biblio.bib

@article{Chushkin:he5573,
author = "Chushkin, Y. and Zontone, F.",
title = "{Upsampling speckle patterns for coherent X-ray diffraction imaging}",
journal = "Journal of Applied Crystallography",
year = "2013",
volume = "46",
number = "2",
pages = "319--323",
month = "Apr",
doi = {10.1107/S0021889813003117},
url = {http://dx.doi.org/10.1107/S0021889813003117},
}

@article{Chushkin:rg5010,
author = "Chushkin, Y. and Caronna, C. and Madsen, A.",
title = "{A novel event correlation scheme for X-ray photon correlation spectroscopy}",
journal = "Journal of Applied Crystallography",
year = "2012",
volume = "45",
number = "4",
pages = "807--813",
month = "Aug",
doi = {10.1107/S0021889812023321},
url = {http://dx.doi.org/10.1107/S0021889812023321},
}
@article{ipython,
Author          = {P\'erez, F. and Granger, B. E.},
Title           = {{IP}ython: a {S}ystem for {I}nteractive {S}cientific {C}omputing},
Journal         = {{C}omput. {S}ci. {E}ng.},
Volume          = {9},
Number          = {3},
Pages           = {21-29},
month           = may,
year            = 2007,
url             = "http://ipython.org",
}

@misc{scipy,
  author =   {Jones, E. and Oliphant, T. E. and  Peterson, P.},
  title =     {{SciPy}: Open source scientific tools for {Python}},
  year =        {2001},
  url = "http://www.scipy.org/"
}

@article{numpy,
author = {Oliphant, T. E.},
title = {Python for Scientific Computing},
publisher = {IEEE},
year = {2007},
journal = {{C}omput. {S}ci. {E}ng.},
volume = {9},
number = {3},
pages = {10-20},
keywords = {high level languages; natural sciences computing},
COMMENTEDurl = {http://link.aip.org/link/?CSX/9/10/1}
}

@article{matplotlib,
 author = {Hunter, J. D.},
 title = {Matplotlib: A 2D Graphics Environment},
 journal = {{C}omput. {S}ci. {E}ng.},
 issue_date = {May 2007},
 volume = {9},
 number = {3},
 month = may,
 year = {2007},
 issn = {1521-9615},
 pages = {90-95},
 numpages = {6},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {Python, Python, scripting languages, application development, scientific programming, application development, scientific programming, scripting languages},
COMMENTEDurl = {http://dx.doi.org/10.1109/MCSE.2007.55},
COMMENTEDdoi = {10.1109/MCSE.2007.55},
COMMENTEDacmid = {1251845},
}
@article{pyhst,
author={Chilingaryan, S. and Mirone, A. and Hammersley, A. and Ferrero, C. and Helfen, L. and Kopmann, A. and dos Santos Rolo, T. and Vagovic, P.},
journal={Nuclear Science, IEEE Transactions on},
title={A GPU-Based Architecture for Real-Time Data Assessment at Synchrotron Experiments},
year={2011},
volume={58},
number={4},
pages={1447-1455},
keywords={data acquisition;high energy physics instrumentation computing;synchrotrons;tomography;GPU memory;GPU-based architecture;computational power;data acquisition;data rates;data transfers;digital detector technology;fast 2D detectors;graphic cards;high photon flux;imaging experiments;memory transfers;microtomography beamlines;quasireal-time visualization;real-time data assessment;reconstruction software;reconstruction time;synchrotron experiments;synchrotron facilities;synchrotron sources;system resources;Graphics processing unit;Image reconstruction;Kernel;Libraries;Pixel;Synchrotrons;Three dimensional displays;Computed tomography;GPU computing;high performance computing;image reconstruction;parallel programming;performance evaluation;software;synchrotrons},
doi={10.1109/TNS.2011.2141686},
ISSN={0018-9499},}

@article{pyhst2,
 title = {PyHST2: an hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities},
journal={ Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms},
 author={Alessandro Mirone and Emmanuelle Gouillart and  Emmanuel Brun and  Paul Tafforeau and Jerome Kieffer},
 year={2013},
 url = {http://arxiv.org/abs/1306.1392},
 status = {submitted},
 COMMENTEDvolume={58},
 COMMENTEDnumber={4},
 COMMENTEDpages={1447-1455}
}

@article{pymca,
 title = {A multiplatform code for the analysis of energy-dispersive X-ray fluorescence spectra},
 journal = {Spectrochim. Acta Part B},
 volume = {62},
 number = {1},
 pages = {63--68},
 year = {2007},
 author = { Solé, V.A. and Papillon, E. and Cotte, M. and Walter, Ph. and Susini, J.},
COMMENTEDissn = "0584-8547",
COMMENTEDdoi = "10.1016/j.sab.2006.12.002",
COMMENTEDkeywords = "X-ray fluorescence",
COMMENTEDurl = "http://www.sciencedirect.com/science/article/pii/S0584854706003764",
}

@article{edna,
author = {Incardona, M-F. and Bourenkov, G and Levik, K. and Pieritz, R and Popov, A. and Svensson, O. },
COMMENTEDauthor = {Incardona, Marie-Fran{\c{c}}oise and Bourenkov, Gleb P. and Levik, Karl and Pieritz, Romeu A. and Popov, Alexander N. and Svensson, Olof},
title = "{{\it EDNA}: a framework for plugin-based applications applied to X-ray experiment online data analysis}",
journal = "J. Synchrotron Rad.",
year = "2009",
volume = "16",
number = "6",
pages = {872-879},
month = "Nov",
COMMENTEDdoi = {10.1107/S0909049509036681},
COMMENTEDurl = {http://dx.doi.org/10.1107/S0909049509036681},
}


@article{cython,
    author={Behnel, S. and Bradshaw, R. and Citro, C. and Dalcin, L. and Seljebotn, D.S. and Smith, K.},
    journal={{C}omput. {S}ci. {E}ng.},
    title={Cython: The Best of Both Worlds},
    year={2011},
    month={march-april},
    volume={13},
    number={2},
    pages={31-39},
    keywords={Cython language;Fortran code;Python language extension;numerical loops;programming language;C language;numerical analysis;},
COMMENTEDdoi={10.1109/MCSE.2010.118},
COMMENTEDISSN={1521-9615},
}

@article{fabio,
  author =  {Knudsen, E. B. and S{\o}rensen, H. O. and Wright, J. P. and Goret, G. and Kieffer, J.},
  title =   {{FabIO}: easy access to two-dimensional X-ray detector images in {P}ython},
  year =    {2013},
  journal = {J. Appl. Cryst.},
  volume = {46},
  pages = {537-539},  
  COMMENTurl = {http://sourceforge.net/projects/fable/files/fabio},
  doi = {10.1107/S0021889813000150}
}
@misc{python,
    author = {van Rossum, G.},
    year = {1989},
    title = {Python programming language},
    url = {http://www.python.org},
}

@article{opencl,
author = {John E. Stone and David Gohara and Guochun Shi},
title = {OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems},
journal ={Computing in Science and Engineering},
volume = {12},
number = {3},
issn = {1521-9615},
year = {2010},
pages = {66-73},
doi = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2010.69},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}

@misc{opencl_khronos,
	author = {Khronos},
	year = {2008},
	title = {The open standard for parallel programming of heterogeneous systems},
	url = {http://www.khronos.org/opencl},
}
@article{pyopencl,
   author = {{Kl{\"o}ckner}, Andreas
        and {Pinto}, Nicolas
        and {Lee}, Yunsup
        and {Catanzaro}, B.
        and {Ivanov}, Paul
        and {Fasih}, Ahmed },
   title = "{PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation}",
   journal = "Parallel Computing",
   volume = "38",
   number = "3",
   pages = "157--174",
   year = "2012",
   issn = "0167-8191",
   doi = "10.1016/j.parco.2011.09.001",
}



@misc{skimage,
     author = {van der Walt, S. and others },
     title = {{scikits-image} is a collection of algorithms for image processing.},
     url = {http://scikits-image.org/},
     year = {2011},
}
@article{pynx,
author = "Favre-Nicolin, Vincent and Coraux, Johann and Richard, Marie-Ingrid and Renevier, Hubert",
title = "{Fast computation of scattering maps of nanostructures using graphical processing units}",
journal = "J. Appl. Cryst.",
year = "2011",
volume = "44",
number = "3",
pages = "635--640",
month = "Jun",
doi = {10.1107/S0021889811009009},
url = {http://dx.doi.org/10.1107/S0021889811009009},
}
@article{fullfield,
  author={B Fayard and E Pouyet and G Berruyer and D Bugnazet and C Cornu and M Cotte and V De Andrade and F Di Chiaro and O Hignette and J
Kieffer and T Martin and E Papillon and M Salomé and V A Solé},
  title={The new ID21 XANES full-field end-station at ESRF},
  journal={Journal of Physics: Conference Series},
  volume={425},
  number={19},
  pages={192001},
  url={http://stacks.iop.org/1742-6596/425/i=19/a=192001},
  year={2013},
  abstract={A new X-ray absorption near-edge spectroscopy (XANES) full-field imaging station has been developed, installed and tested on beamline ID21 at the European Synchrotron Radiation Facility (ESRF). The set-up operates in the 2-9 keV energy range and allows for the simultaneous acquisition of up to 4.10 6 XANES spectra over large sample areas with preserved sub-micron spatial resolution. The versatile set-up is compatible with various types of cameras and magnifying objectives. It accommodates spatial resolutions ranging from 0.3 ?m to 1.4 ?m and fields of view from 600 ?m up to 2 mm. The range of potential applications is broad: from geology, cultural heritage, environmental sciences to medicine.}
}
@article{pyFAI,
  author={Jerome Kieffer and Dimitrios Karkoulis},
  title={PyFAI, a versatile library for azimuthal regrouping},
  journal={Journal of Physics: Conference Series},
  volume={425},
  number={20},
  pages={202012},
  url={http://stacks.iop.org/1742-6596/425/i=20/a=202012},
  year={2013},
  abstract={2D area detectors like CCD or pixel detectors have become popular in the last 15 years for diffraction experiments (e.g. for WAXS, SAXS, single crystal and powder diffraction (XRPD)). These detectors have a large sensitive area of millions of pixels with high spatial resolution. The software package pyFAI has been designed to reduce SAXS, WAXS and XRPD images taken with those detectors into 1 D curves (azimuthal integration) usable by other software for in-depth analysis such as Rietveld refinement, or 2 D images (a radial transformation named caking ). As a library, the aim of pyFAI is to be integrated into other tools like PyMca or EDNA with a clean pythonic interface. However pyFAI features also command line tools for batch processing, converting data into q-space (q being the momentum transfer) or 2 ? -space ( ? being the Bragg angle) and a calibration graphical interface for optimizing the geometry of the experiment using the Debye-Scherrer rings of a reference sample. PyFAI shares the geometry definition of SPD but can directly import geometries determined by the software FIT2D. PyFAI has been designed to work with any kind of detector and geometry (transmission or reflection) and relies on FabIO, a library able to read more than 20 image formats produced by detectors from 12 different manufacturers. During the transformation from cartesian space (x,y) to polar space (2?, ?), both local and total intensities are conserved in order to obtain accurate quantitative results. Technical details on how this integration is implemented and how it has been ported to native code and parallelized on graphic cards are discussed in this paper.}
}

@inproceedings{pyFAI_gpu,
author = {Kieffer, J. and Ashiotis, G.}, 
title = {PyFAI: a Python library for high performance azimuthal integration on GPU}, 
booktitle = {PROC. OF THE 7th EUR. CONF. ON PYTHON IN SCIENCE (EUROSCIPY 2014)}, 
year = 2014,
url = {http://arxiv.org/pdf/1412.6367.pdf}
}

@article{pyFAI_2015,
author = "Ashiotis, Giannis and Deschildre, Aurore and Nawaz, Zubair and Wright, Jonathan P. and Karkoulis, Dimitrios and Picca, Fr{\'{e}}d{\'{e}}ric Emmanuel and Kieffer, J{\'{e}}r{\^{o}}me",
title = "{The fast azimuthal integration Python library: {\it pyFAI}}",
journal = "Journal of Applied Crystallography",
year = "2015",
volume = "48",
number = "2",
pages = "510--519",
month = "Apr",
doi = {10.1107/S1600576715004306},
url = {http://dx.doi.org/10.1107/S1600576715004306},
abstract = {{\it pyFAI} is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the {\it pyFAI} library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.},
keywords = {powder diffraction, small-angle X-ray scattering, geometry calibration, data reduction, image analysis, GPU programming, Python, computer programs},
}


@ARTICLE{Lowe04,
    author = {David G. Lowe},
    title = {Distinctive Image Features from Scale-Invariant Keypoints},
    journal = {International Journal of Computer Vision},
    year = {2004},
    volume = {60},
    pages = {91--110}
}
@article{Lowe99,
    author = {David G. Lowe},
    title = {Object Recognition from Local Scale-Invariant Features},
    journal = {Proc. of the International Conference on Computer Vision},
    year = {1999},
    doi = {10.1109/ICCV.1999.790410},
    pages = {1150 -- 1157},
    volume = {2},
}

@misc{SIFT_pat,
 author = {David G. Lowe},
 assignee = {The University Of British Columbia},
 holder = {The University Of British Columbia},
 title = {Method and apparatus for identifying scale invariant features in an image and use of same for locating an object in an image },
 year = {2003},
 month = {03},
 day = {23},
 url = {http://www.google.co.in/patents/US6711293},
 number = {US 6711293 B1},
 type = {Patent},
 filing_num = {10684114},
 yearfiled = {1999},
 monthfiled = {03},
 dayfiled = {08},
 abstract = {A method and apparatus for identifying scale invariant features in an image and a further method and apparatus for using such scale invariant features to locate an object in an image are disclosed. The method and apparatus for identifying scale invariant features may involve the use of a processor circuit for producing a plurality of component subregion descriptors for each subregion of a pixel region about pixel amplitude extrema in a plurality of difference images produced from the image. This may involve producing a plurality of difference images by blurring an initial image to produce a blurred image and by subtracting the blurred image from the initial image to produce the difference image. For each difference image, pixel amplitude extrema are located and a corresponding pixel region is defined about each pixel amplitude extremum. Each pixel region is divided into subregions and a plurality of component subregion descriptors are produced for each subregion. These component subregion descriptors are correlated with component subregion descriptors of an image under consideration and an object is indicated as being detected when a sufficient number of component subregion descriptors (scale invariant features) define an aggregate correlation exceeding a threshold correlation with component subregion descriptors (scale invariant features) associated with the object.}
}

@article{ASIFT,
    title   = {{ASIFT: An Algorithm for Fully Affine Invariant Comparison}},
    author  = {Yu, Guoshen and Morel, Jean-Michel},
    journal = {{Image Processing On Line}},
    volume  = {2011},
    year    = {2011},
    doi     = {10.5201/ipol.2011.my-asift},
    url     = {http://dx.doi.org/10.5201/ipol.2011.my-asift}
}

@article{lu,
   title={Fast Implementation of Scale Invariant Feature Transform Based on CUDA},
   author={Lu, Meng},
   journal={Appl. Math},
   volume={7},
   pages={717--722},
   year={2013},
   url={http://hgpu.org/?p=9337}
}
@article{rister,
   title={A FAST AND EFFICIENT SIFT DETECTOR USING THE MOBILE GPU},
   author={Rister, Blaine and Wang, Guohui and Wu, Michael and Cavallaro, Joseph R},
   year={2013},
   url={http://hgpu.org/?p=8983},
   journal = {IEEE International Conference on Acoustics, Speech, and Signal Processing},
   status = {submitted}
}
@article{vasilyev,
   title={Parallel SIFT-detector implementation for images matching},
   author={Vasilyev, Anton I. and Boguslavskiy, Andrey A. and Sokolov, Sergey M.},
   year={2011},
   journal = {International Conference on Computer Graphics and Vision (GraphiCon)},
   url={http://hgpu.org/?p=7017}
}
@article{surf_ipol,
	title = "An Analysis and Implementation of the SURF Method, and its Comparison to SIFT",
	author = "Oyallon, Edouard and  Rabin, Julien",
	journal = {{Image Processing On Line}},
	year = {2013},
	url	= {http://www.ipol.im/pub/pre/69}
}
@article{surf,
  author = {Bay, Herbert and Ess, Andreas and Tuytelaars, Tinne and Van Gool, Luc},
  title = {Speeded-Up Robust Features (SURF)},
  journal = {Comput. Vis. Image Underst.},
  issue_date = {June, 2008},
  volume = {110},
  number = {3},
  month = jun,
  year = {2008},
  issn = {1077-3142},
  pages = {346--359},
  numpages = {14},
  url = {http://dx.doi.org/10.1016/j.cviu.2007.09.014},
  doi = {10.1016/j.cviu.2007.09.014},
  acmid = {1370556},
  publisher = {Elsevier Science Inc.},
  address = {New York, NY, USA},
  keywords = {Camera calibration, Feature description, Interest points, Local features, Object recognition},
}
@misc{sift_pyocl,
    author = {Pierre Paleo and Jérôme Kieffer},
    year = {2013},
    title = {An implementation of SIFT on GPU with OpenCL},
    url = {https://github.com/kif/sift\_pyocl/archive/master.zip},
}
@article{andrade,
author = {De Andrade, Vincent and Susini, Jean and Salomé, Murielle and Beraldin, Olivier and Rigault, Cecile and Heymes, Thomas and Lewin, Eric and Vidal, Olivier},
title = {Submicrometer Hyperspectral X-ray Imaging of Heterogeneous Rocks and Geomaterials: Applications at the Fe K-Edge},
journal = {Anal. Chem.},
volume = {83},
number = {11},
pages = {4220-4227},
year = {2011},
doi = {10.1021/ac200559r},
URL = {http://pubs.acs.org/doi/abs/10.1021/ac200559r},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ac200559r}
}
@article{orsa,
    title   = {{Automatic Homographic Registration of a Pair of Images, with A Contrario Elimination of Outliers}},
    author  = {Moisan, Lionel and Moulon, Pierre and Monasse, Pascal},
    journal = {{Image Processing On Line}},
    volume  = {2012},
    year    = {2012},
    doi     = {10.5201/ipol.2012.mmm-oh},
    url     = {http://dx.doi.org/10.5201/ipol.2012.mmm-oh}
}
% if your bibliography style doesn't support doi fields:
%    note    = {\url{}}

@misc{cufft,
    author = {Nvidia},
    title = {{CUDA CUFFT Library}},
    year = {2007-2013},
    url = {http://docs.nvidia.com/cuda/cufft/}
}

@article{supcomb,
author = "Kozin, M. B. and Svergun, D. I.",
title = "{Automated matching of high- and low-resolution structural models}",
journal = "Journal of Applied Crystallography",
year = "2001",
volume = "34",
number = "1",
pages = "33--41",
month = "Feb",
doi = {10.1107/S0021889800014126},
url = {http://dx.doi.org/10.1107/S0021889800014126},
}

@article{damaver,
author = "Volkov, Vladimir V. and Svergun, Dmitri I.",
title = "{Uniqueness of {\it ab initio} shape determination in small-angle scattering}",
journal = "Journal of Applied Crystallography",
year = "2003",
volume = "36",
number = "3 Part 1",
pages = "860--864",
month = "Jun",
doi = {10.1107/S0021889803000268},
url = {http://dx.doi.org/10.1107/S0021889803000268},
}

@article{dammin,
journal = {Biophysical Journal},
volume = 76,
month = "June",
year = 1999, 
pages = "2879--2886",
title = "Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing",
author = "Svergun, D. I.",
}

@book{pyqt,
author = {Summerfield, Mark},
year = {2007},
month = {October},
day = {28},
title = {Rapid GUI Programming with Python and Qt},
publisher = {Prentice Hall},
edition = {first},
pages = {648},
isbn = {978-0-13-235418-9},
}

@InProceedings{DiamondSE,
author = {Aishima, Jun and Sikharulidze, Irakli and  Lehane, Conor and   Richter,Tobias and   Levik,Karl and Gerring, Matthew and Doutch,James  and Tully,Mark  and  Inoue, Katsuaki and  Terrill, Nick and Gibbons,Paul  and  Ashton, Alun},
title = {Integration of Data Acquisition and Data Analysis for SAXS Experiments at Diamond Light Source},
year= {2014},
booktitle = {American crystallographic Association},
month = {May}, 
note = {session M010.3}
}

@misc{freesas,
  author =   {Bonamis, G. and Kieffer, J},
  title =     {{FreeSAS}: Open source small angle scattering tools for {Python}},
  year =        {2015},
  url = "https://github.com/kif/freesas"
}

@article{Hura2009,
  author = {Hura, Greg L and Menon, Angeli L and Hammel, Michal and Rambo, Robert
	P and Poole II, Farris L and Tsutakawa, Susan E and Jenney Jr, Francis
	E and Classen, Scott and Frankel, Kenneth A and Hopkins, Robert C
	and Yang, Sung-jae and Scott, Joseph W and Dillard, Bret D and Adams,
	Michael W W and Tainer, John A},
  title = {Robust, high-throughput solution structural analyses by small angle
	X-ray scattering (SAXS)},
  journal = {Nat Meth},
  year = {2009},
  volume = {6},
  pages = {606--612},
  number = {8},
  month = aug,
  comment = {10.1038/nmeth.1353},
  issn = {1548-7091},
  publisher = {Nature Publishing Group},
  url = {http://dx.doi.org/10.1038/nmeth.1353}
}

@article{Graewert2013,
  author = {Melissa A Graewert and Dmitri I Svergun},
  title = {Impact and progress in small and wide angle X-ray scattering (SAXS
	and WAXS) },
  journal = {Current Opinion in Structural Biology },
  year = {2013},
  volume = {23},
  pages = {748 - 754},
  number = {5},
  note = {Protein-carbohydrate interactions / Biophysical methods },
  doi = {http://dx.doi.org/10.1016/j.sbi.2013.06.007},
  issn = {0959-440X},
  url = {http://www.sciencedirect.com/science/article/pii/S0959440X13001103}
}

@INCOLLECTION{Reyes2014,
  author = {Francis E. Reyes and Camille R. Schwartz and John A. Tainer and Robert
	P. Rambo},
  title = {Chapter Eleven - Methods for Using New Conceptual Tools and Parameters
	to Assess \{RNA\} Structure by Small-Angle X-Ray Scattering },
  booktitle = {Riboswitch Discovery, Structure and Function},
  publisher = {Academic Press},
  year = {2014},
  editor = {Donald H. Burke-Aguero},
  volume = {549},
  series = {Methods in Enzymology },
  pages = {235 - 263},
  doi = {http://dx.doi.org/10.1016/B978-0-12-801122-5.00011-8},
  issn = {0076-6879},
  keywords = {\{RNA\}},
  url = {http://www.sciencedirect.com/science/article/pii/B9780128011225000118}
}

@ARTICLE{P12,
  author = {Blanchet, Clement E. and Spilotros, Alessandro and Schwemmer, Frank
	and Graewert, Melissa A. and Kikhney, Alexey and Jeffries, Cy M.
	and Franke, Daniel and Mark, Daniel and Zengerle, Roland and Cipriani,
	Florent and Fiedler, Stefan and Roessle, Manfred and Svergun, Dmitri
	I.},
  title = {{Versatile sample environments and automation for biological solution
	X-ray scattering experiments at the P12 beamline (PETRA III, DESY)}},
  journal = {Journal of Applied Crystallography},
  year = {2015},
  volume = {48},
  pages = {431--443},
  number = {2},
  month = {Apr},
  doi = {10.1107/S160057671500254X},
  keywords = {biological small-angle X-ray scattering, high-brilliance P12 synchrotron
	beamline, automated hardware and software systems},
  url = {http://dx.doi.org/10.1107/S160057671500254X}
}


@ARTICLE{BM29paper,
  author = {Pernot, Petra and Round, Adam and Barrett, Ray and De Maria Antolinos,
	Alejandro and Gobbo, Alexandre and Gordon, Elspeth and Huet, Julien
	and Kieffer, Jer{\^{o}}me and Lentini, Mario and Mattenet, Muriel
	and Morawe, Christian and Mueller-Dieckmann, Christoph and Ohlsson,
	Staffan and Schmid, Werner and Surr, John and Theveneau, Pascal and
	Zerrad, Louiza and McSweeney, Sean},
  title = {{Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution}},
  journal = {Journal of Synchrotron Radiation},
  year = {2013},
  volume = {20},
  pages = {660--664},
  number = {4},
  month = {Jul},
  doi = {10.1107/S0909049513010431},
  keywords = {small-angle X-ray scattering, proteins in solution, automation and
	high throughput, online HPLC, structural biology},
  url = {http://dx.doi.org/10.1107/S0909049513010431}
}

@ARTICLE{B21,
  author = {Materlik, Gerhard and Rayment, Trevor and Stuart, David I.},
  title = {Diamond Light Source: status and perspectives},
  journal = {Philosophical Transactions of the Royal Society of London A: Mathematical,
	Physical and Engineering Sciences},
  year = {2015},
  volume = {373},
  number = {2036},
  doi = {10.1098/rsta.2013.0161},
  isbn = {1471-2962},
  issn = {1364-503X},
  publisher = {The Royal Society}
}

@article{scslac,
doi = {10.1107/S0909049512008072},
volume = {19},
year = {2012},
title = {An integrated high-throughput data acquisition system for biological solution X-ray scattering studies},
abstract = {A fully automated high-throughput solution X-ray scattering data collection system, developed for protein structure studies at beamline 4-2 of the Stanford Synchrotron Radiation Lightsource, is described.}, 
author = {Martel, Anne and  Liu, Ping and  Weiss, Thomas M and Niebuhr, Marc and Tsuruta, Hiro},
journal = {Journal of Synchrotron Radiation},
pages = {431--434},
}

@ARTICLE{SCpaper,
  author = {Round, Adam and Felisaz, Franck and Fodinger, Lukas and Gobbo, Alexandre
	and Huet, Julien and Villard, Cyril and Blanchet, Clement E. and
	Pernot, Petra and McSweeney, Sean and Roessle, Manfred and Svergun,
	Dmitri I. and Cipriani, Florent},
  title = {{BioSAXS Sample Changer: a robotic sample changer for rapid and reliable
	high-throughput X-ray solution scattering experiments}},
  journal = {Acta Crystallographica Section D},
  year = {2015},
  volume = {71},
  pages = {67--75},
  number = {1},
  month = {Jan},
  doi = {10.1107/S1399004714026959},
  keywords = {small-angle X-ray scattering, BioSAXS Sample Changer, high-throughput,
	automation},
  url = {http://dx.doi.org/10.1107/S1399004714026959}
}

@ARTICLE{SECPaper2012,
  author = {Round, Adam and Brown, Elizabeth and Marcellin, Romain and Kapp,
	Ulrike and Westfall, Corey S. and Jez, Joseph M. and Zubieta, Chloe},
  title = {{Determination of the GH3.12 protein conformation through HPLC-integrated
	SAXS measurements combined with X-ray crystallography}},
  journal = {Acta Crystallographica Section D},
  year = {2013},
  volume = {69},
  pages = {2072--2080},
  number = {10},
  month = {Oct},
  doi = {10.1107/S0907444913019276},
  keywords = {small-angle X-ray scattering, GH3 family, acyl acid-amido synthetase,
	hormone amino-acid conjugates},
  url = {http://dx.doi.org/10.1107/S0907444913019276}
}

@article{SECbiocat,
author = "Mathew, Elizabeth and Mirza, Ahmed and Menhart, Nick",
title = "{Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins}",
journal = "Journal of Synchrotron Radiation",
year = "2004",
volume = "11",
number = "4",
pages = "314--318",
month = "Jul",
doi = {10.1107/S0909049504014086},
url = {http://dx.doi.org/10.1107/S0909049504014086},
abstract = {Small-angle X-ray scattering and size-exclusion chromatography have been combined within a unified experimental set-up to obtain molecular size information. Besides providing simultaneous corroborative data bearing on the same question from two distinct experimental techniques, passing the samples over a gel filtration column immediately prior to illumination by X-rays provides both a more homogeneous sample and a continuous set of data as the concentration is extrapolated to zero. This greatly facilitates analysis of data from oligomerizing or aggregating proteins and increases the reliability of the results.},
keywords = {SAXS, liquid chromatography, Guinier, aggregation},
}

@article{DPDAK,
author = "Benecke, Gunthard and Wagermaier, Wolfgang and Li, Chenghao and Schwartzkopf, Matthias and Flucke, Gero and Hoerth, Rebecca and Zizak, Ivo and Burghammer, Manfred and Metwalli, Ezzeldin and M{\"{u}}ller-Buschbaum, Peter and Trebbin, Martin and F{\"{o}}rster, Stephan and Paris, Oskar and Roth, Stephan V. and Fratzl, Peter",
title = "{A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new {\it DPDAK} package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering}",
journal = "Journal of Applied Crystallography",
year = "2014",
volume = "47",
number = "5",
pages = "1797--1803",
month = "Oct",
doi = {10.1107/S1600576714019773},
url = {http://dx.doi.org/10.1107/S1600576714019773},
abstract = {X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, {\it DPDAK} (directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of {\it DPDAK} for on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure of {\it DPDAK} and the possibilities and limitations are discussed.},
keywords = {small-angle X-ray scattering, grazing-incidence small-angle X-ray scattering, data reduction, data analysis, computer programs}
}

@article{SCchess,
author = "Nielsen, S. S. and M{\o}ller, M. and Gillilan, R. E.",
title = "{High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell}",
journal = "Journal of Applied Crystallography",
year = "2012",
volume = "45",
number = "2",
pages = "213--223",
month = "Apr",
doi = {10.1107/S0021889812000957},
url = {http://dx.doi.org/10.1107/S0021889812000957},
abstract = {With the rise in popularity of biological small-angle X-ray scattering (BioSAXS) measurements, synchrotron beamlines are confronted with an ever-increasing number of samples from a wide range of solution conditions. To meet these demands, an increasing number of beamlines worldwide have begun to provide automated liquid-handling systems for sample loading. This article presents an automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell. The design incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination. Both the robot-control and the data-processing systems are written in Python. The data-processing code, {\it RAW}, has been enhanced with several new features to form a user-friendly BioSAXS pipeline for the robot. The flow cell also supports efficient manual loading and sample recovery. An effective rinse protocol for the sample cell is developed and tested. Fluid dynamics within the sample capillary reveals a vortex ring pattern of circulation that redistributes radiation-damaged material. Radiation damage is most severe in the boundary layer near the capillary surface. At typical flow speeds, capillaries below 2mm in diameter are beginning to enter the Stokes (creeping flow) regime in which mixing due to oscillation is limited. Analysis within this regime shows that single-pass exposure and multiple-pass exposure of a sample plug are functionally the same with regard to exposed volume when plug motion reversal is slow. The robot was tested on three different beamlines at the Cornell High-Energy Synchrotron Source, with a variety of detectors and beam characteristics, and it has been used successfully in several published studies as well as in two introductory short courses on basic BioSAXS methods.},
keywords = {biological small-angle X-ray scattering, robotics, microfluidics},
}

@article{BioXTASraw,
author = "Nielsen, S. S. and Toft, K. Noergaard and Snakenborg, D. and Jeppesen, M. G. and Jacobsen, J. K. and Vestergaard, B. and Kutter, J. P. and Arleth, L.",
title = "{{\it BioXTAS RAW}, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis}",
journal = "Journal of Applied Crystallography",
year = "2009",
volume = "42",
number = "5",
pages = "959--964",
month = "Oct",
doi = {10.1107/S0021889809023863},
url = {http://dx.doi.org/10.1107/S0021889809023863},
abstract = {A fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering (SAXS) data is presented. The program is freely distributed, following the open-source philosophy, and does not rely on any commercial software packages. {\it BioXTAS RAW} is a fully automated program that, {\it via} an online feature, reads raw two-dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averaging, error bar calculation, artifact removal, normalization and {\it q} calibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easy {\it via} the graphical user interface. {\it BioXTAS RAW} also provides preliminary analysis of one-dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair-distance distribution function, PDDF, and is thereby a free and open-source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII-format input files and is currently compatible with one-dimensional data files from SAXS beamlines at a number of synchrotron facilities. {\it BioXTAS RAW} is written in Python with C++ extensions.},
keywords = {BioXTAS RAW, open-source software, computer programs, small-angle X-ray scattering (SAXS)}
}

@misc{SAXSUtilities,
author = "Sztucki, M.",
title = {On-line processing and analysis of SAXS data},
url = {http://www.sztucki.de/SAXSutilities},
note = {Accessed: 2015-06-15},
year = {2015}
}

@ARTICLE{X33P,
author = {Daniel Franke and Alexey G. Kikhney and Dmitri I. Svergun},
title = {Automated acquisition and analysis of small angle X-ray scattering data },
journal = {Nuclear Instruments and Methods in Physics Research Section A: Accelerators,	Spectrometers, Detectors and Associated Equipment },
year = {2012},
volume = {689},
pages = {52 - 59},
COMnumber = {0},
doi = {http://dx.doi.org/10.1016/j.nima.2012.06.008},
issn = {0168-9002},
keywords = {\{SAXS\}},
url = {http://www.sciencedirect.com/science/article/pii/S0168900212006444}
}

@article{ATSAS1,
  title={ATSAS 2.1-towards automated and web-supported small-angle scattering data analysis},
  author={Petoukhov, Maxim V and Konarev, Peter V and Kikhney, Alexey G and Svergun, Dmitri I},
  journal={Applied Crystallography},
  year={2007},
  publisher={International Union of Crystallography}
}


@article{ATSAS2,
author = "Petoukhov, Maxim V. and Franke, Daniel and Shkumatov, Alexander V. and Tria, Giancarlo and Kikhney, Alexey G. and Gajda, Michal and Gorba, Christian and Mertens, Haydyn D. T. and Konarev, Petr V. and Svergun, Dmitri I.",
title = "{New developments in the {\it ATSAS} program package for small-angle scattering data analysis}",
journal = "Journal of Applied Crystallography",
year = "2012",
volume = "45",
number = "2",
pages = "342--350",
month = "Apr",
doi = {10.1107/S0021889812007662},
url = {http://dx.doi.org/10.1107/S0021889812007662},
abstract = {New developments in the program package {\it ATSAS} (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new {\it ATSAS} release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run {\it ATSAS} programs, are also presented.},
keywords = {isotropic scattering, small-angle scattering, data analysis, biological macromolecules, structural modelling, ATSAS, computer programs},
}

@ARTICLE{SECP12,
author = {Graewert, Melissa A. and Franke, Daniel and Jeffries, Cy M. and Blanchet,
	Clement E. and Ruskule, Darja and Kuhle, Katja and Flieger, Antje
	and Sch{\"a}fer, Bernd and Tartsch, Bernd and Meijers, Rob and Svergun,
	Dmitri I.},
title = {Automated Pipeline for Purification, Biophysical and X-Ray Analysis of Biomacromolecular Solutions},
journal = {Sci. Rep.},
year = {2015},
volume = {5},
pages = {--},
month = jun,
abstract = {Small angle X-ray scattering (SAXS), an increasingly popular method
	for structural analysis of biological macromolecules in solution,
	is often hampered by inherent sample polydispersity. We developed
	an all-in-one system combining in-line sample component separation
	with parallel biophysical and SAXS characterization of the separated
	components. The system coupled to an automated data analysis pipeline
	provides a novel tool to study difficult samples at the P12 synchrotron
	beamline (PETRA-3, EMBL/DESY, Hamburg).},
publisher = {Macmillan Publishers Limited},
url = {http://dx.doi.org/10.1038/srep10734}
}

@article{SCtainer2009,
author= {Hura, Greg L and Menon, Angeli L and Hammel, Michal and Rambo, Robert P and Poole II, Farris L and Tsutakawa, Susan E and Jenney Jr, Francis E and Classen, Scott and Frankel, Kenneth A and Hopkins, Robert C and Yang, Sung-jae and Scott, Joseph W and AU  - Dillard, Bret D and Adams, Michael W W and Tainer, John A},
title = {Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)},
journal = {Nature Meth.},
pages = {606--612},
doi = {10.1038/nmeth.1353},
year = {2009},
vol = {6},
}

@article{SECSWING,
author = "David, G. and P{\'{e}}rez, J.",
title = "{Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline}",
journal = "Journal of Applied Crystallography",
year = "2009",
volume = "42",
number = "5",
pages = "892--900",
month = "Oct",
doi = {10.1107/S0021889809029288},
url = {http://dx.doi.org/10.1107/S0021889809029288},
abstract = {Small-angle X-ray scattering for macromolecules in solution is now widely used in structural biology to complement high-resolution structure determination obtained by X-ray crystallography or NMR. In the context of third-generation synchrotron sources, this increasing interest leads to developments in sample environments and automation. The presence of an online purification system is justified by the need for sample monodispersity. A combined system including an auto-sampler robot and online high-performance liquid chromatography (HPLC) has been developed and optimized at the SWING beamline of Synchrotron SOLEIL (Gif-sur-Yvette, France). In the sample changer mode, a few microlitres of sample can be injected between two air bubbles and circulated at a controlled speed of typically 40{$\mu$}lmin${\sp {$-$}1}$. A maximum of 14 samples per hour could be measured in this mode by remote controlling the sample injections. In the HPLC mode, an initially polydisperse sample can be separated into each of its components before immediate data acquisition. The sample cell is thermostated, and offers a visualization control and online UV{--}Vis absorption monitoring.},
keywords = {monodisperse protein solutions, low-resolution structures, liquid chromatography, circulation cell, solution sample changer, small-angle X-ray scattering (SAXS), macromolecular crystallography},
}

@article{ISPYBB,
author = "De Maria Antolinos, Alejandro and Pernot, Petra and Brennich, Martha E. and Kieffer, J{\'{e}}r{\^{o}}me and Bowler, Matthew W. and Delageniere, Solange and Ohlsson, Staffan and Malbet Monaco, Stephanie and Ashton, Alun and Franke, Daniel and Svergun, Dmitri and McSweeney, Sean and Gordon, Elspeth and Round, Adam",
title = "{ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments}",
journal = "Acta Crystallographica Section D",
year = "2015",
volume = "71",
number = "1",
pages = "76--85",
month = "Jan",
doi = {10.1107/S1399004714019609},
url = {http://dx.doi.org/10.1107/S1399004714019609},
abstract = {Logging experiments with the laboratory-information management system ISPyB (Information System for Protein crystallography Beamlines) enhances the automation of small-angle X-ray scattering of biological macromolecules in solution (BioSAXS) experiments. The ISPyB interface provides immediate user-oriented online feedback and enables data cross-checking and downstream analysis. To optimize data quality and completeness, ISPyBB (ISPyB for BioSAXS) makes it simple for users to compare the results from new measurements with previous acquisitions from the same day or earlier experiments in order to maximize the ability to collect all data required in a single synchrotron visit. The graphical user interface (GUI) of ISPyBB has been designed to guide users in the preparation of an experiment. The input of sample information and the ability to outline the experimental aims in advance provides feedback on the number of measurements required, calculation of expected sample volumes and time needed to collect the data: all of this information aids the users to better prepare for their trip to the synchrotron. A prototype version of the ISPyBB database is now available at the European Synchrotron Radiation Facility (ESRF) beamline BM29 and is already greatly appreciated by academic users and industrial clients. It will soon be available at the PETRA III beamline P12 and the Diamond Light Source beamlines I22 and B21.},
keywords = {small-angle X-ray scattering, proteins in solution, automation, laboratory information-management system},
}


@article{dammif,
author = "Franke, Daniel and Svergun, Dmitri I.",
title = "{{\it DAMMIF}, a program for rapid {\it ab-initio} shape determination in small-angle scattering}",
journal = "Journal of Applied Crystallography",
year = "2009",
volume = "42",
number = "2",
pages = "342--346",
month = "Apr",
doi = {10.1107/S0021889809000338},
url = {http://dx.doi.org/10.1107/S0021889809000338},
abstract = {{\it DAMMIF}, a revised implementation of the {\it ab}-{\it initio} shape-determination program {\it DAMMIN} for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to {\it DAMMIN}. In equivalent conditions, {\it DAMMIF} is 25{--}40 times faster than {\it DAMMIN} on a single CPU. The possibility to utilize multiple CPUs is added to {\it DAMMIF}. The application is available in binary form for major platforms.},
keywords = {computer programs, DAMMIF, DAMMIN, small-angle scattering, particle shape determination},
}

@ARTICLE{RamboTainerNature2013,
  author = {Rambo, Robert P. and Tainer, John A.},
  title = {Accurate assessment of mass, models and resolution by small-angle
	scattering},
  journal = {Nature},
  year = {2013},
  volume = {496},
  pages = {477--481},
  number = {7446},
  month = apr,
  issn = {0028-0836},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited.
	All Rights Reserved.},
  url = {http://dx.doi.org/10.1038/nature12070}
}

@article{cwt,
author = {Du, Pan and Kibbe, Warren A. and Lin, Simon M.}, 
title = {Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
volume = {22}, 
number = {17}, 
pages = {2059-2065}, 
year = {2006}, 
doi = {10.1093/bioinformatics/btl355}, 
abstract ={Motivation: A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods.Results: Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, ‘true’ peaks have characteristic shapes, and providing a shape-matching function that provides a ‘goodness of fit’ coefficient should provide a more robust peak identification method. Based on these observations, a continuous wavelet transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and in addition provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2D CWT coefficients can greatly enhance the effective signal-to-noise ratio. Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low.Availability: The algorithm is implemented in R and will be included as an open source module in the Bioconductor project.Contact:s-lin2@northwestern.eduSupplementary material:http://basic.northwestern.edu/publications/peakdetection/. Colour versions of the figures in this article can be found at Bioinformatics Online.}, 
URL = {http://bioinformatics.oxfordjournals.org/content/22/17/2059.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/22/17/2059.full.pdf+html}, 
journal = {Bioinformatics} 
}

@inproceedings{tango,
author = {G{\"o}tz, A. and  Taurel, E. and  Pons, J.L. and Verdier, P. and  Chaize, J.M. and  Meyer, J. and Poncet, F.  and Heunen, G. and G{\"o}tz, E.},
title = {TANGO A CORBA BASED CONTROL SYSTEM},
booktitle = {Proceedings of ICALEPCS2003},
year = 2003,
note = {MP705}, 
address = {Gyeongju, Korea},
}

@inproceedings{pytango,
author = {Rubio-Manrique, S. and Coutinho, T. and  Su{\~n}{\'e}, R. and Taurel, E.},
title = {DYNAMIC ATTRIBUTES AND OTHER FUNCTIONAL FLEXIBILITIES OF PyTango},
booktitle = {Proceedings of ICALEPCS2009},
year = 2009,
note = {THP07}, 
address = {Kobe, Japan}
}

@article{xrdua,
author = "De Nolf, Wout and Vanmeert, Frederik and Janssens, Koen",
title = "{{\it XRDUA}: crystalline phase distribution maps by two-dimensional scanning and tomographic (micro) X-ray powder diffraction}",
journal = "Journal of Applied Crystallography",
year = "2014",
volume = "47",
number = "3",
pages = "1107--1117",
month = "Jun",
doi = {10.1107/S1600576714008218},
url = {http://dx.doi.org/10.1107/S1600576714008218},
abstract = {Imaging of crystalline phase distributions in heterogeneous materials, either plane projected or in virtual cross sections of the object under investigation, can be achieved by scanning X-ray powder diffraction employing X-ray micro beams and X-ray-sensitive area detectors. Software exists to convert the two-dimensional powder diffraction patterns that are recorded by these detectors to one-dimensional diffractograms, which may be analysed by the broad variety of powder diffraction software developed by the crystallography community. However, employing these tools for the construction of crystalline phase distribution maps proves to be very difficult, especially when employing micro-focused X-ray beams, as most diffraction software tools have mainly been developed having structure solution in mind and are not suitable for phase imaging purposes. {\it XRDUA} has been developed to facilitate the execution of the complete sequence of data reduction and interpretation steps required to convert large sequences of powder diffraction patterns into a limited set of crystalline phase maps in an integrated fashion.},
keywords = {scanning X-ray powder diffraction, tomography, crystalline phase distribution maps, computer programs},
}

@ARTICLE{SHANUM,
  author = {Konarev, Petr V. and Svergun, Dmitri I.},
  title = {{{\it A posteriori} determination of the useful data range for small-angle
	scattering experiments on dilute monodisperse systems}},
  journal = {IUCrJ},
  year = {2015},
  volume = {2},
  pages = {352--360},
  number = {3},
  month = {May},
  abstract = {Small-angle X-ray and neutron scattering (SAXS and SANS) experiments
	on solutions provide rapidly decaying scattering curves, often with
	a poor signal-to-noise ratio, especially at higher angles. On modern
	instruments, the noise is partially compensated for by oversampling,
	thanks to the fact that the angular increment in the data is small
	compared with that needed to describe adequately the local behaviour
	and features of the scattering curve. Given a (noisy) experimental
	data set, an important question arises as to which part of the data
	still contains useful information and should be taken into account
	for the interpretation and model building. Here, it is demonstrated
	that, for monodisperse systems, the useful experimental data range
	is defined by the number of meaningful Shannon channels that can
	be determined from the data set. An algorithm to determine this number
	and thus the data range is developed, and it is tested on a number
	of simulated data sets with various noise levels and with different
	degrees of oversampling, corresponding to typical SAXS/SANS experiments.
	The method is implemented in a computer program and examples of its
	application to analyse the experimental data recorded under various
	conditions are presented. The program can be employed to discard
	experimental data containing no useful information in automated pipelines,
	in modelling procedures, and for data deposition or publication.
	The software is freely accessible to academic users.},
  doi = {10.1107/S2052252515005163},
  keywords = {small-angle scattering, WAXS, SAXS, solution scattering, protein structure,
	Shanum},
  url = {http://dx.doi.org/10.1107/S2052252515005163}
}


@article{workflow,
author = "Brockhauser, Sandor and Svensson, Olof and Bowler, Matthew W. and Nanao, Max and Gordon, Elspeth and Leal, Ricardo M. F. and Popov, Alexander and Gerring, Matthew and McCarthy, Andrew A. and Gotz, Andy",
title = "{The use of workflows in the design and implementation of complex experiments in macromolecular crystallography}",
journal = "Acta Crystallographica Section D",
year = "2012",
volume = "68",
number = "8",
pages = "975--984",
month = "Aug",
doi = {10.1107/S090744491201863X},
url = {http://dx.doi.org/10.1107/S090744491201863X},
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 {\it Data Analysis WorkBench} ({\it DAWB}) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using {\it 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 {\it MXCuBE}.},
keywords = {workflows, automation, data processing, macromolecular crystallography, experimental protocols, characterization, reorientation, radiation damage},
}


@article{CORMAP,
	Author = {Franke, Daniel and Jeffries, Cy M and Svergun, Dmitri I},
	Date = {2015/05//print},
	Journal = {Nat Meth},
	Month = {05},
	Number = {5},
	Pages = {419--422},
	Title = {Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra},
	Volume = {12},
	Year = {2015},
	}
	
	
@article{jacques,
  title={Small-angle scattering for structural biologyÑExpanding the frontier while avoiding the pitfalls},
  author={Jacques, David A and Trewhella, Jill},
  journal={Protein Science},
  volume={19},
  number={4},
  pages={642--657},
  year={2010},
  publisher={Wiley Online Library}
}


@article{USSOMO,
  title={Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module},
  author={Brookes, Emre and P{\'e}rez, Javier and Cardinali, Barbara and Profumo, Aldo and Vachette, Patrice and Rocco, Mattia},
  journal={Journal of applied crystallography},
  volume={46},
  number={6},
  pages={1823--1833},
  year={2013},
  publisher={International Union of Crystallography}
}