The thrust for automation in synchrotron-based macromolecular crystallography

Sweet, Robert M.; Skinner, John M.; Cowan, Matt

doi:10.1080/08940880108261141

Cited by 7 publications

(5 citation statements)

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“…To make communication secure we chose OpenSSL, an open-source implementation of the SSL (Secure Sockets Layer) and TLS (Transport Layer Security) protocols, which is one of the most popular protocols used in Internet programming. This scheme is reliable and well designed under all operating systems for inter-process/program asynchronous communication (Pugliese et al, 1998;Ohata et al, 1998;Sweet et al, 2001). It allows the server and client to authenticate each other and to negotiate an encryption algorithm and cryptographic keys before any data will be transmitted between server and client.…”

Section: Unix Tcp/ip Secure Socket Client/server Schemementioning

confidence: 99%

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments

Gaponov

Igarashi

Hiraki

et al. 2003

J Synchrotron Radiat

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A control system for high‐throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X‐ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

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Section: Unix Tcp/ip Secure Socket Client/server Schemementioning

confidence: 99%

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments

Gaponov

Igarashi

Hiraki

et al. 2003

J Synchrotron Radiat

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“…A number of researchers have already studied and implemented remote access to synchrotrons [1][2][3] and other scientific instruments [4][5][6][7][8]. The Internet has also been used to access laboratories for educational purposes [9] and for remote collaboration during experiments at scientific facilities [3,4].…”

Section: Introductionmentioning

confidence: 99%

Experimenter's portal

Bauer

McIntyre

Sherry

et al. 2012

Proceedings of the 10th International Workshop on Middleware for Grids, Clouds and E-Science

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This paper describes an e-Science initiative to enable teams of scientists to run experiments with secure links at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens via common browsers to operate, observe and record essential parts of an experiment and to access remote cloud-based analysis software to process the large data sets that are often involved in complex experiments. This paper describes the architecture of the software, the underlying web services used for remote access to research facilities and describes the cloud-based approach for data analysis. The core services are general and can be used as the basis for access to a variety of systems, though specific screen interfaces and analysis software must be tailored to a facility. For illustrative purposes, we focus on use of the system to access a single site -a synchrotron beamline at the Canadian Light Source. We conclude with a discussion of the generality and extensibility of the software and services.

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“…These include the first electronic area-sensitive detector at a beamline in the US and on-site computer resources for real-time data reduction (1991). We developed the first graphical user interface (GUI) for diffractometer and data-reduction control (Skinner et al, 1993), an integrated GUI for beamline control and data collection (Skinner et al, 1996), automated spectrum analysis and energy optimization during MAD data collection (1995), 'one-button' data reduction with graphical analysis tools (Skinner & Sweet, 1998), integrated data-collection strategy prediction (Ravelli et al, 1997), web-based remote observation of the experiment (1998), web-based experimental control (1999), and automatic experiment logging into a webviewable log file (Sweet et al, 2001). We also have developed a broad and deep mail-in program for collaboration and service wherein specimens are shipped to our scientific staff for measurement 2 (Robinson et al, 2006).…”

Section: Background and Introductionmentioning

confidence: 99%

Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database

Skinner

Cowan

Buono

et al. 2006

Acta Crystallogr D Biol Cryst

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This manuscript chronicles the evolution of software used originally to control a diffractometer at a macromolecular crystallography beamline. The system has been augmented and rewritten. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. It provides automatic logging of the experiment and communication with the user, all the way from an initial proposal to perform the work to the end of data collection. This has included construction of a relational database to organize all details of the experiment and incorporation of a robotic specimen changer to provide automation for high-throughput applications.

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The thrust for automation in synchrotron-based macromolecular crystallography

Cited by 7 publications

References 0 publications

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments

Experimenter's portal

Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database

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