[kepler-users] The use of Ptolemy 2 and clusters for data analysis at the Diamond Synchrotron

[Christopher Brooks]

We had a talk that might be of interest to the Kepler community about how
Matt Gerring and others are using Ptolemy II as an engine at the Diamond
Light Souce Synchrotron in the UK.

Basically, they use Ptolemy II inside Passerelle, inside Eclipse as an RCP
app.

The slides from the talk are at
http://embedded.eecs.berkeley.edu/seminar/#0b88c9

=====
The use of Ptolemy 2 and clusters for data analysis at the Diamond
Synchrotron

Mar 18, 2014, 4.10-5pm, Matt Gerring <http://www.diamond.ac.uk/>, Diamond
Light Source, United Kingdom.

Slides <http://chess.eecs.berkeley.edu/pubs/x.html>
Abstract

Diamond Light Source is a synchrotron radiation facility conducting
experiments in diverse areas such as crystallography, tomography,
microscopy, spectroscopy and radiography. The synchrotron machine produces
high energy light and requires automated systems to execute experiments
because of the extreme environment required. We will look at some of the
robots operating in this environment and how data is collected at Diamond.
We will also look at how data, once collected, is treated using Ptolemy 2 -
based actors. The seminar will include demonstrations of the Data Analysis
Workbench or DAWN which is open source software used to visualize and treat
data for users. DAWN is a collaboration between Diamond Light Source, the
ESRF and EMBL Grenoble.
Bio:

Matthew Gerring is a software developer and is enthusiastic about Ptolemy
2, Eclipse RCP and design patterns. He works on the DAWN product and
manages the DAWN collaboration at Diamond Synchrotron near Oxford in the
United Kingdom. He has been a keen Java developer for around 15 years and
is a committer to several open source projects, including Eclipse Nebula
and DAWN. When not glued to a screen and weather allowing, he can be found
outdoors walking with the family and dogs or doing a little fly fishing.
===

There is also a paper:

*The use of workflows in the design and implementation of complex
experiments in macromolecular crystallography.*
*Sandor Brockhauser, Olof Svensson, Matthew W. Bowler, Max Nanao, Elspeth
Gordon, Ricardo M.F. Leal, Alexander Popov, Matthew Gerring, Andrew
McCarthy, Andy Gotz*

*Citation*
Sandor Brockhauser, Olof Svensson, Matthew W. Bowler, Max Nanao, Elspeth
Gordon, Ricardo M.F. Leal, Alexander Popov, Matthew Gerring, Andrew
McCarthy, Andy Gotz. "The use of workflows in the design and implementation
of complex experiments in macromolecular crystallography.". *Acta
Crystallographica Section D*, 68(8):975-984, August 2012; (The workflows
use Ptolemy II as an engine.).

*Abstract*
The automation of beam delivery, sample handling and data analysis,
together with increasing photon flux, diminishing focal spot size and the
appearance of fast-readout detectors on synchrotron beamlines, have changed
the way that many macromolecular crystallography experiments are planned
and executed. Screening for the best diffracting crystal, or even the best
diffracting part of a selected crystal, has been enabled by the development
of microfocus beams, precise goniometers and fast-readout detectors that
all require rapid feedback from the initial processing of images in order
to be effective. All of these advances require the coupling of data
feedback to the experimental control system and depend on immediate online
data-analysis results during the experiment. To facilitate this, a Data
Analysis WorkBench (DAWB) for the flexible creation of complex automated
protocols has been developed. Here, example workflows designed and
implemented using DAWB are presented for enhanced multi-step crystal
characterizations, experiments involving crystal re-orientation with kappa
goniometers, crystal-burning experiments for empirically determining the
radiation sensitivity of a crystal system and the application of mesh scans
to find the best location of a crystal to obtain the highest diffraction
quality. Beamline users interact with the prepared workflows through a
specific brick within the beamline-control GUI *MXCuBE*.

*Electronic downloads*

   - http://dx.doi.org/10.1107%2FS090744491201863X

_Christopher
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