text:
02.005}
}

@Article{Verstichel2014,
  Title                    = {Variational optimization of the {2DM}: approaching three-index accuracy using extended cluster constraints},
  Author                   = {Verstichel, Brecht and Poelmans, Ward and De Baerdemacker, Stijn and Wouters, Sebastian and Van Neck, Dimitri},
  Journal                  = {European Physical Journal B: Condensed Matter and Complex Systems},
  Year                     = {2014},

  Month                    = {Mar},
  Number                   = {3},
  Volume                   = {87},

  Doi                      = {10.1140/epjb/e2014-40788-x},
  ISSN                     = {1434-6036},
  Owner                    = {ward},
  Publisher                = {Springer Science + Business Media},
  Timestamp                = {23.06.2015},
  Url                      = {http://dx.doi.org/10.1140/epjb/e2014-40788-x}
}

@Article{verstraete,
  Title                    = {Matrix product states, projected entangled pair states, and variational renormalization group methods for quantum spin systems},
  Author                   = {Verstraete, F. and Murg, V. and Cirac, J.I.},
  Journal                  = {Advances in Physics},
  Year                     = {2008},
  Number                   = {2},
  Pages                    = {143-224},
  Volume                   = {57}
}

@Article{voorhis_benchmark_2000,
  Title                    = {Benchmark variational coupled cluster doubles results},
  Author                   = {Voorhis, Troy Van and Head-Gordon, Martin},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2000},

  Month                    = nov,
  Number                   = {20},
  Pages                    = {8873--8879},
  Volume                   = {113},

  Abstract                 = {We present the first application of the Rayleigh–Ritz variational procedure to the coupled cluster doubles trial function. The variational approach is applied to the potential surface of H 4 , the double dissociation of water and the dissociation of N 2 , and the results are compared to standard coupled cluster doubles calculations. It is found that the variational approach gives a greatly improved description of strongly correlated systems, where the standard approach is known to fail. Some examination of the basis set dependence of the results is presented.},
  Doi                      = {10.1063/1.1319643},
  File                     = {Snapshot:/home/ward/.mozilla/firefox/u1pwfk5g.default/zotero/storage/5BHJUPE7/1.html:text/html},
  ISSN                     = {0021-9606, 1089-7690},
  Keywords                 = {Coupled cluster, Dissociation, Potential energy surfaces},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/113/20/10.1063/1.1319643},
  Urldate                  = {2015-06-11}
}

@Article{Wales1997,
  Title                    = {Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110~{A}toms},
  Author                   = {Wales, David J. and Doye, Jonathan P. K.},
  Journal                  = {The Journal of Physical Chemistry A},
  Year                     = {1997},

  Month                    = {Jul},
  Number                   = {28},
  Pages                    = {5111–5116},
  Volume                   = {101},

  __markedentry            = {[ward:]},
  Doi                      = {10.1021/jp970984n},
  ISSN                     = {1520-5215},
  Owner                    = {ward},
  Publisher                = {American Chemical Society (ACS)},
  Timestamp                = {07.09.2015},
  Url                      = {http://dx.doi.org/10.1021/jp970984n}
}

@Article{weinhold,
  Title                    = {Reduced Density Matrices of atoms and molecules. \mbox{II}. On the \mbox{$N$}-representability problem},
  Author                   = {Weinhold, Frank and Wilson, E.B.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1967},

  Month                    = {Oct},
  Pages                    = {2298--2311},
  Volume                   = {47},

  Myurl                    = {http://link.aps.org/doi/10.1103/PhysRev.138.B1338}
}

@Article{weinhold1,
  Title                    = {Reduced Density Matrices of Atoms and Molecules. \mbox{I}. The 2 Matrix of Double-Occupancy, Configuration-Interaction Wavefunctions for Singlet States},
  Author                   = {Weinhold, Frank and Wilson, E. Bright},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1967},
  Number                   = {7},
  Pages                    = {2752-2758},
  Volume                   = {46},

  Doi                      = {10.1063/1.1841109},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/46/7/10.1063/1.1841109}
}

@Article{weinhold2,
  Title                    = {Reduced Density Matrices of Atoms and Molecules. \mbox{II}. On the \mbox{$N$}-Representability Problem},
  Author                   = {Weinhold, Frank and Wilson, E. Bright},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1967},
  Number                   = {7},
  Pages                    = {2298-2311},
  Volume                   = {47},

  Doi                      = {10.1063/1.1703311},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/47/7/10.1063/1.1703311}
}

@Article{Wen2010,
  Title                    = {Alternating direction augmented Lagrangian methods for semidefinite programming},
  Author                   = {Wen, Zaiwen and Goldfarb, Donald and Yin, Wotao},
  Journal                  = {Math. Prog. Comp.},
  Year                     = {2010},

  Month                    = {Sep},
  Number                   = {3-4},
  Pages                    = {203–230},
  Volume                   = {2},

  Doi                      = {10.1007/s12532-010-0017-1},
  ISSN                     = {1867-2957},
  Owner                    = {ward},
  Publisher                = {Springer Science + Business Media},
  Timestamp                = {23.06.2015},
  Url                      = {http://dx.doi.org/10.1007/s12532-010-0017-1}
}

@Manual{molpro,
  Title                    = {MOLPRO, version 2006.1, a package of ab initio programs},
  Author                   = {H.-J. Werner and P. J. Knowles and R. Lindh and F. R. Manby and M. Schütz and P. Celani and T. Korona and G. Rauhut and R. D. Amos and A. Bernhardsson and A. Berning and D. L. Cooper and M. J. O. Deegan and A. J. Dobbyn and F. Eckert and C. Hampel and G. Hetzer and A. W. Lloyd and S. J. McNicholas and W. Meyer and M. E. Mura and A. Nicklass and P. Palmieri and R. Pitzer and U. Schumann and H. Stoll and A. J. Stone and R. Tarroni and T. Thorsteinsson},
  Year                     = {2006}
}

@Article{dmrg1,
  Title                    = {Density matrix formulation for quantum renormalization groups},
  Author                   = {White, Steven R.},
  Journal                  = {Physical Review Letters},
  Year                     = {1992},

  Month                    = {Nov},
  Pages                    = {2863--2866},
  Volume                   = {69},

  Doi                      = {10.1103/PhysRevLett.69.2863},
  Issue                    = {19},
  Myurl                    = {http://link.aps.org/doi/10.1103/PhysRevLett.69.2863},
  Numpages                 = {0},
  Publisher                = {American Physical Society}
}

@Article{:/content/aip/journal/jcp/110/9/10.1063/1.478295,
  Title                    = {Ab initio quantum chemistry using the density matrix renormalization group},
  Author                   = {White, Steven R. and Martin, Richard L.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1999},
  Number                   = {9},
  Pages                    = {4127-4130},
  Volume                   = {110},

  Doi                      = {http://dx.doi.org/10.1063/1.478295},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/110/9/10.1063/1.478295}
}

@Article{PhysRevB.40.506,
  Title                    = {Numerical study of the two-dimensional Hubbard model},
  Author                   = {White, S. R. and Scalapino, D. J. and Sugar, R. L. and Loh, E. Y. and Gubernatis, J. E. and Scalettar, R. T.},
  Journal                  = {Physical Review B},
  Year                     = {1989},

  Month                    = {Jul},
  Pages                    = {506--516},
  Volume                   = {40},

  Doi                      = {10.1103/PhysRevB.40.506},
  Issue                    = {1},
  Numpages                 = {0},
  Publisher                = {American Physical Society},
  Url                      = {http://link.aps.org/doi/10.1103/PhysRevB.40.506}
}

@Article{C2CP42695A,
  Title                    = {Computational complexity in electronic structure},
  Author                   = {Whitfield, James Daniel and Love, Peter John and Aspuru-Guzik, Alan},
  Journal                  = {Physical Chemistry Chemical Physics},
  Year                     = {2013},
  Pages                    = {397-411},
  Volume                   = {15},

  Doi                      = {10.1039/C2CP42695A},
  Issue                    = {2},
  Myurl                    = {http://dx.doi.org/10.1039/C2CP42695A},
  Publisher                = {The Royal Society of Chemistry}
}

@Article{woon,
  Title                    = {Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon},
  Author                   = {David E. Woon and Thom H. Dunning, Jr.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1993},
  Number                   = {2},
  Pages                    = {1358-1371},
  Volume                   = {98},

  Doi                      = {10.1063/1.464303},
  Keywords                 = {ALUMINIUM; SILICON; PHOSPHORUS; SULFUR; CHLORINE; ARGON; GAUSS FUNCTION; WAVE FUNCTIONS; ELECTRON CORRELATION},
  Publisher                = {AIP},
  Url                      = {http://link.aip.org/link/?JCP/98/1358/1}
}

@PhdThesis{phdseba,
  Title                    = {Accurate variational electronic structure calculations with the density matrix renormalization group},
  Author                   = {Sebastian Wouters},
  School                   = {Ghent University},
  Year                     = {2014},

  Owner                    = {ward},
  Timestamp                = {21.05.2015},
  Url                      = {http://arxiv.org/abs/1405.1225}
}

@Article{seba-salen,
  Title                    = {Communication: {DMRG-SCF} study of the singlet, triplet, and quintet states of oxo-Mn(Salen)},
  Author                   = {Wouters, Sebastian and Bogaerts, Thomas and Van Der Voort, Pascal and Van Speybroeck, Veronique and Van Neck, Dimitri},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2014},
  Number                   = {24},
  Pages                    = {241103},
  Volume                   = {140},

  Doi                      = {10.1063/1.4885815},
  Eid                      = {241103},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/140/24/10.1063/1.4885815}
}

@Article{233Wouters_2012,
  Title                    = {Longitudinal static optical properties of hydrogen chains: Finite field extrapolations of matrix product state calculations},
  Author                   = {Wouters, S. and Limacher, P. A. and Van Neck, D. and Ayers, P. W.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2012},
  Number                   = {13},
  Pages                    = {134110},
  Volume                   = {136},

  Date-added               = {2014-01-15 16:56:01 +0000},
  Date-modified            = {2014-01-15 16:56:01 +0000},
  Doi                      = {10.1063/1.3700087},
  ISSN                     = {0021-9606},
  Owner                    = {ward},
  Timestamp                = {10.03.2015},
  Type                     = {Journal Article},
  Url                      = {<Go to ISI>://WOS:000302596500012}
}

@Article{seba-h-chains,
  Title                    = {Longitudinal static optical properties of hydrogen chains: Finite field extrapolations of matrix product state calculations},
  Author                   = {Wouters, Sebastian and Limacher, Peter A. and Van Neck, Dimitri and Ayers, Paul W.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2012},
  Number                   = {13},
  Pages                    = {-},
  Volume                   = {136},

  Doi                      = {10.1063/1.3700087},
  Eid                      = {134110},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/136/13/10.1063/1.3700087}
}

@Article{113Wouters_2013,
  Title                    = {Thouless theorem for matrix product states and subsequent post density matrix renormalization group methods},
  Author                   = {Wouters, S. and Nakatani, N. and Van Neck, D. and Chan, G. K. L.},
  Journal                  = {Physical Review B},
  Year                     = {2013},
  Number                   = {7},
  Pages                    = {075122},
  Volume                   = {88},

  Date-added               = {2014-01-15 16:56:01 +0000},
  Date-modified            = {2014-01-15 16:56:01 +0000},
  Doi                      = {10.1103/PhysRevB.88.075122},
  ISSN                     = {1098-0121},
  Owner                    = {ward},
  Timestamp                = {10.03.2015},
  Type                     = {Journal Article},
  Url                      = {<Go to ISI>://WOS:000323032700003}
}

@Article{chemps1,
  Title                    = {{CheMPS2}: A free open-source spin-adapted implementation of the density matrix renormalization group for ab initio quantum chemistry },
  Author                   = {Sebastian Wouters and Ward Poelmans and Paul W. Ayers and Dimitri Van Neck},
  Journal                  = {Computer Physics Communications },
  Year                     = {2014},
  Number                   = {6},
  Pages                    = {1501 - 1514},
  Volume                   = {185},

  Doi                      = {10.1016/j.cpc.2014.01.019},
  ISSN                     = {0010-4655},
  Keywords                 = {Density matrix renormalization group},
  Url                      = {http://www.sciencedirect.com/science/article/pii/S0010465514000496}
}

@Article{chemps3,
  Title                    = {{CheMPS2}: Improved {DMRG-SCF} routine and correlation functions },
  Author                   = {Sebastian Wouters and Ward Poelmans and Stijn De Baerdemacker and Paul W. Ayers and Dimitri Van Neck},
  Journal                  = {Computer Physics Communications},
  Year                     = {2015},
  Number                   = {0},
  Pages                    = {235 - 237},
  Volume                   = {191},

  Doi                      = {10.1016/j.cpc.2015.01.007},
  ISSN                     = {0010-4655},
  Keywords                 = {SU(2) spin-adapted \{DMRG\}},
  Url                      = {http://www.sciencedirect.com/science/article/pii/S0010465515000168}
}

@Article{seba1,
  Title                    = {The density matrix renormalization group for ab initio quantum chemistry},
  Author                   = {Wouters, Sebastian and Van Neck, Dimitri},
  Journal                  = {The European Physical Journal D},
  Year                     = {2014},
  Number                   = {9},
  Volume                   = {68},

  Doi                      = {10.1140/epjd/e2014-50500-1},
  Eid                      = {272},
  ISSN                     = {1434-6060},
  Keywords                 = {Molecular Physics and Chemical Physics},
  Language                 = {English},
  Myurl                    = {http://dx.doi.org/10.1140/epjd/e2014-50500-1},
  Publisher                = {Springer Berlin Heidelberg}
}

@Article{yablonovitch_inhibited_1987,
  Title                    = {Inhibited {Spontaneous} {Emission} in {Solid}-{State} {Physics} and {Electronics}},
  Author                   = {Yablonovitch, Eli},
  Journal                  = {Physical Review Letters},
  Year                     = {1987},

  Month                    = may,
  Number                   = {20},
  Pages                    = {2059--2062},
  Volume                   = {58},

  Abstract                 = {It has been recognized for some time that the spontaneous emission by atoms is not necessarily a fixed and immutable property of the coupling between matter and space, but that it can be controlled by modification of the properties of the radiation field. This is equally true in the solid state, where spontaneous emission plays a fundamental role in limiting the performance of semiconductor lasers, heterojunction bipolar transistors, and solar cells. If a three-dimensionally periodic dielectric structure has an electromagnetic band gap which overlaps the electronic band edge, then spontaneous emission can be rigorously forbidden.},
  Doi                      = {10.1103/PhysRevLett.58.2059},
  File                     = {APS Snapshot:/home/ward/.mozilla/firefox/u1pwfk5g.default/zotero/storage/INJ63STB/p2059_1.html:text/html},
  Myurl                    = {http://link.aps.org/doi/10.1103/PhysRevLett.58.2059},
  Urldate                  = {2012-07-24}
}

@Book{sdpa1,
  Title                    = {Latest Developments in the SDPA Family for Solving Large-Scale SDPs},
  Author                   = {Yamashita, Makoto and Fujisawa, Katsuki and Fukuda, Mituhiro and Kobayashi, Kazuhiro and Nakata, Kazuhide and Nakata, Maho},
  Editor                   = {Anjos, Miguel F. and Lasserre, Jean B.},
  Publisher                = {Springer US},
  Year                     = {2012},
  Series                   = {International Series in Operations Research \& Management Science},
  Volume                   = {166},

  Booktitle                = {Handbook on Semidefinite, Conic and Polynomial Optimization},
  Doi                      = {10.1007/978-1-4614-0769-0_24},
  ISBN                     = {978-1-4614-0768-3},
  Language                 = {english},
  Myurl                    = {http://dx.doi.org/10.1007/978-1-4614-0769-0_24},
  Pages                    = {687-713}
}

@Article{sdpa2,
  Title                    = {Implementation and evaluation of {SDPA} 6.0 (semidefinite programming algorithm 6.0)},
  Author                   = {Yamashita, Makoto and Fujisawa, Katsuki and Kojima, Masakazu},
  Journal                  = {Optimization Methods and Software},
  Year                     = {2003},
  Number                   = {4},
  Pages                    = {491--505},
  Volume                   = {18},

  Publisher                = {Taylor \& Francis}
}

@Article{frac_N_2,
  Title                    = {Degenerate Ground States and a Fractional Number of Electrons in Density and Reduced Density Matrix Functional Theory},
  Author                   = {Yang, Weitao and Zhang, Yingkai and Ayers, Paul W.},
  Journal                  = {Physical Review Letters},
  Year                     = {2000},

  Month                    = {May},
  Pages                    = {5172--5175},
  Volume                   = {84},

  Doi                      = {10.1103/PhysRevLett.84.5172},
  Issue                    = {22},
  Myurl                    = {http://link.aps.org/doi/10.1103/PhysRevLett.84.5172},
  Publisher                = {American Physical Society}
}

@Article{zgid_density_2008,
  Title                    = {The density matrix renormalization group self-consistent field method: {Orbital} optimization with the density matrix renormalization group method in the active space},
  Author                   = {Zgid, Dominika and Nooijen, Marcel},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2008},

  Month                    = apr,
  Number                   = {14},
  Pages                    = {144116},
  Volume                   = {128},

  Doi                      = {10.1063/1.2883981},
  ISSN                     = {0021-9606, 1089-7690},
  Keywords                 = {Coupled cluster, Eigenvalues, Optimization, Subspaces, Wave functions},
  Shorttitle               = {The density matrix renormalization group self-consistent field method},
  Url                      = {http://scitation.aip.org/content/aip/journal/jcp/128/14/10.1063/1.2883981},
  Urldate                  = {2015-06-12}
}

@Article{zhao,
  Title                    = {The reduced density matrix method for electronic structure calculations and the role of three-index representability conditions},
  Author                   = {Z. Zhao and B. J. Braams and M. Fukuda and M. L. Overton and J. K. Percus},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {2004},
  Pages                    = {5},
  Volume                   = {120}
}

@Book{wilson_methods_2013,
  Title                    = {Methods in {Computational} {Chemistry}: {Volume} 3: {Concurrent} {Computation} in {Chemical} {Calculations}},
  Editor                   = {Wilson, Stephen},
  Publisher                = {Springer},
  Year                     = {2013},
  Edition                  = {1989 edition},
  Month                    = dec,

  Abstract                 = {Recent years have seen the proliferation of new computer designs that employ parallel processing in one form or another in order to achieve maximum performance. Although the idea of improving the performance of computing machines by carrying out parts of the computation concurrently is not new (indeed, the concept was known to Babbage ), such machines have, until fairly recently, been confined to a few specialist research laboratories. Nowadays, parallel computers are commercially available and they are finding a wide range of applications in chemical calculations. The purpose of this volume is to review the impact that the advent of concurrent computation is already having, and is likely to have in the future, on chemical calculations. Although the potential of concurrent computation is still far from its full realization, it is already clear that it may turn out to be second in importance only to the introduction of the electronic digital computer itself.},
  ISBN                     = {9781461574187},
  Language                 = {English},
  Shorttitle               = {Methods in {Computational} {Chemistry}}
}

@Book{yarkony_modern_1995,
  Title                    = {Modern {Electronic} {Structure} {Theory}},
  Editor                   = {Yarkony, David},
  Publisher                = {World Scientific Pub Co Inc},
  Year                     = {1995},
  Month                    = jun,

  Abstract                 = {Reviews current methods of computation in electronic structure and its use in describing various aspects of physical chemistry. The book is aimed at first year graduate students, college seniors considering graduate study and researchers who want to acquire a wider knowledge of this field.},
  ISBN                     = {9789810229887},
  Language                 = {English}
}

@Misc{jmol,
  Title                    = {Jmol: an open-source Java viewer for chemical structures in {3D}},
  HowPublished             = {\url{http://www.jmol.org}},
  Note                     = {(accessed May 3, 2015)},
  Year                     = {2015},

  Owner                    = {ward},
  Timestamp                = {19.03.2015}
}

@Misc{sdpa3,
  Title                    = {{SDPA} (SemiDefinite Programming Algorithm)},
  HowPublished             = {\url{http://sdpa.sourceforge.net}},
  Note                     = {(accessed May 3, 2015)},
  Year                     = {2015}
}

@Misc{gplv3,
  Title                    = {{GNU} General Public License},
  HowPublished             = {\url{http://www.gnu.org/licenses/gpl.html}},
  Month                    = {June},
  Note                     = {(accessed May 3, 2015)},
  Year                     = {2007},

  Date                     = {2007-06-29},
  Organization             = {Free Software Foundation},
  Pagination               = {section},
  Shorthand                = {GPL},
  Url                      = {http://www.gnu.org/licenses/gpl.html},
  Version                  = {3}
}

gha_language: TeX


text:
@inproceedings{perez2018detecting,
 author = {Pérez-Peló, Sergio and Sánchez-Oro, Jesús and Duarte, Abraham},
 booktitle = {International Conference on Variable Neighborhood Search},
 organization = {Springer, Cham},
 pages = {141--151},
 title = {Detecting Weak Points in Networks Using Variable Neighborhood Search},
 year = {2018}
}

license: MIT

repository: jesussanchezoro/academic-kickstart

license_type: permissive

repo_name: jesussanchezoro/academic-kickstart

branch_name: refs/heads/master

gha_license_id: MIT

extension: bib


text:
@InProceedings{wangf15,
  title = {Safe Screening for Multi-Task Feature Learning with Multiple Data Matrices},
  author = {Jie Wang and Jieping Ye},
  pages = {1747-1756},
  abstract = {Multi-task feature learning (MTFL) is a powerful technique in boosting the predictive performance by learning multiple related classification/regression/clustering tasks simultaneously. However, solving the MTFL problem remains challenging when the feature dimension is extremely large. In this paper, we propose a novel screening rule---that is based on the dual projection onto convex sets (DPC)---to quickly identify the inactive features---that have zero coefficients in the solution vectors across all tasks. One of the appealing features of DPC is that: it is safe in the sense that the detected inactive features are guaranteed to have zero coefficients in the solution vectors across all tasks. Thus, by removing the inactive features from the training phase, we may have substantial savings in the computational cost and memory usage without sacrificing accuracy. To the best of our knowledge, it is the first screening rule that is applicable to sparse models with multiple data matrices. A key challenge in deriving DPC is to solve a nonconvex problem. We show that we can solve for the global optimum efficiently via a properly chosen parametrization of the constraint set. Moreover, DPC has very low computational cost and can be integrated with any existing solvers. We have evaluated the proposed DPC rule on both synthetic and real data sets. The experiments indicate that DPC is very effective in identifying the inactive features---especially for high dimensional data---which leads to a speedup up to several orders of magnitude.},
}

repository: mreid/papersite

repo_name: mreid/papersite


text:
#
# Copyright (C) 2014 Wind River Systems, Inc.
#
SUMMARY = "An implementation of the JSON specification according to RFC 4627"
DESCRIPTION = "An implementation of the JSON specification according to RFC 4627"

LICENSE = "Ruby"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Ruby;md5=105fc57d3f4d3122db32912f3e6107d0"

SRCREV = "7f4cfd853f2c919d854fb95548a19980feff17e8"

S = "${WORKDIR}/git"

RUBY_GEM_NAME="json"
RUBY_BUILD_GEMS="${RUBY_GEM_NAME}.gemspec"
RUBY_INSTALL_GEMS ?= "${RUBY_GEM_NAME}-${PV}.gem"

SRC_URI = " \
    git://github.com/flori/json.git;protocol=https;branch=v1.8 \
    "

inherit ruby

DEPENDS += " \
    ruby \
    virtual/crypt \
"

BBCLASSEXTEND = "native"

repository: YoeDistro/meta-webkit

repo_name: YoeDistro/meta-webkit

extension: bb


text:
DESCRIPTION = "AppWeb is an embedded HTTP Web server that has been designed with security in mind."
SECTION = "console/network"
LICENSE = "GPL"
LIC_FILES_CHKSUM = "file://LICENSE.md;md5=df7cfb0d4723489d25aecb8f2a879818"
SRC_URI = "http://appwebserver.org/software/appweb-5.2.0-src.tgz"
SRC_URI += "file://fix_path.patch \
	file://appweb.conf \
	file://install.conf \
	"

SRC_URI[md5sum] = "e959abec9244eb535179cd1cff0c038b"
SRC_URI[sha256sum] = "dea8fd9d967c149d0ca4e22d034fc995827ae7a1eda881f5a9d72d4d7b2287f0"

inherit update-rc.d
#
# implications - used by update-rc.d scripts
#
INITSCRIPT_NAME = "appweb"
INITSCRIPT_PARAMS = "defaults 70"

FILES_${PN}-dbg =+ "${libdir}/appweb/5.2.0/bin/.debug \
               ${libdir}/.debug"

do_configure () {
    ./configure
}

do_compile () {
	oe_runmake compile
}

do_install () {
    oe_runmake 'ME_ROOT_PREFIX=${D}' installBinary
	install -m 0644 ${WORKDIR}/appweb.conf  ${D}/etc/appweb/appweb.conf
	install -m 0644 ${WORKDIR}/install.conf  ${D}/etc/appweb/install.conf
}


text:
require xorg-app-common.inc
DEPENDS += " libxaw libxt libxmu"
PE = "1"
PR = "${INC_PR}.0"

SRC_URI[archive.md5sum] = "3c0d5d8d6abaf411cd0647bc7073ac38"
SRC_URI[archive.sha256sum] = "4d9e24b95619bc961936d241106ffcc483995de55629567113ad78ba0b37ffb7"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
DESCRIPTION = "libConfuse is a configuration file parser library"
LICENSE = "ISC"
LIC_FILES_CHKSUM = "file://README;md5=4883145883ae2d1bb2d003f204e5e744"

PR = "r0"

SRC_URI = "http://savannah.nongnu.org/download/confuse/confuse-2.7.tar.gz"

SRC_URI[md5sum] = "45932fdeeccbb9ef4228f1c1a25e9c8f"
SRC_URI[sha256sum] = "e32574fd837e950778dac7ade40787dd2259ef8e28acd6ede6847ca895c88778"

inherit autotools pkgconfig gettext

repository: kolibre/meta-kolibre

repo_name: kolibre/meta-kolibre

gha_language: Python


text:
@incollection{rosengren_uses_1974,
  title = {Uses and Gratifications: {{A}} Paradigm Outlined},
  booktitle = {The Uses of Mass Communications: {{Current}} Perspectives on Gratifications Research},
  author = {Rosengren, Karl Erik},
  editor = {Blumler, Jay G. and Katz, Elihu},
  year = {1974},
  pages = {269--286},
  publisher = {{SAGE Publications}},
  note = {In Valkenburg (2016):
\par
Uses-and-gratifications theory: Attempts to understand why and how people actively seek out specific media to satisfy specific needs}
}

url: https://raw.githubusercontent.com/retorquere/bibtex-parser/05fd68b215b96634dea5a7e6ea5e1be187caf3ed/test/better-bibtex/export/Book chapter citation using p. instead of pp. #1375.bibtex

repository: retorquere/bibtex-parser

repo_name: retorquere/bibtex-parser

extension: bibtex


text:
PR = "r9"

SRC_URI = "${GNU_MIRROR}/ncurses/ncurses-${PV}.tar.gz \
	   file://visibility.patch;patch=1"
S = "${WORKDIR}/ncurses-${PV}"

require ncurses.inc

repository: jdegges/gumstix-pip-oe

repo_name: jdegges/gumstix-pip-oe


text:
DESCRIPTION = "D-Bus interfaces for querying and manipulating user account information"
HOMEPAGE="http://www.fedoraproject.org/wiki/Features/UserAccountDialog"
SECTION = "x11"

inherit gnome systemd

PR = "r5"

LICENSE = "GPLv3"
LIC_FILES_CHKSUM = "file://COPYING;md5=d32239bcb673463ab874e80d47fae504"

DEPENDS = "glib-2.0 dbus-glib polkit gobject-introspection-native libxslt"

SRC_URI = "http://www.freedesktop.org/software/${PN}/${P}.tar.xz"
SRC_URI[md5sum] = "47b5af77b544528c02d82761bd574c09"
SRC_URI[sha256sum] = "9feb3d58c5c739f2df4b5410404b29f16e3f4aa6739b685ceb12903f4d5ea867"

PACKAGES += "accounts-daemon"
SYSTEMD_PACKAGES = "accounts-daemon-systemd"
SYSTEMD_SERVICE_accounts-daemon-systemd = "accounts-daemon.service"

FILES_accounts-daemon = " \
    ${libexecdir}/accounts-daemon \
    ${sysconfdir}/dbus-1/* \
    ${datadir}/dbus-1/* \
    ${datadir}/polkit-1/* \
    ${datadir}/${localstatedir}/lib/AccountsService \
    "
FILES_accounts-daemon-systemd = "${systemd_unitdir}"

EXTRA_OECONF = " \
    --disable-static \
    --disable-more-warnings \
    "

repository: tworaz/oe-tworaz

repo_name: tworaz/oe-tworaz

gha_language: Shell


text:
package main

import "fmt"

var container = []string{"0", "1", "2"}

func main() {
	container := map[int]string{0: "zero", 1: "one", 2:"two"} // 可重名变量 屏蔽全局container变量
	container = map[int]string{1: "one", 2: "two", 3:"three"} // 变量重声明
	fmt.Printf("The element is %q.\n", container[1])
}

repository: sharelinux/StudyGolang

repo_name: sharelinux/StudyGolang

extension: go


text:
require qt5.inc
require qt5-git.inc
require qt5-ptest.inc

HOMEPAGE = "http://www.qt.io"
LICENSE = "GFDL-1.3 & BSD & ( GPL-3.0 & The-Qt-Company-GPL-Exception-1.0 | The-Qt-Company-Commercial ) & ( GPL-2.0+ | LGPL-3.0 | The-Qt-Company-Commercial )"
LIC_FILES_CHKSUM = " \
    file://LICENSE.LGPL3;md5=e6a600fd5e1d9cbde2d983680233ad02 \
    file://LICENSE.GPL2;md5=b234ee4d69f5fce4486a80fdaf4a4263 \
    file://LICENSE.GPL3;md5=d32239bcb673463ab874e80d47fae504 \
    file://LICENSE.GPL3-EXCEPT;md5=763d8c535a234d9a3fb682c7ecb6c073 \
    file://LICENSE.FDL;md5=6d9f2a9af4c8b8c3c769f6cc1b6aaf7e \
"

DEPENDS += "qtbase"

PACKAGECONFIG ?= ""
PACKAGECONFIG_class-target ?= "qtdeclarative"
PACKAGECONFIG[qtdeclarative] = ",,qtdeclarative"

do_configure_prepend() {
    # disable qtdeclarative test if it isn't enabled by PACKAGECONFIG
    sed -e 's/qtHaveModule(qml)/OE_QTDECLARATIVE_ENABLED/' -i ${S}/src/src.pro
}

EXTRA_QMAKEVARS_PRE += "${@bb.utils.contains('PACKAGECONFIG', 'qtdeclarative', 'CONFIG+=OE_QTDECLARATIVE_ENABLED', '', d)}"

SRCREV = "0fa22b3674db3d48bbd0b091b7710158ae152daa"

BBCLASSEXTEND =+ "native nativesdk"


text:
/*
Copyright (C) 2019-Present Pivotal Software, Inc. All rights reserved.

This program and the accompanying materials are made available under the terms
of the under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License.  You may obtain a copy of the
License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed
under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied.  See the License for the
specific language governing permissions and limitations under the License.
*/

package repositories_test

import (
	"context"

	. "github.com/onsi/ginkgo"
	. "github.com/onsi/gomega"
	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
	"k8s.io/apimachinery/pkg/types"

	"github.com/pivotal-cf/ism/pkg/apis/osbapi/v1alpha1"
	. "github.com/pivotal-cf/ism/pkg/internal/repositories"
)

var _ = Describe("KubeBrokerRepo", func() {
	var (
		repo           *KubeBrokerRepo
		existingBroker *v1alpha1.Broker
		resource       types.NamespacedName
	)

	BeforeEach(func() {
		resource = types.NamespacedName{Name: "broker-1", Namespace: "default"}

		existingBroker = &v1alpha1.Broker{
			ObjectMeta: metav1.ObjectMeta{
				Name:      resource.Name,
				Namespace: resource.Namespace,
			},
			Spec: v1alpha1.BrokerSpec{
				Name:     "broker-1",
				URL:      "http://example.org/broker",
				Username: "admin",
				Password: "password",
			},
		}

		repo = NewKubeBrokerRepo(kubeClient)
	})

	AfterEach(func() {
		kubeClient.Delete(context.Background(), existingBroker)
	})

	Describe("Get", func() {
		When("the broker exists", func() {
			BeforeEach(func() {
				err := kubeClient.Create(context.Background(), existingBroker)
				Expect(err).NotTo(HaveOccurred())
			})

			It("returns broker", func() {
				broker, err := repo.Get(resource)
				Expect(err).NotTo(HaveOccurred())

				Expect(broker).To(Equal(existingBroker))
			})
		})

		When("the broker doesn't exist", func() {
			It("returns an error", func() {
				_, err := repo.Get(resource)

				Expect(err).To(MatchError("brokers.osbapi.ism.io \"broker-1\" not found"))
			})
		})
	})

	Describe("UpdateStatus", func() {
		When("the broker exists", func() {
			BeforeEach(func() {
				err := kubeClient.Create(context.Background(), existingBroker)
				Expect(err).NotTo(HaveOccurred())
			})

			It("updates status", func() {
				newState := v1alpha1.BrokerStateRegistered
				Expect(existingBroker.Status.State).NotTo(Equal(newState))

				err := repo.UpdateState(existingBroker, newState)
				Expect(err).NotTo(HaveOccurred())

				updatedBroker, err := repo.Get(resource)
				Expect(err).NotTo(HaveOccurred())

				Expect(updatedBroker.Status.State).To(Equal(newState))
				Expect(existingBroker.Status.State).To(Equal(newState))
			})
		})

		When("the broker doesn't exist", func() {
			It("returns an error", func() {
				newState := v1alpha1.BrokerStateRegistered
				err := repo.UpdateState(existingBroker, newState)

				Expect(err).To(MatchError("brokers.osbapi.ism.io \"broker-1\" not found"))
			})
		})
	})
})

repository: jamesjoshuahill/ism

repo_name: jamesjoshuahill/ism


text:
# Copyright 2019 Google LLC
#
# Use of this source code is governed by an MIT-style
# license that can be found in the LICENSE file or at
# https://opensource.org/licenses/MIT.

set(PIK_TESTS
  ac_predictions_test
  adaptive_reconstruction_test
  ans_encode_test
  ans_test
  approx_cube_root_test
  bit_reader_test
  bits_test
  brotli_test
  byte_order_test
  chroma_from_luma_test
  codec_impl_test
  color_encoding_test
  color_management_test
  compressed_image_test
  convolve_test
  data_parallel_test
  dc_predictor_test
  dct_test
  dct_util_test
  deconvolve_test
  descriptive_statistics_test
  entropy_coder_test
  epf_test
  external_image_test
  fields_test
  gaborish_test
  gamma_correct_test
  gradient_test
  headers_test
  image_test
  linalg_test
  lossless8_test
  lossless16_test
  opsin_image_test
  opsin_inverse_test
  optimize_test
  padded_bytes_test
  pik_test
  quantizer_test
  rational_polynomial_test
  resample_test
  robust_statistics_test
  yuv_convert_test
  yuv_opsin_convert_test
)
foreach (TEST IN LISTS PIK_TESTS)
  add_executable("${TEST}" "${CMAKE_CURRENT_LIST_DIR}/${TEST}.cc")
  target_compile_definitions("${TEST}" PRIVATE -DTEST_DATA_PATH="${CMAKE_CURRENT_SOURCE_DIR}/third_party/testdata")
  target_link_libraries("${TEST}" pikcommon gmock gtest gtest_main)
  gtest_add_tests(TARGET "${TEST}")
endforeach ()

repository: google/pik

repo_name: google/pik

extension: cmake


text:
#ifndef NB_CONFIG_H_INCLUDED
#define NB_CONFIG_H_INCLUDED

/*
 * This file is generated by CMake. The original file is called
 * config.h.cmake. Please do not modify.
 */

#cmakedefine HAVE_LEVELDB 1
#cmakedefine HAVE_NESSDB_V1 1
#cmakedefine HAVE_NESSDB_V2 1

#endif /* NB_CONFIG_H_INCLUDED */

repository: tarantool/nosqlbench

repo_name: tarantool/nosqlbench

gha_license_id: NOASSERTION

gha_language: C


text:
@InProceedings{hazan12b,
  title = {Near-Optimal Algorithms for Online Matrix Prediction},
  author = {Elad   Hazan and Satyen Kale and Shai Shalev-Shwartz},
  pages = {38.1--38.13},
  abstract = {In several online prediction problems of recent interest the comparison class is composed of matrices with bounded entries. For example, in the online max-cut problem, the comparison class is matrices which represent cuts of a given graph and in online gambling the comparison class is matrices which represent permutations over n teams. Another important example is online collaborative filtering in which a widely used comparison class is the set of matrices with a small trace norm. In this paper we isolate a property of matrices, which we call (β,τ)-decomposability, and derive an efficient online learning algorithm, that enjoys a regret bound of \emph{Õ(√βτT )} for all problems in which the comparison class is composed of (β,τ)-decomposable matrices. By analyzing the decomposability of cut matrices, low trace-norm matrices and triangular matrices, we derive near optimal regret bounds for online max-cut, online collaborative filtering and online gambling. In particular, this resolves (in the affirmative) an open problem posed by Abernethy (2010); Kleinberg et al. (2010). Finally, we derive lower bounds for the three problems and show that our upper bounds are optimal up to logarithmic factors. In particular, our lower bound for the online collaborative filtering problem resolves another open problem posed by Shamir and Srebro (2011).},
  pdf = {http://jmlr.org/proceedings/papers/v23/hazan12b/hazan12b.pdf},
}


text:
package cmd

import (
	"encoding/json"
	"fmt"
	"io"
	"os"
	"strings"

	"github.com/spf13/cobra"
	vfs "github.com/twpayne/go-vfs"
	yaml "gopkg.in/yaml.v2"
)

type dumpCommandConfig struct {
	format    string
	recursive bool
}

var dumpCommand = &cobra.Command{
	Use:   "dump",
	Short: "Write a dump of the target state to stdout",
	RunE:  makeRunE(config.runDumpCommand),
}

var dumpFuncFormatMap = map[string]func(io.Writer, interface{}) error{
	"json": func(w io.Writer, value interface{}) error {
		e := json.NewEncoder(w)
		e.SetIndent("", "  ")
		return e.Encode(value)
	},
	"yaml": func(w io.Writer, value interface{}) error {
		return yaml.NewEncoder(w).Encode(value)
	},
}

func init() {
	rootCommand.AddCommand(dumpCommand)

	persistentFlags := dumpCommand.PersistentFlags()
	persistentFlags.StringVarP(&config.dump.format, "format", "f", "json", "format (JSON or YAML)")
	persistentFlags.BoolVarP(&config.dump.recursive, "recursive", "r", true, "recursive")
}

func (c *Config) runDumpCommand(fs vfs.FS, args []string) error {
	dumpFunc, ok := dumpFuncFormatMap[strings.ToLower(c.dump.format)]
	if !ok {
		return fmt.Errorf("unknown format: %s", c.dump.format)
	}
	ts, err := c.getTargetState(fs)
	if err != nil {
		return err
	}
	var concreteValue interface{}
	if len(args) == 0 {
		concreteValue, err = ts.ConcreteValue(c.dump.recursive)
		if err != nil {
			return err
		}
	} else {
		entries, err := c.getEntries(ts, args)
		if err != nil {
			return err
		}
		var concreteValues []interface{}
		for _, entry := range entries {
			entryConcreteValue, err := entry.ConcreteValue(ts.DestDir, ts.TargetIgnore.Match, ts.SourceDir, c.dump.recursive)
			if err != nil {
				return err
			}
			if concreteValue != nil {
				concreteValues = append(concreteValues, entryConcreteValue)
			}
		}
		concreteValue = concreteValues
	}
	return dumpFunc(os.Stdout, concreteValue)
}

repository: beejhuff/chezmoi

repo_name: beejhuff/chezmoi


text:
SUMMARY = "mkpimage for signing u-boot images as Altera bootloader."
DESCRIPTION = "mkpimage for signing u-boot images as Altera bootloader."
HOMEPAGE = "https://github.com/maximeh/mkpimage/"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://LICENSE;md5=495c7193849c054119b27d35029e6449"

EXTRA_OEMAKE = "GOPATH=${B}"

SRCREV="d64752876a6185853400498d3a43a5e18681cab7"

SRC_URI = "git://github.com/maximeh/mkpimage.git;branch=master"

SRC_URI += "file://fix-docopt-dependency-url.patch"

S = "${WORKDIR}/git"

PV = "1.0+git${SRCREV}"

do_install () {
	install -d ${D}/bin
	install -m 755 ${S}/bin/mkpimage ${D}/bin
}

inherit native

DEPENDS = "golang golang-docopt-native"
RDEPENDS_${PN} = ""

repository: Muurikas/meta-mka

repo_name: Muurikas/meta-mka


text:
@INPROCEEDINGS{Brodbeck2003,
  author = {Dominique Brodbeck and Luc Girardin},
  title = {Visualization of Large-Scale Customer Satisfaction Surveys Using a Parallel Coordinate Tree},
  pages = {197--201},
  abstract = {Satisfaction surveys are an important measurement tool in fields such as market research or human resources management. Serious studies consist of numerous questions and contain answers from large population samples. Aggregation on both sides, the questions asked as well as the answers received, turns the multidimensional problem into a complex system of interleaved hierarchies. Traditional ways of presenting the results are limited to one-dimensional charts and cross-tables. We developed a visualization method called the Parallel Coordinate Tree that combines multidimensional analysis with a tree structure representation. Distortion-oriented focus+context techniques are used to facilitate interaction with the visualization. In this paper we present a design study of a commercial application that we built, using this method to analyze and communicate results from large-scale customer satisfaction surveys.},
  doi = {10.1109/INFVIS.2003.1249026},
  year = {2003},
  booktitle = {InfoVis'03: Proceedings of the IEEE Symposium on Information Visualization},
  editor = {Tamara Munzner and Stephen North},
  publisher = {IEEE Computer Society},
  isbn = {0780381548}
}

repository: vis-au/treevisnet

repo_name: vis-au/treevisnet


text:
SUMMARY = "Lightweight and flexible command-line JSON processor"
DESCRIPTION = "jq is like sed for JSON data, you can use it to slice and \
               filter and map and transform structured data with the same \
               ease that sed, awk, grep and friends let you play with text."
HOMEPAGE = "http://stedolan.github.io/jq/"
BUGTRACKER = "https://github.com/stedolan/jq/issues"
SECTION = "utils"

LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://COPYING;md5=244a1fb9cf472474a062d67069dec653"

DEPENDS = "flex-native bison-native"

SRC_URI = "http://stedolan.github.io/${BPN}/download/source/${BP}.tar.gz \
"
SRC_URI[md5sum] = "e3c75a4f805bb5342c9f4b3603fb248f"
SRC_URI[sha256sum] = "998c41babeb57b4304e65b4eb73094279b3ab1e63801b6b4bddd487ce009b39d"

inherit autotools

# Don't build documentation (generation requires ruby)
EXTRA_OECONF = "--disable-docs"

branch_name: refs/heads/fido

gha_language: BitBake


text:
package util

import (
	"errors"
	"github.com/astaxie/beego/validation"
	"github.com/gin-gonic/gin"
	"reflect"
	"strings"
)

func GenerateErrors(obj interface{}, errors []*validation.Error, bindString string) (errs []string) {
	if len(errors) == 0 {
		return
	}
	valueObj := reflect.TypeOf(obj)
	for _, err := range errors{
		field, _ := valueObj.FieldByName(err.Field)
		key := field.Tag.Get(bindString)
		if key == "" {
			key = err.Field
		}
		errString := strings.Join([]string{key, err.Message}, " ")
		errs = append(errs, errString)
	}
	return
}

func ValidStructure(obj interface{}, c *gin.Context) (err error) {
	valid := validation.Validation{}
	ok, err := valid.Valid(obj)
	if err != nil {
		return err
	}

	if !ok {
		errs := GenerateErrors(obj, valid.Errors, "json")
		return errors.New(strings.Join(errs, ", "))
	}
	return nil
}

repository: caicaiget/gin-blog

repo_name: caicaiget/gin-blog


text:
@article{Sinha2016,
abstract = {BACKGROUND: The need to develop valid methods for sampling and analyzing fecal specimens for microbiome studies is increasingly important, especially for large population studies.

METHODS: Some of the most important attributes of any sampling method are reproducibility, stability, and accuracy. We compared seven fecal sampling methods [no additive, RNAlater, 70% ethanol, EDTA, dry swab, and pre/post development fecal occult blood test (FOBT)] using 16S rRNA microbiome profiling in two laboratories. We evaluated nine commonly used microbiome metrics: abundance of three phyla, two alpha-diversities, and four beta-diversities. We determined the technical reproducibility, stability at ambient temperature, and accuracy.

RESULTS: Although microbiome profiles showed systematic biases according to sample method and time at ambient temperature, the highest source of variation was between individuals. All collection methods showed high reproducibility. FOBT and RNAlater resulted in the highest stability without freezing for 4 days. In comparison with no-additive samples, swab, FOBT, and 70% ethanol exhibited the greatest accuracy when immediately frozen.

CONCLUSIONS: Overall, optimal stability and reproducibility were achieved using FOBT, making this a reasonable sample collection method for 16S analysis.

IMPACT: Having standardized method of collecting and storing stable fecal samples will allow future investigations into the role of gut microbiota in chronic disease etiology in large population studies. Cancer Epidemiol Biomarkers Prev; 25(2); 407-16. {\textcopyright}2015 AACR.},
author = {Sinha, Rashmi and Chen, Jun and Amir, Amnon and Vogtmann, Emily and Shi, Jianxin and Inman, Kristin S and Flores, Roberto and Sampson, Joshua and Knight, Rob and Chia, Nicholas},
doi = {10.1158/1055-9965.EPI-15-0951},
file = {::},
issn = {1538-7755},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
month = {mar},
number = {2},
pages = {407--16},
pmid = {26604270},
title = {{Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies.}},
url = {http://cebp.aacrjournals.org/content/early/2015/11/24/1055-9965.EPI-15-0951.abstract},
volume = {25},
year = {2016}
}

@article{Wu2010,
abstract = {Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80 degrees C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method.},
author = {Wu, Gary D and Lewis, James D and Hoffmann, Christian and Chen, Ying-Yu and Knight, Rob and Bittinger, Kyle and Hwang, Jennifer and Chen, Jun and Berkowsky, Ronald and Nessel, Lisa and Li, Hongzhe and Bushman, Frederic D},
doi = {10.1186/1471-2180-10-206},
file = {:Users/nolson/Documents/Mendeley Desktop/Wu et al. - 2010 - Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.pdf:pdf},
issn = {1471-2180},
journal = {BMC microbiology},
keywords = {Adult,Bacteria,Bacteria: classification,Bacteria: genetics,Bacteria: isolation & purification,Base Sequence,DNA, Bacterial,DNA, Bacterial: genetics,DNA, Ribosomal,DNA, Ribosomal: genetics,Feces,Feces: microbiology,Female,Gastrointestinal Tract,Gastrointestinal Tract: microbiology,Humans,Male,Middle Aged,Molecular Sequence Data,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Specimen Handling,Specimen Handling: methods,Young Adult},
mendeley-groups = {Metagenomics,16S rRNA},
month = {jan},
pages = {206},
pmid = {20673359},
title = {{Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2921404&tool=pmcentrez&rendertype=abstract},
volume = {10},
year = {2010}
}

@article{Lauber2011,
author = {Lauber, Christian L and Zhou, Nicholas and Gordon, Jeffrey I and Knight, Rob},
doi = {10.1111/j.1574-6968.2010.01965.x.Effect},
file = {:Users/nolson/Documents/Mendeley Desktop/Lauber et al. - 2011 - Effect of storage conditions on the assessment of bacterial community sturture in soil nad human-associated sampl.pdf:pdf},
journal = {FEMS microbiology letters},
keywords = {barcoded bacterial 16s rrna,community analyses,environmental and human metagenomic,gene pyrosequencing,human fecal and human,microbial community storage conditions,phylogenetic- and taxonomic-based,sample processing,skin microbiota,soil,storage conditions,studies},
mendeley-groups = {16S rRNA/16S diversitystudies,16S rRNA},
mendeley-tags = {sample processing,storage conditions},
number = {1},
pages = {80--86},
title = {{Effect of storage conditions on the assessment of bacterial community sturture in soil nad human-associated samples}},
volume = {307},
year = {2011}
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@article{Hill2016,
author = {Hill, Cian J and Brown, Jillian R M and Lynch, Denise B and Jeffery, Ian B and Ryan, C Anthony and Ross, R Paul and Stanton, Catherine and O'Toole, Paul W},
doi = {10.1186/s40168-016-0164-3},
file = {:Users/nolson/Documents/Mendeley Desktop/Hill et al. - 2016 - Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elde.pdf:pdf},
issn = {2049-2618},
journal = {Microbiome},
keywords = {16S assessment dataset,Bioinformatics,DNA storage,Medical Microbiology,Microbial Ecology,Microbial Genetics and Genomics,Microbiology,Virology},
language = {En},
mendeley-tags = {16S assessment dataset,DNA storage},
month = {jan},
number = {1},
pages = {19},
pmid = {27160322},
publisher = {BioMed Central},
title = {{Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.}},
url = {http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0164-3},
volume = {4},
year = {2016}
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@article{Marx2016,
author = {Marx, Vivien},
doi = {10.1038/nmeth.3868},
file = {:Users/nolson/Documents/Mendeley Desktop/Marx - 2016 - PCR the price of infidelity.pdf:pdf},
issn = {1548-7105},
journal = {Nature methods},
month = {may},
number = {6},
pages = {475--9},
pmid = {27243470},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
shorttitle = {Nat Meth},
title = {{PCR: the price of infidelity.}},
url = {http://dx.doi.org/10.1038/nmeth.3868},
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year = {2016}
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@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.name/knitr/},
}

@article{Schmidt2015,
author = {Schmidt, Thomas S B and {Matias Rodrigues}, Jo??o F. and von Mering, Christian},
doi = {10.1111/1462-2920.12610},
file = {:Users/nolson/Documents/Mendeley Desktop/Schmidt, Matias Rodrigues, von Mering - 2015 - Limits to robustness and reproducibility in the demarcation of operational taxonomic unit.pdf:pdf},
isbn = {1462-2920 (Electronic)\n1462-2912 (Linking)},
issn = {14622920},
journal = {Environmental Microbiology},
number = {5},
pages = {1689--1706},
pmid = {25156547},
title = {{Limits to robustness and reproducibility in the demarcation of operational taxonomic units}},
volume = {17},
year = {2015}
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@article{Amore2016,
author = {D'Amore, Rosalinda and Ijaz, Umer Zeeshan and Schirmer, Melanie and Kenny, John G and Gregory, Richard and Darby, Alistair C and Quince, Christopher and Hall, Neil and {D 'amore}, Rosalinda and {Zeeshan Ijaz}, Umer and Schirmer, Melanie and Kenny, John G and Gregory, Richard and Darby, Alistair C and Shakya, Migun and Podar, Mircea and Quince, Christopher and Hall, Neil},
doi = {10.1186/s12864-015-2194-9},
file = {:Users/nolson/Documents/Mendeley Desktop//D'Amore et al. - 2016 - A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
mendeley-groups = {16S rRNA,16S rRNA/16S taxonomic classification},
pages = {1--40},
publisher = {BMC Genomics},
title = {{A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling}},
url = {http://dx.doi.org/10.1186/s12864-015-2194-9},
volume = {17},
year = {2016}
}

@article{Westcott2015,
author = {Westcott, Sarah L and Schloss, Patrick D},
doi = {10.7287/peerj.preprints.1466v1},
file = {:Users/nolson/Documents/Mendeley Desktop/Westcott, Schloss - 2015 - De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to opera.pdf:pdf;:Users/nolson/Documents/Mendeley Desktop/Westcott, Schloss - 2015 - De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to op(2).pdf:pdf},
issn = {2167-8359},
journal = {PeerJ},
keywords = {16S rRNA gene sequences,Bioinformatics,Culture-independent,Microbial ecology,Microbiome,Next generation sequencing,OTU,QIIME,mothur},
mendeley-groups = {16S rRNA/16S taxonomic classification},
pages = {e1487},
pmid = {26664811},
title = {{De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26664811\nhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4675110},
volume = {3},
year = {2015}
}

@article{Wu2013,
archivePrefix = {arXiv},
arxivId = {1308.6333},
author = {Wu, Dongying and Doroud, Ladan and Eisen, Jonathan a.},
eprint = {1308.6333},
file = {:Users/nolson/Documents/Mendeley Desktop/Wu, Doroud, Eisen - 2013 - TreeOTU Operational Taxonomic Unit Classification Based on Phylogenetic Trees.pdf:pdf},
journal = {Arxiv.Org},
mendeley-groups = {16S rRNA/16S taxonomic classification,Missing PDF},
pages = {23},
title = {{TreeOTU\: Operational Taxonomic Unit Classification Based on Phylogenetic Trees}},
url = {http://arxiv.org/abs/1308.6333},
year = {2013}
}

@article{Kopylova2014,
author = {Kopylova, Evguenia and Navas-molina, Jose A and Mercier, C{\'{e}}line and Xu, Zech},
doi = {10.1128/mSystems.00003-15.Editor},
file = {:Users/nolson/Documents/Mendeley Desktop/Kopylova et al. - 2014 - Open-Source Sequence Clustering Methods Improve the State Of the Art.pdf:pdf;:Users/nolson/Documents/Mendeley Desktop/Kopylova et al. - 2014 - Open-Source Sequence Clustering Methods Improve the State Of the Art(2).pdf:pdf;:Users/nolson/Documents/Mendeley Desktop/Kopylova et al. - 2014 - Open-Source Sequence Clustering Methods Improve the State Of the Art(3).pdf:pdf;:Users/nolson/Documents/Mendeley Desktop/Kopylova et al. - 2014 - Open-Source Sequence Clustering Methods Improve the State Of the Art(4).pdf:pdf},
issn = {2379-5077},
journal = {mSystems},
keywords = {amplicon sequencing,analysis,enabled new detailed investigations,generate hundreds of gigabytes,into the human micro-,microbial community,of data in a,operational taxonomic units,sequence clustering,single run and have,urrent dna sequencing technologies},
mendeley-groups = {16S rRNA/16S Clustering},
number = {1},
pages = {1--16},
title = {{Open-Source Sequence Clustering Methods Improve the State Of the Art}},
volume = {1},
year = {2014}
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@article{Schloss2016,
author = {Schloss, Patrick D},
file = {:Users/nolson/Documents/Mendeley Desktop/Schloss - 2016 - Application of database-independent approach to assess the quality of OTU picking methods.pdf:pdf},
mendeley-groups = {16S rRNA},
title = {{Application of database-independent approach to assess the quality of OTU picking methods}},
year = {2016}
}

@article{He2015,
author = {He, Yan and Caporaso, J Gregory and Jiang, Xiao-Tao and Sheng, Hua-Fang and Huse, Susan M and Rideout, Jai Ram and Edgar, Robert C and Kopylova, Evguenia and Walters, William A and Knight, Rob and Zhou, Hong-Wei},
doi = {10.1186/s40168-015-0081-x},
file = {:Users/nolson/Documents/Mendeley Desktop/He et al. - 2015 - Stability of operational taxonomic units an important but neglected property for analyzing microbial diversity.pdf:pdf},
issn = {2049-2618},
journal = {Microbiome},
language = {en},
mendeley-groups = {16S rRNA,16S rRNA/16S Clustering},
month = {may},
number = {1},
pages = {20},
pmid = {25995836},
publisher = {???},
title = {{Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity}},
url = {http://www.microbiomejournal.com/content/3/1/20},
volume = {3},
year = {2015}
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@article{Ghodsi2011,
author = {Ghodsi, Mohammadreza and Liu, Bo and Pop, Mihai},
doi = {10.1186/1471-2105-12-271},
file = {:Users/nolson/Documents/Mendeley Desktop/Ghodsi, Liu, Pop - 2011 - DNACLUST accurate and efficient clustering of phylogenetic marker genes.pdf:pdf},
isbn = {10.1186/1471-2105-12-271},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Algorithms,Cluster Analysis,Genetic Markers,Phylogeny,Sequence Alignment,Sequence Analysis, DNA,Software},
language = {en},
mendeley-groups = {16S rRNA/16S Clustering},
month = {jan},
number = {1},
pages = {271},
pmid = {21718538},
publisher = {BioMed Central Ltd},
title = {{DNACLUST: accurate and efficient clustering of phylogenetic marker genes.}},
url = {http://www.biomedcentral.com/1471-2105/12/271},
volume = {12},
year = {2011}
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@article{Schmidt2015,
author = {Schmidt, Thomas S B and {Matias Rodrigues}, Jo??o F. and von Mering, Christian},
doi = {10.1111/1462-2920.12610},
file = {:Users/nolson/Documents/Mendeley Desktop/Schmidt, Matias Rodrigues, von Mering - 2015 - Limits to robustness and reproducibility in the demarcation of operational taxonomic unit.pdf:pdf},
isbn = {1462-2920 (Electronic)\n1462-2912 (Linking)},
issn = {14622920},
journal = {Environmental Microbiology},
number = {5},
pages = {1689--1706},
pmid = {25156547},
title = {{Limits to robustness and reproducibility in the demarcation of operational taxonomic units}},
volume = {17},
year = {2015}
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@article{Schloss2011,
author = {Schloss, Patrick D. and Westcott, Sarah L.},
doi = {10.1128/AEM.02810-10},
file = {:Users/nolson/Desktop/Appl. Environ. Microbiol.-2011-Schloss-3219-26.pdf:pdf;:Users/nolson/Documents/Mendeley Desktop/Schloss, Westcott - 2011 - Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequenc.pdf:pdf},
issn = {0099-2240},
journal = {Applied and Environmental Microbiology},
keywords = {16S,16S: genetics,Bacterial,Bacterial: chemistry,Bacterial: genetics,Cluster Analysis,Computational Biology,Computational Biology: methods,DNA,Metagenomics,Metagenomics: methods,Phylogeny,RNA,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Sequence Analysis,Sequence Analysis: methods},
mendeley-groups = {16S rRNA,16S rRNA/16S taxonomic classification,16S rRNA/16S Clustering},
month = {may},
number = {10},
pages = {3219--3226},
pmid = {21421784},
title = {{Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis}},
url = {http://aem.asm.org/cgi/doi/10.1128/AEM.02810-10},
volume = {77},
year = {2011}
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author = {Huse, Susan M and Welch, David Mark and Morrison, Hilary G and Sogin, Mitchell L},
doi = {10.1111/j.1462-2920.2010.02193.x},
file = {:Users/nolson/Documents/Mendeley Desktop/Huse et al. - 2010 - Ironing out the wrinkles in the rare biosphere through improved OTU clustering.pdf:pdf},
issn = {1462-2920},
journal = {Environmental microbiology},
keywords = {Biodiversity,Cluster Analysis,DNA, Bacterial,DNA, Bacterial: chemistry,DNA, Bacterial: genetics,DNA, Ribosomal,DNA, Ribosomal: chemistry,DNA, Ribosomal: genetics,Environmental Microbiology,Escherichia coli,Escherichia coli: genetics,Metagenomics,Metagenomics: methods,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, DNA,Staphylococcus epidermidis,Staphylococcus epidermidis: genetics},
mendeley-groups = {16S rRNA/16S diversitystudies,16S rRNA,16S rRNA/16S Seq errors,16S rRNA/16S Clustering},
month = {jul},
number = {7},
pages = {1889--98},
pmid = {20236171},
title = {{Ironing out the wrinkles in the rare biosphere through improved OTU clustering.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2909393&tool=pmcentrez&rendertype=abstract},
volume = {12},
year = {2010}
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@article{Chen2013,
author = {Chen, Wei and Zhang, Clarence K. and Cheng, Yongmei and Zhang, Shaowu and Zhao, Hongyu},
doi = {10.1371/journal.pone.0070837},
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issn = {19326203},
journal = {PLoS ONE},
mendeley-groups = {16S rRNA/16S Clustering},
number = {8},
pmid = {23967117},
title = {{A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs}},
volume = {8},
year = {2013}
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@article{Chao2014,
author = {Chao, Anne and Gotelli, Nicholas J. and Hsieh, T. C. and Sander, Elizabeth L. and Ma, K. H. and Colwell, Robert K. and Ellison, Aaron M.},
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file = {:Users/nolson/Documents/Mendeley Desktop/Chao et al. - 2014 - Rarefaction and extrapolation with Hill numbers A framework for sampling and estimation in species diversity studie.pdf:pdf},
isbn = {0012-9615},
issn = {00129615},
journal = {Ecological Monographs},
keywords = {Abundance data,Diversity,Extrapolation,Hill numbers,Incidence data,Interpolation,Prediction,Rarefaction,Sample coverage,Species richness},
mendeley-groups = {Ecology Diversity},
number = {1},
pages = {45--67},
title = {{Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies}},
volume = {84},
year = {2014}
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author = {Ricotta, Carlo},
doi = {10.1007/s10441-007-9008-7},
file = {:Users/nolson/Documents/Mendeley Desktop/Ricotta - 2007 - A semantic taxonomy for diversity measures.pdf:pdf},
isbn = {00015342 (ISSN)},
issn = {00015342},
journal = {Acta Biotheoretica},
keywords = {Complexity,Compositional diversity matrix,Divergence,Evenness,Pairwise species distances,Richness},
mendeley-groups = {Ecology Diversity},
number = {1},
pages = {23--33},
pmid = {17486413},
title = {{A semantic taxonomy for diversity measures}},
volume = {55},
year = {2007}
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@article{Tuomisto2012,
annote = {species diversity - two components richness and evenness},
author = {Tuomisto, Hanna},
doi = {10.1111/j.1600-0706.2011.19897.x},
file = {:Users/nolson/Documents/Mendeley Desktop/Tuomisto - 2012 - An updated consumer's guide to evenness and related indices.pdf:pdf},
isbn = {1600-0706},
issn = {00301299},
journal = {Oikos},
keywords = {alpha diversity,evenness,richness},
mendeley-groups = {Ecology Diversity/Diversity Metric Performance,Ecology Diversity/alpha diversity},
mendeley-tags = {alpha diversity,evenness,richness},
number = {8},
pages = {1203--1218},
title = {{An updated consumer's guide to evenness and related indices}},
volume = {121},
year = {2012}
}

@article{Bunge2014,
author = {Bunge, John and Willis, Amy and Walsh, Fiona},
doi = {10.1146/annurev-statistics-022513-115654},
file = {:Users/nolson/Documents/Mendeley Desktop/Bunge, Willis, Walsh - 2014 - Estimating the Number of Species in Microbial Diversity Studies.pdf:pdf},
issn = {2326-8298},
journal = {Annual Review of Statistics and Its Application},
keywords = {mixed,number of classes,poisson,sample coverage,species richness,zero truncation,$\alpha$ -diversity},
mendeley-groups = {16S rRNA},
number = {1},
pages = {427--445},
title = {{Estimating the Number of Species in Microbial Diversity Studies}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-statistics-022513-115654},
volume = {1},
year = {2014}
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@article{Chiu2015,
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doi = {10.7287/peerj.preprints.11},
file = {:Users/nolson/Documents/Mendeley Desktop/Chiu, Chao - 2015 - Estimating and comparing microbial diversity in the presence of sequencing errors.pdf:pdf},
isbn = {2255782855},
issn = {2167-9843},
journal = {PeerJ},
mendeley-groups = {Ecology Diversity},
pages = {1--13},
title = {{Estimating and comparing microbial diversity in the presence of sequencing errors}},
year = {2015}
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isbn = {1362-4962 (Electronic)\r0305-1048 (Linking)},
issn = {13624962},
journal = {Nucleic Acids Research},
mendeley-groups = {16S rRNA/16S Seq errors},
number = {6},
pmid = {25586220},
title = {{Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform}},
volume = {43},
year = {2015}
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@article{Amore2016,
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doi = {10.1186/s12864-015-2194-9},
file = {:Users/nolson/Documents/Mendeley Desktop/Amore et al. - 2016 - A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
mendeley-groups = {16S rRNA,16S rRNA/16S taxonomic classification},
pages = {1--40},
publisher = {BMC Genomics},
title = {{A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling}},
url = {http://dx.doi.org/10.1186/s12864-015-2194-9},
volume = {17},
year = {2016}
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journal = {Applied and Environmental Microbiology},
keywords = {16S assessment dataset},
mendeley-groups = {16S rRNA/16S sequencing evaluation},
mendeley-tags = {16S assessment dataset},
number = {18},
pages = {5717--5722},
pmid = {25002428},
title = {{Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles}},
volume = {80},
year = {2014}
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issn = {1932-6203},
journal = {PloS one},
keywords = {16S assessment dataset},
mendeley-groups = {16S rRNA/16S sequencing evaluation},
mendeley-tags = {16S assessment dataset},
number = {2},
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isbn = {0099-2240},
issn = {0099-2240},
journal = {Applied and Environmental Microbiology},
mendeley-groups = {16S rRNA/16S analysis pipelines,16S rRNA/16S taxonomic classification},
number = {17},
pages = {5112--5120},
pmid = {23793624},
title = {{Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform}},
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year = {2013}
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journal = {BMC Genomics},
keywords = {Animal Genetics and Genomics,Life Sciences,Microarrays,Microbial Genetics and Genomics,Plant Genetics & Genomics,Proteomics,general},
language = {En},
mendeley-groups = {16S rRNA/16S differential abundance},
month = {jan},
number = {1},
pages = {78},
publisher = {BioMed Central},
title = {{Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics}},
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doi = {10.1093/nar/gkq873},
institution = {Department of Microbiology, University College Cork, Cork, Ireland. mclaesson@bioinfo.ucc.ie},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {16S,16S: genetics,DNA,DNA: methods,Feces,Feces: microbiology,Genes,Genetic Variation,Humans,Metagenome,Phylogeny,Polymerase Chain Reaction,RNA,Ribosomal,Sequence Analysis,rRNA},
mendeley-groups = {16S rRNA/16S diversitystudies,16S rRNA},
month = {dec},
number = {22},
pages = {e200},
pmid = {20880993},
publisher = {Oxford University Press},
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keywords = {16S,16S: genetics,Bacterial,Bacterial: genetics,Climate Change,DNA,DNA: methods,Metagenomics,Metagenomics: methods,Oklahoma,RNA,Ribosomal,Sequence Analysis,Shewanella,Shewanella: genetics,Shewanella: isolation & purification,Soil Microbiology,reference data,reproducibility},
mendeley-groups = {16S rRNA/16S diversitystudies,16S rRNA,16S rRNA/16S taxonomic classification},
mendeley-tags = {reference data,reproducibility},
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number = {8},
pages = {1303--13},
pmid = {21346791},
publisher = {Nature Publishing Group},
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mendeley-groups = {16S rRNA},
mendeley-tags = {16S bias},
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pmid = {26196512},
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@article{Schirmer2015,
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doi = {10.1093/nar/gku1341},
file = {:Users/nolson/Documents/Mendeley Desktop/Schirmer et al. - 2015 - Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
keywords = {16S rRNA,error correction,sequencing errors},
mendeley-tags = {16S rRNA,error correction,sequencing errors},
month = {jan},
number = {6},
pages = {gku1341--},
title = {{Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform}},
url = {http://nar.oxfordjournals.org/content/43/6/e37 http://nar.oxfordjournals.org/content/early/2015/01/13/nar.gku1341.long},
volume = {43},
year = {2015}
}

@article{Goodrich2014,
author = {Goodrich, Julia K. and {Di Rienzi}, Sara C. and Poole, Angela C. and Koren, Omry and Walters, William A. and Caporaso, J. Gregory and Knight, Rob and Ley, Ruth E.},
doi = {10.1016/j.cell.2014.06.037},
file = {:Users/nolson/Documents/Mendeley Desktop/Goodrich et al. - 2014 - Conducting a Microbiome Study.pdf:pdf},
issn = {00928674},
journal = {Cell},
mendeley-groups = {16S rRNA},
number = {2},
pages = {250--262},
publisher = {Elsevier Inc.},
title = {{Conducting a Microbiome Study}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867414008642},
volume = {158},
year = {2014}
}

@article{Albertsen2015,
author = {Albertsen, Mads and Karst, S{\o}ren M and Ziegler, Anja S and Kirkegaard, Rasmus H and Nielsen, Per H},
doi = {10.1371/journal.pone.0132783},
file = {:Users/nolson/Documents/Mendeley Desktop/Albertsen et al. - 2015 - Back to Basics - The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludg.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {16S,DNA extraction,PCR primers,reference data},
mendeley-groups = {16S rRNA},
mendeley-tags = {16S,DNA extraction,PCR primers,reference data},
month = {jan},
number = {7},
pages = {e0132783},
pmid = {26182345},
publisher = {Public Library of Science},
title = {{Back to Basics - The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities.}},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132783},
volume = {10},
year = {2015}
}

@article{Brooks2015,
author = {Brooks, J Paul and Edwards, David J and Harwich, Michael D and Rivera, Maria C and Fettweis, Jennifer M and Serrano, Myrna G and Reris, Robert A and Sheth, Nihar U and Huang, Bernice and Girerd, Philippe and Consortium, Vaginal Microbiome and Strauss, Jerome F and Jefferson, Kimberly K and Buck, Gregory A},
doi = {10.1186/s12866-015-0351-6},
file = {:Users/nolson/Documents/Mendeley Desktop/Brooks et al. - 2015 - The truth about metagenomics quantifying and counteracting bias in 16S rRNA studies.pdf:pdf},
isbn = {1471-2180 (Electronic)\r1471-2180 (Linking)},
issn = {1471-2180},
journal = {BMC microbiology},
keywords = {1 department of statistical,16S bias,assessments of microbial community,correspondence,dna extraction bias,edu,jpbrooks,next generation sequencing,pcr bias,quality control,sciences and operations research,structure via metagenomics,vcu,virginia},
mendeley-groups = {16S rRNA},
mendeley-tags = {16S bias},
month = {mar},
number = {1},
pages = {66},
pmid = {25880246},
title = {{The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.}},
url = {http://www.biomedcentral.com/1471-2180/15/66},
volume = {15},
year = {2015}
}

@article{Kunin2010,
author = {Kunin, Victor and Engelbrektson, Anna and Ochman, Howard and Hugenholtz, Philip},
doi = {10.1111/j.1462-2920.2009.02051.x},
file = {:Users/nolson/Documents/Mendeley Desktop/Kunin et al. - 2010 - Wrinkles in the rare biosphere pyrosequencing errors can lead to artificial inflation of diversity estimates.pdf:pdf},
issn = {1462-2920},
journal = {Environmental microbiology},
keywords = {Biodiversity,Cluster Analysis,DNA, Bacterial,DNA, Bacterial: genetics,Escherichia coli,Escherichia coli: genetics,Genes, Bacterial,Genetic Variation,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics,Sequence Alignment,Sequence Analysis, DNA,Sequence Analysis, DNA: methods},
mendeley-groups = {Metagenomics,16S rRNA,16S rRNA/16S taxonomic classification},
month = {jan},
number = {1},
pages = {118--23},
pmid = {19725865},
title = {{Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19725865},
volume = {12},
year = {2010}
}

@article{Esling2015,
author = {Esling, Philippe and Lejzerowicz, Franck and Pawlowski, Jan},
doi = {10.1093/nar/gkv107},
file = {:Users/nolson/Documents/Mendeley Desktop/Esling, Lejzerowicz, Pawlowski - 2015 - Accurate multiplexing and filtering for high-throughput amplicon-sequencing.pdf:pdf},
journal = {Nucleic Acids Research},
mendeley-groups = {16S rRNA},
number = {10},
pages = {2513--2524},
title = {{Accurate multiplexing and filtering for high-throughput amplicon-sequencing}},
volume = {43},
year = {2015}
}

@article{Flores2015,
author = {Flores, Roberto and Shi, Jianxin and Yu, Guoqin and Ma, Bing and Ravel, Jacques and Goedert, James J. and Sinha, Rashmi},
doi = {10.1186/s40168-015-0092-7},
file = {:Users/nolson/Documents/Mendeley Desktop/Flores et al. - 2015 - Collection media and delayed freezing effects on microbial composition of human stool.pdf:pdf},
issn = {2049-2618},
journal = {Microbiome},
language = {en},
mendeley-groups = {16S rRNA},
month = {aug},
number = {1},
pages = {33},
pmid = {26269741},
publisher = {BioMed Central Ltd},
title = {{Collection media and delayed freezing effects on microbial composition of human stool}},
url = {http://www.microbiomejournal.com/content/3/1/33},
volume = {3},
year = {2015}
}

@article{Engelbrektson2010,
author = {Engelbrektson, Anna and Kunin, Victor and Wrighton, Kelly C and Zvenigorodsky, Natasha and Chen, Feng and Ochman, Howard and Hugenholtz, Philip},
doi = {10.1038/ismej.2009.153},
file = {:Users/nolson/Documents/Mendeley Desktop/Engelbrektson et al. - 2010 - Experimental factors affecting PCR-based estimates of microbial species richness and evenness.pdf:pdf},
issn = {1751-7370},
journal = {The ISME journal},
keywords = {16S,16S: genetics,Animals,Bacteria,Bacteria: classification,Bacteria: genetics,Bacterial,Bacterial Typing Techniques,Bacterial Typing Techniques: economics,Bacterial Typing Techniques: methods,Bacterial: genetics,DNA,DNA Primers,DNA: economics,DNA: methods,Isoptera,Isoptera: microbiology,Polymerase Chain Reaction,RNA,Ribosomal,Sequence Analysis},
mendeley-groups = {16S rRNA/PCR bias,Metagenomics/Metagenomics DNA extraction/DNA extraction,16S rRNA},
month = {may},
number = {5},
pages = {642--7},
pmid = {20090784},
publisher = {Nature Publishing Group},
title = {{Experimental factors affecting PCR-based estimates of microbial species richness and evenness.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20090784},
volume = {4},
year = {2010}
}

@article{Cangelosi2014,
author = {Cangelosi, Gerard A and Meschke, John S},
doi = {10.1128/AEM.01763-14},
file = {:Users/nolson/Documents/Mendeley Desktop/Cangelosi, Meschke - 2014 - Dead or alive molecular assessment of microbial viability.pdf:pdf},
issn = {1098-5336},
journal = {Applied and environmental microbiology},
mendeley-groups = {16S rRNA},
month = {oct},
number = {19},
pages = {5884--91},
pmid = {25038100},
title = {{Dead or alive: molecular assessment of microbial viability.}},
url = {http://aem.asm.org/content/80/19/5884.long},
volume = {80},
year = {2014}
}
@article{Blazewicz2013,
author = {Blazewicz, Steven J and Barnard, Romain L and Daly, Rebecca A and Firestone, Mary K},
doi = {10.1038/ismej.2013.102},
issn = {1751-7362},
journal = {The ISME Journal},
keywords = {community rRNA,ecosystem processes,environmental samples,microbial activity,microbial growth,ribosomes},
mendeley-groups = {16S rRNA},
month = {jul},
number = {11},
pages = {2061--2068},
publisher = {International Society for Microbial Ecology},
shorttitle = {ISME J},
title = {{Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses}},
url = {http://dx.doi.org/10.1038/ismej.2013.102},
volume = {7},
year = {2013}
}
@techreport{Carini2016,
author = {Carini, Paul and Marsden, Patrick J and Leff, Jonathan W and Morgan, Emily E and Strickland, Michael S and Fierer, Noah},
booktitle = {bioRxiv},
doi = {10.1101/043372},
file = {:Users/nolson/Documents/Mendeley Desktop/Carini et al. - 2016 - Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.pdf:pdf},
keywords = {DNA extraction},
language = {en},
mendeley-groups = {16S rRNA},
mendeley-tags = {DNA extraction},
month = {mar},
pages = {043372},
publisher = {Cold Spring Harbor Labs Journals},
title = {{Relic DNA is abundant in soil and obscures estimates of soil microbial diversity}},
url = {http://biorxiv.org/content/early/2016/03/17/043372.1.abstract},
year = {2016}
}

@article{Carrigg2007,
author = {Carrigg, Cora and Rice, Olivia and Kavanagh, Siobh{\'{a}}n and Collins, Gavin and O'Flaherty, Vincent},
doi = {10.1007/s00253-007-1219-y},
file = {:Users/nolson/Documents/Mendeley Desktop/Carrigg et al. - 2007 - DNA extraction method affects microbial community profiles from soils and sediment.pdf:pdf},
issn = {0175-7598},
journal = {Applied microbiology and biotechnology},
keywords = {16S,16S: genetics,Bacteria,Bacteria: genetics,Bacterial,Bacterial: genetics,Bacterial: isolation & purification,DNA,Electrophoresis,Environmental Microbiology,Geologic Sediments,Geologic Sediments: microbiology,Nucleic Acid Denaturation,Polyacrylamide Gel,Polyacrylamide Gel: methods,RNA,Ribosomal,Ribosomal: analysis,Soil Microbiology},
mendeley-groups = {Metagenomics/Metagenomics DNA extraction/DNA extraction,Missing PDF},
month = {dec},
number = {4},
pages = {955--64},
pmid = {17960375},
title = {{DNA extraction method affects microbial community profiles from soils and sediment.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17960375},
volume = {77},
year = {2007}
}

@article{Olson2012,
author = {Olson, Nathan D and Morrow, Jayne B},
doi = {10.1186/1756-0500-5-668},
issn = {1756-0500},
journal = {BMC research notes},
keywords = {Biodetection,dna characterization,dna concentration,dna extraction,dna purity,pcr inhibition,qpcr,shearing},
month = {dec},
number = {1},
pages = {668},
pmid = {23206278},
publisher = {BMC Research Notes},
title = {{DNA extract characterization process for microbial detection methods development and validation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23206278},
volume = {5},
year = {2012}
}

@article{Ettenauer2012,
author = {Ettenauer, J{\"{o}}rg D and Pi{\~{n}}ar, Guadalupe and Lopandic, Ksenija and Spangl, Bernhard and Ellersdorfer, G{\"{u}}nther and Voitl, Christian and Sterflinger, Katja},
doi = {10.1016/j.scitotenv.2012.09.005},
issn = {1879-1026},
journal = {The Science of the total environment},
keywords = {Building materials,DNA extraction,DNA purity,DNA yield,PCR},
mendeley-groups = {Missing PDF},
month = {oct},
pages = {44--53},
pmid = {23063637},
publisher = {Elsevier B.V.},
title = {{Microbes on building materials - Evaluation of DNA extraction protocols as common basis for molecular analysis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23063637},
volume = {439C},
year = {2012}
}

@article{Jonsson2016,
abstract = {Metagenomics is the study of microbial communities by sequencing of genetic material directly from environmental or clinical samples. The genes present in the metagenomes are quantified by annotating and counting the generated DNA fragments. Identification of differentially abundant genes between metagenomes can provide important information about differences in community structure, diversity and biological function. Metagenomic data is however high-dimensional, contain high levels of biological and technical noise and have typically few biological replicates. The statistical analysis is therefore challenging and many approaches have been suggested to date.},
author = {Jonsson, Viktor and {\"{O}}sterlund, Tobias and Nerman, Olle and Kristiansson, Erik},
doi = {10.1186/s12864-016-2386-y},
file = {:Users/nolson/Documents/Mendeley Desktop/Jonsson et al. - 2016 - Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomic.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Animal Genetics and Genomics,Life Sciences,Microarrays,Microbial Genetics and Genomics,Plant Genetics & Genomics,Proteomics,general},
language = {En},
mendeley-groups = {16S rRNA/16S differential abundance},
month = {jan},
number = {1},
pages = {78},
publisher = {BioMed Central},
title = {{Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics}},
url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2386-y},
volume = {17},
year = {2016}
}

@article{zhang2014pear,
  title={PEAR: a fast and accurate Illumina Paired-End reAd mergeR},
  author={Zhang, Jiajie and Kobert, Kassian and Flouri, Tom{\'a}{\v{s}} and Stamatakis, Alexandros},
  journal={Bioinformatics},
  volume={30},
  number={5},
  pages={614--620},
  year={2014},
  publisher={Oxford Univ Press}
}

@article{masella2012pandaseq,
  title={PANDAseq: paired-end assembler for illumina sequences},
  author={Masella, Andre P and Bartram, Andrea K and Truszkowski, Jakub M and Brown, Daniel G and Neufeld, Josh D},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={31},
  year={2012},
  publisher={BioMed Central Ltd}
}

@article{anders2010differential,
  title={Differential expression analysis for sequence count data},
  author={Anders, Simon and Huber, Wolfgang},
  journal={Genome biology},
  volume={11},
  number={10},
  pages={1},
  year={2010},
  publisher={BioMed Central}
}

@article{love2014moderated,
  title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
  journal={Genome biology},
  volume={15},
  number={12},
  pages={1},
  year={2014},
  publisher={BioMed Central}
}

@article{mcmurdie2014waste,
  title={Waste not, want not: why rarefying microbiome data is inadmissible},
  author={McMurdie, Paul J and Holmes, Susan},
  journal={PLoS Comput Biol},
  volume={10},
  number={4},
  pages={e1003531},
  year={2014},
  publisher={Public Library of Science}
}

repository: nate-d-olson/mgmgnotes

repo_name: nate-d-olson/mgmgnotes


text:
package problems

func isPalindrome(x int) bool {
	if x < 0 || x%10 == 0 && x != 0 {
		return false
	}
	var y = 0
	for {
		y = y*10 + x%10
		x /= 10
		if y >= x {
			break
		}
	}
	return x == y || x == y/10
}

branch_name: refs/heads/main


text:
package message

import (
	"github.com/atlassian/go-sentry-api"
	"strconv"
	"strings"
)

const MdFormatType = "md"

type MD struct {
}

func (m MD) Build(project sentry.Project, issue sentry.Issue) string {
	message := []string{
		"*" + project.Organization.Name + " [" + *project.Organization.ID + "]*",
		"-------------------------------------",
		"*Project:* " + project.Name,
		"*Project ID:* " + project.ID,
		"",
		"*Issue ID:* " + *issue.ID,
		"*Title:* " + *issue.Title,
		"*Type:* " + *issue.Type,
		"*FirstSeen:* " + issue.FirstSeen.Format("02.01.2006 15:04:05"),
		"*LastSeen:* " + issue.LastSeen.Format("02.01.2006 15:04:05"),
		"*Status:* " + string(*issue.Status),
		"*Short ID:* " + *issue.ShortID,
		"*Level:* " + *issue.Level,
		"*Culprit:* " + *issue.Culprit,
		"*UserCount:* " + strconv.Itoa(*issue.UserCount),
		"*Permalink:* " + *issue.Permalink,
		"",
	}

	return strings.Join(message, "\n")
}

repository: evgeny-klyopov/sentry-notifier

repo_name: evgeny-klyopov/sentry-notifier


text:
# Base this image on core-image-minimal
include recipes-core/images/core-image-minimal.bb

IMAGE_INSTALL += " \
		vim-tiny \
		dropbear \
		lmsensors \
		pciutils \
		e2fsprogs \
		sysbench \
		phoronix-test-suite \
		"


text:
@article{elbaz2018hydrogen,
 author = {Elbaz, Yuval and Furman, David and ,Caspary-Toroker, Maytal},
 journal = {Physical Chemistry Chemical Physics},
 number = {20},
 pages = {25169--25178},
 publisher = {Royal Society of Chemistry},
 title = {Hydrogen Transfer through Different Crystal Phases of Nickel Oxy/hydroxide},
 year = {2018}
}


text:
@Article{Feldman2010,
  author="Feldman, Ronen
  and Govindaraj, Suresh
  and Livnat, Joshua
  and Segal, Benjamin",
  title="Management's tone change, post earnings announcement drift and accruals",
  journal="Review of Accounting Studies",
  year="2010",
  month="Dec",
  day="01",
  volume="15",
  number="4",
  pages="915--953",
  abstract="This study explores whether the management discussion and analysis (MD{\&}A) section of Forms 10-Q and 10-K has incremental information content beyond financial measures such as earnings surprises and accruals. It uses a classification scheme of words into positive and negative categories to measure the tone change in the MD{\&}A section relative to prior periodic SEC filings. Our results indicate that short window market reactions around the SEC filing are significantly associated with the tone change of the MD{\&}A section, even after controlling for accruals and earnings surprises. We show that management's tone change adds significantly to portfolio drift returns in the window of 2 days after the SEC filing date through 1 day after the subsequent quarter's preliminary earnings announcement, beyond financial information conveyed by accruals and earnings surprises. The drift returns are affected by the ability of the tone change signals to help predict the subsequent quarter's earnings surprise but cannot be completely attributed to this ability. We also find that the incremental information of management's tone change depends on the strength of the firm's information environment.",
  issn="1573-7136",
  doi="10.1007/s11142-009-9111-x",
  url="https://doi.org/10.1007/s11142-009-9111-x"
}

@misc{Vaswani2017,
    title={Attention Is All You Need},
    author={Ashish Vaswani and Noam Shazeer and Niki Parmar and Jakob Uszkoreit and Llion Jones and Aidan N. Gomez and Lukasz Kaiser and Illia Polosukhin},
    year={2017},
    eprint={1706.03762},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}

@article{Devlin2018,
  author    = {Jacob Devlin and
               Ming{-}Wei Chang and
               Kenton Lee and
               Kristina Toutanova},
  title     = {{BERT:} Pre-training of Deep Bidirectional Transformers for Language
               Understanding},
  journal   = {CoRR},
  volume    = {abs/1810.04805},
  year      = {2018},
  url       = {http://arxiv.org/abs/1810.04805},
  archivePrefix = {arXiv},
  eprint    = {1810.04805},
  timestamp = {Tue, 30 Oct 2018 20:39:56 +0100},
  biburl    = {https://dblp.org/rec/bib/journals/corr/abs-1810-04805},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{Mikolov2014,
  author    = {Quoc V. Le and
               Tomas Mikolov},
  title     = {Distributed Representations of Sentences and Documents},
  journal   = {CoRR},
  volume    = {abs/1405.4053},
  year      = {2014},
  url       = {http://arxiv.org/abs/1405.4053},
  archivePrefix = {arXiv},
  eprint    = {1405.4053},
  timestamp = {Mon, 13 Aug 2018 16:48:49 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/corr/LeM14},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@book{Hastie2009,
  title={The Elements of Statistical Learning},
  author={Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
  publisher={Springer Science+Business Media, LLC},
  year={2009}
}

@inproceedings{Popel2018,
  title={Training Tips for the Transformer Model},
  booktitle={The Prague Bulletin of Mathematical Linguistics},
  author="Popel, Martin and Bojar, Ondřej",
  year={2018},
  crossref={PragueBulletin2018},
  pages={43--70}
}

@proceedings{PragueBulletin2018,
  title={The Prague Bulletin of Mathematical Linguistics},
  year=2018,
  number=110
}

@misc{DeSola2019,
  author = {DeSola, Vinicio and Hanna, Kevin and Nonis, Pri},
  year = {2019},
  title = {FinBERT: pre-trained model on SEC filings for financial natural language tasks},
}

@book{Russel2016,
  author = {Russell, Stuart and Norvig Peter},
  title = {Artificial Intelligence - A Modern Approach},
  year = 2016,
  edition = 3
}

@book{Goodfellow2016,
    title={Deep Learning},
    author={Ian Goodfellow and Yoshua Bengio and Aaron Courville},
    publisher={MIT Press},
    note={\url{http://www.deeplearningbook.org}},
    year={2016}
}

@article{Hochreiter1997,
  title={Long Short-Term Memory},
  author={Hochreiter, Sepp and Schmidhuber, Jürgen},
  journal={Neural Computation},
  volume=9,
  year=1997,
  pages={1735--1780},
}

@techreport{Azimi2019,
  title={Is Positive Sentiment in Corporate Annual Reports Informative? Evidence from Deep Learning},
  author={Azimi, Mehran and Agrawal, Anup},
  institution={University of Alabama},
  year=2019
}

@techreport{Shlens2014,
  title={A Tutorial on Principal Component Analysis},
  author={Shlens, Jonathon},
  institution={Google Research},
  year=2014
}

@techreport{Fletcher2008,
  title={Support Vector Machines Explained},
  author={Fletcher, Tristan},
  institution={University College London},
  year=2008
}

@article{Lipton2015,
  author    = {Lipton, Zachary Chase and Berkowitz, John},
  title     = {A Critical Review of Recurrent Neural Networks for Sequence Learning},
  journal   = {CoRR},
  volume    = {abs/1506.00019},
  year      = 2015
}

@phdthesis{Grzegorczyk2018,
  author = {Grzegorczyk, Karol},
  title = {Vector representations of text data in deep learning},
  school = {AGH University of Science and Technology},
  year = 2018
}

@misc{Mikolov2013,
  author = {Mikolov, Thomas and Chen, Kai and Corrado, Greg and Dean, Jeffrey},
  title = {Efficient Estimation of Word Representations in Vector Space},
  year = 2013
}

@article{Heo2016,
  author = {Heo, Junyoung and Yang, Jin Yong},
  title = {Stock Price Prediction Based on Financial Statements Using SVM},
  journal = {International Journal of Hybrid Information Technology},
  volume = 9,
  number = 2,
  year = 2016,
  pages = {57--66}
}

@techreport{Milosevic2016,
  author = {Milosevic, Nikola},
  title = {Equity forecast: Predicting long term stock price movement using machine learning},
  institution = {School of Computer Science, University of Manchester},
  year = 2016
}

@techreport{Moukalled2019,
  author = {Moukalled, Mariam and El-Hajj, Wassim and Jaber, Mohamad},
  title = {Automated Stock Price Prediction Using Machine Learning},
  institution = {Computer Science Department, American University of Beirut},
  year = 2019
}

@techreport{Li2006,
  author = {Li, Feng},
  title = {Do Stock Market Investors Understand the Risk Sentiment of Corporate Annual Reports?},
  institution = {Stephen M. Ross School of Business, University of Michigan},
  year = 2006
}


text:
require midori.inc

SRC_URI = "http://goodies.xfce.org/releases/midori/midori-${PV}.tar.bz2"

SRC_URI[md5sum] = "0b9298d00c598137431beb51dbe1f302"
SRC_URI[sha256sum] = "e561f66262eaf6b9cbd8e84688184b7f3ba6cba0e34e9791e578bdef9adc7731"