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<title>About — DIALS documentation</title>
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<section id="about">
<h1>About<a class="headerlink" href="#about" title="Link to this heading">¶</a></h1>
<p>Atomic structures are vital for scientific research. From understanding
the mechanisms of biology to the design of new materials for industrial applications,
knowing the placement of atoms in a molecule assists in the control of disease progression,
drug design, the development of therapies such as vaccines, building new compounds
for better batteries, and finding new methods of carbon sequestration.</p>
<p>Crystallography is one of the prime technologies used to generate high quality structures,
generated from crystallographic data collected at large facilities like synchrotrons and
X-ray free electron lasers, on large micro electron diffraction instruments, at neutron
sources, or at home in a lab. At these facilities and instruments, crystals are either
rotated in a beam of photons, neutrons, or electrons, or are exposed one at a time in a
serial experiment, and diffraction data from detectors are collected and stored in image
files. The DIALS software package (Diffraction Integration for Advanced Light Sources) is
used throughout the world for processing crystallographic data in automated pipelines or
through graphical user interfaces.</p>
<p>The DIALS software is developed in a fully open-source, collaborative
environment. The main development teams are based at <a class="reference external" href="http://www.diamond.ac.uk/Home.html">Diamond Light Source</a>
and <a class="reference external" href="http://www.ccp4.ac.uk/">CCP4</a>, in the UK, and at <a class="reference external" href="http://www.lbl.gov/">Lawrence Berkeley National Laboratory</a>, USA.
However, in the spirit of the open source movement, we welcome
collaboration from anyone who wishes to contribute to the project.</p>
<p>To avoid “reinventing the wheel” as much as possible, the DIALS project builds
on knowledge accumulated over many decades in the field of crystallographic
data processing. We benefit greatly from the altruism of experts who contribute their ideas
and advice, either directly or via their detailed publications on existing
algorithms and packages such as XDS <a class="footnote-reference brackets" href="#xds" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>2<span class="fn-bracket">]</span></a> and MOSFLM <a class="footnote-reference brackets" href="#mosflm" id="id2" role="doc-noteref"><span class="fn-bracket">[</span>3<span class="fn-bracket">]</span></a>. At the heart
of the DIALS framework lies a design philosophy of hardware abstraction and a
generalised model of the experiment
that is inspired directly by material published on the seminal workshops on
position sensitive detector software <a class="footnote-reference brackets" href="#lure" id="id3" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a>. Continuing in the spirit of these
workshops we held our own series of meetings, with talks from invited speakers, and code
camps in which specific problems are addressed by intensive effort across the
collaboration. Summaries of these meetings and copies of slides given as
presentations are available <a class="reference internal" href="workshops/index.html"><span class="doc">here</span></a>.</p>
<p>DIALS is written using Python and C++, making heavy use of the <a class="reference external" href="https://github.com/cctbx">cctbx</a> <a class="footnote-reference brackets" href="#rwgk" id="id4" role="doc-noteref"><span class="fn-bracket">[</span>4<span class="fn-bracket">]</span></a>
for core crystallographic calculations and much infrastructure including a
complete build system. Seamless interaction between the C++ and Python
components of this <em>hybrid system</em> is enabled by <a class="reference external" href="http://www.boost.org/doc/libs/1_59_0/libs/python/doc/index.html">Boost.Python</a>. Python provides
a useful ground for rapid prototyping, after which core algorithms and data
structures may be transferred over to C++ for speed. High level interfaces of
the hybrid system remain in Python, facilitating further development and code
reuse both within DIALS and by third parties.</p>
<section id="development-teams">
<h2>Development Teams<a class="headerlink" href="#development-teams" title="Link to this heading">¶</a></h2>
<section id="dials-uk">
<h3>DIALS UK<a class="headerlink" href="#dials-uk" title="Link to this heading">¶</a></h3>
<p>Development of DIALS in the UK is funded by the <a class="reference external" href="https://wellcome.ac.uk/">Wellcome Trust</a>,
<a class="reference external" href="http://www.diamond.ac.uk/Home.html">Diamond Light Source</a> and <a class="reference external" href="http://www.ccp4.ac.uk/">CCP4</a>, and led by <a class="reference external" href="http://www.diamond.ac.uk/Beamlines/Mx/VMXm/Staff/Evans.html">Dr Gwyndaf Evans</a>.</p>
</section>
<section id="dials-us">
<h3>DIALS US<a class="headerlink" href="#dials-us" title="Link to this heading">¶</a></h3>
<p>Development of DIALS at <a class="reference external" href="http://www.lbl.gov/">Lawrence Berkeley National Laboratory</a>, USA is led by
<a class="reference external" href="https://biosciences.lbl.gov/profiles/aaron-brewster/">Dr Aaron Brewster</a> and supported by <a class="reference external" href="http://www.nih.gov/">National Institutes of Health</a> /
<a class="reference external" href="http://www.nigms.nih.gov/">National Institute of General Medical Sciences</a> grant R24GM154040: <em>DIALS:
supporting structural biology through open source diffraction processing software</em>.
Work at LBNL is performed under <a class="reference external" href="http://www.energy.gov/">Department of Energy</a> contract
DE-AC02-05CH11231.</p>
</section>
</section>
<section id="acknowledgements">
<h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Link to this heading">¶</a></h2>
<p>We are grateful to all those who have contributed to the development
of DIALS.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Contributors include:
Aaron Brewster
Ammaar Saeed
Amy Thompson
Asmit Bhowmick
Benjamin Williams
Billy Poon
Daniel Paley
Daniel Tchon
David Waterman
Derek Mendez
Graeme Winter
Huw Jenkins
Hans-Christian Stadler
Ian Rees
Iris Young
James Beilsten-Edmands
James Parkhurst
Johan Hattne
Katrin Leinweber
Kevin Dalton
Lee James O'Riordan
Luis Fuentes-Montero
Marcin Wojdyr
Markus Gerstel
Nathaniel Echols
Nicholas Devenish
Nicholas Sauter
Nigel Moriarty
Oliver Zeldin
Richard Gildea
Robert Bolotovsky
Stef Smeets
Takanori Nakane
Tara Michels-Clark
Tarik Drevon
Yash Karan
Marko Petrovic
</pre></div>
</div>
<p>In addition, we acknowledge guidance and ideas gained through numerous
intellectual discussions with the following:</p>
<p>Alun Ashton,
Gleb Bourenkov,
Gerard Bricogne,
Phil Evans,
Andrew Leslie,
Nigel Moriarty,
Garib Murshudov,
Jim Pflugrath,
Harry Powell,
Jon Schuermann
and
Matthew Webber.</p>
<aside class="footnote-list brackets">
<aside class="footnote brackets" id="lure" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id3">1</a><span class="fn-bracket">]</span></span>
<p><cite>Bricogne, G. (1987). Proceedings of the CCP4 Daresbury Study Weekend, pp. 120-145.</cite></p>
</aside>
<aside class="footnote brackets" id="xds" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">2</a><span class="fn-bracket">]</span></span>
<p><cite>Kabsch, W. (2010). Acta Cryst. D66, 125-132.</cite></p>
</aside>
<aside class="footnote brackets" id="mosflm" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id2">3</a><span class="fn-bracket">]</span></span>
<p><cite>Leslie, A. G. W. and Powell H. R. (2007), Evolving Methods for Macromolecular Crystallography, 245, 41-51. ISBN 978-1-4020-6314-5.</cite></p>
</aside>
<aside class="footnote brackets" id="rwgk" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">4</a><span class="fn-bracket">]</span></span>
<p><cite>Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W., & Adams, P. D. (2002). Journal of Applied Crystallography. 35, 126–136.</cite></p>
</aside>
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