic neutron scattering |
In this work we describe the different steps followed to obtain momentum distributions from time-of-flight inelastic neutron scattering measured at spectrometer MARI (Rutherford Appleton Laboratory, United Kingdom). In the first part of the work Multiple Scattering and Attenuation effects are calculated based on a Monte Carlo algorithm that employs the experimental data as a starting point. From the numeric runs, correction factors are defined, that are applied to the experimental data. Thus the corrected data serve as input for the next run, thus defining an iterative procedure. We discuss the preparation of the input data, the relevant magnitudes that must be considered and the minimum input dataset necessary to tackle this problem. The second part of this work is devoted to the algorithm of data analysis. A parameterized model is introduced to fit the experimental data of S(Q,w). The fitting algorithm has a visual user interface based on the program Grace called as a subroutine from a Fortran main program. All the described procedures are based on free software running on Linux (Debian GNU/Linux in this case). We show recent results obtained in the study of liquid Hydrogen at different pressures. |
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| Organization: | RIKEN SPring-8 Center |
| Author(s): | Go Ueno, Kazuya Hasegawa, Nobuo Okazaki, Hironori Murakami, Raita Hirose, Takashi Kumasaka, Masaki Yamamoto |
| Session: | Poster (Tuesday evening) |
| Title: | Automatic beamline operation system for protein crystallography beamlines at SPring-8 |
Structural genomics projects progressing worldwide have been accelerated by high throughput protein crystallography with the automation of beamlines at synchrotron radiation facilities. Here in SPring-8, the automatic system to execute successive diffraction experiments with sample auto-changer SPACE was developed at RIKEN Structural Genomics Beamlines (BL26B1 & BL26B2) [1]. The operation software BSS [2] provides the intuitive GUI and centralized control of beamline instruments with the networked client-server architecture. In 2005, more than twenty crystals a day have been constantly delivered and screened at BL26B2, at rates of 5 min/sample, and seven data sets in daily average have been constantly collected. Up to now, a public beamline BL38B1 (Structural Biology III) and another beamline in SPring-8, other than BL26s, and also five laboratories inside and outside SPring-8 have implemented SPACE robotic system to carry out the automated data collection. [1] Ueno, G., Kanda, H., Hirose, R., Ida, K., Kumasaka, T. and Yamamoto, M. (2006). J. Struct. Funct. Genomics. 7, 15-22. [2] Ueno, G., Kanda, H., Kumasaka, T., and Yamamoto, M. (2005). J. Synchrotron Rad. 12, 380-384. |
|
| Organization: | Illinois Institute of Technology / Southeast Regional CAT |
| Author(s): | Andrew J Howard, James F Fait, Zheng-Qing Fu, William M Lavender, John J Chrzas |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | SER-CAT automation and controls |
Southeast Regional Collaborative Access Team (SER-CAT) operates an automated end-station at beamline 22-BM at the Advanced Photon Source. The sample-loading robot is a modification of the ALS design: most of the novel elements are in the controls and in the sample-holding Dewar. The reliability of the system is high, and user acceptance of the system has increased substantially in recent months. The overall SER-CAT control system, based on mx (http://mx.iit.edu/) and SERGUI (NOBUGS 2004, paper 112), has straightforward interfaces for user operations with the sample-loading system. It includes both a fully automatic loop-centering system and a point-and-click interface. SERGUI now features an effective strategy facility that employs X-GEN (http://xgen.iit.edu/) as its computational engine. Users can enter symmetry information or rely entirely on the strategy-sample data. Plans for the future include increasing the ruggedness and reliability of the robotics, controls, and strategy systems; tighter integration with data processing and structure determination functions using X-GEN, SGXPRO and other packages; and employment of a larger, more sophisticated sample-loading robot on SER-CAT's other beamline, 22-ID. |
|
| Organization: | Diamond Light Source |
| Author(s): | Karl Levik, Richard Woolliscroft, Katherine McAuley, Liz Duke, Bill Pulford, Alun Ashton |
| Session: | Poster (Tuesday evening) |
| Title: | High throughput MX data collection at Diamond |
The process of collecting experimental measurements in the area of macromolecular crystallography (MX) at synchrotrons is becoming highly automated. This is due to the availability of advances in both hardware and software. To permit automatic decision making at the beamline the process of harvesting sample information will begin in the user’s home or collaborator laboratory, before experimental measurement and potentially full structure solution occurs at a synchrotron. Diamond will utilise the work of a number of international high throughput computing and eScience initiatives to allow a high level of experiment logging and secured, authorised data access and processing. |
|
| Organization: | Diamond Light Source |
| Author(s): | Richard Woolliscroft |
| Session: | Poster (Tuesday evening) |
| Title: | The embedded scripting environment in the GDA |
The Generic Data Acquisition (GDA) system is a Java-based beamline control system developed jointly between Diamond Light Source and CCLRC Daresbury. It provides both users with a choice of graphical or command-line based control. The command-line control embedded into the GDA is based on the Jython scripting language. It provides users with a powerful scripting environment, yet via a simple syntax. This was presented at NoBUGS 2004. The poster outlines the GDA scripting environment and progress since the last NoBUGS. |
|
| Organization: | University of Chicago |
| Author(s): | Mark Rivers |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | X-ray Detector Support with EPICS |
There are a large number of synchrotron beamlines that are using EPICS for control and data acquisition. An important capability required for these applications is to control x-ray detectors. These range from solid-state detectors with multi-channel analyzers to CCD detectors for diffraction. This talk will discuss EPICS support for the following detector types:
The use of the asyn module to support these applications will be discussed. |
|
| Organization: | Diamond Light Source Ltd |
| Author(s): | Fajin Yuan, Richard Woolliscroft, Bill Pulford |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | GDA – an Integrated Science Experiment Environment for synchrotron users at Diamond and SRS |
Synopsis The Generic Data Acquisition or GDA is a software suite jointly developed at the SRS Daresbury and Diamond Light Source in the UK for synchrotron experiment control and data collection. In recent years the teams from Diamond and SRS have collaborated to transform and improve the system to make it more configurable, extensible, and user friendly. GDA is built using Java programming language with an embedded Jython scripting engine. This paper or presentation provides an overview of GDA, its design, components, and functionalities. It also describes aspects of the GDA system including user interface design, beamline configurability, embedded scripting tools, interface and integration with other 3rd party software such as EPICS, IDL, and DNA. Other features of the GDA include an extensible mechanism or plug-in. that allows tight integration with user developed software, such as user-specific environment control programs and data analysis software. We believe this could significantly improve our users’ experiment experience at the Diamond Light Source. Our aim is eventually to provide an Integrated Science Experiment Environment from which users can carry out their science exploration, access, manage, and visualise their data, obtain online help at their finger tips. |
|
| Organization: | NIST/University of Maryland |
| Author(s): | L.R. Kneller, R.T. Azuah, R.M. Dimeo |
| Session: | Poster (Tuesday evening) |
| Title: | DAVE--Software Facilitating Science at the NCNR |
The DAVE software package is a free suite of tools for reducing, visualizing, and analyzing data collected on the inelastic neutron spectrometers at the NIST Center for Neutron Research. The design goal for the software is to provide easy-to-use, powerful tools that facilitate data reduction and interpretation. This poster will present some key capabilities with emphasis on recent developments of the software package. This work is based upon activities supported by the National Science Foundation under Agreement No. DMR-0086210. |
|
| Organization: | ISIS Facility |
| Author(s): | J. D. M. Champion, F. A. Akeroyd, T. G. Perring, P. Amin, S. J. Levett and D. A. J. Whittaker |
| Session: | Poster (Tuesday evening) |
| Title: | LIBISISEXC: A FORTRAN90 library for inelastic neutron data reduction |
With the arrival of the MERLIN chopper spectrometer an update of the existing ISIS VMS based inelastic data reduction program (HOMER) has being undertaken. To make best use of existing and available resources we have programmed the data manipulation routines as a FORTRAN90 library and added a control and graphics front end using the MATLABŽ® package from The MathWorks, Inc. Though not a fully Object Oriented (OO) language, FORTRAN90 provides many of the necessary features and the OO paradigm has been used where possible in the design and coding. Derived data types (classes) have been based on those defined by the NeXus standard - instances can exist in both MATLAB and FORTRAN90 and share memory where possible for efficiency. While only a MATLAB front end has been used to date, work has begun on providing a PYTHON based one. |
|
| Organization: | Lawrence Berkeley National Lab |
| Author(s): | Hanjing Huang |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | Labview-based User Interface for Beamline Equipment Protection System at the Advanced Light Source |
Equipment Protection System is a system of hardware and software components used to protect the storage ring vacuum from contamination and beamline components from thermal damage. It also provides operator control of beamline valves and shutters. EPS has two basic components -- computer-based control system (PLC) and graphic user interface (PanelMate or Labview). This talk is devoted to an explanation of the hardware and software components, as well as features and functionalities of the current EPS. It covers the design philosophy, history, motivations for and efforts to upgrade the legacy system. A comparison between Labview-based and PanelMate user interface is also presented. A complete hardware and software simulation is presented at the end of talk. |
|
| Organization: | ORNL - SNS |
| Author(s): | P.F. Peterson and J.-C. Bilheux |
| Session: | Data Formats and Data Management (Monday morning) |
| Title: | Translation Service – life cycle of the data at the SNS |
The life cycle of the data starts when events are detected and files are created by the Data Acquisition System (DAS). But there is a long way to go before the user can work with the data. The Translation Service (TS) takes care of making data useable by converting preNeXus files (DAS internal files) into NeXus and sending appropriate files and information to the Data Management system to be cataloged and archived. The full picture of the Translation Service and what it interfaces will be presented. |
|
| Organization: | SLAC |
| Author(s): | A. Gonzalez, P. Moorhead, S. McPhillips, J. Song, N. Sauter |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| ** Combined with presentation 58 ** | |
| Title: | Integration of data analysis and collection at SSRL |
The Blu-Ice/DCS (Distributed Control Software) beamline control software implemented at the SSRL has enabled a high degree of automation for macromolecular crystallography data collection. The next step towards the final aim to integrate data analysis and data acquisition to the point where only minimal input by the user will be required to carry out a complete experiment. In order to achieve this, we are developing a set of applications for beamline monitoring, automated autoindexing and evaluation of diffraction images and data collection strategy determination from two diffraction images. These tools are accessible through a web-browser based interface, Web-Ice. A connection between the DCS server and Web-Ice makes it possible to access the data analysis applications automatically as the images as being collected; this has been exploited to implement totally automated - on-the-fly crystal screening, scoring and strategy calculation. In addition, because Web-Ice can also be run as a stand-alone application, the users can access the experiment results and re-analyze the data at any time before or after scheduled beamtime. |
|
| Organization: | Indiana University |
| Author(s): | P.A. Zolnierczuk, D.V. Baxter, H. Kaiser, C.M. Lavelle, M.B. Leuschner, W.R. Lozowski, N.B. Remmes, T. Rinckel, W.M. Snow and P.E. Sokol |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | Data Acquisition, Analysis and Visualization at LENS |
The Low Energy Neutron Source (LENS) is a novel, university-based pulsed neutron source under construction at the Indiana University Cyclotron Facility. The source utilizes a low energy p-n reaction in beryllium coupled with a high-current, variable-pulse-width proton accelerator to produce either short or long neutron pulses. Highly optimized moderators produce cold and very cold neutrons for use by a suite of neutron scattering instruments and development facilities. The LENS facility will initially provide four neutron scattering beamlines: a small angle neutron scattering (SANS), an instrument for high-precision measurement of scattering angles using Spin-echo (SESAME), a neutron optics test bench and a radiography instrument. We will present an overview of LENS data acquisition, analysis and visualization systems. And we will also discuss plans to migrate/upgrade existing systems in order to integrate LENS instrumentation with SNS computing environment. The LENS project is supported by the National Science Foundation (under grants DMR-0220560 and DMR-0320627), the 21st Century Science and Technology fund of Indiana, Indiana University, and the Department of Defense. |
|
| Organization: | Brookhaven National Lab |
| Author(s): | Skinner, John M; Buono, Rick; Sweet, Robert M; Cowan, Matt; Nolan, William; Bosshard, Heinz; Robinson, Howard H; Heroux, Annie; Soares, Alexei S; Schneider, Dieter K |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | Integrated Software for Macromolecular Crystallography Synchrotron Beamlines |
The software used by the Brookhaven Biology Department at the NSLS was designed originally to control a diffractometer at a macromolecular crystallography beamline. Over the years this system has been systematically augmented and rewritten. For over a decade, it has been recognized that efficient use of a Macromolecular Protein Crystallography beamline demands software that is easy to use. While designing an intuitive interface to the experiment presents significant difficulties, the implementation of the underlying control code is further complicated by the ever-changing hardware that it controls. Hardware has traditionally been limited to beamline motors, scalers, diffractometers, and X-ray detectors. New challenges for the designers of integrated software are arising as sample changing robots, the need for remote observation or operation, and associated project-management database systems are developed to meet the demands of high-throughput crystallography. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. Our system provides automatic logging of the experiment and communication with the user, from the initial proposal to perform the work, all the way through to the end of data collection. In order to meet our strict standards for automation and data collection, we have designed a synergetic system of integrated software. This includes the construction of the PXDB relational database system, using PostgreSQL as the underlying database and Perl/Javascript/HTML for the application code, to collect and organize all details of the experiment. We have also incorporated a robotic specimen changer to provide automation for high-throughput applications. The NSLS PXRR data collection and beamline control software, CBASS, is a Python-based system that is under continuous development to meet ongoing requirements. Recent enhancements to the software have included integration with DNA, the product of a collaboration of several European Labs, and the utilization of the ESRF's C3D program for use in automatic crystal centering. |
|
| Organization: | Spallation Neutron Source |
| Author(s): | P.F.Peterson |
| Session: | Data Formats and Data Management (Monday morning) |
| Title: | The State of NeXus |
The NeXus International Advisory Committee (NIAC) has been hard at work solidifying the standard. In addition to an overview of NeXus, the results of the last NIAC meeting and changes in the v4.0.0 of the NeXus API will be presented. |
|
| Organization: | Oak Ridge National Laboratory |
| Author(s): | Carol Tang |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | Chopper Control System at SNS |
We present details of the Chopper Control System (CCS) including software architecture, hardware interfaces, and network environment. The CCS can currently control both Astrium and Revolve choppers in any combination but can easily be extended to control other types of choppers. The software can be operated locally through a sophisticated GUI or can be remotely controlled using a custom UDP protocol. We will also describe how this application works within the data acquisition system. |
|
| Organization: | Spallation Neutron Source |
| Author(s): | M.A.Reuter, P.F.Peterson, and J.Bilheux |
| Session: | Data Visualization / Analysis / Simulation (Wednesday morning) |
| Title: | SNS Common Libraries - A Base for Neutron Scattering Software |
The SNS Common Libraries (SCL) is a flexible set of static calculations that operate on an abstract data object. The cross-platform libraries are implemented in C++ using templates, allowing flexible primitive data types. In addition it is wrapped in swig for use from Python. The tenets, format, and contents of the SCL will be presented. |
|
| Organization: | Illinois Institute of Technology |
| Author(s): | W. M. Lavender |
| Presentation Type: | poster |
| Title: | Progress with the MX Data Acquisition and Control Toolkit |
This report discusses recent progress with the MX data acquisition and control toolkit. MX is a portable toolkit for distributed data acquisition and control with over 440 device driver for devices commonly found at synchrotron radiation sources and laboratory X-ray facilities. Since the last NOBUGS meeting, a variety of improvements have been made that have significantly increased the performance of MX network communication. In addition, MX has been modified to be compatible with running on 64-bit operating system. Also, support has been added for video capture boards, Camera Link I/O, pan/tilt/zoom modules, and for connections to Blu-Ice servers. A variety of drivers for already existing device classes has been added as well. A significant new development is the use of MX as part of the control system for a new commercial X-ray detector system. This system is the PCCD-170170 CCD detector and streak camera from Aviex, LLC, which is primarily designed for SAXS experiments. Other new developments include new graphical user interfaces for lithography and microfocussing experiments. In addition, MX has now been packaged for Debian, along with supporting packages for EPICS base and MEDM. |
|
| Organization: | University of Tennessee |
| Author(s): | William T. Swain, Peter F. Peterson, Stephen D. Miller |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | Software Engineering Best Practices for 21st Century Computational Science |
Within the past decade, the character of computational science has changed dramatically. Both the collaborative nature of computational science and the potential for near term societal impact now demand a new level of diligence to achieve reliability and productivity. In a general sense, the necessary software engineering methods are immediately available in some segments of industry and government. However the specific applicability of these methods in computational science is not well established. The core strategy is to extend the usual mathematical rigor of science into the task of scientific software production. This objective is achieved through the application of theory-based specification and verification practices. The proposed presentation will identify a core set of practices and methods to achieve this objective. Specifically the presentation will describe a rigorous, seamless method for transforming requirements to code and a quantitative approach to software certification and process improvement. These practices have been introduced as part of the initial software development process adopted by the SNS Science Software group. In addition to providing a basic description of the practices and methods, the presentation will include discussion of process implementation issues and lessons learned to date. |
|
| Organization: | Brookhaven Nat'l Lab Biology Department |
| Author(s): | Robert M. Sweet, Biology Dept., Brookhaven Nat’l Laboratory, Upton, LI, New York Herbert J. Bernstein, Mathematics and Computer Science, Dowling College, Oakdale, LI, New York |
| Session: | Data Formats and Data Management (Monday morning) |
| Title: | Management of Synchrotron Image Data for Macromolecular Crystallography: The imgCIF File System |
Motivation: There are over a dozen synchrotron x-ray sources around the world where macromolecular crystallography (PX) measurements are made. There are three or four major area-detector vendors who supply the equipment for recording diffraction patterns, with about ten detector types in lower abundance. Finally, there are three or four different data-reduction programs that have significant use in this discipline, with another half dozen others getting some use. However, there is only one repository for the structural results of these studies, and that is the Protein Data Bank. It is the purpose of the PDB to archive reduced structure factors, the atomic structures that result from the analysis, and a substantial quantity of meta data that describe how the measurements were made and the molecular structure was determined. The value of imgCIF: It is the goal of the imgCIF project to develop and promote the universal adoption of a self-defining format that will contain all of the meta-data pertaining to the execution of the experiment, and will allow any data-reduction program or image-visualization tool to treat data from any detector. CIF (the Crystallographic Information Framework) is a data-definition and -storage schema that is approved by the International Union of Crystallography. The imgCIF format includes meta data items from the CIF dictionary and then one or more diffraction images. The existing standard for imgCIF will lend itself to elaboration in NeXus or XML formats. This lecture will describe some features of imgCIF and the state of the process of adoption of a standard. This work is supported by grants to BNL from the US Department of Energy’s Office of Biological and Environmental Research and the National Institute of Health’s National Center for Research Resources, and to Dowling College from the National Science Foundation and the DOE’s BER. | |
| Organization: | Advanced Light Source |
| Author(s): | Edward E. Domning, Yunian Lou, Brian V. Smith |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | The Beamline Controls System: A LabVIEW Based System for Beamline and Endstation Control at the ALS |
The Beamline Controls Section of the Advanced Light Source (ALS) Controls Group has implemented a LabVIEW based data acquisition and control system for control of ALS beamlines and endstations. The original intention of the design was to create a system that integrates the sensors and actuators of a beamline into a package that allows a beamline scientist to tune up a beamline. Once implemented the system proved to be flexible enough to be used as a general control system for beamline and endstation control at the ALS. At the lowest level this system interfaces to motion controllers, analog and digital I/O devices, amplifiers, and vision systems. For each hardware type (motor, analog input, etc) we can have levels of abstraction that allow for coordinated moves (i.e. monochromators), feedback (i.e. beam position maintenance from a beam image) or calculated values (i.e. beam position). The information for each hardware type is stored in a generic form and made accessible to higher-level features. These features include basic user interface screens, network access, scripting, basic scanning (time, single motor, two motor), beamline specific tuning or scanning routines, beamline automation, and instrument scanning (MAR CCD, SCIENTA). There are currently 46 installations of varying complexity with 22 controlling beamlines and 24 controlling endstations. There are interfaces to 22 different types of “motor” controllers (power supplies, analog outputs and temperature controllers are considered motors for scanning), and 13 different analog inputs devices. |
|
| Organization: | Paul Scherrer Institute |
| Author(s): | Mark Koennecke, Uwe Filges |
| Session: | Poster (Tuesday evening) |
| Title: | Integration of McStas Simulations into the Instrument Control Software SICS |
It is now possible to simulate whole neutron instruments together with sample using the McStas simulation package. Faster computers and the release of the paralellized McStas version 1.9 allow such simulations to be performed within reasonable time intervalls. Thus it became possible to link such a simulation with an instrument control program. The result is a virtual instrument. In this contribution we show how a McStas simulation was linked to PSI's SICS instrument control software. This is for the powder diffractometer DMC, but the solution found is general enough to be useful for other instruments as well. |
|
| Organization: | Lawrence Berkeley National Laboratory |
| Author(s): | Brian V. Smith, Edward E. Domning, Yunian Lou |
| Session: | Poster (Tuesday evening) |
| Title: | Automated Endstation Control Using The LBNL Beamline Controls Software |
The Advanced Light Source Controls Group at the Lawrence Berkeley National Laboratory has implemented a software package to control roughly two dozen of the beamlines using LabVIEW. This software has also proven useful for automation of endstation operations. This includes sample insertion/manipulation using coordinated motion of positioning systems, scanning of spectrometers, video cameras and microchannel plate (MCP) detectors using an architecture that is fairly flexible, allowing new motors, spectrometers/detectors and cameras to be integrated with moderate effort. There is also a network-based interface to allow the endstation to control the main beamline system (e.g. monochromator, undulator, etc). The devices currently supported use a variety of interfaces: Ethernet, EPICS (XIA DXP Saturn and Roentec Xflash Max detectors), CameraLink (Dalsa and Basler CCD cameras), LabVIEW VIs (Spectral Instruments CCD camera), DLLs (Scienta series spectrometers), and digital I/O (Quantar Position Analyzer used with an MCP). Features include CCD image calibration (bad pixel handling, polynomial intensity correction) and detector setup (number of channels, "live time", etc.). Automated sample insertion/manipulation allows the user to specify a coordinated sequence of multiple axis motions to automatically load and position experimental samples. The PEEM3 microscope developed at LBNL will integrate this feature along with video capture and scanning of samples using this software. |
|
| Organization: | LBNL |
| Author(s): | H. Nishimura, C. Timossi |
| Session: | Poster (Tuesday evening) |
| Title: | Experience with .NET for controls and modeling |
Since the release of .NET Framework in 2001, we have been slowly gaining experience in using it for accelerator simulation and controls. Our primary areas of concern have been:
We present a report on our evaluation of the first two items and some early impressions of the second two. (1) We have ported a CPU-intensive numerical code for particle tracking to C#. By using a .NET profiler to find and improve the runtime performance, we have attained very satisfactory result [1]. (2) We have rewritten the EPICS Simple Channel Access ActiveX control as a .NET assembly in C#. We then compared it's performance against the original control[2]. We have also ported it to Windows XP x64. (3) We have found that the Linux implementation, MONO[3], allows .NET 1.1 applications on windows to run unmodified on Linux. (4) We will cover the other potentially useful features of .NET : remoting, object database, dynamic scripting and the .NET security model. References [1] http://accelconf.web.cern.ch/AccelConf/e06/PAPERS/WEPCH145.PDF [2] http://conference.kek.jp/pcapac2005/paper/TUB2.pdf [3] http://www.mono-project.com |
|
| Organization: | ISIS Facility, CCLRC Rutherford Appleton Laboratory |
| Author(s): | C M Moreton-Smith |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | A Crisis of Identity - the Promise (and pain) of "Single Sign on" |
Surprised and delighted are not adjectives which most people would attribute to the "dry" subject of user authentication. But imagine yourself, arriving at a facility where the swipe of a smart card could register your presence on site, set up the beam line as you last used it and ensure all data collected was routed automatically to your home institution at the end of an experiment. Not only this, but the restaurant had registered your vegetarian preference and the guest house selected the south facing ground floor room you liked so much the last time you visited; and imagine this worked at every institute you visited! Whilst not quite at the level described above, the CCLRC Single Sign on Project is particularly interesting in that it aims, pragmatically to join disparate systems; corporate administrative systems, scientific instrument control and desktop systems and e-Science grids and archives. Users of all the facilities will be able to work from the identity of a single account and password whatever they are doing be it on Linux, Windows or on a remote grid node or web site. In particular, visitors to the Diamond Light Source and ISIS facilities will use exactly the same accounts and password system as CLRC corporate users. In this talk I'll discuss some basics of the pragmatic approach to single sign on that was adopted as well as some of the technologies and breakthroughs which were particularly significant. Finally, I'll broaden the discussion to look at some possible approaches to going global and linking facilities on separate sites and continents to gain the same benefits for our itinerant user communities. |
|
| Organization: | JAEA |
| Author(s): | Takeshi Nakatani, Setsuo Satoh, Toshiya Otomo, Masatoshi Arai |
| Session: | Poster (Tuesday evening) |
| Title: | Architecture of Data Acquisition Software at MLF / J-PARC |
In neutron scattering experiments at Materials and Life Science Facility (MLF) of Japan Proton Accelerator Research Complex (J-PARC), large amount of data will be acquired. We have decided to adopt network distributed computing to manage these data. Our data acquisition software executed on these computers is message driven client / server architecture. The control messages are communicated between the user interface client and the data acquisition server via TCP/IP socket / Ethernet. Because the messages and the application program interface for the communication are opened to the public, the users will be able to experiment with not only the ready-made software but also the software which they wrote themselves. We show the details of software architecture and the prototype of this system in this presentation. |
|
| Organization: | Sincrotrone Trieste SCpA |
| Author(s): | Fabio Asnicar, Fulvio Bille', Roberto Borghes, Alessandro Busato, Valentina Chenda, Alessio Curri, Laura Del Cano, Daniele Favretto, Enrico Mariotti, Milan Prica, Roberto Pugliese, Michele Turcinovich |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | E2Science: The Elettra E-Science Platform |
We will describe the evolutions of the Elettra Virtual Collaboratory software resulting from the developments in the framework of the FP6 EU projects BIOXHIT, EUROTeV and GridCC, the related technologies and approaches and their application to remote operations of an accelerator and experimental stations. |
|
| Organization: | Sincrotrone Trieste SCpA |
| Author(s): | Fabio Asnicar, Fulvio Bille', Roberto Borghes, Alessandro Busato, Valentina Chenda, Alessio Curri, Laura Del Cano, Daniele Favretto, Enrico Mariotti, Milan Prica, Roberto Pugliese, Michele Turcinovich |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | The Open Virtual Unified Office |
We will describe the Open Virtual Unified Office, a facility management system developed in the framework of the FP6 EU project IA-SFS. The system is the evolution of the Elettra Virtual Users Office based on webservices and open source technologies. We will describe the many functionalities of the system and a possible solution to implement an European wide Clearing House for the management of beamtime applications based on network of systems integrated via webservices. |
|
| Organization: | Sincrotrone Trieste SCpA |
| Author(s): | Fabio Asnicar, Fulvio Bille', Roberto Borghes, Alessandro Busato, Valentina Chenda, Alessio Curri, Laura Del Cano, Daniele Favretto, Enrico Mariotti, Milan Prica, Roberto Pugliese, Michele Turcinovich |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | A New Platform for Experimental Stations At Elettra: the Upgrade of Xray Diffraction Beamline |
We will describe the new platform for experimental stations at Elettra developed in the framework of the upgrade of the Xray diffraction beamline. The platform based on the TANGO control system, CORBA and webservices was developed to support the challenging requirements of High Throughput protein crystallography in the framework of BIOXHIT FP6 EU project and integrates smothly with systems like DNA and the Elettra E-Science platform. |
|
| Organization: | Lawrence Berkeley National Lab |
| Authors: | J. M. Weber and M. J. Chin |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | Using FPGAs with Embedded Processors for Complete Hardware and Software Systems |
Field Programmable Gate Arrays (FPGAs) with embedded processors allow the instrumentation designer to field a system that tightly couples high speed (>500MHz) digital logic to a Control Systems-friendly software platform (i.e. Linux, VxWorks, EPICs). This technology merges CPU and I/O functions onto a single board allowing greater flexibility in physical form factor, power requirements, and data management. Without being constrained by a bus standard, hardware and software can join in a malleable design template. LBNL is currently using this technique to design a control system module for ALS booster top off operation and has completed designs for PEP-II transverse feedback electronics and ALS bunch cleaning. This presentation will include a hands-on demo of an FPGA evaluation board running a simplified example of a control system interface. |
|
| Organization: | ESRF |
| Authors: | Andrew Gotz, Jaroslaw Butanowicz, Lukasz Slezak |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | The moral of FABLE |
The moral of FABLE FABLE is a project to develop an integrated software solution for doing 3d xray diffraction (3DXRD). FABLE is also an attempt to develop professional applications for science. Put differently FABLE asks the question - can the professionals help us develop better scientific applications ? FABLE has chosen the Eclipse Rich Client Platform for developing graphical applications. The applications developed for FABLE make extensive use of the framework and patterns offered by Eclipse/RCP. FABLE follows the GUM theory of integrating the data taking process, online processing and offline data analysis. FABLE uses Gumtree (an Eclipse/RCP application being developed by ANSTO) services whenever possible. FABLE uses different protocols for talking to hardware (TANGO) and analysis programs (XMLRPC) and the grid (SOAP). Nexus is FABLE's data format of choice for storing data. This talk will present the lessons learned while developing the first FABLE applications for 3DXRD on ID11. FABLE home page : http://www.sourceforge.net/fable/wiki |
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| Organization: | Argonne National Laboratory, Intense Pulsed Neutron Source |
| Authors: | Rodney R. Porter |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | Sample Environment Control using EPICS on LINUX |
Sample environment control for the beam lines at Argonne National Laboratory's Intense Pulsed Neutron Source (IPNS) uses dedicated controllers, which connect to the EPICS control system through serial interfaces connected to port Servers. The programming for these interfaces was originally implemented in EPICS 3.13 on VME IOCs running VxWorks. These interfaces feature implementation of the majority of the serial command set for the controllers, auto sensing of device models for similar controllers, such as the LakeShore 330, 332, and 340, and a veto implementation with selectable equilibration times. They also implement a state notation program to control the serial throughput and for implementation of more complex features. These interfaces have now been converted to EPICS 3.14, which allows operation on a greater variety of hardware and operating systems. Testing of these interfaces was done on PCs running LINUX, to maintain compatibility with other computers in our data acquisition system, to take advantage of the faster Ethernet cards, and to maximize cost benefits. Running EPICS on LINUX PCs offers a tremendous cost savings compared to VME hardware, when real time performance is not needed. |
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| Organization: | LBNL/UCSF |
| Authors: | James M Holton |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| Title: | Why are we not solving more structures? |
Most X-ray data sets collected at synchrotron sources do not produce usable results. An analysis of data collected in 2003 at the ALS beamline 8.3.1 shows that 2346 datasets were collected and 48 structures were deposited in the PDB. Although it is understandable that not every dataset leads to a published structure, it is hard to explain how ~98% of them do not. This suggests that a great deal of improvement in scientific productivity can be attained if the reasons for failed projects are better understood. To clarify the nature of this gap, we have measured the success rates of each stage in the structure determination process. These statistics have allowed us to identify the most important stumbling blocks and we have now designed data collection strategies for avoiding them. Spot overlap is the most common cause of failure in data processing. Careful attention to collection strategy and appropriately bending the sample pin is a simple way to avoid this problem. Failure of MAD/SAD data sets to produce an interpretable map appears to be mainly due to insufficient signal-to-noise ratio in the data or rapid radiolysis of heavy atom sites. Simulations suggest that the average anomalous signal-to-noise ratio (delta-F/sigma(delta-F)) must be greater than unity for a MAD/SAD structure to succeed, and this fact has now been incorporated into the automated strategy program at 8.3.1. Experimental studies of the radiolysis rate of selenomethionine under different conditions are also underway. We have measured the rate of destruction of selenomethionine sites and found that it can be as much as six times faster than the rate of degradation of the diffraction pattern, making it difficult to detect. Although the exact mechanisms of radiation damage are still unclear, we now have an understanding of the "worst case scenario" and how to prepare for it. Another important cause of inefficiency is user fatigue. We have eliminated the need for late-night user presence with our new robotics system. Interactive screening of samples is conducted as usual during the day, but data collection runs can now be "postponed" until the midnight-8:00am shift. Individual user shifts can now be made shorter and more frequent. We expect this new feature will lead to more efficient use of beamline resources as well as faster optimization of crystal growth conditions, because users will be getting more rapid feedback on the quality of their samples. Future plans include mounting crystallization trays directly into the x-ray beam. Fluidigm's TOPAZ crystallizers are particularly well-suited for this task because they are not only well-optimized crystallization systems, but the trays can be easily shipped at room temperature without damaging the crystals. Preliminary experiments have demonstrated that background scattering is the major impediment to the quality of in-tray diffraction patterns. We are now working with Fluidigm Corporation to create a new line of low-background crystallizer chips as well as a plate goniometer for shooting any SBS compatible tray. |
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| Organization: | Oak Ridge National Laboratory |
| Authors: | M.D. Lumsden, J.L. Robertson, M. Yethiraj, W.T. Heller, S. Kulan, B. Larkins, and D.L. Maierhafer |
| Session: | Data Acquisition and Controls (II) (Wednesday morning) |
| Title: | The SPICE Data Acquisition System |
SPICE (Spectrometer and Instrument Control Environment) is a LabVIEW-based data acquisition system which has been designed for controlling the instrumentation at the High Flux Isotope Reactor (HFIR). The system has at its core a command processing engine which receives commands from several sources, including a text command line, graphical user interface, and web based interface and processes these through a first-in-first-out execution stack. All commands and hardware components are dynamically loaded and not part of the engine allowing for easy porting to various instrument types. The hardware interface layer uses a modular method-based approach which allows for control of both local and remote hardware. There are various built-in structures in the command processing engine that improve flexibility including an alias structure, the ability to perform mathematical functions in the commands, a simple macro language and full scripting capability through a COM link to Python. The instrument can be fully controlled remotely using a CGI interface and the instrument status is always available through a LabVIEW remote panel interface. The original implementation of SPICE was for the triple-axis spectrometers and this has been used successfully for several years. Several features of note include a full UB matrix implementation improving the handling of single crystals, simple one-button instrument alignment, and a spurion calculator. The interface has been well received by users and SPICE is now being implemented to control triple-axis spectrometers at University of Missouri, the MIT reactor, South Korea, and Japan. Very active development is taking place to port SPICE to the new SANS instruments at HFIR. All device drivers are now complete, including a LabVIEW driver for the ORDELA 21000N 2d position sensitive detector and we are fully controlling the SANS instruments using SPICE. We have developed a prototype GUI whose appearance can be tailored to the experience level of the user. The data is stored in an XML file format and routines are being written to allow on-the-fly 2d and 1d data reduction and visualization. |
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| Organization: | LBNL |
| Authors: | Mary Thompson |
| Session: | Software Development: Methods, Toolkits, and Frameworks (Tuesday morning) |
| Title: | An Introduction to Grid and Web Services and What They are Good for |
Web and Grid services are the latest "easy to write and use" solution to client/server applications. This talk will attempt to explain what it means to be web or grid service, how they differ. It will include a brief overview of the XML standards used such as SOAP, WSDL, WS-Basic Profile, and the WS-RF standards. It will also survey some of the Web services frameworks and tools with emphasis on Tomcat and Axis and what they provide to fullfil the promise of "ease of use and deployment". For Grid services we will look at the Globus Toolkit 4 (GT4), pyGridware and WSRF::Lite. I will try to clarify the advantages and disadvantages of the "service" approach in order help with a decision as to whether this technology would be useful in a particular application. |
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| Organization: | LBNL |
| Authors: | Robert F Gunion; Ron Tackaberry; Hanjing Huang |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | The Berkeley Device Server Architecture |
We have designed a device server to simplify the development of powerful, flexible, extensible, and easily maintained interfaces between users and hardware drivers. The Berkeley Device Server (BDS) architecture is written in C/C++, uses MICO/CORBA, and has been ported to Linux and Windows. BDS has enabled us to connect with a variety of hardware and software devices with a minimum of effort, including realistic simulations of hardware. By creating a simple and intuitive C client layer around the C++/CORBA middleware, we have been able to program for a wide variety of user interface environments including LabVIEW, IDL, and PHP; also, because BDS is CORBA based, integration with Java has been simple and painless. One of the most powerful capabilities of BDS is the dynamic creation and destruction of devices as the corresponding hardware is activated or deactivated. We will describe the issues that led to the development of BDS, the problems it has solved and its future directions. |
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| Organization: | Stanford Synchrotron Radiation Laboratory |
| Authors: | Clyde Smith, Aina Cohen, Mike Soltis |
| Session: | X-Ray Experimental Systems (Monday afternoon) |
| ** Combined with presentation 33 ** | |
| Title: | Remote access to SSRL Protein Crystallography beamlines |
Since June 2005, the protein crystallography users of the Stanford Synchrotron Radiation Laboratory (SSRL) have had the option to conduct diffraction experiments from their home institutions by means of advanced software tools that enable network-based control of the highly automated beamlines. Remote experimenters have access to the same tools as local users, and have the capability to mount, center, and screen pre-frozen samples, and to collect, analyze, and backup diffraction data. Automated sample mounting is accomplished with the Stanford Auto-Mounting System (SAM), beamline and experimental control is carried out using Blu-Ice/DCS, and additional remote monitoring of the experiment and data backup is supported with several web-based applications. The highly graphical applications and computational resources at SSRL are accessed through a client/server application that uses minimal resources on the client side and has a typical response similar to that obtained locally at the beamline console. This remote capability is now available on all six SSRL macromolecular crystallography beamlines. During the last user run, 75% of the user groups used the SAM robot, and 50% of the groups used the remote access tools, some from as far away as Australia and New Zealand. For pre-frozen samples the new technologies implemented at SSRL has eliminated the distinction between remote and local access to synchrotron resources. I will present a live remote access demonstration and connect to several SSRL beamlines to present the features accessible to remote users. |
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| Organization: | Division of Applied Science and Engineering, California Institute of Technology |
| Authors: | Jiao Lin, Max Kresch, Patrick Hung, John McCorquodale, Olivier Delaire, Mike McKerns, Michael Aivazis, Brent Fultz |
| Session: | Poster (Tuesday evening) |
| Title: | Reduction Package for Neutron Inelastic Time-of-Flight Instruments in DANSE |
DANSE (Distributed Data Analysis for Neutron Scattering Experiments, http://wiki.cacr.caltech.edu/danse/index.php) is a $12M NSF-funded effort to construct data analysis and reduction software to support the neutron science community. The DANSE project was prompted by the growing software needs of the newly constructed Spallation Neutron Source in Oak Ridge, Tennessee. A core data reduction package, that currently supports three inelastic TOF instruments, has been constructed. This package provides basic operations such as binning and rebinning, calibrations, and background corrections, and can be adpated fairly easily to support other instruments. The reduction library is written in C++, and is exported to python for better flexibility, extensibility, and interoperability. The reduction applications are built on top of the pyre framework, which provides a uniform way for applications to accept user inputs, and staging computing engines. Pyre also provides or will soon provide facilities like remote launching, remote monitoring, and parallel computing. Reduction applications for the LRMECS and PHAROS instruments are now available, and their GUI interfaces are based on wxPython. Using pyre's mpi bindings, a parallel version of the PHAROS reduction application can reduce a dataset to S(Q,E) in 7 seconds on 10 2GHz AMD Opteron processors, or in 35 seconds on a single processor. |
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| Organization: | Materials Science Division, California Institute of Technology |
| Authors: | Michael M. McKerns, Michael A.G. Aivazis, and Brent Fultz |
| Session: | Data Acquisition and Controls (I) (Tuesday afternoon) |
| Title: | DANSE (Distributed Data Analysis for Neutron Scattering Experiments): Extending the Scientific Toolkit for the Neutron Community |
The DANSE system will merge the various computational tasks of neutron scattering into a unified, component based run-time environment. Standard components will implement data analysis, visualization, modeling, and instrument simulation for all areas of neutron scattering. A core technology of DANSE is an open source framework that supports the software components and mediates their interactions. DANSE will provide tools to help instrument scientists and expert users migrate their existing routines to components, and allow new and casual users to access a stock set of standard analysis applications or configure their own new computing procedures for novel experiments. The modular structure of DANSE parallels the steps of data analysis performed by scientists, thus making it a natural environment for creating flexible computing procedures. DANSE will lower barriers to sharing software, and extend the experimentalist's toolkit with capabilities of analysis and interpretation such as high-performance simulations (band structure, molecular dynamics, etc.), co-analysis of data from multiple experiments, and real-time feedback for experimental control. |
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