text:
ymers,Polymers: chemistry,Solutions},
number = {28},
pages = {284131},
pmid = {22739124},
title = {{Non-equilibrium relaxation and tumbling times of polymers in semidilute solution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22739124},
volume = {24},
year = {2012}
}
@article{Halpin-Healy1995,
abstract = {Kinetic interfaces form the basis of a fascinating, interdisciplinary branch of statistical mechanics. Diverse stochastic growth processes can be unified via an intriguing nonlinear stochastic partial differential equation whose consequences and generalizations have mobilized a sizeable community of physicists concerned with a statistical description of kinetically roughened surfaces. Substantial analytical, experimental and numerical effort has already been expended. Despite impressive successes, however, there remain many open questions, with much richness and subtlety still to be revealed. In this review, we give an unorthodox account of this rapidly growing field, concentrating on two main lines — the interface growth equations themselves, and their directed polymer counterparts. We emphasize the intrinsic links among the topics discussed, as well as the relationships to other branches of natural science. Our aim is to persuade the reader that multidisciplinary statistical mechanics can be challenging, enjoyable pursuit of surprising depth.},
author = {Halpin-Healy, Timothy and Zhang, Yi-Cheng},
doi = {10.1016/0370-1573(94)00087-J},
file = {:Users/wenwen/Documents/MendeleyRefs/Halpin-Healy, Zhang{\_}Physics Reports{\_}1995.pdf:pdf},
isbn = {0370-1573},
issn = {03701573},
journal = {Phys. Rep.},
number = {4-6},
pages = {215--414},
title = {{Kinetic roughening phenomena, stochastic growth, directed polymers and all that. Aspects of multidisciplinary statistical mechanics}},
volume = {254},
year = {1995}
}
@book{Teraoka2002,
author = {Teraoka, Iwao},
file = {:Users/wenwen/Documents/MendeleyRefs/Teraoka{\_}Unknown{\_}2002.pdf:pdf},
publisher = {John Wiley {\&} Sons},
title = {{Plymer solutions}},
year = {2002}
}
@article{Meloni2008,
author = {Meloni, Sandro and G{\'{o}}mez-Garde{\~{n}}es, Jes{\'{u}}s and Latora, Vito and Moreno, Yamir},
doi = {10.1103/PhysRevLett.100.208701},
file = {:Users/wenwen/Documents/MendeleyRefs/Meloni et al.{\_}Physical Review Letters{\_}2008.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {20},
pages = {1--4},
title = {{Scaling Breakdown in Flow Fluctuations on Complex Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.208701},
volume = {100},
year = {2008}
}
@article{Shargel2003,
author = {Shargel, Benjamin and Sayama, Hiroki and Epstein, Irving and Bar-Yam, Yaneer},
doi = {10.1103/PhysRevLett.90.068701},
file = {:Users/wenwen/Documents/MendeleyRefs/Shargel et al.{\_}Physical Review Letters{\_}2003.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {feb},
number = {6},
pages = {068701},
title = {{Optimization of Robustness and Connectivity in Complex Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.90.068701},
volume = {90},
year = {2003}
}
@article{Hahn1996,
abstract = {The diffusion of particles in single-file systems is investigated by means of molecular dynamics simulation. For three different system configurations, the mean square displacements are calculated and compared with the result of analytical considerations. For a straight tube the mean square displacement is proportional to the time t. For a straight tube, where random forces act on the particles, and for a periodic tube potential it is proportional to the square root of time.},
author = {Hahn, K. and K{\"{a}}rger, J.},
doi = {10.1021/jp951807u},
file = {:Users/wenwen/Documents/MendeleyRefs/Hahn, K{\"{a}}rger{\_}The Journal of Physical Chemistry{\_}1996.pdf:pdf},
issn = {0022-3654},
journal = {J. Phys. Chem.},
keywords = {diffusion,single-file},
month = {jan},
number = {1},
pages = {316--326},
title = {{Molecular Dynamics Simulation of Single-File Systems}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp951807u},
volume = {100},
year = {1996}
}
@book{Dawkins2007a,
author = {Dawkins, Paul},
file = {:Users/wenwen/Documents/MendeleyRefs/Dawkins{\_}Unknown{\_}2007.pdf:pdf},
title = {{Differential Equations}},
year = {2007}
}
@article{Matthews1991,
abstract = {We consider the interaction of a large number of limit-cycle oscillators with linear, all-to-all coupling and a distribution of natural frequencies. The system exhibits extremely rich dynamics as the coupling strength and the width of the frequency distribution are varied. We find a variety of steady behaviors that can be described by a stationary distribution in phase space: frequency locking, amplitude death, incoherence and partial locking. An unexpected result is that the system can also exhibit unsteady behavior, in which the phase space distribution evolves periodically, quasiperiodically or even chaotically. The simple form of the model allows us to derive several analytical results. The stability boundaries of amplitude death and incoherence are found explicitly. Rigorous results on the existence and stability of frequency locking are also obtained. ?? 1991.},
author = {Matthews, Paul C. and Mirollo, Renato E. and Strogatz, Steven H.},
doi = {10.1016/0167-2789(91)90129-W},
file = {:Users/wenwen/Documents/MendeleyRefs/Matthews, Mirollo, Strogatz{\_}Physica D Nonlinear Phenomena{\_}1991.pdf:pdf},
isbn = {0167-2789},
issn = {01672789},
journal = {Phys. D Nonlinear Phenom.},
month = {sep},
number = {2-3},
pages = {293--331},
title = {{Dynamics of a large system of coupled nonlinear oscillators}},
url = {http://linkinghub.elsevier.com/retrieve/pii/016727899190129W},
volume = {52},
year = {1991}
}
@article{Motegi2012a,
abstract = {The relaxation dynamics of the one-dimensional totally asymmetric simple exclusion process on a ring is considered in the case of step initial condition. Analyzing the time evolution of the local particle densities and currents by the Bethe ansatz method, we examine their full relaxation dynamics. As a result, we observe peculiar behaviors, such as the emergence of a ripple in the density profile and the existence of the excessive particle currents. Moreover, by making a finite-size scaling analysis of the asymptotic amplitudes of the local densities and currents, we find the scaling exponents with respect to the total number of sites to be −3/2 and −1, respectively.},
archivePrefix = {arXiv},
arxivId = {arXiv:1201.2749v1},
author = {Motegi, Kohei and Sakai, Kazumitsu and Sato, Jun},
doi = {10.1103/PhysRevE.85.042105},
eprint = {arXiv:1201.2749v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Motegi, Sakai, Sato{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {042105},
title = {{Exact relaxation dynamics in the totally asymmetric simple exclusion process}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.042105},
volume = {85},
year = {2012}
}
@article{Howard2011,
author = {Howard, Michael P. and Milner, Scott T.},
doi = {10.1103/PhysRevE.84.051804},
file = {:Users/wenwen/Documents/MendeleyRefs/Howard, Milner{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {5},
pages = {051804},
title = {{Numerical simulation methods for the Rouse model in flow}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.051804},
volume = {84},
year = {2011}
}
@book{Morse2004,
author = {Morse, DC},
file = {:Users/wenwen/Documents/MendeleyRefs/Morse{\_}Unknown{\_}2004.pdf:pdf},
isbn = {0471445282},
publisher = {John Wiley {\&} Sons},
title = {{Theory of constrained Brownian motion}},
volume = {128},
year = {2004}
}
@article{Parshani2011,
abstract = {Current network models assume one type of links to define the relations between the network entities. However, many real networks can only be correctly described using two different types of relations. Connectivity links that enable the nodes to function cooperatively as a network and dependency links that bind the failure of one network element to the failure of other network elements. Here we present an analytical framework for studying the robustness of networks that include both connectivity and dependency links. We show that a synergy exists between the failure of connectivity and dependency links that leads to an iterative process of cascading failures that has a devastating effect on the network stability. We present exact analytical results for the dramatic change in the network behavior when introducing dependency links. For a high density of dependency links, the network disintegrates in a form of a first-order phase transition, whereas for a low density of dependency links, the network disintegrates in a second-order transition. Moreover, opposed to networks containing only connectivity links where a broader degree distribution results in a more robust network, when both types of links are present a broad degree distribution leads to higher vulnerability.},
author = {Parshani, Roni and Buldyrev, Sergey V and Havlin, Shlomo},
doi = {10.1073/pnas.1008404108},
file = {:Users/wenwen/Documents/MendeleyRefs/Parshani, Buldyrev, Havlin{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2011.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
keywords = {Computer Communication Networks,Computer Simulation,Information Services,Models,Social Support,Theoretical},
month = {jan},
number = {3},
pages = {1007--1010},
pmid = {21191103},
title = {{Critical effect of dependency groups on the function of networks}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3024657{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.1008404108},
volume = {108},
year = {2011}
}
@article{Mansfield2008a,
author = {Mansfield, Marc L},
doi = {10.1063/1.454443},
file = {:Users/wenwen/Documents/MendeleyRefs/Mansfield{\_}The Journal of Chemical Physics{\_}1988.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {10},
pages = {6570},
title = {{The coil–stretch transition of polymers in external fields}},
url = {http://scitation.aip.org/content/aip/journal/jcp/88/10/10.1063/1.454443},
volume = {88},
year = {1988}
}
@article{Daido2011,
author = {Daido, Hiroaki},
doi = {10.1103/PhysRevE.83.026209},
file = {:Users/wenwen/Documents/MendeleyRefs/Daido{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {feb},
number = {2},
pages = {026209},
title = {{Dynamics of a large ring of coupled active and inactive oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.83.026209},
volume = {83},
year = {2011}
}
@article{Dekker2013,
abstract = {How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.},
author = {Dekker, Job and Marti-Renom, Marc a and Mirny, Leonid a},
doi = {10.1038/nrg3454},
file = {:Users/wenwen/Documents/MendeleyRefs/Dekker, Marti-Renom, Mirny{\_}Nature Reviews Genetics{\_}2013.pdf:pdf},
isbn = {1471-0064 (Electronic) 1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
month = {may},
number = {6},
pages = {390--403},
pmid = {23657480},
publisher = {Nature Publishing Group},
title = {{Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data}},
volume = {14},
year = {2013}
}
@article{Mizuguchi2015a,
abstract = {Advanced techniques including the chromosome conformation capture (3C) methodology and its derivatives are complementing microscopy approaches to study genome organization, and are revealing new details of three-dimensional (3D) genome architecture at increasing resolution. The fission yeast Schizosaccharomyces pombe (S. pombe) comprises a small genome featuring organizational elements of more complex eukaryotic systems, including conserved heterochromatin assembly machinery. Here we review key insights into genome organization revealed in this model system through a variety of techniques. We discuss the predominant role of Rabl-like configuration for interphase chromosome organization and the dynamic changes that occur during mitosis and meiosis. High resolution Hi-C studies have also revealed the presence of locally crumpled chromatin regions called "globules" along chromosome arms, and implicated a critical role for pericentromeric heterochromatin in imposing fundamental constraints on the genome to maintain chromosome territoriality and stability. These findings have shed new light on the connections between genome organization and function. It is likely that insights gained from the S. pombe system will also broadly apply to higher eukaryotes. Published by Elsevier B.V.},
author = {Mizuguchi, Takeshi and Barrowman, Jemima and Grewal, Shiv I.S.},
doi = {10.1016/j.febslet.2015.06.008},
file = {:Users/wenwen/Documents/MendeleyRefs/Mizuguchi, Barrowman, Grewal{\_}FEBS Letters{\_}2015.pdf:pdf},
isbn = {0014-5793},
issn = {00145793},
journal = {FEBS Lett.},
keywords = {Cohesin,Fission yeast,Genome organization,Heterochromatin,Hi-C,Rabl,cohesin,fission yeast,genome organization,heterochromatin,hi-c,rabl},
month = {oct},
number = {20PartA},
pages = {2975--2986},
pmid = {26096785},
publisher = {Federation of European Biochemical Societies},
title = {{Chromosome domain architecture and dynamic organization of the fission yeast genome}},
url = {http://dx.doi.org/10.1016/j.febslet.2015.06.008 http://doi.wiley.com/10.1016/j.febslet.2015.06.008},
volume = {589},
year = {2015}
}
@article{Lepri2003,
author = {Lepri, S},
doi = {10.1016/S0370-1573(02)00558-6},
file = {:Users/wenwen/Documents/MendeleyRefs/Lepri{\_}Physics Reports{\_}2003.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
keywords = {classical lattices,thermal conductivity},
month = {apr},
number = {1},
pages = {1--80},
title = {{Thermal conduction in classical low-dimensional lattices}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157302005586},
volume = {377},
year = {2003}
}
@techreport{Prellberg2012,
author = {Prellberg, Thomas},
file = {:Users/wenwen/Documents/MendeleyRefs/Prellberg{\_}Unknown{\_}2012.pdf:pdf},
pages = {1--24},
title = {{From Rosenbluth Sampling to PERM - rare event sampling with stochastic growth algorithms Sampling of Simple Random Walks}},
year = {2012}
}
@article{Morino2013,
author = {Morino, Kai and Tanaka, Gouhei and Aihara, Kazuyuki},
doi = {10.1103/PhysRevE.88.032909},
file = {:Users/wenwen/Documents/MendeleyRefs/Morino, Tanaka, Aihara{\_}Physical Review E{\_}2013.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {032909},
title = {{Efficient recovery of dynamic behavior in coupled oscillator networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.88.032909},
volume = {88},
year = {2013}
}
@article{DaCosta2010,
author = {da Costa, R. and Dorogovtsev, S. and Goltsev, a. and Mendes, J.},
doi = {10.1103/PhysRevLett.105.255701},
file = {:Users/wenwen/Documents/MendeleyRefs/da Costa et al.{\_}Physical Review Letters{\_}2010.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {25},
pages = {2--5},
title = {{Explosive Percolation Transition is Actually Continuous}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.105.255701},
volume = {105},
year = {2010}
}
@article{Soriano2008,
abstract = {We introduce an approach for the quantitative assessment of the connectivity in neuronal cultures, based on the statistical mechanics of percolation on a graph. This allows us to monitor the development of the culture and to see the emergence of connectivity in the network. The culture becomes fully connected at a time equivalent to the expected time of birth. The spontaneous bursting activity that characterizes cultures develops in parallel with the connectivity. The average number of inputs per neuron can be quantitatively determined in units of m(0), the number of activated inputs needed to excite the neuron. For m(0) approximately 15 we find that hippocampal neurons have on average approximately 60-120 inputs, whereas cortical neurons have approximately 75-150, depending on neuronal density. The ratio of excitatory to inhibitory neurons is determined by using the GABA(A) antagonist bicuculine. This ratio changes during development and reaches the final value at day 7-8, coinciding with the expected time of the GABA switch. For hippocampal cultures the inhibitory cells comprise approximately 30{\%} of the neurons in the culture whereas for cortical cultures they are approximately 20{\%}. Such detailed global information on the connectivity of networks in neuronal cultures is at present inaccessible by any electrophysiological or other technique.},
author = {Soriano, Jordi and {Rodriguez Martinez}, M. and Tlusty, Tsvi and Moses, Elisha},
doi = {10.1073/pnas.0707492105},
file = {:Users/wenwen/Documents/MendeleyRefs/Soriano et al.{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2008.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
keywords = {Cells,Cultured,Electrophysiology,Hippocampus,Hippocampus: cytology,Hippocampus: drug effects,Nerve Net,Nerve Net: cytology,Nerve Net: drug effects,Tissue Culture Techniques},
month = {sep},
number = {37},
pages = {13758--13763},
pmid = {18772389},
title = {{Development of input connections in neural cultures}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2544527{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.0707492105},
volume = {105},
year = {2008}
}
@book{Durrentt1991,
author = {Durrent, Rick and Kesten, Harry},
file = {:Users/wenwen/Documents/MendeleyRefs/Durrent, Kesten{\_}Unknown{\_}1991.pdf:pdf},
publisher = {Springer},
title = {{Random walks, Brownian motion, and interacting particle systems}},
year = {1991}
}
@article{Taloni2014,
author = {Taloni, Alessandro and Marchesoni, Fabio},
doi = {10.1142/S1793048014400050},
file = {:Users/wenwen/Documents/MendeleyRefs/Taloni, Marchesoni{\_}Biophysical Reviews and Letters{\_}2014.pdf:pdf},
issn = {1793-0480},
journal = {Biophys. Rev. Lett.},
keywords = {diffusion noise equation,fractional langevin equation,single file model},
number = {04},
pages = {381--396},
title = {{Interacting Single-File System: Fractional Langevin Formulation Versus Diffusion-Noise Approach}},
url = {http://www.worldscientific.com/doi/10.1142/S1793048014400050},
volume = {09},
year = {2014}
}
@book{Bressloff2014,
address = {Cham},
author = {Bressloff, Paul C.},
doi = {10.1007/978-3-319-08488-6},
file = {:Users/wenwen/Documents/MendeleyRefs/Bressloff{\_}Unknown{\_}2014.pdf:pdf},
isbn = {978-3-319-08487-9},
publisher = {Springer International Publishing},
series = {Interdisciplinary Applied Mathematics},
title = {{Stochastic Processes in Cell Biology}},
url = {http://link.springer.com/10.1007/978-3-319-08488-6},
volume = {41},
year = {2014}
}
@article{Zhang2011a,
abstract = {We introduce a new polymer model for mitotic chromosomes. The key assumption of the model is the ability of the chromatin fibre to cross-link to itself due to binding proteins. These protein-chromatin interactions are included by a probabilistic and dynamic mechanism. The hypothesis is motivated by the observation of high repulsive forces between ring polymers. We performed computer simulations to validate our model. Our results show that the presence of loops leads to a tight compaction and contributes significantly to the bending rigidity of chromosomes. Moreover, our qualitative prediction of the force elongation behaviour is close to experimental findings. The Dynamic Loop Model presented here indicates that the internal structure of mitotic chromosomes is based on self-organization of the chromatin fibre rather than attachment of chromatin to a protein scaffold. It also shows that the number and size of loops have a strong influence on the mechanical properties. We suggest that changes in the mechanical characteristics of chromosomes in different stages of the cell cycle, for example, can be explained by an altered internal loop structure.},
author = {Zhang, Yang and Heermann, Dieter W.},
doi = {10.1371/journal.pone.0029225},
editor = {Kreplak, Laurent},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang, Heermann{\_}PLoS ONE{\_}2011.pdf:pdf},
isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)},
issn = {19326203},
journal = {PLoS One},
month = {dec},
number = {12},
pages = {e29225},
pmid = {22216220},
publisher = {Public Library of Science},
title = {{Loops determine the mechanical properties of mitotic chromosomes}},
url = {http://dx.plos.org/10.1371/journal.pone.0029225},
volume = {6},
year = {2011}
}
@article{Ghosh2009,
author = {Ghosh, Surya K. and Singh, Kulveer and Sain, Anirban},
doi = {10.1103/PhysRevE.80.051904},
file = {:Users/wenwen/Documents/MendeleyRefs/Ghosh, Singh, Sain{\_}Physical Review E{\_}2009.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {5},
pages = {051904},
title = {{Effect of intrinsic curvature on semiflexible polymers}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.80.051904},
volume = {80},
year = {2009}
}
@article{Milo2002,
abstract = {Complex networks are studied across many fields of science. To uncover their structural design principles, we defined "network motifs," patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.},
author = {Milo, R},
doi = {10.1126/science.298.5594.824},
file = {:Users/wenwen/Documents/MendeleyRefs/Milo et al.{\_}Science (New York, N.Y.){\_}2002.pdf:pdf},
issn = {00368075},
journal = {Science (80-. ).},
keywords = {Algorithms,Animals,Caenorhabditis elegans,Caenorhabditis elegans: anatomy {\&} histology,Caenorhabditis elegans: physiology,Electronics,Escherichia coli,Escherichia coli: genetics,Food Chain,Gene Expression Regulation,Internet,Nerve Net,Nerve Net: physiology,Neurons,Neurons: physiology,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Synapses,Synapses: physiology},
month = {oct},
number = {5594},
pages = {824--827},
pmid = {12399590},
title = {{Network Motifs: Simple Building Blocks of Complex Networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12399590 http://www.sciencemag.org/cgi/doi/10.1126/science.298.5594.824},
volume = {298},
year = {2002}
}
@article{Williams2016a,
author = {Williams, Jennifer L and Kendall, Bruce E and Levine, Jonathan M},
doi = {10.1126/science.aaf6268},
file = {:Users/wenwen/Documents/MendeleyRefs/Williams, Kendall, Levine{\_}Science{\_}2016.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {jul},
number = {6298},
pages = {482--485},
title = {{Rapid evolution accelerates plant population spread in fragmented experimental landscapes}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aaf6268},
volume = {353},
year = {2016}
}
@article{Chatterjee2007,
author = {Chatterjee, Abhijit and Vlachos, Dionisios G.},
doi = {10.1007/s10820-006-9042-9},
file = {:Users/wenwen/Documents/MendeleyRefs/Chatterjee, Vlachos{\_}Journal of Computer-Aided Materials Design{\_}2007.pdf:pdf},
issn = {0928-1045},
journal = {J. Comput. Mater. Des.},
keywords = {accelerated algorithms,binary tree,coarse-graining,computational singular perturbation,crystal growth,defects,diffusion,efficient search,efficient update,low-dimensional manifold,materials,mesoscopic modeling,monte carlo,multiscale simulation,phase transitions,review,stiff,stochastic,tau-leap},
month = {mar},
number = {2},
pages = {253--308},
title = {{An overview of spatial microscopic and accelerated kinetic Monte Carlo methods}},
url = {http://link.springer.com/10.1007/s10820-006-9042-9},
volume = {14},
year = {2007}
}
@article{Costa2004,
author = {Costa, Luciano},
doi = {10.1103/PhysRevE.70.056106},
file = {:Users/wenwen/Documents/MendeleyRefs/Costa{\_}Physical Review E{\_}2004.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {056106},
title = {{L-percolations of complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.70.056106},
volume = {70},
year = {2004}
}
@book{Press1996,
author = {Press, Wh and Teukolsky, Sa and Vetterling, Wt},
issn = {01609327},
pmid = {847},
publisher = {Cambridge University Press},
title = {{Numerical Recipes in Fortran 90: The Art of Parallel Scientific Computing}},
year = {1996}
}
@article{Belovs2006,
abstract = {On the basis of the model of a flexible magnetic filament, the characteristics of their thermal fluctuations are considered. The crossover of the time dependence of the mean quadratic displacement from t(3/4) to t(1/2) at the magnetic field increase is found. Two characteristic mechanisms of the magnetization relaxation time distribution--straightening of the thermal undulations and excitation of the bending modes of the free ends under the action of an ac magnetic field--are described. In both cases, the characteristic scaling law omega(-3/4) of the magnetic susceptibility in a high-frequency range is found.},
author = {Everaers, R. and J{\"{u}}licher, F. and Ajdari, A. and Maggs, A. C.},
doi = {10.1103/PhysRevLett.82.3717},
file = {:Users/wenwen/Documents/MendeleyRefs/Belovs, Cēbers{\_}Physical review. E, Statistical, nonlinear, and soft matter physics{\_}2006.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {18},
pages = {3717--3720},
pmid = {16605342},
title = {{Dynamic Fluctuations of Semiflexible Filaments}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.3717},
volume = {82},
year = {1999}
}
@article{Arkin2013,
abstract = {In a recent computational study, we found highly structured conformations for the polymer-attractive sphere model system. Those conformations are of highly ordered spherical shape or form two-dimensional planar, compact to extended, random coil structures. The observed conformations range from desorbed to partially or even completely adsorbed. In order to present their shape characteristics, here we calculate the gyration tensor and related shape descriptors.},
author = {Arkin, Handan and Janke, Wolfhard},
doi = {10.1063/1.4788616},
file = {:Users/wenwen/Documents/MendeleyRefs/Arkin, Janke{\_}Journal of Chemical Physics{\_}2013.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
pages = {1--9},
pmid = {23406146},
title = {{Gyration tensor based analysis of the shapes of polymer chains in an attractive spherical cage}},
volume = {138},
year = {2013}
}
@article{Walter2012,
author = {Walter, JC and Ferrantini, A and Carlon, E and Vanderzande, C.},
doi = {10.1103/PhysRevE.85.031120},
file = {:Users/wenwen/Documents/MendeleyRefs/Walter et al.{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--7},
title = {{Fractional Brownian motion and the critical dynamics of zipping polymers}},
url = {http://arxiv.org/abs/1111.4323 http://link.aps.org/doi/10.1103/PhysRevE.85.031120},
volume = {85},
year = {2012}
}
@article{Lizana2008,
author = {Lizana, L. and Ambj{\"{o}}rnsson, T.},
doi = {10.1103/PhysRevLett.100.200601},
file = {:Users/wenwen/Documents/MendeleyRefs/Lizana, Ambj{\"{o}}rnsson{\_}Physical Review Letters{\_}2008.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {20},
pages = {200601},
title = {{Single-File Diffusion in a Box}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.200601},
volume = {100},
year = {2008}
}
@book{Huang1987,
author = {Huang, Kerson},
edition = {2},
file = {:Users/wenwen/Documents/MendeleyRefs/Huang{\_}Unknown{\_}1987.pdf:pdf},
pages = {493},
publisher = {John Wiley {\&} Sons},
title = {{Statistical Mechanics}},
year = {1987}
}
@article{Tao2012,
abstract = {An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.},
author = {Tao, Peng and Wu, Xiongwu and Brooks, Bernard R.},
doi = {10.1063/1.4756796},
file = {:Users/wenwen/Documents/MendeleyRefs/Tao, Wu, Brooks{\_}The Journal of Chemical Physics{\_}2012.pdf:pdf},
isbn = {0021-9606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {13},
pages = {134110},
pmid = {23039588},
title = {{Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations}},
url = {http://scitation.aip.org/content/aip/journal/jcp/137/13/10.1063/1.4756796},
volume = {137},
year = {2012}
}
@article{Speck2008,
abstract = {For configurational changes of soft matter systems affected or caused by external hydrodynamic flow, we identify applied work, exchanged heat, and entropy change on the level of a single trajectory. These expressions guarantee invariance of stochastic thermodynamics under a change of frame of reference. As criterion for equilibrium versus nonequilibrium, zero versus nonzero applied work replaces detailed balance versus nonvanishing currents, since both latter criteria are shown to depend on the frame of reference. Our results are illustrated quantitatively by calculating the large deviation function for the entropy production of a dumbbell in shear flow.},
archivePrefix = {arXiv},
arxivId = {0712.0232},
author = {Speck, Thomas and Mehl, Jakob and Seifert, Udo},
doi = {10.1103/PhysRevLett.100.178302},
eprint = {0712.0232},
file = {:Users/wenwen/Documents/MendeleyRefs/Speck, Mehl, Seifert{\_}Physical Review Letters{\_}2008.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {apr},
number = {17},
pages = {178302},
pmid = {18518344},
title = {{Role of External Flow and Frame Invariance in Stochastic Thermodynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.178302},
volume = {100},
year = {2008}
}
@article{Albert2002,
author = {Albert, R{\'{e}}ka and Barab{\'{a}}si, Albert-L{\'{a}}szl{\'{o}}},
doi = {10.1103/RevModPhys.74.47},
file = {:Users/wenwen/Documents/MendeleyRefs/Albert, Barab{\'{a}}si{\_}Reviews of Modern Physics{\_}2002.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {jan},
number = {1},
pages = {47--97},
title = {{Statistical mechanics of complex networks}},
url = {http://arxiv.org/abs/0704.3702 http://link.aps.org/doi/10.1103/RevModPhys.74.47},
volume = {74},
year = {2002}
}
@article{Voigt2002,
abstract = {Borrowing concepts from the schema theory of genetic algorithms, we have developed a computational algorithm to identify the fragments of proteins, or schemas, that can be recombined without disturbing the integrity of the three-dimensional structure. When recombination leaves these schemas undisturbed, the hybrid proteins are more likely to be folded and functional. Crossovers found by screening libraries of several randomly shuffled proteins for functional hybrids strongly correlate with those predicted by this approach. Experimental results from the construction of hybrids of two beta-lactamases that share 40{\%} amino acid identity demonstrate a threshold in the amount of schema disruption that the hybrid protein can tolerate. To the extent that introns function to promote recombination within proteins, natural selection would serve to bias their locations to schema boundaries.},
author = {Voigt, Christopher a and Martinez, Carlos and Wang, Zhen-Gang and Mayo, Stephen L and Arnold, Frances H},
doi = {10.1038/nsb805},
file = {:Users/wenwen/Documents/MendeleyRefs/Voigt et al.{\_}Nature structural biology{\_}2002.pdf:pdf},
isbn = {1072-8368 (Print)$\backslash$r1072-8368 (Linking)},
issn = {10728368},
journal = {Nat. Struct. Biol.},
number = {7},
pages = {553--558},
pmid = {12042875},
title = {{Protein building blocks preserved by recombination.}},
volume = {9},
year = {2002}
}
@article{Ponmurugan2011,
author = {Ponmurugan, M. and Vemparala, Satyavani},
doi = {10.1103/PhysRevE.84.060101},
file = {:Users/wenwen/Documents/MendeleyRefs/Ponmurugan, Vemparala{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {6},
pages = {060101},
title = {{Transient-state fluctuationlike relation for the driving force on a biomolecule}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.060101},
volume = {84},
year = {2011}
}
@article{Newman2001b,
abstract = {We describe in detail a new and highly efficient algorithm for studying site or bond percolation on any lattice. The algorithm can measure an observable quantity in a percolation system for all values of the site or bond occupation probability from zero to one in an amount of time which scales linearly with the size of the system. We demonstrate our algorithm by using it to investigate a number of issues in percolation theory, including the position of the percolation transition for site percolation on the square lattice, the stretched exponential behavior of spanning probabilities away from the critical point, and the size of the giant component for site percolation on random graphs.$\backslash$n$\backslash$nPublished in: Phys. Rev. E 64, 016706 (2001)},
archivePrefix = {arXiv},
arxivId = {cond-mat/0101295},
author = {Newman, M E J and Ziff, R M},
doi = {10.1103/PhysRevE.64.016706},
eprint = {0101295},
file = {:Users/wenwen/Documents/MendeleyRefs/Newman, Ziff{\_}Physical Review E{\_}2001.pdf:pdf},
isbn = {1063-651X},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {jun},
number = {1},
pages = {016706},
pmid = {11461441},
primaryClass = {cond-mat},
title = {{Fast Monte Carlo algorithm for site or bond percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.64.016706{\%}5Cnpapers3://publication/doi/10.1103/PhysRevE.64.016706{\%}5Cnhttp://link.aps.org/doi/10.1103/PhysRevE.64.016706 http://link.aps.org/doi/10.1103/PhysRevE.64.016706},
volume = {64},
year = {2001}
}
@article{Huang2014,
author = {Huang, Wenwen and Zhang, Xiyun and Hu, Xin and Zou, Yong and Liu, Zonghua and Guan, Shuguang},
doi = {10.1063/1.4881215},
file = {:Users/wenwen/Documents/MendeleyRefs/Huang et al.{\_}Chaos An Interdisciplinary Journal of Nonlinear Science{\_}2014.pdf:pdf},
issn = {10541500},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
number = {2},
pages = {1--8},
title = {{Variation of critical point of aging transition in a networked oscillators system}},
volume = {24},
year = {2014}
}
@article{Cho2011a,
author = {Cho, Y. and Kahng, B.},
doi = {10.1103/PhysRevE.84.050102},
file = {:Users/wenwen/Documents/MendeleyRefs/Cho, Kahng{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {1--5},
title = {{Discontinuous percolation transitions in real physical systems}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.050102},
volume = {84},
year = {2011}
}
@article{Breskin2006,
author = {Breskin, Ilan and Soriano, Jordi and Moses, Elisha and Tlusty, Tsvi},
doi = {10.1103/PhysRevLett.97.188102},
file = {:Users/wenwen/Documents/MendeleyRefs/Breskin et al.{\_}Physical Review Letters{\_}2006.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {oct},
number = {18},
pages = {1--4},
title = {{Percolation in Living Neural Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.97.188102},
volume = {97},
year = {2006}
}
@article{Croxton1984,
abstract = {The principal geometric features of self-avoiding hard sphere ring polymers are determined on the basis of the iterative convolution technique. The results are in good qualitative agreement with Monte Carlo estimates. ?? 1984.},
author = {Croxton, Clive A.},
doi = {10.1016/0375-9601(84)90500-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Croxton{\_}Physics Letters A{\_}1984.pdf:pdf},
issn = {03759601},
journal = {Phys. Lett. A},
number = {1-2},
pages = {86--88},
title = {{Statistics of self-avoiding ring polymers}},
volume = {106},
year = {1984}
}
@article{Derrida1993,
abstract = {Several recent works have shown that the one-dimensional fully asymmetric exclusion model, which describes a system of particles hopping in a preferred direction with hard core interactions, can be solved exactly in the case of open boundaries. Here the authors present a new approach based on representing the weights of each configuration in the steady state as a product of noncommuting matrices. With this approach the whole solution of the problem is reduced to finding two matrices and two vectors which satisfy very simple algebraic rules. They obtain several explicit forms for these non-commuting matrices which are, in the general case, infinite-dimensional. Their approach allows exact expressions to be derived for the current and density profiles. Finally they discuss briefly two possible generalizations of their results: the problem of partially asymmetric exclusion and the case of a mixture of two kinds of particles.},
author = {Derrida, B. and Evans, M R and Hakim, V and Pasquier, V},
doi = {10.1088/0305-4470/26/7/011},
file = {:Users/wenwen/Documents/MendeleyRefs/Derrida et al.{\_}J. Phys. A Math. Gen.{\_}1993(2).pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Derrida et al.{\_}J. Phys. A Math. Gen.{\_}1993.pdf:pdf},
isbn = {0305-4470},
issn = {0305-4470},
journal = {J. Phys. A Math. Gen.},
number = {7},
pages = {1493--1517},
pmid = {21316277},
title = {{Exact solution of a 1D asymmetric exclusion model using a matrix formulation}},
url = {http://dx.doi.org/10.1088/0305-4470/26/7/011},
volume = {26},
year = {1993}
}
@article{Tree2013,
abstract = {The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer $\lambda$-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.},
author = {Tree, Douglas R. and Muralidhar, Abhiram and Doyle, Patrick S. and Dorfman, Kevin D.},
doi = {10.1021/ma401507f},
file = {:Users/wenwen/Documents/MendeleyRefs/Tree et al.{\_}Macromolecules{\_}2013.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {oct},
number = {20},
pages = {8369--8382},
pmid = {24347685},
title = {{Is DNA a Good Model Polymer}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma401507f},
volume = {46},
year = {2013}
}
@article{Cozzo2012,
author = {Cozzo, Emanuele and Arenas, Alex and Moreno, Yamir},
doi = {10.1103/PhysRevE.86.036115},
file = {:Users/wenwen/Documents/MendeleyRefs/Cozzo, Arenas, Moreno{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {036115},
title = {{Stability of Boolean multilevel networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.86.036115},
volume = {86},
year = {2012}
}
@article{Rulkov1995,
author = {Rulkov, NF and Sushchik, MM and Tsimring, LS and Abarbanel, HDI},
file = {:Users/wenwen/Documents/MendeleyRefs/Rulkov et al.{\_}Physical Review E{\_}1995.pdf:pdf},
journal = {Phys. Rev. E},
title = {{Generalized synchronization of chaos in directionally coupled chaotic systems}},
url = {http://pre.aps.org/abstract/PRE/v51/i2/p980{\_}1},
year = {1995}
}
@article{Ding2012,
abstract = {Pairing and recombination of homologous chromosomes are essential for ensuring reductional segregation in meiosis. However, the mechanisms by which chromosomes recognize their homologous partners are poorly understood. Here, we report that the sme2 gene encodes a meiosis-specific noncoding RNA that mediates homologous recognition in the fission yeast Schizosaccharomyces pombe. The sme2 locus shows robust pairing from early in meiotic prophase. The sme2 RNA transcripts accumulate at their respective gene loci and greatly enhance pairing of homologous loci: Deletion of the sme2 sequence eliminates this robust pairing, whereas transposition to other chromosomal sites confers robust pairing at those ectopic sites. Thus, we propose that RNA transcripts retained on the chromosome play an active role in recognition of homologous chromosomes for pairing.},
author = {Ding, Da-Qiao and Okamasa, Kasumi and Yamane, Miho and Tsutsumi, Chihiro and Haraguchi, Tokuko and Yamamoto, Masayuki and Hiraoka, Yasushi},
doi = {10.1126/science.1219518},
file = {:Users/wenwen/Documents/MendeleyRefs/Ding et al.{\_}Science{\_}2012.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
keywords = {Chromosome Pairing,Chromosomes,Fungal,Fungal: genetics,Fungal: physiology,Genes,Genetic,Meiosis,Models,Prophase,RNA,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Recombination,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Schizosaccharomyces pombe Proteins: genetics,Schizosaccharomyces pombe Proteins: metabolism,Schizosaccharomyces: genetics,Schizosaccharomyces: physiology,Telomere,Telomere: physiology,Transcription,Untranslated,Untranslated: genetics,mRNA Cleavage and Polyadenylation Factors,mRNA Cleavage and Polyadenylation Factors: genetic},
month = {may},
number = {6082},
pages = {732--736},
pmid = {22582262},
title = {{Meiosis-Specific Noncoding RNA Mediates Robust Pairing of Homologous Chromosomes in Meiosis}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22582262 http://www.sciencemag.org/cgi/doi/10.1126/science.1219518},
volume = {336},
year = {2012}
}
@article{Uehara2014,
author = {Uehara, Erica and Deguchi, Tetsuo},
doi = {10.1063/1.4862500},
file = {:Users/wenwen/Documents/MendeleyRefs/Uehara, Deguchi{\_}Journal of Chemical Physics{\_}2014.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {4},
title = {{Statistical and hydrodynamic properties of double-ring polymers with a fixed linking number between twin rings}},
volume = {140},
year = {2014}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
# QWT port for LotOS
# Based on code by Mikhail Kuchuk, https://github.com/mikuka
#
# This software is a part of LotOS framework.
#
# Copyright (c) 2016, ilbers GmbH

DESCRIPTION = "Qt Widget Extension for Technical Applications"
SECTION = "libs"
PR = "r1"

# LGPLv2.1 + some exceptions
LICENSE = "QWTv1.0"
LIC_FILES_CHKSUM = "file://COPYING;md5=dac2743472b0462ff3cfb4af42051c88"

SRC_URI = "${SOURCEFORGE_MIRROR}/qwt/qwt-${PV}.tar.bz2"

SRC_URI[md5sum] = "9c88db1774fa7e3045af063bbde44d7d"
SRC_URI[sha256sum] = "2b08f18d1d3970e7c3c6096d850f17aea6b54459389731d3ce715d193e243d0c"

inherit qmake5 qmake5_paths

DEPENDS = "qtbase"

PACKAGES += "${PN}-mkspecs"
FILES_${PN}-mkspecs = "\
    ${OE_QMAKE_PATH_QT_ARCHDATA}/mkspecs \
"

S = "${WORKDIR}/qwt-${PV}"

QWT_OPENGL = "QWT_CONFIG     += QwtOpenGL"
QWT_EXAMPLES = "QWT_CONFIG     += QwtExamples"
QWT_DESIGNER = "QWT_CONFIG     += QwtDesigner"

python __anonymous() {
    packageconfig = d.getVar("PACKAGECONFIG", True)
    if packageconfig.find("opengl") == -1:
        d.prependVar("QWT_OPENGL", "#")
    if packageconfig.find("qwt-examples") == -1:
        d.prependVar("QWT_EXAMPLES", "#")
    if packageconfig.find("qwt-plugins") == -1:
        d.prependVar("QWT_DESIGNER", "#")
}

do_configure_prepend () {
    sed -i -e 's:QT += designer:LIBS += ${OE_QMAKE_PATH_LIBS}/qtcreator/plugins -lQt5Designer:' ${S}/designer/designer.pro
    sed -i -e 's:/usr/local/qwt-$$QWT_VERSION:${D}${prefix}:g' ${S}/qwtconfig.pri
    sed -i -e 's:QWT_CONFIG     += QwtDesigner:${QWT_DESIGNER}:' ${S}/qwtconfig.pri
    sed -i -e 's:QWT_CONFIG     += QwtOpenGL:${QWT_OPENGL}:' ${S}/qwtconfig.pri
    sed -i -e 's:QWT_CONFIG     += QwtExamples:${QWT_EXAMPLES}:' ${S}/qwtconfig.pri
    sed -i -e 's:QWT_CONFIG     += QwtSvg:#QWT_CONFIG     += QwtSvg:' ${S}/qwtconfig.pri
}

do_install () {
    oe_runmake -e install
    install -d ${D}${datadir}/doc/${PN}
    mv ${D}${prefix}/doc/* ${D}${datadir}/doc/${PN}/
    rmdir ${D}${prefix}/doc
    if [ -e ${S}/../build/examples/bin ] ; then
        cd ${S}/examples
        install -d ${D}/${bindir}
        cd bin/
        for i in * ; do
            cp -pPR ${i} ${D}/${bindir}/${i}
        done
    fi
    if [ -e ${S}/../build/build/designer ] ; then
        mv ${D}${prefix}/plugins ${D}${libdir}${QT_DIR_NAME}
    fi
    install -d ${D}/usr/${feature}
    install -d ${D}${libdir}${QT_DIR_NAME}
}

INSANE_SKIP_${PN} = "installed-vs-shipped"
PACKAGES_prepend = "${PN}-examples ${PN}-features ${PN}-plugins "

FILES_${PN}-examples = "${bindir}/*"
FILES_${PN}-features = "${prefix}/features"
FILES_${PN}-plugins = "${libdir}${QT_DIR_NAME}/plugins/designer/*.so"
FILES_${PN}-dbg += "${libdir}${QT_DIR_NAME}/plugins/designer/.debug"

repository: ilbers/meta-lotos

repo_name: ilbers/meta-lotos

gha_language: C

extension: bb


text:
DESCRIPTION = "Magic is Perl's way of enhancing variables. This mechanism lets the user \
add extra data to any variable and hook syntactical operations (such as \
access, assignment or destruction) that can be applied to it. With this \
module, you can add your own magic to any variable without having to write \
a single line of XS."

SECTION = "libs"
LICENSE = "Artistic-1.0 | GPL-1.0-or-later"
PR = "r0"

MAINTAINER=	"Poky <poky@yoctoproject.org>"
HOMEPAGE=	"https://metacpan.org/release/Variable-Magic"

LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Artistic-1.0;md5=cda03bbdc3c1951996392b872397b798 \
file://${COMMON_LICENSE_DIR}/GPL-1.0-or-later;md5=30c0b8a5048cc2f4be5ff15ef0d8cf61"

SRC_URI = "https://cpan.metacpan.org/authors/id/V/VP/VPIT/Variable-Magic-0.62.tar.gz"

SRC_URI[md5sum] = "588d94ec3d98dece878a776d161c1dda"
SRC_URI[sha256sum] = "3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c"

S = "${WORKDIR}/Variable-Magic-${PV}"

inherit cpan

BBCLASSEXTEND = "native"

repository: rehsack/meta-cpan

repo_name: rehsack/meta-cpan

gha_license_id: MIT

gha_language: BitBake


text:
@article{HaojiedongWhat2016,
 abstract = {Previous work has shown that feature maps of deep convolutional neural networks (CNNs) can be interpreted as feature representation of a particular image region. Features aggregated from these feature maps have been exploited for image retrieval tasks and achieved state-of-the-art performances in recent years. The key to the success of such methods is the feature representation. However, the different factors that impact the effectiveness of features are still not explored thoroughly. There are much less discussion about the best combination of them. The main contribution of our paper is the thorough evaluations of the various factors that affect the discriminative ability of the features extracted from CNNs. Based on the evaluation results, we also identify the best choices for different factors and propose a new multi-scale image feature representation method to encode the image effectively. Finally, we show that the proposed method generalises well and outperforms the state-of-the-art methods on four typical datasets used for visual instance retrieval.},
 archiveprefix = {arXiv},
 arxivid = {1611.01640},
 author = {Hao, Jiedong and Dong, Jing and Wang, Wei and Tan, Tieniu},
 eprint = {1611.01640},
 journal = {arXiv preprint arXiv:1611.01640},
 month = {nov},
 title = {What Is the Best Practice for CNNs Applied to Visual Instance Retrieval?},
 url = {http://arxiv.org/abs/1611.01640},
 year = {2016}
}


text:
%%% -*-BibTeX-*-
@article{Liu2023TPAMI,
    author  = {Jing Liu  and   Bohan Zhuang  and  Peng Chen  and  Chunhua Shen  and  Jianfei Cai  and  Mingkui Tan},
    title   = {Single-path Bit Sharing for Automatic Loss-aware Model Compression},
    journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
    year    = {2023},
    eprint  = {2101.04935},
    project = {},
    venue   = {TPAMI},
}


text:
@article{alexander_association_2007,
 abstract = {OBJECTIVE: This was an open-label study to asses the association of changes in hemoglobin with changes in health related quality of life (HRQOL) in patients treated with darbepoetin alfa. METHODS: Originally, 81 chronic kidney disease (CKD) patients not on dialysis and naive to erythropoiesis stimulating agents (ESA) were randomly assigned into two open-label groups (3 : 1). As a majority of control group patients opted out of control status, this study reports on the single arm study analysis that was performed on the 48 patients who received the drug through week 16. Sixty-two patients received once-weekly darbepoetin alfa in addition to conservative management for CKD. Instruments that measured general (SF-36, FACTanemia, FACT-fatigue, ADL and IADL) and disease specific (KDQOL) HRQOL domains were administered at baseline and after 8, 16, and 24 weeks. RESULTS: Compared to baseline values, mean HRQOL subscales were significantly improved in the treatment group at 16 weeks (p \textless 0.05 for SF-36 physical function; p \textless 0.001 for SF-36 vitality, FACT anemia and FACT fatigue scales). At week 16, the SF-36 mean increase for 48 treatment patients in the Vitality Subscale Score was 14.9 (SD 3.2) and the mean increase in the KDQOL Burden of Kidney Disease Subscale was 5.5 (SD 3.3). Multivariate regression analysis demonstrated a statistically significant association (p \textless 0.05) between hemoglobin levels and higher HRQOL scores on several physical function, energy and fatigue scales. CONCLUSION: Improvements in hemoglobin in CKD patients not on dialysis were associated with statistically significant (p \textless 0.05), clinically meaningful (\textgreater 5 points) HRQOL improvements on scales measuring physical activity, vitality and fatigue. Our study did not show an association between increased hemoglobin levels and other aspects of HRQOL, such as those relating to emotional status, sexual activity or cognition. The interpretation of our results is limited by the lack of a control arm to assess whether conservative therapy for CKD, in the absence of ESA administration, would have a comparable effect on patients' HRQOL scores. Further research needs to examine whether other aspects of HRQOL improve with anemia treatment, in the same way as those aspects of HRQOL more closely related to physical activity and fatigue.},
 author = {Alexander, Marcus and Kewalramani, Reshma and Agodoa, Irene and Globe, Denise},
 doi = {10.1185/030079907X242502},
 issn = {1473-4877 0300-7995},
 journal = {Current medical research and opinion},
 keywords = {*Quality of Life, Adolescent, Adult, Anemia/*drug therapy/etiology, Darbepoetin alfa, Erythropoietin/*analogs & derivatives/therapeutic use, Female, Hematinics/*therapeutic use, Hemoglobins/analysis, Humans, Kidney Failure, Chronic/*complications, Male, Middle Aged, Renal Dialysis, Treatment Outcome},
 language = {eng},
 month = {December},
 note = {Place: England},
 number = {12},
 pages = {2997--3008},
 pmid = {17958944},
 title = {Association of anemia correction with health related quality of life in patients not on dialysis.},
 volume = {23},
 year = {2007}
}


text:
SUMMARY = "Fast Math Parser Library"
HOMEPAGE = "http://beltoforion.de/article.php?a=muparser"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://License.txt;md5=7330c66af0fadfe6e8c17069e8e726f2"

SRC_URI = "https://github.com/beltoforion/${BPN}/archive/v${PV}.tar.gz"
SRC_URI[md5sum] = "02dae671aa5ad955fdcbcd3fee313fb7"
SRC_URI[sha256sum] = "0666ef55da72c3e356ca85b6a0084d56b05dd740c3c21d26d372085aa2c6e708"

inherit autotools pkgconfig

EXTRA_OECONF = "--enable-samples=no"


text:
require u-boot-ti.inc

# u-boot needs devtree compiler to parse dts files
DEPENDS += "dtc-native"

DESCRIPTION = "u-boot bootloader for TI devices"

LIC_FILES_CHKSUM = "file://Licenses/README;md5=0507cd7da8e7ad6d6701926ec9b84c95"

PR = "r13"
PV_append = "+git${SRCPV}"

SRC_URI = "git://git.ti.com/ti-u-boot/ti-u-boot.git;protocol=git;branch=${BRANCH}"

BRANCH ?= "ti-u-boot-2015.07"

SRCREV = "f3171e0a0d41bc79f819a1b85563ef7c643bf59b"

SPL_BINARY = "MLO"
SPL_UART_BINARY = "u-boot-spl.bin"

# Keystone specifics
UBOOT_SUFFIX_keystone = "bin"
SPL_UART_BINARY_keystone = ""

# SPI NOR Flash binaries
UBOOT_SPI_SPL_BINARY = "u-boot-spl.bin"
UBOOT_SPI_BINARY = "u-boot.img"
UBOOT_SPI_GPH_BINARY = "u-boot-spi.gph"

# SPI NOR Flash deployed images
UBOOT_SPI_SPL_IMAGE = "u-boot-spl-${MACHINE}-${PV}-${PR}.bin"
UBOOT_SPI_SPL_SYMLINK = "u-boot-spl-${MACHINE}.bin"
UBOOT_SPI_IMAGE = "u-boot-${MACHINE}-${PV}-${PR}.img"
UBOOT_SPI_SYMLINK = "u-boot-${MACHINE}.img"
UBOOT_SPI_GPH_IMAGE = "u-boot-spi-${MACHINE}-${PV}-${PR}.gph"
UBOOT_SPI_GPH_SYMLINK = "u-boot-spi-${MACHINE}.gph"

do_install_append_keystone () {
	install ${S}/spl/${UBOOT_SPI_SPL_BINARY} ${D}/boot/${UBOOT_SPI_SPL_IMAGE}
	ln -sf ${UBOOT_SPI_SPL_IMAGE} ${D}/boot/${UBOOT_SPI_SPL_BINARY}

	install ${S}/${UBOOT_SPI_BINARY} ${D}/boot/${UBOOT_SPI_IMAGE}
	ln -sf ${UBOOT_SPI_IMAGE} ${D}/boot/${UBOOT_SPI_BINARY}

	install ${S}/${UBOOT_SPI_GPH_BINARY} ${D}/boot/${UBOOT_SPI_GPH_IMAGE}
	ln -sf ${UBOOT_SPI_GPH_IMAGE} ${D}/boot/${UBOOT_SPI_GPH_BINARY}
}

do_deploy_append_keystone () {
	install ${S}/spl/${UBOOT_SPI_SPL_BINARY} ${DEPLOYDIR}/${UBOOT_SPI_SPL_IMAGE}
	rm -f ${UBOOT_SPI_SPL_BINARY} ${UBOOT_SPI_SPL_SYMLINK}
	ln -sf ${UBOOT_SPI_SPL_IMAGE} ${UBOOT_SPI_SPL_SYMLINK}
	ln -sf ${UBOOT_SPI_SPL_IMAGE} ${UBOOT_SPI_SPL_BINARY}

	install ${S}/${UBOOT_SPI_BINARY} ${DEPLOYDIR}/${UBOOT_SPI_IMAGE}
	rm -f ${UBOOT_SPI_BINARY} ${UBOOT_SPI_SYMLINK}
	ln -sf ${UBOOT_SPI_IMAGE} ${UBOOT_SPI_SYMLINK}
	ln -sf ${UBOOT_SPI_IMAGE} ${UBOOT_SPI_BINARY}

	install ${S}/${UBOOT_SPI_GPH_BINARY} ${DEPLOYDIR}/${UBOOT_SPI_GPH_IMAGE}
	rm -f ${UBOOT_SPI_GPH_BINARY} ${UBOOT_SPI_GPH_SYMLINK}
	ln -sf ${UBOOT_SPI_GPH_IMAGE} ${UBOOT_SPI_GPH_SYMLINK}
	ln -sf ${UBOOT_SPI_GPH_IMAGE} ${UBOOT_SPI_GPH_BINARY}
}

repository: joelagnel/meta-ti

repo_name: joelagnel/meta-ti


text:
DESCRIPTION = "A daemon to manage CPUfreq states"
HOMEPAGE = "http://www.deater.net/john/powernowd.html"
LICENSE = "GPLv2"

SRC_URI = "http://www.deater.net/john/${P}.tar.gz \
		   file://fix-makefile.patch"

do_install() {
	install -d ${D}${sbindir}
	install -m 755 powernowd ${D}${sbindir}/
}

SRC_URI[md5sum] = "9c7131bce36bbb3e8b688478e8dc34c7"
SRC_URI[sha256sum] = "44ea3e6777c471a514d1e0a53b60cd5a4e2e56802ba23ec67331b69f122ec3d7"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
@inproceedings{paszke2017automatic,
  title={Automatic Differentiation in {PyTorch}},
  author={Paszke, Adam and Gross, Sam and Chintala, Soumith and Chanan, Gregory and Yang, Edward and DeVito, Zachary and Lin, Zeming and Desmaison, Alban and Antiga, Luca and Lerer, Adam},
  booktitle={NIPS {A}utodiff {W}orkshop},
  year={2017}
}
@misc{tensorflow2015-whitepaper,
title={ {TensorFlow}: Large-Scale machine learning on heterogeneous systems},
url={https://www.tensorflow.org/},
note={Software available from tensorflow.org},
author={
    Mart\'{\i}n~Abadi and
    Ashish~Agarwal and
    Paul~Barham and
    Eugene~Brevdo and
    Zhifeng~Chen and
    Craig~Citro and
    Greg~S.~Corrado and
    Andy~Davis and
    Jeffrey~Dean and
    Matthieu~Devin and
    Sanjay~Ghemawat and
    Ian~Goodfellow and
    Andrew~Harp and
    Geoffrey~Irving and
    Michael~Isard and
    Yangqing Jia and
    Rafal~Jozefowicz and
    Lukasz~Kaiser and
    Manjunath~Kudlur and
    Josh~Levenberg and
    Dandelion~Man\'{e} and
    Rajat~Monga and
    Sherry~Moore and
    Derek~Murray and
    Chris~Olah and
    Mike~Schuster and
    Jonathon~Shlens and
    Benoit~Steiner and
    Ilya~Sutskever and
    Kunal~Talwar and
    Paul~Tucker and
    Vincent~Vanhoucke and
    Vijay~Vasudevan and
    Fernanda~Vi\'{e}gas and
    Oriol~Vinyals and
    Pete~Warden and
    Martin~Wattenberg and
    Martin~Wicke and
    Yuan~Yu and
    Xiaoqiang~Zheng},
  year={2015},
}

@article{DBLP:journals/corr/ChenLLLWWXXZZ15,
  author    = {Tianqi Chen and
               Mu Li and
               Yutian Li and
               Min Lin and
               Naiyan Wang and
               Minjie Wang and
               Tianjun Xiao and
               Bing Xu and
               Chiyuan Zhang and
               Zheng Zhang},
  title     = {MXNet: {A} Flexible and Efficient Machine Learning Library for Heterogeneous
               Distributed Systems},
  journal   = {CoRR},
  volume    = {abs/1512.01274},
  year      = {2015},
  url       = {http://arxiv.org/abs/1512.01274},
  archivePrefix = {arXiv},
  eprint    = {1512.01274},
  timestamp = {Mon, 13 Aug 2018 16:48:04 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/corr/ChenLLLWWXXZZ15},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{mckinney-proc-scipy-2010,
author = {McKinney, Wes},
booktitle = {Proceedings of the 9th {P}ython in {S}cience {C}onference},
editor = {van der Walt, St{\'{e}}fan and Millman, Jarrod},
pages = {51--56},
title = {{Data Structures for Statistical Computing in Python}},
year = {2010}
}

@article{spark,
 author = {Zaharia, Matei and Xin, Reynold S. and Wendell, Patrick and Das, Tathagata and Armbrust, Michael and Dave, Ankur and Meng, Xiangrui and Rosen, Josh and Venkataraman, Shivaram and Franklin, Michael J. and Ghodsi, Ali and Gonzalez, Joseph and Shenker, Scott and Stoica, Ion},
 title = {Apache Spark: A unified engine for big data processing},
 journal = {Commun. ACM},
 issue_date = {November 2016},
 volume = {59},
 number = {11},
 month = oct,
 year = {2016},
 issn = {0001-0782},
 pages = {56--65},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/2934664},
 doi = {10.1145/2934664},
 acmid = {2934664},
 publisher = {ACM},
 address = {New York, NY, USA},
}

@article{10.1093/bib/bbw068,
    author = {Lee, Byunghan and Min, Seonwoo and Yoon, Sungroh},
    title = "{Deep learning in bioinformatics}",
    journal = {Briefings in Bioinformatics},
    volume = {18},
    number = {5},
    pages = {851-869},
    year = {2016},
    month = {07},
    abstract = "{In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.}",
    issn = {1467-5463},
    doi = {10.1093/bib/bbw068},
    url = {https://doi.org/10.1093/bib/bbw068},
    eprint = {http://oup.prod.sis.lan/bib/article-pdf/18/5/851/25581102/bbw068.pdf},
}
@article{Zaharia:2016:ASU:3013530.2934664,
 author = {Zaharia, Matei and Xin, Reynold S. and Wendell, Patrick and Das, Tathagata and Armbrust, Michael and Dave, Ankur and Meng, Xiangrui and Rosen, Josh and Venkataraman, Shivaram and Franklin, Michael J. and Ghodsi, Ali and Gonzalez, Joseph and Shenker, Scott and Stoica, Ion},
 title = {Apache Spark: A Unified Engine for Big Data Processing},
 journal = {Commun. ACM},
 issue_date = {November 2016},
 volume = {59},
 number = {11},
 month = oct,
 year = {2016},
 issn = {0001-0782},
 pages = {56--65},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/2934664},
 doi = {10.1145/2934664},
 acmid = {2934664},
 publisher = {ACM},
 address = {New York, NY, USA},
}
@article{Hutter2015,
  doi = {10.1007/s13218-015-0381-0},
  url = {https://doi.org/10.1007/s13218-015-0381-0},
  year = {2015},
  month = jul,
  publisher = {Springer Nature},
  volume = {29},
  number = {4},
  pages = {329--337},
  author = {Frank Hutter and J\"{o}rg L\"{u}cke and Lars Schmidt-Thieme},
  title = {Beyond Manual Tuning of Hyperparameters},
  journal = {{KI} - K\"{u}nstliche Intelligenz}
}
@article{Craig1988,
  doi = {10.1007/bf00140399},
  url = {https://doi.org/10.1007/bf00140399},
  year = {1988},
  publisher = {Springer Nature},
  volume = {2},
  number = {2},
  pages = {103--118},
  author = {I. D. Craig},
  title = {Blackboard systems},
  journal = {Artificial Intelligence Review}
}
@incollection{sqlalchemy, place={Mountain View}, title={SQLalchemy}, booktitle={The architecture of open source applications volume II: structure, scale, and a few more fearless hacks.}, publisher={aosabook.org}, author={Bayer, Michael}, editor={Brown, Amy and Wilson, Greg}, year={2012}
}
@article{LeCun2015,
  doi = {10.1038/nature14539},
  url = {https://doi.org/10.1038/nature14539},
  year = {2015},
  month = may,
  publisher = {Springer Nature},
  volume = {521},
  number = {7553},
  pages = {436--444},
  author = {Yann LeCun and Yoshua Bengio and Geoffrey Hinton},
  title = {Deep learning},
  journal = {Nature}
}
@article{DBLP:journals/corr/ChetlurWVCTCS14,
  author    = {Sharan Chetlur and
               Cliff Woolley and
               Philippe Vandermersch and
               Jonathan Cohen and
               John Tran and
               Bryan Catanzaro and
               Evan Shelhamer},
  title     = {cuDNN: Efficient Primitives for Deep Learning},
  journal   = {CoRR},
  volume    = {abs/1410.0759},
  year      = {2014},
  url       = {http://arxiv.org/abs/1410.0759},
  archivePrefix = {arXiv},
  eprint    = {1410.0759},
  timestamp = {Mon, 13 Aug 2018 16:48:28 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/corr/ChetlurWVCTCS14},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@misc{chollet2015keras,
  title={Keras},
  author={Chollet, Fran\c{c}ois and others},
  year={2015},
  howpublished={\url{https://keras.io}},
}
@misc{arya.ai, title={Tools to simplify the process of building deep learning systems}, howpublished={https://arya.ai/}, journal={Arya.ai}
}
@misc{google, title={Cloud AutoML - Custom Machine Learning Models  |  AutoML  |  Google Cloud}, howpublished={https://cloud.google.com/automl/}, journal={Google}, publisher={Google}
}
@article{DBLP:journals/corr/abs-1708-02709,
  author    = {Tom Young and
               Devamanyu Hazarika and
               Soujanya Poria and
               Erik Cambria},
  title     = {Recent Trends in Deep Learning Based Natural Language Processing},
  journal   = {CoRR},
  volume    = {abs/1708.02709},
  year      = {2017},
  url       = {http://arxiv.org/abs/1708.02709},
  archivePrefix = {arXiv},
  eprint    = {1708.02709},
  timestamp = {Mon, 13 Aug 2018 16:46:22 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/corr/abs-1708-02709},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{scikit-learn,
 title={Scikit-learn: Machine Learning in {P}ython},
 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
         and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
         and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
         Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
 journal={Journal of Machine Learning Research},
 volume={12},
 pages={2825--2830},
 year={2011}
}
@misc{pypi, title={PyPI – the Python Package Index}, url={https://pypi.org/}, journal={PyPI}
}
@misc{kubeflow_2019, title={Kubeflow}, howpublished={\url{https://www.kubeflow.org/}}, year={2019}, month={Jan}
}

repository: kellylab/Fireworks

repo_name: kellylab/Fireworks

gha_language: Python


text:
@inproceedings{Abe2018b,
 abstract = {There are several studies that propose identity management that utilizes blockchain technology. In Ethereum, the main programmable blockchain system, data on a blockchain are saved as encoded binaries for executing automatic verification. To decode a binary, users need to know the application binary interfaces (ABI) that describes the data structure of the registered information. However, the manner by which ABI are shared in the current blockchain protocol is opaque. To resolve this problem, we describe a new protocol for embedding the ABI on a blockchain transaction when a registrant registers information. Our method enables users to read registered data with information on the blockchain alone, and it guarantees transparency without requiring users to trust third parties.},
 author = {Abe, Ryosuke and Watanabe, Hiroki and Ohashi, Shigenori and Fujimura, Shigeru and Nakadaira, Atsushi},
 booktitle = {2018 IEEE 42nd Annual Computer Software and Applications Conference (COMPSAC)},
 doi = {10.1109/COMPSAC.2018.10298},
 isbn = {978-1-5386-2666-5},
 month = {Jul},
 title = {Storage Protocol for Securing Blockchain Transparency},
 year = {2018}
}


text:
@article{activeobject1996,
  author = {R. Greg Lavender and Douglas C. Schmidt},
  title = {Active Object -- An Object Behavioral Pattern for Concurrent Programming},
  year = {1996},
}

@article{board2007rss,
  author = {{RSS Advisory Board}},
  title = {RSS 2.0 Specification},
  year = {2007},
}

@article{dice1945,
  author = {Dice, Lee R.},
  journal = {Ecology},
  number = {3},
  pages = {297},
  title = {Measures of the Amount of Ecologic Association Between Species},
  volume = {26},
  year = {1945},
  doi = {10.2307/1932409},
  issn = {00129658},
}

@article{dudani1976,
  author = {Dudani, Sahibsingh A.},
  journal = {{IEEE} Transactions on Systems, Man and Cybernetics},
  number = {4},
  pages = {325--327},
  title = {The {Distance-Weighted} {k-Nearest-Neighbor} Rule},
  volume = {{SMC-6}},
  year = {1976},
  doi = {10.1109/TSMC.1976.5408784},
  issn = {0018-9472},
}

@article{heydon99mercator,
 author = {Heydon, Allan and Najork, Marc},
 title = {Mercator: A Scalable, Extensible Web Crawler},
 journal = {World Wide Web},
 volume = {2},
 number = {4},
 year = {1999},
 issn = {1386-145X},
 pages = {219--229},
 numpages = {11},
 url = {http://dx.doi.org/10.1023/A:1019213109274},
 doi = {10.1023/A:1019213109274},
 acmid = {598733},
 publisher = {Kluwer Academic Publishers},
 address = {Hingham, MA, USA},
}

@article{johnson2008blogs,
  author = {Johnson, Kay},
  journal = {Serials review},
  number = {3},
  pages = {199--204},
  title = {Are Blogs Here to Stay?: An Examination of the Longevity and Currency of a Static List of Library and Information Science Weblogs},
  volume = {34},
  year = {2008},
}

@article{kasioumis2013towards,
  author = {Kasioumis, Nikos and Banos, Vangelis and Kalb, Hendrik},
  journal = {World Wide Web},
  pages = {1--27},
  title = {Towards building a blog preservation platform},
  year = {2013},
}

@article{levenshtein1966,
  author = {Levenshtein, {VI}},
  journal = {Soviet Physics Doklady.},
  number = {8},
  pages = {707--710},
  title = {Binary codes capable of correcting deletions, insertions and reversals.},
  volume = {10},
  year = {1966},
}

@article{lindahl2003weblogs,
  author = {Lindahl, Charlie and Blount, Elise},
  journal = {Computer},
  number = {11},
  pages = {114--116},
  title = {Weblogs: simplifying web publishing},
  volume = {36},
  year = {2003},
}

@article{stalker,
  author = {Ion Muslea and Steven Minton and Craig A. Knoblock},
  journal = {Journal of Autonomous Agents and Multi-Agent Systems},
  pages = {93--114},
  title = {Hierarchical Wrapper Induction for Semistructured Information Sources},
  volume = {4},
  year = {2001},
}

@inproceedings{berger2011,
  author = {Berger, P. and Hennig, P. and Bross, J. and Meinel, C.},
  booktitle = {Third International Conference on Social Computing},
  pages = {672--677},
  title = {Mapping the {Blogosphere{\textendash}Towards} a Universal and Scalable {Blog-Crawler}},
  year = {2011},
  doi = {10.1109/PASSAT/SocialCom.2011.57},
}

@inproceedings{boldi2003,
  author = {Boldi, Paolo and Codenotti, Bruno and Santini, Massimo and Vigna, Sebastiano},
  title = {{UbiCrawler:} a scalable fully distributed web crawler},
  year = {2003},
}

@inproceedings{burton2011,
  author = {Burton, K. and Kasch, N. and Soboroff, I.},
  booktitle = {Fifth Annual Conference on Weblogs and Social Media},
  title = {The {ICWSM} 2011 Spinn3r Dataset},
  year = {2011},
}

@inproceedings{faheem2012intelligent,
  author = {Faheem, Muhammad},
  booktitle = {Proceedings of the 21st international conference companion on World Wide Web},
  pages = {127--132},
  title = {Intelligent crawling of Web applications for Web archiving},
  year = {2012},
}

@inproceedings{gkotsis2013,
  address = {Berlin, Heidelberg},
  author = {Gkotsis, George and Stepanyan, Karen and Cristea, Alexandra I. and Joy, Mike},
  booktitle = {Proceedings of the 29th British National Conference on Big Data},
  pages = {292--302},
  series = {BNCOD'13},
  title = {Self-supervised Automated Wrapper Generation for Weblog Data Extraction},
  year = {2013},
  doi = {10.1007/978-3-642-39467-6_26},
  isbn = {978-3-642-39466-9},
}

@inproceedings{hundt2011,
  author = {Hundt, Robert},
  booktitle = {Proceedings of Scala Days},
  title = {Loop Recognition in {C++/Java/Go/Scala}},
  year = {2011},
}

@inproceedings{kohlschuetter2010,
  address = {New York, {NY}, {USA}},
  author = {Kohlsch\"{u}tter, Christian and Fankhauser, Peter and Nejdl, Wolfgang},
  booktitle = {Proceedings of the Third {ACM} International Conference on Web Search and Data Mining},
  pages = {441{\textendash}450},
  series = {{WSDM} '10},
  title = {Boilerplate Detection Using Shallow Text Features},
  year = {2010},
  doi = {10.1145/1718487.1718542},
  isbn = {978-1-60558-889-6},
}

@inproceedings{lixto,
  author = {Georg Gottlob and Christoph Koch and Robert Baumgartner and Marcus Herzog and Sergio Flesca},
  booktitle = {Proceedings of the Twenty-third Symposium on Principles of Database Systems},
  pages = {1--12},
  title = {The Lixto Data Extraction Project: Back and Forth Between Theory and Practice},
  year = {2004},
  doi = {10.1145/1055558.1055560},
  isbn = {158113858X},
}

@inproceedings{oita2010,
  author = {Oita, Marilena and Senellart, Pierre},
  title = {Archiving Data Objects using Web Feeds},
  year = {2010},
}

@inproceedings{shkapenyuk2002,
  author = {Shkapenyuk, V. and Suel, Torsten},
  booktitle = {18th International Conference on Data Engineering, 2002. Proceedings},
  pages = {357--368},
  title = {Design and implementation of a high-performance distributed Web crawler},
  year = {2002},
  doi = {10.1109/ICDE.2002.994750},
}

@inproceedings{treeedit,
  address = {New York, NY, USA},
  author = {Reis, D. C. and Golgher, P. B. and Silva, A. S. and Laender, A. F.},
  booktitle = {Proceedings of the 13th International Conference on World Wide Web},
  pages = {502--511},
  series = {WWW '04},
  title = {Automatic Web News Extraction Using Tree Edit Distance},
  year = {2004},
  doi = {10.1145/988672.988740},
  isbn = {1-58113-844-X},
}

@misc{andrewrogers2014,
  author = {Andrew Rogers and Gary Brewer},
  howpublished = {\url{http://trends.builtwith.com/docinfo/Microdata}},
  note = {\lastvisited},
  title = {Microdata Usage Statistics},
}

@misc{antinharasymiv2011,
  author = {Antin Harasymiv},
  howpublished = {\href{http://buzz.blogger.com/2011/09/dynamic-views-seven-new-ways-to-share.html}{\nolinkurl{http://buzz.blogger.com/2011/09/dynamic-views-}}\\\href{http://buzz.blogger.com/2011/09/dynamic-views-seven-new-ways-to-share.html}{\nolinkurl{seven-new-ways-to-share.html}}},
  note = {\lastvisited},
  title = {Blogger Dynamic Views},
}

@misc{brianwilson2008,
  author = {Brian Wilson},
  howpublished = {\url{http://dev.opera.com/articles/view/mama}},
  note = {\lastvisited},
  title = {Metadata Analysis and Mining Application},
}

@misc{nahedeltantawy2012,
  author = {Nahed Eltantawy and Julie B. Wiest},
  journal = {Ikkevold},
  title = {Social Media in the Egyptian Revolution: Reconsidering Resource Mobilization Theory (1-3)},
  year = {2012},
}

@misc{thereactivemanifesto2013,
  author = {{Various authors}},
  howpublished = {\url{http://reactivemanifesto.org}},
  note = {\lastvisited},
  title = {The Reactive Manifesto},
}

@misc{w3c2002,
  author = {{Various authors, WC3}},
  howpublished = {\url{http://www-mit.w3.org/QA/Tips/Use\_h1\_for\_Title}},
  note = {\lastvisited},
  title = {Use h1 for top level heading},
}

@misc{w3c2014,
  author = {{Various authors, W3C}},
  howpublished = {\url{http://w3.org/standards}},
  note = {\lastvisited},
  title = {{W3C} standards},
}

@misc{whatwg2014,
  author = {{WHATWG}},
  howpublished = {\href{http://whatwg.org/specs/web-apps/current-work/multipage}{\nolinkurl{http://whatwg.org/specs/web-apps/current-}}\\\href{http://whatwg.org/specs/web-apps/current-work/multipage}{\nolinkurl{work/multipage}}},
  note = {\lastvisited},
  title = {Microdata - {HTML5} Draft Standard},
}

@misc{wordpress2014,
  author = {{WordPress}},
  howpublished = {\url{http://wordpress.com/stats/posting}},
  note = {\lastvisited},
  title = {Posting Activity},
}


text:
@article{193220,
author = {Unser, M and Aldroubi, A and Eden, M},
doi = {10.1109/78.193220},
issn = {1053-587X},
journal = {Signal Processing, IEEE Transactions on},
keywords = {data compression;differentiation;digital filters;filtering and prediction theory;image processing;interference suppression;interpolation;least squares approximations;signal processing;splines (mathematics);B-spline coefficients;B-spline signal processing;data compressions;differentiation;digital filters;digital images;filtering;higher-dimensional signals;interpolation;least squares splines;linear filtering;linear transformation;noise reduction;smoothing splines;transfer functions;Data compression;Filtering;Interpolation;Least squares approximation;Maximum likelihood detection;Noise reduction;Nonlinear filters;Signal processing;Smoothing methods;Spline},
month = {feb},
number = {2},
pages = {821--833},
title = {{B-spline signal processing. I. Theory}},
volume = {41},
year = {1993}
}
@article{193221,
author = {Unser, M and Aldroubi, A and Eden, M},
doi = {10.1109/78.193221},
issn = {1053-587X},
journal = {Signal Processing, IEEE Transactions on},
keywords = {digital filters;filtering and prediction theory;image processing;least squares approximations;signal processing;splines (mathematics);B-spline signal processing;cubic spline image pyramid;design;digital filters;least-squares approximation;recursive filtering algorithms;smoothing spline;Computational complexity;Filtering algorithms;Image edge detection;Interpolation;Low pass filters;Process design;Signal processing;Signal processing algorithms;Smoothing methods;Spline},
month = {feb},
number = {2},
pages = {834--848},
title = {{B-spline signal processing. II. Efficiency design and applications}},
volume = {41},
year = {1993}
}
@article{Krips2011,
author = {Krips, Kristjan and Petmanson, Timo},
file = {:C$\backslash$:/Users/dcona/Documents/Mendeley/petmanson-krips-algo-project.pdf:pdf},
pages = {1--7},
title = {{The constellation database}},
year = {2011}
}
@article{Ji,
author = {Ji, Suyao and Wang, Jinzhi and Liu, Xiaoge},
file = {:C$\backslash$:/Users/dcona/Documents/Mendeley/Ji{\_}Liu{\_}Wang.pdf:pdf},
keywords = {constellation,constellation detection,detection approach,first,image processing,star pattern,steps in our constellation,template matching,the image is preprocessed,there are three important,to a},
title = {{Constellation Detection}}
}
@article{Renken,
abstract = {An unmanned system for automatically 3-axis attitude determination by star constellation matching is a very useful tool for applications primary in the field of satellite technology, where stars are visible all the time. A special designed CCD camera system, which is sensitive enough to detect stars, points to the direction (attitude) to be determinated and captures stars within the camera field of view (fov). By comparing this imaged star pattern with celestial coordinates out of a database-like star catalogue, a star pattern can be matched and the attitude (3-axis) can be calculated by using simple vector algebra. In partnership with other attitude determination systems, the accuracy and reliability for an attitude control system is increasing. Including camera hardware and image processing software, we realized a transputer based (Inmos T8XX, Occam, Parallel C) onboard computer system for our own satellite missions. For terrestrial and ground based pointing applications or post-mission attitude determination a powerful PC-based system (Pentium, Pascal, C) is available with additional visualization features of certain steps during the image processing via an userfriendly desktop.},
author = {Renken, Hartmut and Rath, H J},
file = {:C$\backslash$:/Users/dcona/Documents/Mendeley/or1997.pdf:pdf},
journal = {Space Technology},
keywords = {attitude determination,image processing,matching,pointing,star tracker},
title = {{A Method for Three-Axis Attitude determination by Image-processed star constellation matching}}
}
@misc{yaleStar,
author = {{Hoffleit, D. and Warren, Jr.}, W.H.},
title = {{The Bright Star Catalog, 5th Revised Edition}},
url = {http://tdc-www.harvard.edu/catalogs/bsc5.html},
year = {1991}
}

repository: jvahala/Space-Doodles

repo_name: jvahala/Space-Doodles

gha_language: TeX


text:
% This file was created with JabRef 2.10.
% Encoding: UTF-8

@Article{luque2014,
  Title                    = {Integrated neural and robotic simulations. Simulation of cerebellar neurobiological substrate for an object-oriented dynamic model abstraction process},
  Author                   = {Luque, Niceto R and Carrillo, Richard R and Naveros, Francisco and Garrido, Jes{\'u}s A and S{\'a}ez-Lara, MJ},
  Journal                  = {Robotics and Autonomous Systems},
  Year                     = {2014},
  Number                   = {12},
  Pages                    = {1702--1716},
  Volume                   = {62},

  Publisher                = {Elsevier}
}

repository: EduardoRosLab/neurorobotics-website

repo_name: EduardoRosLab/neurorobotics-website


text:
# This is a hack because $*#($*($# e17 doesn't check if firefox is present and puts it in the menu blindly
LICENSE = "MIT"

RDEPENDS_${PN} = "epiphany"
RCONFLICTS_${PN} = "firefox"
PR = "r1"

do_install() {
	install -d ${D}/${bindir}
	ln -sf ${bindir}/epiphany ${D}/${bindir}/firefox
}