===== About ===== Information about ``nextPYP`` Developers ========== | Jeff Martin |jwm| |0000-0002-9773-3256| .. |jwm| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/jeffrey.martin :width: 16 :height: 16 :alt: GitLab commits from jwm .. |0000-0002-9773-3256| image:: _static/orcid.svg :target: https://orcid.org/0000-0002-9773-3256 :width: 16 :height: 16 :alt: ORCID profile for 0000-0002-9773-3256 | Ye Zhou |yez| |0000-0002-0489-3614| .. |yez| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/ye.zhou867 :width: 16 :height: 16 :alt: GitLab commits from yez .. |0000-0002-0489-3614| image:: _static/orcid.svg :target: https://orcid.org/0000-0002-0489-3614 :width: 16 :height: 16 :alt: ORCID profile for 0000-0002-0489-3614 | Hsuan-Fu Liu |hfl| |0000-0001-9302-7648| .. |hfl| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/tofushan :width: 16 :height: 16 :alt: GitLab commits from hfl .. |0000-0001-9302-7648| image:: _static/orcid.svg :target: https://orcid.org/0000-0001-9302-7648 :width: 16 :height: 16 :alt: ORCID profile for 0000-0001-9302-7648 | Xiaochen Du |dux| |0000-0001-6228-0907| .. |dux| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/xiaochen.du :width: 16 :height: 16 :alt: GitLab commits from dux .. |0000-0001-6228-0907| image:: _static/orcid.svg :target: https://orcid.org/0000-0001-6228-0907 :width: 16 :height: 16 :alt: ORCID profile for 0000-0001-6228-0907 | Qinwen Huang |qwh| |0000-0002-7082-5257| .. |qwh| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/qinwen.huang :width: 16 :height: 16 :alt: GitLab commits from qwh .. |0000-0002-7082-5257| image:: _static/orcid.svg :target: https://orcid.org/0000-0002-7082-5257 :width: 16 :height: 16 :alt: ORCID profile for 0000-0002-7082-5257 | Alberto Bartesaghi |alberto| |0000-0002-7360-1523| .. |alberto| image:: _static/gitlab.svg :target: https://gitlab.cs.duke.edu/alberto :width: 16 :height: 16 :alt: GitLab commits from alberto .. |0000-0002-7360-1523| image:: _static/orcid.svg :target: https://orcid.org/0000-0002-7360-1523 :width: 16 :height: 16 :alt: ORCID profile for 0000-0002-7360-1523 References ========== ``nextPYP`` implements algorithms reported in the following publications: - Liu, HF., Zhou, Y., Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J., Bartesaghi, A. (2023), `nextPYP: a comprehensive and scalable platform for characterizing protein variability in-situ using single-particle cryo-electron tomography `_, Nature Methods. - Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) `Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-Electron Microscopy `_, IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), pp. 3246-3255. - Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) `Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels `_, European Conference on Computer Vision (ECCV) 13681, pp. 644-660. - Liu, HF., Zhou, Y., Bartesaghi, A. (2022) `High-resolution structure determination using high-throughput electron cryo-tomography `_, Acta Crystallographica Section D: Structural Biology 78 (7), pp. 817-824. - Bouvette, J., Liu, HF., Du, X., Zhou, Y., Sikkema, AP., da Fonseca Rezende e Mello, J., Klemm, BP., Huang, R., Schaaper, RM., Borgnia, MJ., Bartesaghi. A., (2021) `Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography `_, Nature Communications 12, 1957. - Zhou, Y., Moscovich, A., Bendory, T., Bartesaghi, A., (2019) `Unsupervised particle sorting for high-resolution single-particle cryo-EM `_, Inverse Problems 36, 044002. - Bartesaghi, A., Aguerrebere, C., Falconieri, V., Banerjee, S., Earl, L. A., Zhu, X., ... & Subramaniam, S. (2018). `Atomic resolution cryo-EM structure of β-galactosidase `_. Structure, 26(6), pp. 848-856. - Bartesaghi, A., Lecumberry, F., Sapiro, G., Subramaniam, S., (2012). `Protein secondary structure determination by constrained single-particle cryo-electron tomography `_, Structure, 20(12), pp. 2003-13. Funding ======= Development of ``nextPYP`` is supported by grants from NIGMS (R01-GM141223), NIAID (U54-AI170752), the Chan Zuckerberg Initiative (2021-234602), and Duke University. Dependencies ============ ``nextPYP`` uses functionality from `IMOD `_, `cisTEM `_, and `CTFFIND4 `_. cisTEM and CTFFIND4 license terms --------------------------------- .. code-block:: bash Copyright © 2023 Howard Hughes Medical Institute Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - Neither the name of HHMI nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 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IMOD license terms ------------------ .. code-block:: bash IMOD Version 4.11 Copyright Notice and Credits -------------------------------------------------------------------------- Except as noted, ALL SOFTWARE LISTED IS Copyright (C) 1994-2020 by the Regents of the University of Colorado. All portions of IMOD, except as noted below, are open source under the General Public License (GPL) version 2.0. A copy of this license is in the file GPL.txt. (All license files referred to here are in the directory 'licenses' in the binary distribution or 'dist' in the source code.) The libraries written entirely in C/C++ are released under the Lesser GPL (see LGPL.txt). Software may be modified and redistributed under the terms of these licenses. The source can be found at http://bio3d.colorado.edu/imod/nightlyBuild and http://bio3d.colorado.edu/imod/openSource THIS SOFTWARE AND/OR DOCUMENTATION IS PROVIDED WITH NO WARRANTY, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. Programs were written by David Mastronarde, James Kremer, Rick Gaudette, Sue Held, Quanren Xiong, and John Heumann at the University of Colorado, some based on work and libraries from the MRC. We thank David Agard and Hans Chen for the original MRC source code, Wah Chiu for a Unix version of low-level MRC file routines used in the FORTRAN parts, and Chuck Robertson for much work on the port to Linux. The program nad_eed_3d by Achilleas Frangakis and Reiner Hegerl is copyright Max-Planck-Institut for Biochemistry, Martinsried, Germany. The LSQR routine by Michael Saunders is used in some programs. IMOD uses a C version of LSQR and some BLAS routines from the BCLS package of Michael Friedlander, which are covered by the Lesser GPL (see LGPL.txt). IMOD uses a subset of the LAPACK routines developed at Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., Courant Institute, Argonne National Lab, and Rice University. They are copyrighted by the University of Tennessee and covered by a BSD-style license (see LAPACK.txt). IMOD also uses a subset of the BLAS routines, developed by: Jack Dongarra, Argonne National Lab; Jeremy Du Croz, NAG Ltd.; Iain Duff, AERE Harwell; Richard Hanson, Sandia National Labs; and Sven Hammarling, NAG Ltd. The program imodwincpu was adapted from code obtained from www.codeproject.com and written by Dudi Abramov. It is excluded from the GPL license and is covered exclusively by the Code Project Open License (see CPOL.html). Routines for computing some statistical functions were adapted from S. J. Zhang and J. M. Jin, Computation of Special Functions. New York: John Wiley & Sons, 1996 and are copyrighted by the authors and publisher. Andrew Noske (originally at the University of Queensland, Australia, then at the University of California, San Diego) contributed the beadhelper, drawingtools, interpolator, namewizard, and stereology plugins. See the help displayed by those plugins for acknowledgements of funding for his work. Jane Ding at California Institute of Technology contributed the Grab with Note plugin. The isosurface display in 3dmod uses contouring and surface smoothing modules from Chimera, developed at the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, supported by NIH/NCRR grant P41-RR01081. RAPTOR was developed by Fernando Amat, Farshid Moussavi, and Mark Horowitz at Stanford University and is copyrighted by them. It is covered by the license in RAPTORlicense.txt. It uses three libraries, parts of which are included in the IMOD source code distribution: OpenCV (http://sourceforge.net/projects/opencvlibrary/), covered by the license in OpenCV.txt, SuiteSparse (http://www.cise.ufl.edu/research/sparse/SuiteSparse/), covered by the licenses in CSparse.txt and LGPL.txt, and Stair Vision Library (http://sourceforge.net/projects/stairvision/), covered by the license in StairVision.txt. The warping library uses modules from Pavel Sakov's 'nn' package, which are copyrighted by Sakov and CSIRO, and covered by the license in nn.txt. The library also uses code from Ken Clarkson's 'hull' program, which is copyrighted by AT&T and covered by the license in hull.txt. Routines for solving 3x3 eigenvectors are copyrighted by Joachim Kopp and covered by the LGPL license. The ctffind library was adapted from the ctffind program of Alexis Rohou and Nikolaus Grigorieff, which is Copyright (c) 2018, Howard Hughes Medical Institute, and is covered by the Janelia Research Campus Software License 1.2. Mauro Maiorca, at the Biochemistry & Molecular Biology Department, Bio21 Institute, University of Melbourne, Australia, contributed the preNAD and preNID programs. His work was supported by funding from the Australian Research Council and the National Health and Medical Research Council. preNAD and preNID use recursive line filter routines from Gregoire Malandain, covered by version 3 of the GPL (see GPL-3.0.txt). IMOD uses TIFF libraries which are Copyright (c) 1988-1997 Sam Leffler and Copyright (c) 1991-1997 Silicon Graphics, Inc. (see TIFF.txt). Because IMOD uses the libjpeg library, this software is based in part on the work of the Independent JPEG Group. IMOD also uses the zlib library, which is Copyright 1995-2010 by Jean-loup Gailly and Mark Adler. IMOD may use FFTW libraries which are Copyright (c) 1997--1999 Massachusetts Institute of Technology, written by Matteo Frigo and Steven G. Johnson, and covered by version 2 of the GPL. IMOD uses HDF5 libraries which are Copyright 1998-2006 by the Board of Trustees of the University of Illinois and Copyright 2006-2014 by The HDF Group and covered by the license in HDF5.txt. The module gcvspl.c is based on an f2c translation of gcvspl.f, which was obtained from http://www.netlib.org. gcvspl.f was written by H.J. Woltring based on routines in Lyche et al. (1983) and other sources as documented in gcvspl.c. IMOD includes a copy of the Mini-XML library which is Copyright 2003-2016 by Michael R. Sweet and is covered by the modified Library GPL in Mini-XML.txt This work is supported by NIH/NIGMS grant GM125074 to David Mastronarde. Contact: mast at colorado dot edu www: http://bio3d.colorado.edu/imod/index.html University of Colorado, Dept. of MCD Biology, 347 UCB, Boulder, CO 80309