rethomics_manuscript.bib

@article{gilestro_pysolo_2009,
  title = {{{pySolo}}: A Complete Suite for Sleep Analysis in {{Drosophila}}},
  volume = {25},
  issn = {1367-4811},
  shorttitle = {{{pySolo}}},
  doi = {10.1093/bioinformatics/btp237},
  abstract = {SUMMARY: pySolo is a multiplatform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website.
AVAILABILITY: Software and documentation are located at (http://www.pysolo.net). pySolo is a free software released under the GNU General Public License.},
  language = {eng},
  number = {11},
  journal = {Bioinformatics (Oxford, England)},
  author = {Gilestro, Giorgio F. and Cirelli, Chiara},
  month = jun,
  year = {2009},
  keywords = {Animals,Sleep,Drosophila melanogaster,Motor Activity,User-Computer Interface,Software,Computational Biology},
  pages = {1466-1467},
  pmid = {19369499},
  pmcid = {PMC2732309}
}

@book{wickham_ggplot2_2016,
  title = {Ggplot2: {{Elegant Graphics}} for {{Data Analysis}}},
  isbn = {978-3-319-24277-4},
  shorttitle = {Ggplot2},
  abstract = {This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to: produce handsome, publication-quality plots with automatic legends created from the plot specificationsuperimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scalesadd customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regressionsave any ggplot2 plot (or part thereof) for later modification or reusecreate custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plotsapproach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page.},
  language = {en},
  publisher = {{Springer}},
  author = {Wickham, Hadley},
  month = jun,
  year = {2016},
  keywords = {Computers / Computer Graphics,Computers / Mathematical \& Statistical Software,Mathematics / Combinatorics,Mathematics / Graphic Methods,Mathematics / Probability \& Statistics / Stochastic Processes}
}

@book{wickham_tidyverse_2017,
  title = {Tidyverse: {{Easily Install}} and {{Load}} the '{{Tidyverse}}'},
  author = {Wickham, Hadley},
  year = {2017}
}

@book{dowle_data.table_2017,
  title = {Data.Table: {{Extension}} of `data.Frame`},
  author = {Dowle, Matt and Srinivasan, Arun},
  year = {2017}
}

@book{r_core_team_r_2017,
  address = {Vienna, Austria},
  title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
  publisher = {{R Foundation for Statistical Computing}},
  author = {{R Core Team}},
  year = {2017}
}

@article{itskov_automated_2014,
  title = {Automated Monitoring and Quantitative Analysis of Feeding Behaviour in {{{\emph{Drosophila}}}}},
  volume = {5},
  copyright = {2014 Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/ncomms5560},
  abstract = {Food ingestion is one of the defining behaviours of all animals, but its quantification and analysis remain challenging. This is especially the case for feeding behaviour in small, genetically tractable animals such as Drosophila melanogaster. Here, we present a method based on capacitive measurements, which allows the detailed, automated and high-throughput quantification of feeding behaviour. Using this method, we were able to measure the volume ingested in single sips of an individual, and monitor the absorption of food with high temporal resolution. We demonstrate that flies ingest food by rhythmically extending their proboscis with a frequency that is not modulated by the internal state of the animal. Instead, hunger and satiety homeostatically modulate the microstructure of feeding. These results highlight similarities of food intake regulation between insects, rodents, and humans, pointing to a common strategy in how the nervous systems of different animals control food intake.},
  language = {en},
  journal = {Nature Communications},
  author = {Itskov, Pavel M. and Moreira, Jos{\'e}-Maria and Vinnik, Ekaterina and Lopes, Gon{\c c}alo and Safarik, Steve and Dickinson, Michael H. and Ribeiro, Carlos},
  month = aug,
  year = {2014},
  pages = {4560},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5AKUWWHQ/Itskov et al. - 2014 - Automated monitoring and quantitative analysis of .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BM3KJKXI/ncomms5560.html}
}

@article{geissmann_ethoscopes_2017,
  title = {Ethoscopes: {{An}} Open Platform for High-Throughput Ethomics},
  volume = {15},
  issn = {1545-7885},
  shorttitle = {Ethoscopes},
  doi = {10.1371/journal.pbio.2003026},
  abstract = {Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.},
  language = {en},
  number = {10},
  journal = {PLOS Biology},
  author = {Geissmann, Quentin and Rodriguez, Luis Garcia and Beckwith, Esteban J. and French, Alice S. and Jamasb, Arian R. and Gilestro, Giorgio F.},
  month = oct,
  year = {2017},
  keywords = {Computer networks,Cameras,Sleep,Drosophila melanogaster,Animal behavior,3D printing,Light-emitting diodes,Sleep deprivation},
  pages = {e2003026},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JRY8ANLY/Geissmann et al. - 2017 - Ethoscopes An open platform for high-throughput e.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FSBVUDBY/article.html}
}

@article{buhl_quasimodo_2016,
  title = {Quasimodo Mediates Daily and Acute Light Effects on {{Drosophila}} Clock Neuron Excitability},
  volume = {113},
  copyright = {\textcopyright{}  . http://www.pnas.org/site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1606547113},
  abstract = {We have characterized a light-input pathway regulating Drosophila clock neuron excitability. The molecular clock drives rhythmic electrical excitability of clock neurons, and we show that the recently discovered light-input factor Quasimodo (Qsm) regulates this variation, presumably via an Na+, K+, Cl- cotransporter (NKCC) and the Shaw K+ channel (dKV3.1). Because of light-dependent degradation of the clock protein Timeless (Tim), constant illumination (LL) leads to a breakdown of molecular and behavioral rhythms. Both overexpression (OX) and knockdown (RNAi) of qsm, NKCC, or Shaw led to robust LL rhythmicity. Whole-cell recordings of the large ventral lateral neurons (l-LNv) showed that altering Qsm levels reduced the daily variation in neuronal activity: qsmOX led to a constitutive less active, night-like state, and qsmRNAi led to a more active, day-like state. Qsm also affected daily changes in K+ currents and the GABA reversal potential, suggesting a role in modifying membrane currents and GABA responses in a daily fashion, potentially modulating light arousal and input to the clock. When directly challenged with blue light, wild-type l-LNvs responded with increased firing at night and no net response during the day, whereas altering Qsm, NKKC, or Shaw levels abolished these day/night differences. Finally, coexpression of ShawOX and NKCCRNAi in a qsm mutant background restored LL-induced behavioral arrhythmicity and wild-type neuronal activity patterns, suggesting that the three genes operate in the same pathway. We propose that Qsm affects both daily and acute light effects in l-LNvs probably acting on Shaw and NKCC.},
  language = {en},
  number = {47},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Buhl, Edgar and Bradlaugh, Adam and Ogueta, Maite and Chen, Ko-Fan and Stanewsky, Ralf and Hodge, James J. L.},
  month = nov,
  year = {2016},
  keywords = {circadian rhythms,GABA reversal potential,light input,membrane excitability,potassium currents},
  pages = {13486-13491},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SIIKPFX9/Buhl et al. - 2016 - Quasimodo mediates daily and acute light effects o.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9B7ACC7N/13486.html},
  pmid = {27821737}
}

@article{ruf_lomb-scargle_1999,
  title = {The {{Lomb}}-{{Scargle Periodogram}} in {{Biological Rhythm Research}}: {{Analysis}} of {{Incomplete}} and {{Unequally Spaced Time}}-{{Series}}},
  volume = {30},
  issn = {0929-1016},
  shorttitle = {The {{Lomb}}-{{Scargle Periodogram}} in {{Biological Rhythm Research}}},
  doi = {10.1076/brhm.30.2.178.1422},
  abstract = {This paper investigates the utility of the Lomb\textendash{}Scargle periodogram for the analysis of biological rhythms. This method is particularly suited to detect periodic components in unequally sampled time-series and data sets with missing values, but restricts all calculations to actually measured values. The Lomb-Scargle method was tested on both real and simulated time-series with even and uneven sampling, and compared to a standard method in biomedical rhythm research, the Chi-square periodogram. Results indicate that the Lomb\textendash{}Scargle algorithm shows a clearly better detection efficiency and accuracy in the presence of noise, and avoids possible bias or erroneous results that may arise from replacement of missing data by interpolation techniques. Hence, the Lomb\textendash{}Scargle periodogram may serve as a useful method for the study of biological rhythms, especially when applied to telemetrical or observational time-series obtained from free-living animals, i.e., data sets that notoriously lack points.},
  number = {2},
  journal = {Biological Rhythm Research},
  author = {Ruf, T.},
  month = apr,
  year = {1999},
  pages = {178-201},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6F749AE7/Ruf - 1999 - The Lomb-Scargle Periodogram in Biological Rhythm .pdf}
}

@article{sokolove_chi_1978,
  title = {The Chi Square Periodogram: {{Its}} Utility for Analysis of Circadian Rhythms},
  volume = {72},
  issn = {0022-5193},
  shorttitle = {The Chi Square Periodogram},
  doi = {10.1016/0022-5193(78)90022-X},
  abstract = {It is proposed that chi-square statistic be employed in constructing periodograms for the analysis of hourly time series data obtained in studies of circadian rhythmicity. We show that even for relatively short (10 day) time series, the integral-valued chi-square periodogram can distinguish circadian-periodic from random series at a level of significance of about 0$\cdot$01. In addition, we describe the effects of serial correlation and examine the resolving power of the method for two periodic components in the circadian range. We suggest how the method can be most profitably employed in the analysis of event-recorder data for detection of rhythmicity in the range 14 to 34 h., and for the estimation of period to $\pm$0$\cdot$2 h.},
  number = {1},
  journal = {Journal of Theoretical Biology},
  author = {Sokolove, Phillip G. and Bushell, Wayne N.},
  month = may,
  year = {1978},
  pages = {131-160}
}

@article{schmid_new_2011,
  title = {A {{New ImageJ Plug}}-in ``{{ActogramJ}}'' for {{Chronobiological Analyses}}},
  volume = {26},
  issn = {0748-7304},
  doi = {10.1177/0748730411414264},
  abstract = {While the rapid development of personal computers and high-throughput recording systems for circadian rhythms allow chronobiologists to produce huge amounts of data, the software to analyze them often lags behind. Here, we announce newly developed chronobiology software that is easy to use, compatible with many different systems, and freely available. Our system can perform the most frequently used analyses: actogram drawing, periodogram analysis, and waveform analysis. The software is distributed as a pure Java plug-in for ImageJ and so works on the 3 main operating systems: Linux, Macintosh, and Windows. We believe that this free software raises the speed of data analyses and makes studying chronobiology accessible to newcomers.},
  language = {en},
  number = {5},
  journal = {Journal of Biological Rhythms},
  author = {Schmid, Benjamin and Helfrich-F{\"o}rster, Charlotte and Yoshii, Taishi},
  month = oct,
  year = {2011},
  pages = {464-467},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q4D9GMGK/Schmid et al. - 2011 - A New ImageJ Plug-in “ActogramJ” for Chronobiologi.pdf}
}

@article{nitabach_organization_2008,
  title = {Organization of the {{Drosophila}} Circadian Control Circuit},
  volume = {18},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2007.11.061},
  abstract = {Molecular genetics has revealed the identities of several components of the fundamental circadian molecular oscillator - an evolutionarily conserved molecular mechanism of transcription and translation that can operate in a cell-autonomous manner. Therefore, it was surprising when studies of circadian rhythmic behavior in the fruit fly Drosophila suggested that the normal operations of circadian clock cells, which house the molecular oscillator, in fact depend on non-cell-autonomous effects - interactions between the clock cells themselves. Here we review several genetic analyses that broadly extend that viewpoint. They support a model whereby the approximately 150 circadian clock cells in the brain of the fly are sub-divided into functionally discrete rhythmic centers. These centers alternatively cooperate or compete to control the different episodes of rhythmic behavior that define the fly's daily activity profile.},
  language = {eng},
  number = {2},
  journal = {Current biology: CB},
  author = {Nitabach, Michael N. and Taghert, Paul H.},
  month = jan,
  year = {2008},
  keywords = {Brain,Animals,Glutamic Acid,Biological Clocks,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,Light,Neuropeptides,Locomotion,Temperature,Environment},
  pages = {R84-93},
  pmid = {18211849}
}

@article{perez-escudero_idtracker_2014,
  title = {{{idTracker}}: Tracking Individuals in a Group by Automatic Identification of Unmarked Animals},
  volume = {11},
  copyright = {2014 Nature Publishing Group},
  issn = {1548-7105},
  shorttitle = {{{idTracker}}},
  doi = {10.1038/nmeth.2994},
  abstract = {Animals in groups touch each other, move in paths that cross, and interact in complex ways. Current video tracking methods sometimes switch identities of unmarked individuals during these interactions. These errors propagate and result in random assignments after a few minutes unless manually corrected. We present idTracker, a multitracking algorithm that extracts a characteristic fingerprint from each animal in a video recording of a group. It then uses these fingerprints to identify every individual throughout the video. Tracking by identification prevents propagation of errors, and the correct identities can be maintained indefinitely. idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. We tested it on fish (Danio rerio and Oryzias latipes), flies (Drosophila melanogaster), ants (Messor structor) and mice (Mus musculus).},
  language = {en},
  number = {7},
  journal = {Nature Methods},
  author = {P{\'e}rez-Escudero, Alfonso and Vicente-Page, Juli{\'a}n and Hinz, Robert C. and Arganda, Sara and {de Polavieja}, Gonzalo G.},
  month = jul,
  year = {2014},
  pages = {743-748},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DEDZ8X6G/Pérez-Escudero et al. - 2014 - idTracker tracking individuals in a group by auto.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/49G3A4RZ/nmeth.html}
}

@article{reiser_ethomics_2009,
  title = {The Ethomics Era?},
  volume = {6},
  copyright = {2009 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth0609-413},
  abstract = {Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.},
  language = {en},
  number = {6},
  journal = {Nature Methods},
  author = {Reiser, Michael},
  month = jun,
  year = {2009},
  pages = {413-414},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GV26AIV4/Reiser - 2009 - The ethomics era.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8S7AMZIK/nmeth0609-413.html}
}

@article{pelkowski_novel_2011,
  title = {A Novel High-Throughput Imaging System for Automated Analyses of Avoidance Behavior in Zebrafish Larvae},
  volume = {223},
  issn = {0166-4328},
  doi = {10.1016/j.bbr.2011.04.033},
  abstract = {Early brain development can be influenced by numerous genetic and environmental factors, with long-lasting effects on brain function and behavior. The identification of these factors is facilitated by recent innovations in high-throughput screening. However, large-scale screening in whole organisms remains challenging, in particular when studying changes in brain function or behavior in vertebrate model systems. In this study, we present a novel imaging system for high-throughput analyses of behavior in zebrafish larvae. The three-camera system can image 12 multiwell plates simultaneously and is unique in its ability to provide local visual stimuli in the wells of a multiwell plate. The acquired images are converted into a series of coordinates, which characterize the location and orientation of the larvae. The developed imaging techniques were tested by measuring avoidance behaviors in seven-day-old zebrafish larvae. The system effectively quantified larval avoidance and revealed an increased edge preference in response to a blue or red `bouncing ball' stimulus. Larvae also avoid a bouncing ball stimulus when it is counter-balanced with a stationary ball, but do not avoid blinking balls counter-balanced with a stationary ball. These results indicate that the seven-day-old larvae respond specifically to movement, rather than color, size, or local changes in light intensity. The imaging system and assays for measuring avoidance behavior may be used to screen for genetic and environmental factors that cause developmental brain disorders and for novel drugs that could prevent or treat these disorders.},
  number = {1},
  journal = {Behavioural Brain Research},
  author = {Pelkowski, Sean D. and Kapoor, Mrinal and Richendrfer, Holly A. and Wang, Xingyue and Colwill, Ruth M. and Creton, Robbert},
  month = sep,
  year = {2011},
  keywords = {Behavior,Zebrafish,Automated image analysis,Avoidance,High-throughput imaging,Thigmotaxis,Visual stimuli},
  pages = {135-144}
}

@article{swierczek_high-throughput_2011,
  title = {High-Throughput Behavioral Analysis in {{{\emph{C}}}}{\emph{. Elegans}}},
  volume = {8},
  copyright = {2011 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth.1625},
  abstract = {We designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three traditional behavioral paradigms using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allowed rapid quantification of behavior with minimal human effort. Thus, this system will enable large-scale forward and reverse genetic screens for complex behaviors.},
  language = {en},
  number = {7},
  journal = {Nature Methods},
  author = {Swierczek, Nicholas A. and Giles, Andrew C. and Rankin, Catharine H. and Kerr, Rex A.},
  month = jul,
  year = {2011},
  pages = {592-598},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9BSAFXZB/Swierczek et al. - 2011 - High-throughput behavioral analysis in iC. elega.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/382LCCBY/nmeth.html}
}

@article{ro_flic_2014,
  title = {{{FLIC}}: {{High}}-{{Throughput}}, {{Continuous Analysis}} of {{Feeding Behaviors}} in {{Drosophila}}},
  volume = {9},
  issn = {1932-6203},
  shorttitle = {{{FLIC}}},
  doi = {10.1371/journal.pone.0101107},
  abstract = {We present a complete hardware and software system for collecting and quantifying continuous measures of feeding behaviors in the fruit fly, Drosophila melanogaster. The FLIC (Fly Liquid-Food Interaction Counter) detects analog electronic signals as brief as 50 $\mathrm{\mu}$s that occur when a fly makes physical contact with liquid food. Signal characteristics effectively distinguish between different types of behaviors, such as feeding and tasting events. The FLIC system performs as well or better than popular methods for simple assays, and it provides an unprecedented opportunity to study novel components of feeding behavior, such as time-dependent changes in food preference and individual levels of motivation and hunger. Furthermore, FLIC experiments can persist indefinitely without disturbance, and we highlight this ability by establishing a detailed picture of circadian feeding behaviors in the fly. We believe that the FLIC system will work hand-in-hand with modern molecular techniques to facilitate mechanistic studies of feeding behaviors in Drosophila using modern, high-throughput technologies.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Ro, Jennifer and Harvanek, Zachary M. and Pletcher, Scott D.},
  month = jun,
  year = {2014},
  keywords = {Behavior,Drosophila melanogaster,Circadian rhythms,Sucrose,Capillary tubes,Chronobiology,Decision making,Food consumption},
  pages = {e101107},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/99GT5HRP/Ro et al. - 2014 - FLIC High-Throughput, Continuous Analysis of Feed.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P9C2KW2P/article.html}
}

@article{faville_how_2015,
  title = {How Deeply Does Your Mutant Sleep? {{Probing}} Arousal to Better Understand Sleep Defects in {{{\emph{Drosophila}}}}},
  volume = {5},
  copyright = {2015 Nature Publishing Group},
  issn = {2045-2322},
  shorttitle = {How Deeply Does Your Mutant Sleep?},
  doi = {10.1038/srep08454},
  abstract = {The fruitfly, Drosophila melanogaster, has become a critical model system for investigating sleep functions. Most studies use duration of inactivity to measure sleep. However, a defining criterion for sleep is decreased behavioral responsiveness to stimuli. Here we introduce the Drosophila ARousal Tracking system (DART), an integrated platform for efficiently tracking and probing arousal levels in animals. This video-based platform delivers positional and locomotion data, behavioral responsiveness to stimuli, sleep intensity measures, and homeostatic regulation effects \textendash{} all in one combined system. We show how insight into dynamically changing arousal thresholds is crucial for any sleep study in flies. We first find that arousal probing uncovers different sleep intensity profiles among related genetic background strains previously assumed to have equivalent sleep patterns. We then show how sleep duration and sleep intensity can be uncoupled, with distinct manipulations of dopamine function producing opposite effects on sleep duration but similar sleep intensity defects. We conclude by providing a multi-dimensional assessment of combined arousal and locomotion metrics in the mutant and background strains. Our approach opens the door for deeper insights into mechanisms of sleep regulation and provides a new method for investigating the role of different genetic manipulations in controlling sleep and arousal.},
  language = {en},
  journal = {Scientific Reports},
  author = {Faville, R. and Kottler, B. and Goodhill, G. J. and Shaw, P. J. and {van Swinderen}, B.},
  month = feb,
  year = {2015},
  pages = {8454},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X6GPV5SL/Faville et al. - 2015 - How deeply does your mutant sleep Probing arousal.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TDX7CFH9/srep08454.html}
}

@article{lopes_bonsai_2015,
  title = {Bonsai: An Event-Based Framework for Processing and Controlling Data Streams},
  volume = {9},
  issn = {1662-5196},
  shorttitle = {Bonsai},
  doi = {10.3389/fninf.2015.00007},
  abstract = {The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation.},
  language = {English},
  journal = {Frontiers in Neuroinformatics},
  author = {Lopes, Gon{\c c}alo and Bonacchi, Niccol{\`o} and Fraz{\~a}o, Jo{\~a}o and Neto, Joana P. and Atallah, Bassam V. and Soares, Sofia and Moreira, Lu{\'\i}s and Matias, Sara and Itskov, Pavel M. and Correia, Patr{\'\i}cia A. and Medina, Roberto E. and Calcaterra, Lorenza and Dreosti, Elena and Paton, Joseph J. and Kampff, Adam R.},
  year = {2015},
  keywords = {Electrophysiology,Behavior Control,closed-loop system,data acquisition system,data stream processing,open-source,parallel processing,Rapid prototyping,video tracking},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T4ZKBTQ3/Lopes et al. - 2015 - Bonsai an event-based framework for processing an.pdf}
}

@article{brown_study_2017,
  title = {The Study of Animal Behaviour as a Physical Science},
  copyright = {\textcopyright{} 2017, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  doi = {10.1101/220855},
  abstract = {Behaviour is the ultimate output of an animal's nervous system and choosing the right action at the right time can be critical for survival. A quantitative understanding of behaviour would therefore advance research in neuroscience as well as ecology and evolution. However, animal posture typically has many degrees of freedom and behavioural dynamics vary on timescales ranging from milliseconds to years, presenting both technical and conceptual challenges. Here we review 1) advances in imaging and computer vision that are making it possible to capture increasingly complete records of animal motion and 2) new approaches to understanding the resulting behavioural data sets. With the right analytical approaches, these data are allowing researchers to revisit longstanding questions about the structure and organisation of animal behaviour and to put unifying principles on a quantitative footing. Contributions from both experimentalists and theorists are leading to the emergence of a physics of behaviour and the prospect of discovering laws and developing theories with broad applicability. We believe that there now exists an opportunity to develop theories of behaviour which can be tested using these data sets leading to a deeper understanding of how and why animals behave.},
  language = {en},
  journal = {bioRxiv},
  author = {Brown, Andre EX and de Bivort, Benjamin},
  month = nov,
  year = {2017},
  pages = {220855},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YXYA6VWX/220855.html}
}

@article{morin_shining_2012,
  title = {Shining {{Light}} into {{Black Boxes}}},
  volume = {336},
  copyright = {Copyright \textcopyright{} 2012, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1218263},
  abstract = {The publication and open exchange of knowledge and material form the backbone of scientific progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs ``black boxes'' in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences. Eliminating this disparity will require concerted policy action by funding agencies and journal publishers, as well as changes in the way research institutions receiving public funds manage their intellectual property (IP).
Funders, publishers, and research institutions must act to ensure that research computer code is made widely available.
Funders, publishers, and research institutions must act to ensure that research computer code is made widely available.},
  language = {en},
  number = {6078},
  journal = {Science},
  author = {Morin, A. and Urban, J. and Adams, P. D. and Foster, I. and Sali, A. and Baker, D. and Sliz, P.},
  month = apr,
  year = {2012},
  pages = {159-160},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QJLFV23U/Morin et al. - 2012 - Shining Light into Black Boxes.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6RCL54SX/159.html},
  pmid = {22499926}
}

@article{stodden_toward_2013,
  title = {Toward {{Reproducible Computational Research}}: {{An Empirical Analysis}} of {{Data}} and {{Code Policy Adoption}} by {{Journals}}},
  volume = {8},
  issn = {1932-6203},
  shorttitle = {Toward {{Reproducible Computational Research}}},
  doi = {10.1371/journal.pone.0067111},
  abstract = {Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38\% had a data policy, 22\% had a code policy, and 66\% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16\% in the number of data policies, a 30\% increase in code policies, and a 7\% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Stodden, Victoria and Guo, Peixuan and Ma, Zhaokun},
  month = jun,
  year = {2013},
  keywords = {Bibliometrics,Computational biology,Data management,Open access publishing,Open data,Reproducibility,Science policy,Scientific publishing},
  pages = {e67111},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PCTW4U6M/Stodden et al. - 2013 - Toward Reproducible Computational Research An Emp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FQT5S9YI/article.html}
}

@article{peng_reproducible_2011,
  title = {Reproducible {{Research}} in {{Computational Science}}},
  volume = {334},
  copyright = {Copyright \textcopyright{} 2011, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1213847},
  abstract = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.},
  language = {en},
  number = {6060},
  journal = {Science},
  author = {Peng, Roger D.},
  month = dec,
  year = {2011},
  pages = {1226-1227},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G3ETMFYF/Peng - 2011 - Reproducible Research in Computational Science.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H5D8SC9E/tab-pdf.html},
  pmid = {22144613}
}

@article{leipzig_review_2017,
  title = {A Review of Bioinformatic Pipeline Frameworks},
  volume = {18},
  issn = {1467-5463},
  doi = {10.1093/bib/bbw020},
  abstract = {High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.},
  language = {en},
  number = {3},
  journal = {Briefings in Bioinformatics},
  author = {Leipzig, Jeremy},
  month = may,
  year = {2017},
  pages = {530-536},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GZAZNITE/Leipzig - 2017 - A review of bioinformatic pipeline frameworks.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DLPWJBRB/2562749.html}
}

@article{roumpeka_review_2017,
  title = {A {{Review}} of {{Bioinformatics Tools}} for {{Bio}}-{{Prospecting}} from {{Metagenomic Sequence Data}}},
  volume = {8},
  issn = {1664-8021},
  doi = {10.3389/fgene.2017.00023},
  abstract = {The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.},
  language = {English},
  journal = {Frontiers in Genetics},
  author = {Roumpeka, Despoina D. and Wallace, R. John and Escalettes, Frank and Fotheringham, Ian and Watson, Mick},
  year = {2017},
  keywords = {bioinformatics,Assembly,Bioprospecting,gene prediction,Metagenomics,next generation sequencing},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/886RJ3LV/Roumpeka et al. - 2017 - A Review of Bioinformatics Tools for Bio-Prospecti.pdf}
}

@article{huber_orchestrating_2015,
  title = {Orchestrating High-Throughput Genomic Analysis with {{Bioconductor}}},
  volume = {12},
  copyright = {2015 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth.3252},
  abstract = {Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.},
  language = {en},
  number = {2},
  journal = {Nature Methods},
  author = {Huber, Wolfgang and Carey, Vincent J. and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S. and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D. and Irizarry, Rafael A. and Lawrence, Michael and Love, Michael I. and MacDonald, James and Obenchain, Valerie and Ole{\'s}, Andrzej K. and Pag{\`e}s, Herv{\'e} and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K. and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin},
  month = feb,
  year = {2015},
  pages = {115-121},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/76L3CFHR/Huber et al. - 2015 - Orchestrating high-throughput genomic analysis wit.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UYFJLFN2/nmeth.html}
}

@article{hashem_rise_2015,
  title = {The Rise of ``Big Data'' on Cloud Computing: {{Review}} and Open Research Issues},
  volume = {47},
  issn = {0306-4379},
  shorttitle = {The Rise of ``Big Data'' on Cloud Computing},
  doi = {10.1016/j.is.2014.07.006},
  abstract = {Cloud computing is a powerful technology to perform massive-scale and complex computing. It eliminates the need to maintain expensive computing hardware, dedicated space, and software. Massive growth in the scale of data or big data generated through cloud computing has been observed. Addressing big data is a challenging and time-demanding task that requires a large computational infrastructure to ensure successful data processing and analysis. The rise of big data in cloud computing is reviewed in this study. The definition, characteristics, and classification of big data along with some discussions on cloud computing are introduced. The relationship between big data and cloud computing, big data storage systems, and Hadoop technology are also discussed. Furthermore, research challenges are investigated, with focus on scalability, availability, data integrity, data transformation, data quality, data heterogeneity, privacy, legal and regulatory issues, and governance. Lastly, open research issues that require substantial research efforts are summarized.},
  journal = {Information Systems},
  author = {Hashem, Ibrahim Abaker Targio and Yaqoob, Ibrar and Anuar, Nor Badrul and Mokhtar, Salimah and Gani, Abdullah and Ullah Khan, Samee},
  month = jan,
  year = {2015},
  keywords = {Big data,Cloud computing,Hadoop},
  pages = {98-115},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D7TDT6E3/Hashem et al. - 2015 - The rise of “big data” on cloud computing Review .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P7EZKGR8/S0306437914001288.html}
}

@article{stephens_big_2015,
  title = {Big {{Data}}: {{Astronomical}} or {{Genomical}}?},
  volume = {13},
  issn = {1545-7885},
  shorttitle = {Big {{Data}}},
  doi = {10.1371/journal.pbio.1002195},
  abstract = {Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a ``four-headed beast''\textemdash{}it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the ``genomical'' challenges of the next decade.},
  language = {en},
  number = {7},
  journal = {PLOS Biology},
  author = {Stephens, Zachary D. and Lee, Skylar Y. and Faghri, Faraz and Campbell, Roy H. and Zhai, Chengxiang and Efron, Miles J. and Iyer, Ravishankar and Schatz, Michael C. and Sinha, Saurabh and Robinson, Gene E.},
  month = jul,
  year = {2015},
  keywords = {Animal genomics,Cancer genomics,Data acquisition,Genome complexity,Genome sequencing,Genomic medicine,Human genomics,Mammalian genomics},
  pages = {e1002195},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E74GMNKX/Stephens et al. - 2015 - Big Data Astronomical or Genomical.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/C3Y84935/article.html}
}

@article{berman_measuring_2018,
  title = {Measuring Behavior across Scales},
  volume = {16},
  issn = {1741-7007},
  doi = {10.1186/s12915-018-0494-7},
  abstract = {The need for high-throughput, precise, and meaningful methods for measuring behavior has been amplified by our recent successes in measuring and manipulating neural circuitry. The largest challenges associated with moving in this direction, however, are not technical but are instead conceptual: what numbers should one put on the movements an animal is performing (or not performing)? In this review, I will describe how theoretical and data analytical ideas are interfacing with recently-developed computational and experimental methodologies to answer these questions across a variety of contexts, length scales, and time scales. I will attempt to highlight commonalities between approaches and areas where further advances are necessary to place behavior on the same quantitative footing as other scientific fields.},
  journal = {BMC Biology},
  author = {Berman, Gordon J.},
  month = feb,
  year = {2018},
  pages = {23},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/46BBE8ZT/Berman - 2018 - Measuring behavior across scales.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IHV92U57/s12915-018-0494-7.html}
}

@misc{schmidbauer_waveletcomp_2018,
  title = {{{WaveletComp}}: {{Computational Wavelet Analysis}}},
  copyright = {GPL-2},
  shorttitle = {{{WaveletComp}}},
  abstract = {Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.},
  author = {Schmidbauer, Angi Roesch and Harald},
  month = mar,
  year = {2018},
  keywords = {TimeSeries}
}

@incollection{liu_wavelet_1994,
  series = {Wavelets in Geophysics},
  title = {Wavelet {{Spectrum Analysis}} and {{Ocean Wind Waves}}},
  volume = {4},
  abstract = {Wavelet spectrum analysis is applied to a set of measured ocean wind waves data collected during the 1990 SWADE (Surface Wave Dynamics Experiment) program. The results reveal significantly new and previously unexplored insights on wave grouping parameterizations, phase relations during wind wave growth, and detecting wave breaking characteristics. These insights are due to the nature of the wavelet transform that would not be immediately evident using a traditional Fourier transform approach.},
  booktitle = {Wavelet {{Analysis}} and {{Its Applications}}},
  publisher = {{Academic Press}},
  author = {Liu, Paul C.},
  editor = {Foufoula-Georgiou, Efi and Kumar, Praveen},
  month = jan,
  year = {1994},
  pages = {151-166},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B9DYZHGR/B9780080520872500128.html},
  doi = {10.1016/B978-0-08-052087-2.50012-8}
}

@article{cazelles_wavelet_2008,
  title = {Wavelet Analysis of Ecological Time Series},
  volume = {156},
  issn = {0029-8549, 1432-1939},
  doi = {10.1007/s00442-008-0993-2},
  abstract = {Wavelet analysis is a powerful tool that is already in use throughout science and engineering. The versatility and attractiveness of the wavelet approach lie in its decomposition properties, principally its time-scale localization. It is especially relevant to the analysis of non-stationary systems, i.e., systems with short-lived transient components, like those observed in ecological systems. Here, we review the basic properties of the wavelet approach for time-series analysis from an ecological perspective. Wavelet decomposition offers several advantages that are discussed in this paper and illustrated by appropriate synthetic and ecological examples. Wavelet analysis is notably free from the assumption of stationarity that makes most methods unsuitable for many ecological time series. Wavelet analysis also permits analysis of the relationships between two signals, and it is especially appropriate for following gradual change in forcing by exogenous variables.},
  language = {en},
  number = {2},
  journal = {Oecologia},
  author = {Cazelles, Bernard and Chavez, Mario and Berteaux, Dominique and M{\'e}nard, Fr{\'e}d{\'e}ric and Vik, Jon Olav and Jenouvrier, St{\'e}phanie and Stenseth, Nils C.},
  month = may,
  year = {2008},
  pages = {287-304},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2L4L5I44/Cazelles et al. - 2008 - Wavelet analysis of ecological time series.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z54QFB5Z/s00442-008-0993-2.html}
}

@article{aguiar-conraria_business_2011,
  title = {Business Cycle Synchronization and the {{Euro}}: {{A}} Wavelet Analysis},
  volume = {33},
  issn = {0164-0704},
  shorttitle = {Business Cycle Synchronization and the {{Euro}}},
  doi = {10.1016/j.jmacro.2011.02.005},
  abstract = {We use wavelet analysis to study business cycle synchronization across the EU-15 and the Euro-12 countries. Based on the wavelet transform, we propose a metric to measure and test for business cycles synchronization. Several conclusions emerge. France and Germany form the core of the Euro land, being the most synchronized countries with the rest of Europe. Portugal, Greece, Ireland and Finland do not show statistically relevant degrees of synchronization with Europe. We also show that some countries (like Spain) have a French accent, while others have a German accent (e.g., Austria). Perhaps surprisingly, we find that the French business cycle has been leading the German business cycle as well as the rest of Europe. Among the countries that may, in the future, join the Euro, the Czech Republic seems the most promising candidate.},
  number = {3},
  journal = {Journal of Macroeconomics},
  author = {Aguiar-Conraria, Lu{\i}\textasciiacute{}s and Joana Soares, Maria},
  month = sep,
  year = {2011},
  keywords = {Business cycle synchronization,Continuous wavelet transform,European Union integration,Multidimensional scaling,Wavelet distance matrix},
  pages = {477-489},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4ZQVLVGY/Aguiar-Conraria and Joana Soares - 2011 - Business cycle synchronization and the Euro A wav.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6LLC544W/S016407041100019X.html}
}

@article{lau_climate_1995,
  title = {Climate {{Signal Detection Using Wavelet Transform}}: {{How}} to {{Make}} a {{Time Series Sing}}},
  volume = {76},
  issn = {0003-0007},
  shorttitle = {Climate {{Signal Detection Using Wavelet Transform}}},
  doi = {10.1175/1520-0477(1995)076<2391:CSDUWT>2.0.CO;2},
  abstract = {In this paper, the application of the wavelet transform (WT) to climate time series analyses is introduced. A tutorial description of the basic concept of WT, compared with similar concepts used in music, is also provided. Using an analogy between WT representation of a time series and a music score, the authors illustrate the importance of local versus global information in the time\textendash{}frequency localization of climate signals. Examples of WT applied to climate data analysis are demonstrated using analytic signals as well as real climate time series. Results of WT applied to two climate time series\textemdash{}that is, a proxy paleoclimate time series with a 2.5-Myr deep-sea sediment record of $\delta$18 O and a 140-yr monthly record of Northern Hemisphere surface temperature\textemdash{}are presented. The former shows the presence of a 40-kyr and a 100-kyr oscillation and an abrupt transition in the oscillation regime at 0.7 Myr before the present, consistent with previous studies. The latter possesses a myriad of oscillatory modes from interannual (2\textendash{}5 yr), interdecadal (10\textendash{}12 yr, 20\textendash{}25 yr, and 40\textendash{}60 yr), and century (\textasciitilde{}180 yr) scales at different periods of the data record. In spite of the large difference in timescales, common features in time\textendash{}frequency characteristics of these two time series have been identified. These features suggest that the variations of the earth's climate are consistent with those exhibited by a nonlinear dynamical system under external forcings.},
  number = {12},
  journal = {Bulletin of the American Meteorological Society},
  author = {Lau, K.-M. and Weng, Hengyi},
  month = dec,
  year = {1995},
  pages = {2391-2402},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IG7BB6HQ/Lau and Weng - 1995 - Climate Signal Detection Using Wavelet Transform .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZZ3VAVPX/1520-0477(1995)0762391CSDUWT2.0.html}
}

@article{grossmann_decomposition_1984,
  title = {Decomposition of {{Hardy Functions}} into {{Square Integrable Wavelets}} of {{Constant Shape}}},
  volume = {15},
  issn = {0036-1410},
  doi = {10.1137/0515056},
  abstract = {An arbitrary square integrable real-valued function (or, equivalently, the associated Hardy function) can be conveniently analyzed into a suitable family of square integrable wavelets of constant shape, (i.e. obtained by shifts and dilations from any one of them.) The resulting integral transform is isometric and self-reciprocal if the wavelets satisfy an ``admissibility condition'' given here. Explicit expressions are obtained in the case of a particular analyzing family that plays a role analogous to that of coherent states (Gabor wavelets) in the usual \$L\_2 \$ -theory. They are written in terms of a modified \$$\backslash$Gamma \$-function that is introduced and studied. From the point of view of group theory, this paper is concerned with square integrable coefficients of an irreducible representation of the nonunimodular \$ax + b\$-group.},
  number = {4},
  journal = {SIAM Journal on Mathematical Analysis},
  author = {Grossmann, A. and Morlet, J.},
  month = jul,
  year = {1984},
  pages = {723-736},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PYC5YMCY/Grossmann and Morlet - 1984 - Decomposition of Hardy Functions into Square Integ.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2C62YAI7/0515056.html}
}

@article{leise_wavelet_2013,
  title = {Wavelet Analysis of Circadian and Ultradian Behavioral Rhythms},
  volume = {11},
  issn = {1740-3391},
  doi = {10.1186/1740-3391-11-5},
  abstract = {We review time-frequency methods that can be useful in quantifying circadian and ultradian patterns in behavioral records. These records typically exhibit details that may not be captured through commonly used measures such as activity onset and so may require alternative approaches. For instance, activity may involve multiple bouts that vary in duration and magnitude within a day, or may exhibit day-to-day changes in period and in ultradian activity patterns. The discrete Fourier transform and other types of periodograms can estimate the period of a circadian rhythm, but we show that they can fail to correctly assess ultradian periods. In addition, such methods cannot detect changes in the period over time. Time-frequency methods that can localize frequency estimates in time are more appropriate for analysis of ultradian periods and of fluctuations in the period. The continuous wavelet transform offers a method for determining instantaneous frequency with good resolution in both time and frequency, capable of detecting changes in circadian period over the course of several days and in ultradian period within a given day. The discrete wavelet transform decomposes a time series into components associated with distinct frequency bands, thereby facilitating the removal of noise and trend or the isolation of a particular frequency band of interest. To demonstrate the wavelet-based analysis, we apply the transforms to a numerically-generated example and also to a variety of hamster behavioral records. When used appropriately, wavelet transforms can reveal patterns that are not easily extracted using other methods of analysis in common use, but they must be applied and interpreted with care.},
  journal = {Journal of Circadian Rhythms},
  author = {Leise, Tanya L.},
  month = jul,
  year = {2013},
  keywords = {Wavelet transform,Circadian rhythms,Time series analysis,Ultradian rhythms,Estrous cycle,Fourier transform,Rodent locomotor activity},
  pages = {5},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KKIKMJ4T/Leise - 2013 - Wavelet analysis of circadian and ultradian behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5NHRVYDN/1740-3391-11-5.html}
}

@article{robie_mapping_2017,
  title = {Mapping the {{Neural Substrates}} of {{Behavior}}},
  volume = {170},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/j.cell.2017.06.032},
  abstract = {\subsection{Summary$<$/h2$>$

Assigning behavioral functions to neural structures has long been a central goal in neuroscience and is a necessary first step toward a circuit-level understanding of how the brain generates behavior. Here, we map the neural substrates of locomotion and social behaviors for \emph{Drosophila melanogaster} using automated machine-vision and machine-learning techniques. From videos of 400,000 flies, we quantified the behavioral effects of activating 2,204 genetically targeted populations of neurons. We combined a novel quantification of anatomy with our behavioral analysis to create brain-behavior correlation maps, which are shared as browsable web pages and interactive software. Based on these maps, we generated hypotheses of regions of the brain causally related to sensory processing, locomotor control, courtship, aggression, and sleep. Our maps directly specify genetic tools to target these regions, which we used to identify a small population of neurons with a role in the control of walking.$<$/p$>$

}},
  language = {English},
  number = {2},
  journal = {Cell},
  author = {Robie, Alice A. and Hirokawa, Jonathan and Edwards, Austin W. and Umayam, Lowell A. and Lee, Allen and Phillips, Mary L. and Card, Gwyneth M. and Korff, Wyatt and Rubin, Gerald M. and Simpson, Julie H. and Reiser, Michael B. and Branson, Kristin},
  month = jul,
  year = {2017},
  pages = {393-406.e28},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D58FZ2M8/Robie et al. - 2017 - Mapping the Neural Substrates of Behavior.pdf},
  pmid = {28709004, 28709004}
}

@article{anderson_toward_2014,
  title = {Toward a {{Science}} of {{Computational Ethology}}},
  volume = {84},
  issn = {0896-6273},
  doi = {10.1016/j.neuron.2014.09.005},
  abstract = {The new field of ``Computational Ethology'' is made possible by advances in technology, mathematics, and engineering that allow scientists to automate the measurement and the analysis of animal behavior. We explore the opportunities and long-term directions of research in this area.},
  number = {1},
  journal = {Neuron},
  author = {Anderson, David J. and Perona, Pietro},
  month = oct,
  year = {2014},
  pages = {18-31},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YK746QDB/Anderson and Perona - 2014 - Toward a Science of Computational Ethology.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P6P48H73/S0896627314007934.html}
}

@article{brown_ethology_2018,
  title = {Ethology as a Physical Science},
  copyright = {2018 The Publisher},
  issn = {1745-2481},
  doi = {10.1038/s41567-018-0093-0},
  abstract = {The study of animal behaviour, ethology, is becoming more quantitative. New theory is emerging, driven by better imaging and novel representations of animal posture dynamics that span the vast range of relevant behavioural timescales.},
  language = {en},
  journal = {Nature Physics},
  author = {Brown, Andr{\'e} E. X. and de Bivort, Benjamin},
  month = apr,
  year = {2018},
  pages = {1},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K9M33RFY/Brown and Bivort - 2018 - Ethology as a physical science.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Y8X7HBD6/s41567-018-0093-0.html}
}

@article{tsai_image_2012,
  title = {Image {{Tracking Study}} on {{Courtship Behavior}} of {{Drosophila}}},
  volume = {7},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0034784},
  abstract = {Background In recent years, there have been extensive studies aimed at decoding the DNA. Identifying the genetic cause of specific changes in a simple organism like Drosophila may help scientists recognize how multiple gene interactions may make some people more susceptible to heart disease or cancer. Investigators have devised experiments to observe changes in the gene networks in mutant Drosophila that responds differently to light, or have lower or higher locomotor activity. However, these studies focused on the behavior of the individual fly or on pair-wise interactions in the study of aggression or courtship. The behavior of these activities has been captured on film and inspected by a well-trained researcher after repeatedly watching the recorded film. Some studies also focused on ways to reduce the inspection time and increase the accuracy of the behavior experiment. Methodology In this study, the behavior of drosophila during courtship was analyzed automatically by machine vision. We investigated the position and behavior discrimination during courtship using the captured images. Identification of the characteristics of drosophila, including sex, size, heading direction, and wing angles, can be computed using image analysis techniques that employ the Gaussian mixture model. The behavior of multiple drosophilae can also be analyzed simultaneously using the motion-prediction model and the variation constraint of heading direction. Conclusions The overlapped fruit flies can be identified based on the relationship between body centers. Moreover, the behaviors and profiles can be correctly recognized by image processing based on the constraints of the wing angle and the size of the body. Therefore, the behavior of the male fruit flies can be discriminated when two or three fruit flies form a close cluster. In this study, the courtship behavior, including wing songs and attempts, can currently be distinguished with accuracies of 95.8\% and 90\%, respectively.},
  language = {en},
  number = {4},
  journal = {PLOS ONE},
  author = {Tsai, Hung-Yin and Huang, Yen-Wen},
  month = apr,
  year = {2012},
  keywords = {Abdomen,Behavior,Biological locomotion,Drosophila,Drosophila melanogaster,Ellipses,Probability density,Wings},
  pages = {e34784},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LQYNR6H7/Tsai and Huang - 2012 - Image Tracking Study on Courtship Behavior of Dros.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/22MK42MF/article.html}
}

@article{kabra_jaaba_2013,
  title = {{{JAABA}}: Interactive Machine Learning for Automatic Annotation of Animal Behavior},
  volume = {10},
  copyright = {2012 Nature Publishing Group},
  issn = {1548-7105},
  shorttitle = {{{JAABA}}},
  doi = {10.1038/nmeth.2281},
  abstract = {We present a machine learning\textendash{}based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, including mice and adult and larval Drosophila.},
  language = {en},
  number = {1},
  journal = {Nature Methods},
  author = {Kabra, Mayank and Robie, Alice A. and Rivera-Alba, Marta and Branson, Steven and Branson, Kristin},
  month = jan,
  year = {2013},
  pages = {64-67},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XBXXCLBC/Kabra et al. - 2013 - JAABA interactive machine learning for automatic .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HPCA7U7H/nmeth.html}
}

@article{branson_high-throughput_2009,
  title = {High-Throughput Ethomics in Large Groups of {{{\emph{Drosophila}}}}},
  volume = {6},
  copyright = {2009 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth.1328},
  abstract = {We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.},
  language = {en},
  number = {6},
  journal = {Nature Methods},
  author = {Branson, Kristin and Robie, Alice A. and Bender, John and Perona, Pietro and Dickinson, Michael H.},
  month = jun,
  year = {2009},
  pages = {451-457},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/75DSN2F5/Branson et al. - 2009 - High-throughput ethomics in large groups of iDro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QTWXSYMQ/nmeth.html}
}

@article{sejnowski_putting_2014,
  title = {{Putting big data to good use in neuroscience}},
  volume = {17},
  issn = {1097-6256},
  doi = {10.1038/nn.3839},
  language = {English (US)},
  number = {11},
  journal = {Nature Neuroscience},
  author = {Sejnowski, Terrence J. and Churchland, Patricia S. and Movshon, J. Anthony},
  month = oct,
  year = {2014},
  pages = {1440-1441},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IFLJF74H/putting-big-data-to-good-use-in-neuroscience.html},
  pmid = {25349909}
}

@article{schatz_biological_2015,
  title = {Biological Data Sciences in Genome Research},
  volume = {25},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.191684.115},
  abstract = {The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.},
  language = {en},
  number = {10},
  journal = {Genome Research},
  author = {Schatz, Michael C.},
  month = jan,
  year = {2015},
  pages = {1417-1422},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JCUKQQZD/Schatz - 2015 - Biological data sciences in genome research.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SCTXNL7J/1417.html},
  pmid = {26430150}
}

@article{sokolowski_drosophila_2001,
  title = {{\emph{Drosophila}}: {{Genetics}} Meets Behaviour},
  volume = {2},
  copyright = {2001 Nature Publishing Group},
  issn = {1471-0064},
  shorttitle = {{\emph{Drosophila}}},
  doi = {10.1038/35098592},
  abstract = {Genes are understandably crucial to physiology, morphology and biochemistry, but the idea of genes contributing to individual differences in behaviour once seemed outrageous. Nevertheless, some scientists have aspired to understand the relationship between genes and behaviour, and their research has become increasingly informative and productive over the past several decades. At the forefront of behavioural genetics research is the fruitfly Drosophila melanogaster, which has provided us with important insights into the molecular, cellular and evolutionary bases of behaviour.},
  language = {en},
  number = {11},
  journal = {Nature Reviews Genetics},
  author = {Sokolowski, Marla B.},
  month = nov,
  year = {2001},
  pages = {879-890},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QKI328NE/Sokolowski - 2001 - iDrosophilai Genetics meets behaviour.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S5UP9NJI/35098592.html}
}

@article{dubowy_circadian_2017,
  title = {Circadian {{Rhythms}} and {{Sleep}} in {{Drosophila}} Melanogaster},
  volume = {205},
  copyright = {Copyright \textcopyright{} 2017 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.115.185157},
  abstract = {The advantages of the model organism Drosophila melanogaster, including low genetic redundancy, functional simplicity, and the ability to conduct large-scale genetic screens, have been essential for understanding the molecular nature of circadian ($\sim$24 hr) rhythms, and continue to be valuable in discovering novel regulators of circadian rhythms and sleep. In this review, we discuss the current understanding of these interrelated biological processes in Drosophila and the wider implications of this research. Clock genes period and timeless were first discovered in large-scale Drosophila genetic screens developed in the 1970s. Feedback of period and timeless on their own transcription forms the core of the molecular clock, and accurately timed expression, localization, post-transcriptional modification, and function of these genes is thought to be critical for maintaining the circadian cycle. Regulators, including several phosphatases and kinases, act on different steps of this feedback loop to ensure strong and accurately timed rhythms. Approximately 150 neurons in the fly brain that contain the core components of the molecular clock act together to translate this intracellular cycling into rhythmic behavior. We discuss how different groups of clock neurons serve different functions in allowing clocks to entrain to environmental cues, driving behavioral outputs at different times of day, and allowing flexible behavioral responses in different environmental conditions. The neuropeptide PDF provides an important signal thought to synchronize clock neurons, although the details of how PDF accomplishes this function are still being explored. Secreted signals from clock neurons also influence rhythms in other tissues. SLEEP is, in part, regulated by the circadian clock, which ensures appropriate timing of sleep, but the amount and quality of sleep are also determined by other mechanisms that ensure a homeostatic balance between sleep and wake. Flies have been useful for identifying a large set of genes, molecules, and neuroanatomic loci important for regulating sleep amount. Conserved aspects of sleep regulation in flies and mammals include wake-promoting roles for catecholamine neurotransmitters and involvement of hypothalamus-like regions, although other neuroanatomic regions implicated in sleep in flies have less clear parallels. Sleep is also subject to regulation by factors such as food availability, stress, and social environment. We are beginning to understand how the identified molecules and neurons interact with each other, and with the environment, to regulate sleep. Drosophila researchers can also take advantage of increasing mechanistic understanding of other behaviors, such as learning and memory, courtship, and aggression, to understand how sleep loss impacts these behaviors. Flies thus remain a valuable tool for both discovery of novel molecules and deep mechanistic understanding of sleep and circadian rhythms.},
  language = {en},
  number = {4},
  journal = {Genetics},
  author = {Dubowy, Christine and Sehgal, Amita},
  month = apr,
  year = {2017},
  keywords = {circadian rhythms,neuroscience,molecular neuroscience,FlyBook: Drosophila,sleep},
  pages = {1373-1397},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MCG6A8MB/Dubowy and Sehgal - 2017 - Circadian Rhythms and Sleep in Drosophila melanoga.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZZNTU666/1373.html},
  pmid = {28360128}
}

@article{dankert_automated_2009,
  title = {Automated {{Monitoring}} and {{Analysis}} of {{Social Behavior}} in {{Drosophila}}},
  volume = {6},
  issn = {1548-7091},
  doi = {10.1038/nmeth.1310},
  abstract = {We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies, and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship ``song'') and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.},
  number = {4},
  journal = {Nature methods},
  author = {Dankert, Heiko and Wang, Liming and Hoopfer, Eric D. and Anderson, David J. and Perona, Pietro},
  month = apr,
  year = {2009},
  pages = {297-303},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RN3SWBNN/Dankert et al. - 2009 - Automated Monitoring and Analysis of Social Behavi.pdf},
  pmid = {19270697},
  pmcid = {PMC2679418}
}

@article{ogueta_maite_2018_1172980,
  title = {{{LL Behaviour}} of {{TIM Gal4}} $>$ {{NKCC OX}} and {{NKCC OX}} / + Flies},
  doi = {10.5281/zenodo.1172980},
  journal = {Zenodo},
  author = {Ogueta, Maite and Stanewsky, Ralf},
  month = feb,
  year = {2018}
}