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@ARTICLE{Sacco2012-sv,
  title    = "The human phosphatase interactome: An intricate family portrait",
  author   = "Sacco, Francesca and Perfetto, Livia and Castagnoli, Luisa and
              Cesareni, Gianni",
  abstract = "The concerted activities of kinases and phosphatases modulate the
              phosphorylation levels of proteins, lipids and carbohydrates in
              eukaryotic cells. Despite considerable effort, we are still
              missing a holistic picture representing, at a proteome level, the
              functional relationships between kinases, phosphatases and their
              substrates. Here we focus on phosphatases and we review and
              integrate the available information that helps to place the
              members of the protein phosphatase superfamilies into the human
              protein interaction network. In addition we show how protein
              interaction domains and motifs, either covalently linked to the
              phosphatase domain or in regulatory/adaptor subunits, play a
              prominent role in substrate selection.",
  journal  = "FEBS Lett.",
  volume   =  586,
  number   =  17,
  pages    = "2732--2739",
  month    =  aug,
  year     =  2012,
  language = "en",
  issn     = "0014-5793, 1873-3468",
  pmid     = "22626554",
  doi      = "10.1016/j.febslet.2012.05.008",
  pmc      = "PMC3437441"
}

% The entry below contains non-ASCII chars that could not be converted
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@ARTICLE{Bostock2011-je,
  title    = "D³: {Data-Driven} Documents",
  author   = "Bostock, Michael and Ogievetsky, Vadim and Heer, Jeffrey",
  abstract = "Data-Driven Documents (D3) is a novel representation-transparent
              approach to visualization for the web. Rather than hide the
              underlying scenegraph within a toolkit-specific abstraction, D3
              enables direct inspection and manipulation of a native
              representation: the standard document object model (DOM). With
              D3, designers selectively bind input data to arbitrary document
              elements, applying dynamic transforms to both generate and modify
              content. We show how representational transparency improves
              expressiveness and better integrates with developer tools than
              prior approaches, while offering comparable notational efficiency
              and retaining powerful declarative components. Immediate
              evaluation of operators further simplifies debugging and allows
              iterative development. Additionally, we demonstrate how D3
              transforms naturally enable animation and interaction with
              dramatic performance improvements over intermediate
              representations.",
  journal  = "IEEE Trans. Vis. Comput. Graph.",
  volume   =  17,
  number   =  12,
  pages    = "2301--2309",
  month    =  dec,
  year     =  2011,
  language = "en",
  issn     = "1077-2626, 1941-0506",
  pmid     = "22034350",
  doi      = "10.1109/TVCG.2011.185"
}

@ARTICLE{Cohen2002-yj,
  title    = "Protein kinases--the major drug targets of the twenty-first
              century?",
  author   = "Cohen, Philip",
  abstract = "Protein phosphorylation regulates most aspects of cell life,
              whereas abnormal phosphorylation is a cause or consequence of
              disease. A growing interest in developing orally active
              protein-kinase inhibitors has recently culminated in the approval
              of the first of these drugs for clinical use. Protein kinases
              have now become the second most important group of drug targets,
              after G-protein-coupled receptors. Here, I give a personal view
              of some of the most important advances that have shaped this
              field.",
  journal  = "Nat. Rev. Drug Discov.",
  volume   =  1,
  number   =  4,
  pages    = "309--315",
  month    =  apr,
  year     =  2002,
  language = "en",
  issn     = "1474-1776",
  pmid     = "12120282",
  doi      = "10.1038/nrd773"
}

@ARTICLE{Chartier2013-es,
  title    = "Kinome Render: a stand-alone and web-accessible tool to annotate
              the human protein kinome tree",
  author   = "Chartier, Matthieu and Ch{\'e}nard, Thierry and Barker, Jonathan
              and Najmanovich, Rafael",
  abstract = "Human protein kinases play fundamental roles mediating the
              majority of signal transduction pathways in eukaryotic cells as
              well as a multitude of other processes involved in metabolism,
              cell-cycle regulation, cellular shape, motility, differentiation
              and apoptosis. The human protein kinome contains 518 members.
              Most studies that focus on the human kinome require, at some
              point, the visualization of large amounts of data. The
              visualization of such data within the framework of a phylogenetic
              tree may help identify key relationships between different
              protein kinases in view of their evolutionary distance and the
              information used to annotate the kinome tree. For example,
              studies that focus on the promiscuity of kinase inhibitors can
              benefit from the annotations to depict binding affinities across
              kinase groups. Images involving the mapping of information into
              the kinome tree are common. However, producing such figures
              manually can be a long arduous process prone to errors. To
              circumvent this issue, we have developed a web-based tool called
              Kinome Render (KR) that produces customized annotations on the
              human kinome tree. KR allows the creation and automatic overlay
              of customizable text or shape-based annotations of different
              sizes and colors on the human kinome tree. The web interface can
              be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A
              stand-alone version is also available and can be run locally.",
  journal  = "PeerJ",
  volume   =  1,
  pages    = "e126",
  month    =  aug,
  year     =  2013,
  keywords = "Annotation; Data visualisation; Human kinome tree; Protein
              kinases",
  language = "en",
  issn     = "2167-8359",
  pmid     = "23940838",
  doi      = "10.7717/peerj.126",
  pmc      = "PMC3740139"
}

@ARTICLE{Tiganis2007-iw,
  title    = "Protein tyrosine phosphatase function: the substrate perspective",
  author   = "Tiganis, Tony and Bennett, Anton M",
  abstract = "It is now well established that the members of the PTP (protein
              tyrosine phosphatase) superfamily play critical roles in
              fundamental biological processes. Although there has been much
              progress in defining the function of PTPs, the task of
              identifying substrates for these enzymes still presents a
              challenge. Many PTPs have yet to have their physiological
              substrates identified. The focus of this review will be on the
              current state of knowledge of PTP substrates and the approaches
              used to identify them. We propose experimental criteria that
              should be satisfied in order to rigorously assign PTP substrates
              as bona fide. Finally, the progress that has been made in
              defining the biological roles of PTPs through the identification
              of their substrates will be discussed.",
  journal  = "Biochem. J",
  volume   =  402,
  number   =  1,
  pages    = "1--15",
  month    =  feb,
  year     =  2007,
  language = "en",
  issn     = "1470-8728, 0264-6021",
  pmid     = "17238862",
  doi      = "10.1042/BJ20061548",
  pmc      = "PMC1783993"
}

@MISC{Winston_Chang_aut_cre_Joe_Cheng_aut_JJ_Allaire_aut_Yihui_Xie_aut_Jonathan_McPherson_aut_RStudio_cph_jQuery_Foundation_cph_jQuery_library2019-nv,
  title        = "shiny: Web Application Framework for {R} version 1.3.2 from
                  {CRAN}",
  author       = "{Winston Chang [aut, cre], Joe Cheng [aut], JJ Allaire [aut],
                  Yihui Xie [aut], Jonathan McPherson [aut], RStudio [cph],
                  jQuery Foundation [cph] (jQuery library} and {jQuery UI
                  library), jQuery contributors [ctb, cph] (jQuery library} and
                  {authors listed in inst/www/shared/jquery-AUTHORS. txt),
                  jQuery UI contributors [ctb, cph] (jQuery UI library} and
                  {authors listed in inst/www/shared/jqueryui/AUTHORS. txt),
                  Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb]
                  (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap
                  library), Twitter, Inc [cph] (Bootstrap library), Alexander
                  Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph]
                  (Respond. js library), Stefan Petre [ctb, cph]
                  (Bootstrap-datepicker library), Andrew Rowls [ctb, cph]
                  (Bootstrap-datepicker library), Dave Gandy [ctb, cph]
                  (Font-Awesome font), Brian Reavis [ctb, cph] (selectize. js
                  library), Kristopher Michael Kowal [ctb, cph] (es5-shim
                  library), es5-shim contributors [ctb, cph] (es5-shim
                  library), Denis Ineshin [ctb, cph] (ion. rangeSlider
                  library), Sami Samhuri [ctb, cph] (Javascript strftime
                  library), SpryMedia Limited [ctb, cph] (DataTables library),
                  John Fraser [ctb, cph] (showdown. js library), John Gruber
                  [ctb, cph] (showdown. js library), Ivan Sagalaev [ctb, cph]
                  (highlight. js library), R Core Team [ctb, cph] (tar
                  implementation from R)}",
  abstract     = "Makes it incredibly easy to build interactive web
                  applications with R. Automatic ``reactive'' binding between
                  inputs and outputs and extensive prebuilt widgets make it
                  possible to build beautiful, responsive, and powerful
                  applications with minimal effort.",
  month        =  apr,
  year         =  2019,
  howpublished = "\url{https://rdrr.io/cran/shiny/}",
  note         = "Accessed: 2019-6-28"
}

@MISC{Bailey2015-ft,
  title    = "{shinyBS}: Twitter Bootstrap Components for Shiny",
  author   = "Bailey, Eric",
  year     =  2015,
  keywords = "libs.bib.bib"
}

@ARTICLE{Begovich2004-nl,
  title    = "A missense single-nucleotide polymorphism in a gene encoding a
              protein tyrosine phosphatase ({PTPN22}) is associated with
              rheumatoid arthritis",
  author   = "Begovich, Ann B and Carlton, Victoria E H and Honigberg, Lee A
              and Schrodi, Steven J and Chokkalingam, Anand P and Alexander,
              Heather C and Ardlie, Kristin G and Huang, Qiqing and Smith,
              Ashley M and Spoerke, Jill M and Conn, Marion T and Chang, Monica
              and Chang, Sheng-Yung P and Saiki, Randall K and Catanese, Joseph
              J and Leong, Diane U and Garcia, Veronica E and McAllister, Linda
              B and Jeffery, Douglas A and Lee, Annette T and Batliwalla,
              Franak and Remmers, Elaine and Criswell, Lindsey A and Seldin,
              Michael F and Kastner, Daniel L and Amos, Christopher I and
              Sninsky, John J and Gregersen, Peter K",
  abstract = "Rheumatoid arthritis (RA) is the most common systemic autoimmune
              disease, affecting approximately 1\% of the adult population
              worldwide, with an estimated heritability of 60\%. To identify
              genes involved in RA susceptibility, we investigated the
              association between putative functional single-nucleotide
              polymorphisms (SNPs) and RA among white individuals by use of a
              case-control study design; a second sample was tested for
              replication. Here we report the association of RA susceptibility
              with the minor allele of a missense SNP in PTPN22
              (discovery-study allelic P=6.6 x 10(-4); replication-study
              allelic P=5.6 x 10(-8)), which encodes a hematopoietic-specific
              protein tyrosine phosphatase also known as ``Lyp.'' We show that
              the risk allele, which is present in approximately 17\% of white
              individuals from the general population and in approximately 28\%
              of white individuals with RA, disrupts the P1 proline-rich motif
              that is important for interaction with Csk, potentially altering
              these proteins' normal function as negative regulators of T-cell
              activation. The minor allele of this SNP recently was implicated
              in type 1 diabetes, suggesting that the variant phosphatase may
              increase overall reactivity of the immune system and may heighten
              an individual carrier's risk for autoimmune disease.",
  journal  = "Am. J. Hum. Genet.",
  volume   =  75,
  number   =  2,
  pages    = "330--337",
  month    =  aug,
  year     =  2004,
  language = "en",
  issn     = "0002-9297",
  pmid     = "15208781",
  doi      = "10.1086/422827",
  pmc      = "PMC1216068"
}

@ARTICLE{Chen2017-bb,
  title    = "Genomics and evolution of protein phosphatases",
  author   = "Chen, Mark J and Dixon, Jack E and Manning, Gerard",
  abstract = "Protein phosphatases are the essential opposite to protein
              kinases; together, these enzymes regulate all protein
              phosphorylation and most cellular processes. To better understand
              the global roles of protein phosphorylation, we cataloged the
              human protein phosphatome, composed of 189 known and predicted
              human protein phosphatase genes. We also identified 79 protein
              phosphatase pseudogenes or retrogenes, some of which may have
              residual function. We traced the origin and diversity of
              phosphatases by building protein phosphatomes for eight other
              eukaryotes, from the protist Dictyostelium to the sea urchin. We
              classified protein phosphatases from all nine species into a
              hierarchy of 10 protein folds, 21 families, and 178 subfamilies.
              We found that >80\% of the 101 human subfamilies were conserved
              across the animal kingdom, but show substantial differences in
              evolution, including losses and expansions of individual
              subfamilies and changes in accessory domains. Protein
              phosphatases show similar evolutionary dynamics to those of
              kinases, with substantial losses in major model organisms.
              Sequence analysis predicts that 26 human protein phosphatase
              domains are catalytically disabled and that this disability is
              mostly conserved across orthologs. This genomic and evolutionary
              perspective on protein phosphatases provides a framework for
              global analysis of protein phosphorylation throughout the animal
              kingdom.",
  journal  = "Sci. Signal.",
  volume   =  10,
  number   =  474,
  month    =  apr,
  year     =  2017,
  language = "en",
  issn     = "1937-9145, 1945-0877",
  pmid     = "28400531",
  doi      = "10.1126/scisignal.aag1796"
}

@MISC{Perrier2019-io,
  title    = "shinyWidgets: Custom Inputs Widgets for Shiny",
  author   = "Perrier, Victor and Meyer, Fanny and Granjon, David",
  year     =  2019,
  keywords = "libs.bib.bib"
}

@ARTICLE{Buchser2010-jb,
  title    = "Kinase/phosphatase overexpression reveals pathways regulating
              hippocampal neuron morphology",
  author   = "Buchser, William J and Slepak, Tatiana I and Gutierrez-Arenas,
              Omar and Bixby, John L and Lemmon, Vance P",
  abstract = "Development and regeneration of the nervous system requires the
              precise formation of axons and dendrites. Kinases and
              phosphatases are pervasive regulators of cellular function and
              have been implicated in controlling axodendritic development and
              regeneration. We undertook a gain-of-function analysis to
              determine the functions of kinases and phosphatases in the
              regulation of neuron morphology. Over 300 kinases and 124
              esterases and phosphatases were studied by high-content analysis
              of rat hippocampal neurons. Proteins previously implicated in
              neurite growth, such as ERK1, GSK3, EphA8, FGFR, PI3K, PKC, p38,
              and PP1a, were confirmed to have effects in our functional
              assays. We also identified novel positive and negative neurite
              growth regulators. These include neuronal-developmentally
              regulated kinases such as the activin receptor, interferon
              regulatory factor 6 (IRF6) and neural leucine-rich repeat 1
              (LRRN1). The protein kinase N2 (PKN2) and choline kinase alpha
              (CHKA) kinases, and the phosphatases PPEF2 and SMPD1, have little
              or no established functions in neuronal function, but were
              sufficient to promote neurite growth. In addition, pathway
              analysis revealed that members of signaling pathways involved in
              cancer progression and axis formation enhanced neurite outgrowth,
              whereas cytokine-related pathways significantly inhibited neurite
              formation.",
  journal  = "Mol. Syst. Biol.",
  volume   =  6,
  pages    = "391",
  month    =  jul,
  year     =  2010,
  language = "en",
  issn     = "1744-4292",
  pmid     = "20664637",
  doi      = "10.1038/msb.2010.52",
  pmc      = "PMC2925531"
}

@ARTICLE{Hendriks2013-fg,
  title    = "Protein tyrosine phosphatases in health and disease",
  author   = "Hendriks, Wiljan J A J and Elson, Ari and Harroch, Sheila and
              Pulido, Rafael and Stoker, Andrew and den Hertog, Jeroen",
  abstract = "Protein tyrosine phosphatases (PTPs) represent a super-family of
              enzymes that play essential roles in normal development and
              physiology. In this review, we will discuss the PTPs that have a
              causative role in hereditary diseases in humans. In addition,
              recent progress in the development and analysis of animal models
              expressing mutant PTPs will be presented. The impact of PTP
              signaling on health and disease will be exemplified for the
              fields of bone development, synaptogenesis and central nervous
              system diseases. Collectively, research on PTPs since the late
              1980's yielded the cogent view that development of PTP-directed
              therapeutic tools is essential to further combat human disease.",
  journal  = "FEBS J.",
  volume   =  280,
  number   =  2,
  pages    = "708--730",
  month    =  jan,
  year     =  2013,
  language = "en",
  issn     = "1742-464X, 1742-4658",
  pmid     = "22938156",
  doi      = "10.1111/febs.12000"
}

@MISC{Chang2018-jb,
  title    = "shiny: Web Application Framework for {R}",
  author   = "Chang, Winston and Cheng, Joe and Allaire, J J and Xie, Yihui and
              McPherson, Jonathan",
  year     =  2018,
  keywords = "libs.bib.bib"
}

@ARTICLE{Robinson2005-ge,
  title    = "The phosphoinositide-3-phosphatase {MTMR2} associates with
              {MTMR13}, a membrane-associated pseudophosphatase also mutated in
              type {4B} {Charcot-Marie-Tooth} disease",
  author   = "Robinson, Fred L and Dixon, Jack E",
  abstract = "Charcot-Marie-Tooth disease type 4B (CMT4B) is a severe,
              demyelinating peripheral neuropathy characterized by distinctive,
              focally folded myelin sheaths. CMT4B is caused by recessively
              inherited mutations in either myotubularin-related 2 (MTMR2) or
              MTMR13 (also called SET-binding factor 2). MTMR2 encodes a member
              of the myotubularin family of phosphoinositide-3-phosphatases,
              which dephosphorylate phosphatidylinositol 3-phosphate (PI(3)P)
              and bisphosphate PI(3,5)P2. MTMR13 encodes a large,
              uncharacterized member of the myotubularin family. The MTMR13
              phosphatase domain is catalytically inactive because the
              essential Cys and Arg residues are absent. Given the genetic
              association of both MTMR2 and MTMR13 with CMT4B, we investigated
              the biochemical relationship between these two proteins. We found
              that the endogenous MTMR2 and MTMR13 proteins are associated in
              human embryonic kidney 293 cells. MTMR2-MTMR13 association is
              mediated by coiled-coil sequences present in each protein. We
              also examined the cellular localization of MTMR2 and MTMR13 using
              fluorescence microscopy and subcellular fractionation. We found
              that (i) MTMR13 is a predominantly membrane-associated protein;
              (ii) MTMR2 and MTMR13 cofractionate in both a light membrane
              fraction and a cytosolic fraction; and (iii) MTMR13 membrane
              association is mediated by the segment of the protein which
              contains the pseudophosphatase domain. This work, which describes
              the first cellular or biochemical investigation of the MTMR13
              pseudophosphatase protein, suggests that MTMR13 functions in
              association with MTMR2. Loss of MTMR13 function in CMT4B2
              patients may lead to alterations in MTMR2 function and subsequent
              alterations in 3-phosphoinositide signaling. Such a mechanism
              would explain the strikingly similar phenotypes of patients with
              recessive mutations in either MTMR2 or MTMR13.",
  journal  = "J. Biol. Chem.",
  volume   =  280,
  number   =  36,
  pages    = "31699--31707",
  month    =  sep,
  year     =  2005,
  language = "en",
  issn     = "0021-9258",
  pmid     = "15998640",
  doi      = "10.1074/jbc.M505159200"
}

@ARTICLE{Metz2018-ad,
  title    = "Coral: Clear and Customizable Visualization of Human Kinome Data",
  author   = "Metz, Kathleen S and Deoudes, Erika M and Berginski, Matthew E
              and Jimenez-Ruiz, Ivan and Aksoy, Bulent Arman and Hammerbacher,
              Jeff and Gomez, Shawn M and Phanstiel, Douglas H",
  abstract = "Protein kinases represent one of the largest gene families in
              eukaryotes and play roles in a wide range of cell signaling
              processes and human diseases. Current tools for visualizing
              kinase data in the context of the human kinome superfamily are
              limited to encoding data through the addition of nodes to a
              low-resolution image of the kinome tree. We present Coral, a
              user-friendly interactive web application for visualizing both
              quantitative and qualitative data. Unlike previous tools, Coral
              can encode data in three features (node color, node size, and
              branch color), allows three modes of kinome visualization (the
              traditional kinome tree as well as radial and dynamic force
              networks), and generates high-resolution scalable vector graphics
              files suitable for publication without the need for refinement
              using graphics editing software. Due to its user-friendly,
              interactive, and highly customizable design, Coral is broadly
              applicable to high-throughput studies of the human kinome. The
              source code and web application are available at
              github.com/dphansti/CORAL and phanstiel-lab.med.unc.edu/Coral,
              respectively.",
  journal  = "Cell Syst",
  volume   =  7,
  number   =  3,
  pages    = "347--350.e1",
  month    =  sep,
  year     =  2018,
  keywords = "data visualization; kinase; kinome",
  language = "en",
  issn     = "2405-4712",
  pmid     = "30172842",
  doi      = "10.1016/j.cels.2018.07.001",
  pmc      = "PMC6366324"
}

@ARTICLE{Pulido2008-by,
  title    = "Protein tyrosine phosphatases: dual-specificity phosphatases in
              health and disease",
  author   = "Pulido, Rafael and Hooft van Huijsduijnen, Rob",
  abstract = "Dual-specificity phosphatases (DSPs) constitute a subfamily of
              protein tyrosine phosphatases (PTPs) that dephosphorylates
              phospho-Tyr, phospho-Ser and nonproteinaceous substrates. DSPs
              are involved in the regulation of both developmental and
              postnatal essential processes, such as early embryogenesis,
              placental development and immune responses. Several DSP genes are
              implicated in familial and sporadic human diseases, including
              tumor-related, neurological and muscle disorders, and
              cardiovascular and inflammatory diseases. This association ranges
              from disease-causative mutations to disease-risk-prone
              single-nucleotide polymorphisms, promoter methylation or gene
              duplication (most often in cancer). Deconvolution of the role of
              DSPs in disease is challenging. The enzymes' activities are
              regulated at many levels and they form part of extensive,
              intricate networks with other signaling components. Here, we
              review current knowledge of the role of cysteine-based PTP-domain
              DSPs in health and disease, and their suitability as putative
              therapeutic targets for drugs is discussed.",
  journal  = "FEBS J.",
  volume   =  275,
  number   =  5,
  pages    = "848--866",
  month    =  mar,
  year     =  2008,
  language = "en",
  issn     = "1742-464X",
  pmid     = "18298792",
  doi      = "10.1111/j.1742-4658.2008.06250.x"
}

@ARTICLE{Andersen2004-cu,
  title    = "A genomic perspective on protein tyrosine phosphatases: gene
              structure, pseudogenes, and genetic disease linkage",
  author   = "Andersen, Jannik N and Jansen, Peter G and Echwald, S{\o}ren M
              and Mortensen, Ole H and Fukada, Toshiyuki and Del Vecchio,
              Robert and Tonks, Nicholas K and M{\o}ller, Niels Peter H",
  abstract = "The protein tyrosine phosphatases (PTPs) are now recognized as
              critical regulators of signal transduction under normal and
              pathophysiological conditions. In this analysis we have explored
              the sequence of the human genome to define the composition of the
              PTP family. Using public and proprietary sequence databases, we
              discovered one novel human PTP gene and defined chromosomal loci
              and exon structure of the additional 37 genes encoding known PTP
              transcripts. Direct orthologs were present in the mouse genome
              for all 38 human PTP genes. In addition, we identified 12 PTP
              pseudogenes unique to humans that have probably contaminated
              previous bioinformatics analysis of this gene family. PCR
              amplification and transcript sequencing indicate that some PTP
              pseudogenes are expressed, but their function (if any) is
              unknown. Furthermore, we analyzed the enhanced diversity
              generated by alternative splicing and provide predicted amino
              acid sequences for four human PTPs that are currently defined by
              fragments only. Finally, we correlated each PTP locus with
              genetic disease markers and identified 4 PTPs that map to known
              susceptibility loci for type 2 diabetes and 19 PTPs that map to
              regions frequently deleted in human cancers. We have made our
              analysis available at http://ptp.cshl.edu or
              http://science.novonordisk.com/ptp and we hope this resource will
              facilitate the functional characterization of these key enzymes.",
  journal  = "FASEB J.",
  volume   =  18,
  number   =  1,
  pages    = "8--30",
  month    =  jan,
  year     =  2004,
  language = "en",
  issn     = "0892-6638, 1530-6860",
  pmid     = "14718383",
  doi      = "10.1096/fj.02-1212rev"
}

@ARTICLE{Ostman2006-aq,
  title    = "Protein-tyrosine phosphatases and cancer",
  author   = "Ostman, Arne and Hellberg, Carina and B{\"o}hmer, Frank D",
  abstract = "Tyrosine phosphorylation is an important signalling mechanism in
              eukaryotic cells. In cancer, oncogenic activation of tyrosine
              kinases is a common feature, and novel anticancer drugs have been
              introduced that target these enzymes. Tyrosine phosphorylation is
              also controlled by protein-tyrosine phosphatases (PTPs). Recent
              evidence has shown that PTPs can function as tumour suppressors.
              In addition, some PTPs, including SHP2, positively regulate the
              signalling of growth-factor receptors, and can be oncogenic. An
              improved understanding of how these enzymes function and how they
              are regulated might aid the development of new anticancer agents.",
  journal  = "Nat. Rev. Cancer",
  volume   =  6,
  number   =  4,
  pages    = "307--320",
  month    =  apr,
  year     =  2006,
  language = "en",
  issn     = "1474-175X",
  pmid     = "16557282",
  doi      = "10.1038/nrc1837"
}

@ARTICLE{Eid2017-gf,
  title    = "{KinMap}: a web-based tool for interactive navigation through
              human kinome data",
  author   = "Eid, Sameh and Turk, Samo and Volkamer, Andrea and Rippmann,
              Friedrich and Fulle, Simone",
  abstract = "BACKGROUND: Annotations of the phylogenetic tree of the human
              kinome is an intuitive way to visualize compound profiling data,
              structural features of kinases or functional relationships within
              this important class of proteins. The increasing volume and
              complexity of kinase-related data underlines the need for a tool
              that enables complex queries pertaining to kinase disease
              involvement and potential therapeutic uses of kinase inhibitors.
              RESULTS: Here, we present KinMap, a user-friendly online tool
              that facilitates the interactive navigation through kinase
              knowledge by linking biochemical, structural, and disease
              association data to the human kinome tree. To this end,
              preprocessed data from freely-available sources, such as ChEMBL,
              the Protein Data Bank, and the Center for Therapeutic Target
              Validation platform are integrated into KinMap and can easily be
              complemented by proprietary data. The value of KinMap will be
              exemplarily demonstrated for uncovering new therapeutic
              indications of known kinase inhibitors and for prioritizing
              kinases for drug development efforts. CONCLUSION: KinMap
              represents a new generation of kinome tree viewers which
              facilitates interactive exploration of the human kinome. KinMap
              enables generation of high-quality annotated images of the human
              kinome tree as well as exchange of kinome-related data in
              scientific communications. Furthermore, KinMap supports multiple
              input and output formats and recognizes alternative kinase names
              and links them to a unified naming scheme, which makes it a
              useful tool across different disciplines and applications. A
              web-service of KinMap is freely available at
              http://www.kinhub.org/kinmap/ .",
  journal  = "BMC Bioinformatics",
  volume   =  18,
  number   =  1,
  pages    = "16",
  month    =  jan,
  year     =  2017,
  keywords = "Human kinome tree; Images; Interactive annotation; Protein
              kinases",
  language = "en",
  issn     = "1471-2105",
  pmid     = "28056780",
  doi      = "10.1186/s12859-016-1433-7",
  pmc      = "PMC5217312"
}

@MISC{Wickham2018-zb,
  title    = "readr: Read Rectangular Text Data",
  author   = "Wickham, Hadley and Hester, Jim and Francois, Romain",
  year     =  2018,
  keywords = "libs.bib.bib"
}

@MISC{Ooms2018-tr,
  title    = "rsvg: Render {SVG} Images into {PDF}, {PNG}, {PostScript}, or
              Bitmap Arrays",
  author   = "Ooms, Jeroen",
  year     =  2018,
  keywords = "libs.bib.bib"
}

@MISC{Chang2018-ef,
  title    = "shinydashboard: Create Dashboards with 'Shiny'",
  author   = "Chang, Winston and Borges Ribeiro, Barbara",
  year     =  2018,
  keywords = "libs.bib.bib"
}

@ARTICLE{Manning2002-tx,
  title    = "The protein kinase complement of the human genome",
  author   = "Manning, G and Whyte, D B and Martinez, R and Hunter, T and
              Sudarsanam, S",
  abstract = "We have catalogued the protein kinase complement of the human
              genome (the ``kinome'') using public and proprietary genomic,
              complementary DNA, and expressed sequence tag (EST) sequences.
              This provides a starting point for comprehensive analysis of
              protein phosphorylation in normal and disease states, as well as
              a detailed view of the current state of human genome analysis
              through a focus on one large gene family. We identify 518
              putative protein kinase genes, of which 71 have not previously
              been reported or described as kinases, and we extend or correct
              the protein sequences of 56 more kinases. New genes include
              members of well-studied families as well as previously
              unidentified families, some of which are conserved in model
              organisms. Classification and comparison with model organism
              kinomes identified orthologous groups and highlighted expansions
              specific to human and other lineages. We also identified 106
              protein kinase pseudogenes. Chromosomal mapping revealed several
              small clusters of kinase genes and revealed that 244 kinases map
              to disease loci or cancer amplicons.",
  journal  = "Science",
  volume   =  298,
  number   =  5600,
  pages    = "1912--1934",
  month    =  dec,
  year     =  2002,
  keywords = "paperRIS.ris",
  language = "en",
  issn     = "0036-8075, 1095-9203",
  pmid     = "12471243",
  doi      = "10.1126/science.1075762"
}

@ARTICLE{Tonks2006-sq,
  title    = "Protein tyrosine phosphatases: from genes, to function, to
              disease",
  author   = "Tonks, Nicholas K",
  abstract = "The protein tyrosine phosphatase (PTP) superfamily of enzymes
              functions in a coordinated manner with protein tyrosine kinases
              to control signalling pathways that underlie a broad spectrum of
              fundamental physiological processes. In this review, I describe
              recent breakthroughs in our understanding of the role of the PTPs
              in the regulation of signal transduction and the aetiology of
              human disease.",
  journal  = "Nat. Rev. Mol. Cell Biol.",
  volume   =  7,
  number   =  11,
  pages    = "833--846",
  month    =  nov,
  year     =  2006,
  language = "en",
  issn     = "1471-0072",
  pmid     = "17057753",
  doi      = "10.1038/nrm2039"
}

@MISC{Neuwirth2014-ux,
  title    = "{RColorBrewer}: {ColorBrewer} Palettes",
  author   = "Neuwirth, Erich",
  year     =  2014,
  keywords = "libs.bib.bib"
}


text:
@inproceedings{Licitra2016,
 author = {Licitra, Giovanni and Sieberling, Sören and Engelen, Sebastiaan and Williams, Paul and Ruiterkamp, Richard and Diehl, Moritz},
 booktitle = {2016 European Control Conference (ECC)},
 doi = {10.1109/ECC.2016.7810515},
 month = {June},
 pages = {1574--1579},
 title = {Optimal control for minimizing power consumption during holding patterns for airborne wind energy pumping system},
 url = {https://cdn.syscop.de/publications/Licitra2016.pdf},
 year = {2016}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
SUMMARY = "OpenBMC org.openbmc.managers.Download example implementation"
DESCRIPTION = "An example implementation for the org.openbmc.managers.Download DBUS API."
PV = "1.0+git${SRCPV}"
PR = "r1"

SKELETON_DIR = "pydownloadmgr"

inherit skeleton-python
inherit obmc-phosphor-dbus-service

RDEPENDS:${PN} += "\
        python-dbus \
        python-pygobject \
        python-subprocess \
        pyphosphor-dbus \
        "

DBUS_SERVICE:${PN} += "org.openbmc.managers.Download.service"

repository: JamesMihm/openbmc

repo_name: JamesMihm/openbmc

extension: bb


text:
@inproceedings{farina2019regret,
 author = {Gabriele Farina and Christian Kroer and Tuomas Sandholm},
 booktitle = {ICML (long oral)},
 title = {Regret Circuits: Composability of Regret Minimizers },
 url = {https://arxiv.org/abs/1811.02540},
 year = {2019}
}

repository: ChrKroer/academic-kickstart

repo_name: ChrKroer/academic-kickstart


text:
@proceedings{ws-2015-linguistics-clinical,
    title = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1200",
    doi = "10.3115/v1/W15-12",
}
@inproceedings{coppersmith-etal-2015-adhd,
    title = "From {ADHD} to {SAD}: Analyzing the Language of Mental Health on Twitter through Self-Reported Diagnoses",
    author = "Coppersmith, Glen  and
      Dredze, Mark  and
      Harman, Craig  and
      Hollingshead, Kristy",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1201",
    doi = "10.3115/v1/W15-1201",
    pages = "1--10",
}
@inproceedings{mitchell-etal-2015-quantifying,
    title = "Quantifying the Language of Schizophrenia in Social Media",
    author = "Mitchell, Margaret  and
      Hollingshead, Kristy  and
      Coppersmith, Glen",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1202",
    doi = "10.3115/v1/W15-1202",
    pages = "11--20",
}
@inproceedings{preotiuc-pietro-etal-2015-role,
    title = "The role of personality, age, and gender in tweeting about mental illness",
    author = "Preo{\c{t}}iuc-Pietro, Daniel  and
      Eichstaedt, Johannes  and
      Park, Gregory  and
      Sap, Maarten  and
      Smith, Laura  and
      Tobolsky, Victoria  and
      Schwartz, H. Andrew  and
      Ungar, Lyle",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1203",
    doi = "10.3115/v1/W15-1203",
    pages = "21--30",
}
@inproceedings{coppersmith-etal-2015-clpsych,
    title = "{CLP}sych 2015 Shared Task: Depression and {PTSD} on Twitter",
    author = "Coppersmith, Glen  and
      Dredze, Mark  and
      Harman, Craig  and
      Hollingshead, Kristy  and
      Mitchell, Margaret",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1204",
    doi = "10.3115/v1/W15-1204",
    pages = "31--39",
}
@inproceedings{preotiuc-pietro-etal-2015-mental,
    title = "Mental Illness Detection at the World Well-Being Project for the {CLP}sych 2015 Shared Task",
    author = "Preo{\c{t}}iuc-Pietro, Daniel  and
      Sap, Maarten  and
      Schwartz, H. Andrew  and
      Ungar, Lyle",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1205",
    doi = "10.3115/v1/W15-1205",
    pages = "40--45",
}
@inproceedings{pedersen-2015-screening,
    title = "Screening Twitter Users for Depression and {PTSD} with Lexical Decision Lists",
    author = "Pedersen, Ted",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1206",
    doi = "10.3115/v1/W15-1206",
    pages = "46--53",
}
@inproceedings{resnik-etal-2015-university,
    title = "The University of {M}aryland {CLP}sych 2015 Shared Task System",
    author = "Resnik, Philip  and
      Armstrong, William  and
      Claudino, Leonardo  and
      Nguyen, Thang",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1207",
    doi = "10.3115/v1/W15-1207",
    pages = "54--60",
}
@inproceedings{del-castillo-etal-2015-computational,
    title = "Computational cognitive modeling of inflectional verb morphology in {S}panish-speakers for the characterization and diagnosis of {A}lzheimer{'}s Disease",
    author = "del Castillo, M. Dolores  and
      Serrano, J. Ignacio  and
      Oliva, Jes{\'u}s",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1208",
    doi = "10.3115/v1/W15-1208",
    pages = "61--70",
}
@inproceedings{tanana-etal-2015-recursive,
    title = "Recursive Neural Networks for Coding Therapist and Patient Behavior in Motivational Interviewing",
    author = "Tanana, Michael  and
      Hallgren, Kevin  and
      Imel, Zac  and
      Atkins, David  and
      Smyth, Padhraic  and
      Srikumar, Vivek",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1209",
    doi = "10.3115/v1/W15-1209",
    pages = "71--79",
}
@inproceedings{murphy-etal-2015-putting,
    title = "Putting Feelings into Words: Cross-Linguistic Markers of the Referential Process",
    author = "Murphy, Sean  and
      Maskit, Bernard  and
      Bucci, Wilma",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1210",
    doi = "10.3115/v1/W15-1210",
    pages = "80--88",
}
@inproceedings{mowery-etal-2015-towards,
    title = "Towards Developing an Annotation Scheme for Depressive Disorder Symptoms: A Preliminary Study using Twitter Data",
    author = "Mowery, Danielle  and
      Bryan, Craig  and
      Conway, Mike",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1211",
    doi = "10.3115/v1/W15-1211",
    pages = "89--98",
}
@inproceedings{resnik-etal-2015-beyond,
    title = "Beyond {LDA}: Exploring Supervised Topic Modeling for Depression-Related Language in Twitter",
    author = "Resnik, Philip  and
      Armstrong, William  and
      Claudino, Leonardo  and
      Nguyen, Thang  and
      Nguyen, Viet-An  and
      Boyd-Graber, Jordan",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1212",
    doi = "10.3115/v1/W15-1212",
    pages = "99--107",
}
@inproceedings{gorman-etal-2015-automated,
    title = "Automated morphological analysis of clinical language samples",
    author = "Gorman, Kyle  and
      Bedrick, Steven  and
      Kiss, G{\'e}za  and
      Morley, Eric  and
      Ingham, Rosemary  and
      Mohammed, Metrah  and
      Papadakis, Katina  and
      van Santen, Jan",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1213",
    doi = "10.3115/v1/W15-1213",
    pages = "108--116",
}
@inproceedings{rouhizadeh-etal-2015-similarity,
    title = "Similarity Measures for Quantifying Restrictive and Repetitive Behavior in Conversations of Autistic Children",
    author = "Rouhizadeh, Masoud  and
      Sproat, Richard  and
      van Santen, Jan",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1214",
    doi = "10.3115/v1/W15-1214",
    pages = "117--123",
}
@inproceedings{rosenstein-etal-2015-practical,
    title = "Practical issues in developing semantic frameworks for the analysis of verbal fluency data: A {N}orwegian data case study",
    author = "Rosenstein, Mark  and
      Foltz, Peter  and
      Vaskinn, Anja  and
      Elvev{\aa}g, Brita",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1215",
    doi = "10.3115/v1/W15-1215",
    pages = "124--133",
}
@inproceedings{maskit-etal-2015-computer,
    title = "A Computer Program for Tracking the Evolution of a Psychotherapy Treatment",
    author = "Maskit, Bernard  and
      Bucci, Wilma  and
      Murphy, Sean",
    booktitle = "Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality",
    month = jun # " 5",
    year = "2015",
    address = "Denver, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W15-1216",
    doi = "10.3115/v1/W15-1216",
    pages = "134--145",
}

repository: emorynlp/nlprankings

repo_name: emorynlp/nlprankings

gha_license_id: NOASSERTION

gha_language: TeX


text:
.form-signin { max-width: 330px;padding: 15px;margin: 0 auto; }
.form-submit {background-image: linear-gradient(to bottom, #c61012 0%, #c61012 100%);background-image: none;border: 1px solid transparent;}
.tips { color: #c12; }

repository: liziczh/lizi-old

repo_name: liziczh/lizi-old

gha_language: Java

extension: css


text:
# Image with cloud9 ide, gfx and hw tools installed

require cloud9-image.bb

IMAGE_INSTALL += " \
                  packagegroup-core-x11-xserver \
                  angstrom-gnome-icon-theme-enable gtk-engine-clearlooks gtk-theme-clearlooks angstrom-clearlooks-theme-enable \
                  e-wm-config-default e-wm-config-standard e-wm-config-illume2 \
                  xserver-nodm-init \
                  xserver-common \
                  ttf-dejavu-sans ttf-dejavu-sans-mono ttf-dejavu-common \
                 "

export IMAGE_BASENAME = "Cloud9-IDE-gfx"

repository: Angstrom-distribution/meta-ti

repo_name: Angstrom-distribution/meta-ti

gha_license_id: MIT

gha_language: BlitzBasic


text:
@inproceedings{moreolo_sdn-enabled_2015,
 abstract = {We experimentally demonstrate multiple advanced functionalities of a cost-effective high-capacity sliceable-BVT using multicarrier technology. It is programmable, adaptive and reconfigurable by an SDN controller for efficient resource usage, enabling unique granularity, flexibility and grid adaptation, even in conventional fixed-grid networks.},
 author = {Moreolo, M. S. and Fabrega, J. M. and Nadal, L. and Vílchez, F. J. and Mayoral, A. and Vilalta, R. and Muñoz, R. and Casellas, R. and Martínez, R. and Nishihara, M. and Tanaka, T. and Takahara, T. and Rasmussen, J. C. and Kottke, C. and Schlosser, M. and Freund, R. and Meng, F. and Yan, S. and Zervas, G. and Simeonidou, D. and Yoshida, Y. and Kitayama, K.},
 booktitle = {2015 European Conference on Optical Communication (ECOC)},
 date = {2015-09},
 doi = {10.1109/ECOC.2015.7341867},
 eventtitle = {2015 European Conference on Optical Communication (ECOC)},
 file = {/Users/sy13201/Zotero/storage/X5KP6QTT/Moreolo et al_2015_SDN-enabled sliceable BVT based on multicarrier technology for multi-flow.pdf;/Users/sy13201/Zotero/storage/GDE6C8K4/articleDetails.html},
 keywords = {Adaptive optics,Arrays,Bandwidth,Bit error rate,Bit rate,fixed-grid networks,multicarrier technology,multiflow distance,multiflow rate,Optical filters,Optical receivers,optical transceivers,SDN controller,SDN-enabled sliceable BVT,software defined networking},
 pages = {1--3},
 title = {SDN-Enabled Sliceable BVT Based on Multicarrier Technology for Multi-Flow Rate/Distance and Grid Adaptation}
}


text:
SUMMARY = "Basic console-based gateway image"

require lmp-image-common.inc

require ${@bb.utils.contains('DISTRO_FEATURES', 'sota', 'lmp-feature-factory.inc', '', d)}
require ${@bb.utils.contains('DISTRO_FEATURES', 'wayland', 'lmp-feature-wayland.inc', '', d)}
require lmp-feature-ota-utils.inc
require lmp-feature-wireguard.inc
require lmp-feature-docker.inc
require lmp-feature-bluetooth.inc
require lmp-feature-wifi.inc
require lmp-feature-nat64.inc
require lmp-feature-jobserv.inc
require lmp-feature-softhsm.inc
require lmp-feature-sysctl-hang-crash-helper.inc
require lmp-feature-sysctl-net-queue-pfifo-fast.inc

require ${@bb.utils.contains('MACHINE_FEATURES', 'optee', 'lmp-feature-optee.inc', '', d)}
require ${@bb.utils.contains('MACHINE_FEATURES', 'tpm2', 'lmp-feature-tpm2.inc', '', d)}
require ${@bb.utils.contains('DISTRO_FEATURES', 'ima', 'lmp-feature-ima.inc', '', d)}

BT_6LOWPAN_NETWORK = "fe80:0:0:0:d4e7::1/80"
require lmp-feature-bt-6lowpan.inc

require lmp-service-bluetooth-disable.inc
require ${@bb.utils.contains('SOTA_CLIENT', 'aktualizr', 'lmp-service-ostree-pending-reboot.inc', '', d)}

IMAGE_FEATURES += "ssh-server-openssh"

# Base packages
CORE_IMAGE_BASE_INSTALL += " \
    cpufrequtils \
    ldd \
    gptfdisk \
    iptables \
    kernel-modules \
    networkmanager-nmcli \
"

CORE_IMAGE_BASE_INSTALL += " \
    ethtool \
    git \
    pciutils \
"

repository: foundriesio/meta-lmp

repo_name: foundriesio/meta-lmp

branch_name: refs/heads/main

gha_language: BitBake


text:
SUMMARY = "Library for parsing configuration files"
DESCRIPTION = "libConfuse is a configuration file parser library written in C. It \
 supports sections and (lists of) values (strings, integers, floats, \
 booleans or other sections), as well as some other features (such as \
 single/double-quoted strings, environment variable expansion, \
 functions and nested include statements)."
HOMEPAGE = "http://www.nongnu.org/confuse/"

LICENSE = "ISC"

S = "${WORKDIR}/git"

LIC_FILES_CHKSUM = "file://LICENSE;md5=42fa47330d4051cd219f7d99d023de3a"

inherit autotools binconfig pkgconfig lib_package gettext

EXTRA_OECONF = "--enable-shared --enable-static --disable-silent-rules"

BBCLASSEXTEND = "native"

SRCREV = "67fac45d54856e3817def4ef49807cf921132158"
SRC_URI = "git://github.com/martinh/libconfuse.git"

do_configure:prepend() {
  touch ${S}/support/config.rpath
}

repository: uglyoldbob/oe-custom

repo_name: uglyoldbob/oe-custom


text:
@book{bodie2003finanzas,
  title={Finanzas},
  author={Bodie, Z. and Merton, R.C.},
  isbn={9789702600978},
  series={{\'A}rea Universitarios},
  url={https://books.google.hn/books?id=jPTppKDvIv8C},
  year={2003},
  publisher={Pearson Educaci{\'o}n}
}

repository: JaimeEscoto/potential-bassoon

repo_name: JaimeEscoto/potential-bassoon

extension: bibtex


text:
@inproceedings{Isstaif2018PerformanceMO,
  title={Performance Model of Apache Cassandra Under Heterogeneous Workload Using the Quantitative Verification Approach},
  author={Al Amjad Tawfiq Isstaif and Nizar Alhafez},
  booktitle={EPEW},
  year={2018}
}

repository: isstaif/starter-academic

repo_name: isstaif/starter-academic


text:
/* this styles did not work and I dont know why? */

Body {
    background-color: light rgba(102, 88, 88, 0.096);
    color: black;
}

div.page {
    margin: 60px auto;
    width: 800px;
    background: rgb(202, 219, 188)
        ;
}

div.page .header {
    padding: 25px 25px 30px 25px;
    border-bottom: 30px rgb(194, 126, 102) solid;
}

div.page .content {
    padding: 25px 25px 15px 65px;
    background-color: rgb(201, 212, 201);
}


text:
file(REMOVE_RECURSE
  "CMakeFiles/quickstep_queryoptimizer_physical_Aggregate.dir/Aggregate.cpp.o"
  "libquickstep_queryoptimizer_physical_Aggregate.pdb"
  "libquickstep_queryoptimizer_physical_Aggregate.a"
)

# Per-language clean rules from dependency scanning.
foreach(lang CXX)
  include(CMakeFiles/quickstep_queryoptimizer_physical_Aggregate.dir/cmake_clean_${lang}.cmake OPTIONAL)
endforeach()

repository: kpgaffney/quickstep-optimizer-rs

repo_name: kpgaffney/quickstep-optimizer-rs

extension: cmake


text:
@article{de2011comparing,
  title={Comparing adult and adolescent transsexuals: an MMPI-2 and MMPI-A study},
  author={De Vries, Annelou LC and Kreukels, Baudewijntje PC and Steensma, Thomas D and Doreleijers, Theo AH and Cohen-Kettenis, Peggy T},
  journal={Psychiatry research},
  volume={186},
  number={2},
  pages={414--418},
  year={2011},
  publisher={Elsevier},
  doi={10.1016/j.psychres.2010.07.033},
  fulltext={http://www.psy-journal.com/article/S0165-1781%2810%2900465-8/abstract},
  conclusion={"Adult FtMs functioned significantly better than MtFs on three clinical scales. Contrary to what is often assumed, no differences in psychological functioning were found in the adult transsexuals with regard to sexual orientation, except on one clinical scale. Most remarkably, significantly more adults with GID scored in the clinical range on two or more clinical scales than adolescents with GID. Therefore, early medical intervention may be recommendable for adolescents with GID."}
}

repository: transcience/paper-dex

repo_name: transcience/paper-dex


text:
SUMMARY = "OpenSwitch"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Apache-2.0;md5=89aea4e17d99a7cacdbeed46a0096b10"

SRC_URI = "git://git.openswitch.net/openswitch/ops;protocol=https"

SRCREV = "42303a345212480a7b00f1178f8c8e1fb2879621"

# When using AUTOREV, we need to force the package version to the revision of git
# in order to avoid stale shared states.
PV = "git${SRCPV}"

S = "${WORKDIR}/git"

FILES_${PN} = "/usr/share/openvswitch/ /usr/share/openvswitch/*.extschema /usr/share/openvswitch/*.xml /usr/share/openvswitch/*.ovsschema"

OPS_SCHEMA_PATH="${S}/schema"

do_compile() {
  ${PYTHON} ${OPS_SCHEMA_PATH}/sanitize.py ${OPS_SCHEMA_PATH}/vswitch.extschema ${OPS_SCHEMA_PATH}/vswitch.ovsschema
  ${PYTHON} ${OPS_SCHEMA_PATH}/sanitize.py ${OPS_SCHEMA_PATH}/dhcp_leases.extschema ${OPS_SCHEMA_PATH}/dhcp_leases.ovsschema
  touch ${OPS_SCHEMA_PATH}/vswitch.xml
}

do_install() {
  install -d ${D}/${prefix}/share/openvswitch
	install -m 0644 ${OPS_SCHEMA_PATH}/vswitch.extschema ${D}/${prefix}/share/openvswitch/vswitch.extschema
	install -m 0644 ${OPS_SCHEMA_PATH}/vswitch.ovsschema ${D}/${prefix}/share/openvswitch/vswitch.ovsschema
	install -m 0644 ${OPS_SCHEMA_PATH}/vswitch.xml ${D}/${prefix}/share/openvswitch/vswitch.xml
	install -m 0644 ${OPS_SCHEMA_PATH}/dhcp_leases.extschema ${D}/${prefix}/share/openvswitch/dhcp_leases.extschema
	install -m 0644 ${OPS_SCHEMA_PATH}/dhcp_leases.ovsschema ${D}/${prefix}/share/openvswitch/dhcp_leases.ovsschema
	install -m 0644 ${OPS_SCHEMA_PATH}/dhcp_leases.xml ${D}/${prefix}/share/openvswitch/dhcp_leases.xml
	install -m 0644 ${OPS_SCHEMA_PATH}/configdb.ovsschema ${D}/${prefix}/share/openvswitch/configdb.ovsschema
	install -m 0644 ${OPS_SCHEMA_PATH}/vtep.ovsschema ${D}/${prefix}/share/openvswitch/vtep.ovsschema
	install -m 0644 ${OPS_SCHEMA_PATH}/vtep.xml ${D}/${prefix}/share/openvswitch/vtep.xml
}

repository: notmem/ops-build

repo_name: notmem/ops-build


text:
@article{salinger_albany_using_component_based_design_to_dev_flex_multiphysics,
author = "Andrew G. Salinger and Roscoe A. Bartless and Andrew M. Bradley and Qiushi Chen and Irina P. Demeshko and Xujiao Gao and Glen A. Hansen and Alejandro Mota and Richard P. Muller and Erik Nielsen and Jakob T. Ostien and Roget P. Pawlowski and Mauro Perego and Eric T. Phipps and WaiChing Sun and Irina K. Tezaur",
title  = "Albany: using Component-Based Design To Develop A Flexible, Generic Mulitphysics Analysis Code",
journal= "International Journal For Multiscale Computaional Engineering",
year   = 2016,
volume = 14,
number = 4,
}

repository: JustinClough/grasp

repo_name: JustinClough/grasp


text:
require acpid.inc

SRC_URI_append = " file://event.c.diff;patch=1 \
                   file://fixfd.diff;patch=1 \
                   file://netlink.diff;patch=1"

repository: demsey/openembedded

repo_name: demsey/openembedded

branch_name: HEAD


text:
def assert_true(status)
    assert(status == true, 'assert(true) failed!')
end

def assert_false(status)
    assert(status == false, 'assert(false) failed!')
end

assert_true(0 == 0)
assert_false(0 != 0)
assert_true(0 != 1)
assert_false(0 == 1)

assert_true(0.0 == 0)
assert_false(0.0 != 0)
assert_true(0.0 != 1.0)
assert_false(0.0 == 1.0)

assert_true(nil == nil)
assert_false(nil != nil)
assert_true(true != nil)
assert_false(true == nil)
assert_true(nil != false)
assert_false(nil == false)

assert_true(list == list)
assert_false(list == map)

assert_true([] == [])
assert_true([true] == [true])
assert_true([[]] == [[]])
assert_false([[]] != [[]])
assert_false([0] == [])
assert_false([] != [])
assert_true([] != nil)
assert_false([] == nil)

assert_true({} != nil)
assert_false({} == nil)

gha_language: C

extension: be


text:
# Digital Twins

@article{Niederer2021,
abstract = {Mathematical modeling and simulation are moving from being powerful development and analysis tools towards having increased roles in operational monitoring, control and decision support, in which models of specific entities are continually updated in the form of a digital twin. However, current digital twins are largely the result of bespoke technical solutions that are difficult to scale. We discuss two exemplar applications that motivate challenges and opportunities for scaling digital twins, and that underscore potential barriers to wider adoption of this technology. Development in digital-twin technology has been rapidly growing across a range of industries and disciplines. However, to ensure a wider and more robust adoption of such technology, various challenges must be addressed by the computational science community.},
author = {Niederer, Steven A. and Sacks, Michael S. and Girolami, Mark and Willcox, Karen},
doi = {10.1038/s43588-021-00072-5},
journal = {Nature Computational Science},
title = {{Scaling digital twins from the artisanal to the industrial}},
year = {2021},
topic = {dt-conceptual}
}

@misc{ward2021continuous,
      title={Continuous calibration of a digital twin: comparison of particle filter and Bayesian calibration approaches},
      author={Rebecca Ward and Ruchi Choudhary and Alastair Gregory and Melanie Jans-Singh and Mark Girolami},
      year={2021},
      eprint={2011.09810},
      archivePrefix={arXiv},
      primaryClass={cs.CE},
      topic = {dt-experimental}
}

@article{Kapteyn2021,
author={Kapteyn, Michael G.
and Pretorius, Jacob V. R.
and Willcox, Karen E.},
title={A probabilistic graphical model foundation for enabling predictive digital twins at scale},
journal={Nature Computational Science},
year={2021},
month={May},
day={01},
volume={1},
number={5},
pages={337-347},
abstract={A unifying mathematical formulation is needed to move from one-off digital twins built through custom implementations to robust digital twin implementations at scale. This work proposes a probabilistic graphical model as a formal mathematical representation of a digital twin and its associated physical asset. We create an abstraction of the asset--twin system as a set of coupled dynamical systems, evolving over time through their respective state spaces and interacting via observed data and control inputs. The formal definition of this coupled system as a probabilistic graphical model enables us to draw upon well-established theory and methods from Bayesian statistics, dynamical systems and control theory. The declarative and general nature of the proposed digital twin model make it rigorous yet flexible, enabling its application at scale in a diverse range of application areas. We demonstrate how the model is instantiated to enable a structural digital twin of an unmanned aerial vehicle (UAV). The digital twin is calibrated using experimental data from a physical UAV asset. Its use in dynamic decision-making is then illustrated in a synthetic example where the UAV undergoes an in-flight damage event and the digital twin is dynamically updated using sensor data. The graphical model foundation ensures that the digital twin calibration and updating process is principled, unified and able to scale to an entire fleet of digital twins.},
issn={2662-8457},
doi={10.1038/s43588-021-00069-0},
topic = {dt-experimental}
}

# Others
@misc{HBR2019Belonging,
	author = {Carr, Evan W. and Reece, Andrew and Kellerman, Gabriella Rosen and Robichaux, Alexi},
	title = {{The Value of Belonging at Work}},
	journal = {Harv. Bus. Rev.},
	year = {2019},
	month = {Dec},
	note = {[Online; accessed 19. Nov. 2020]},
	url = {https://hbr.org/2019/12/the-value-of-belonging-at-work}
}

@misc{Lifehack2020pomodoro,
	author = {Cummings, Tucker},
	title = {{Does the Pomodoro Technique Work for Your Productivity?}},
	journal = {Lifehack},
	year = {2020},
	month = {Apr},
	publisher = {Lifehack},
	url = {https://www.lifehack.org/articles/productivity/the-pomodoro-technique-is-it-right-for-you.html}
}

# Demonstrators

## forest

### forest-modelling-treecrown_deepforest

@article{Weinstein2020_MEE,
   abstract = {Abstract Remote sensing of forested landscapes can transform the speed, scale and cost of forest research. The delineation of individual trees in remote sensing images is an essential task in forest analysis. Here we introduce a new Python package, DeepForest that detects individual trees in high resolution RGB imagery using deep learning. While deep learning has proven highly effective in a range of computer vision tasks, it requires large amounts of training data that are typically difficult to obtain in ecological studies. DeepForest overcomes this limitation by including a model pretrained on over 30 million algorithmically generated crowns from 22 forests and fine-tuned using 10,000 hand-labelled crowns from six forests. The package supports the application of this general model to new data, fine tuning the model to new datasets with user labelled crowns, training new models and evaluating model predictions. This simplifies the process of using and retraining deep learning models for a range of forests, sensors and spatial resolutions. We illustrate the workflow of DeepForest using data from the National Ecological Observatory Network, a tropical forest in French Guiana, and street trees from Portland, Oregon.},
   author = {Ben G Weinstein and Sergio Marconi and Mélaine Aubry-Kientz and Gregoire Vincent and Henry Senyondo and Ethan P White},
   doi = {https://doi.org/10.1111/2041-210X.13472},
   issue = {12},
   journal = {Methods in Ecology and Evolution},
   keywords = {NEON,RGB,crown delineation,deep learning,forests,remote sensing,tree crowns},
   pages = {1743-1751},
   title = {DeepForest: A Python package for RGB deep learning tree crown delineation},
   volume = {11},
   url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13472},
   year = {2020},
   topic = {forest-modelling-treecrown_deepforest}
}

@article{Weinstein2020_EI,
   abstract = {Tree crown detection is a fundamental task in remote sensing for forestry and ecosystem ecology. While many individual tree segmentation algorithms have been proposed, the development and testing of these algorithms is typically site specific, with few methods evaluated against data from multiple forest types simultaneously. This makes it difficult to determine the generalization of proposed approaches, and limits tree detection at broad scales. Using data from the National Ecological Observatory Network, we extend a recently developed deep learning approach to include data from a range of forest types to determine whether information from one forest can be used for tree detection in other forests, and explore the potential for building a universal tree detection algorithm. We find that the deep learning approach works well for overstory tree detection across forest conditions. Performance was best in open oak woodlands and worst in alpine forests. When models were fit to one forest type and used to predict another, performance generally decreased, with better performance when forests were more similar in structure. However, when models were pretrained on data from other sites and then fine-tuned using a relatively small amount of hand-labeled data from the evaluation site, they performed similarly to local site models. Most importantly, a model fit to data from all sites performed as well or better than individual models trained for each local site.},
   author = {Ben G Weinstein and Sergio Marconi and Stephanie A Bohlman and Alina Zare and Ethan P White},
   doi = {https://doi.org/10.1016/j.ecoinf.2020.101061},
   issn = {1574-9541},
   journal = {Ecological Informatics},
   keywords = {Airborne LiDAR,Object detection,RGB deep learning,Tree crown detection},
   pages = {101061},
   title = {Cross-site learning in deep learning RGB tree crown detection},
   volume = {56},
   url = {https://www.sciencedirect.com/science/article/pii/S157495412030011X},
   year = {2020},
   topic = {forest-modelling-treecrown_deepforest}
}

@article{Weinstein2019,
   abstract = {Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detection network. Individual crown delineation has been a long-standing challenge in remote sensing and available algorithms produce mixed results. We show that deep learning models can leverage existing Light Detection and Ranging (LIDAR)-based unsupervised delineation to generate trees that are used for training an initial RGB crown detection model. Despite limitations in the original unsupervised detection approach, this noisy training data may contain information from which the neural network can learn initial tree features. We then refine the initial model using a small number of higher-quality hand-annotated RGB images. We validate our proposed approach while using an open-canopy site in the National Ecological Observation Network. Our results show that a model using 434,551 self-generated trees with the addition of 2848 hand-annotated trees yields accurate predictions in natural landscapes. Using an intersection-over-union threshold of 0.5, the full model had an average tree crown recall of 0.69, with a precision of 0.61 for the visually-annotated data. The model had an average tree detection rate of 0.82 for the field collected stems. The addition of a small number of hand-annotated trees improved the performance over the initial self-supervised model. This semi-supervised deep learning approach demonstrates that remote sensing can overcome a lack of labeled training data by generating noisy data for initial training using unsupervised methods and retraining the resulting models with high quality labeled data.},
   author = {Ben G Weinstein and Sergio Marconi and Stephanie Bohlman and Alina Zare and Ethan White},
   doi = {10.3390/rs11111309},
   issn = {2072-4292},
   issue = {11},
   journal = {Remote Sensing},
   title = {Individual Tree-Crown Detection in RGB Imagery Using Semi-Supervised Deep Learning Neural Networks},
   volume = {11},
   url = {https://www.mdpi.com/2072-4292/11/11/1309},
   year = {2019},
   topic = {forest-modelling-treecrown_deepforest}
}

## polar

### polar-modelling-icenet

@article{Andersson2021,
   abstract = {Anthropogenic warming has led to an unprecedented year-round reduction in Arctic sea ice extent. This has far-reaching consequences for indigenous and local communities, polar ecosystems, and global climate, motivating the need for accurate seasonal sea ice forecasts. While physics-based dynamical models can successfully forecast sea ice concentration several weeks ahead, they struggle to outperform simple statistical benchmarks at longer lead times. We present a probabilistic, deep learning sea ice forecasting system, IceNet. The system has been trained on climate simulations and observational data to forecast the next 6 months of monthly-averaged sea ice concentration maps. We show that IceNet advances the range of accurate sea ice forecasts, outperforming a state-of-the-art dynamical model in seasonal forecasts of summer sea ice, particularly for extreme sea ice events. This step-change in sea ice forecasting ability brings us closer to conservation tools that mitigate risks associated with rapid sea ice loss.},
   author = {Tom R Andersson and J Scott Hosking and María Pérez-Ortiz and Brooks Paige and Andrew Elliott and Chris Russell and Stephen Law and Daniel C Jones and Jeremy Wilkinson and Tony Phillips and James Byrne and Steffen Tietsche and Beena Balan Sarojini and Eduardo Blanchard-Wrigglesworth and Yevgeny Aksenov and Rod Downie and Emily Shuckburgh},
   doi = {10.1038/s41467-021-25257-4},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications},
   pages = {5124},
   title = {Seasonal Arctic sea ice forecasting with probabilistic deep learning},
   volume = {12},
   url = {https://doi.org/10.1038/s41467-021-25257-4},
   year = {2021},
   topic = {polar-modelling-icenet}
}

## urban

### urban-sensors-climate_ukv

@misc{MetOffice,
 author = {McCaie, Theo},
 editor = {{Met Office Informatics Lab}},
 title = {Met Office and partners offer data and compute platform for COVID-19 researchers},
 url = {https://medium.com/informatics-lab/met-office-and-partners-offer-data-and-compute-platform-for-covid-19-researchers-83848ac55f5f},
 lastchecked = {27.10.2021},
 originalyear = {09.04.2020},
 topic = {urban-sensors-climate_ukv}
}

## wildfires

### wildfires-sensors-fires_modis

@techreport{firms,
     title = {{MODIS Collection 6 Active Fire Product User’s Guide Revision B}},
     author = {Louis Giglio and Wilfrid Schroeder and Joanne V. Hall and Christopher O. Justice},
     group = {csg},
     year = {2018},
     institution = {NASA},
     Date-Added = {2015-03-01},
     Date-Modified = {2018-12-01},
     url = {https://modis-fire.umd.edu/files/MODIS_C6_Fire_User_Guide_B.pdf},
     topic = {wildfires-sensors-fires_modis}
}


text:
@Article{gonzalez-cabrera_exploratory_2019,
  title = {Exploratory study on bullying in gifted students: prevalence and psychological wellbeing},
  issn = {1988-592X},
  shorttitle = {Estudio exploratorio sobre acoso escolar en alumnado con altas capacidades},
  url = {http://doi.org/10.4438/1988-592X-RE-2019-386-432},
  doi = {10.4438/1988-592X-RE-2019-386-432},
  abstract = {Introduction: The distinguishing characteristics of gifted students can leave them vulnerable to being bullied. Evidence on school violence and gifted students is scarce and it has still not been explored in Spain. The aim is to establish the prevalence of bullying among gifted students, its distribution across the different roles and its relationship with other psychological variables. Method: We employed a cross-sectional and analytic study of 285 gifted students (Mage = 11.77; SD = 2.28; range 9–18) from all over Spain (175 male, 61.6%). The Spanish versions of the European Bullying Intervention Project Questionnaire, Depression, Anxiety, Stress Scales-21, Interpersonal Support Evaluation List and KIDSCREEN-10 were used. Results: 50.9% is involved in bullying, with 36.9% being victims, 1.1% bullies, and 10.2% bully-victims. Bully-victims and victims present worse health-related quality of life scores (p \textless .001), depression (p \textless .001), stress (p \textless .001) and, and anxiety (p \textless .001) than uninvolved individuals. Discussion: This paper provides empirical evidence of the high prevalence of victimization among gifted Spanish students. Being a victim or bully-victims has an impact on psychological wellbeing and, particularly, on health-related quality of life, stress, anxiety, and depression.},
  number = {386},
  urldate = {2020-08-14},
  journal = {Revista de Educacion},
  author = {Joaquin Gonzalez-Cabrera and Javier Touron and Juan Manuel Machimbarrena and Ana Leon-Mejia and Monica Gutierrez-Ortega},
  year = {2019},
  pages = {187--206},
  pubtype = {2},
}

repository: mmachimbarrena/Pruebaweb

repo_name: mmachimbarrena/Pruebaweb


text:
SUMMARY = "TestDisk is powerful free data recovery software!"
DESCRIPTION = "It was primarily designed to help recover lost partitions and/or make non-booting disks bootable again when these symptoms are caused by faulty software: certain types of viruses or human error (such as accidentally deleting a Partition Table). Partition table recovery using TestDisk is really easy."
HOMEPAGE = "http://www.cgsecurity.org/wiki/TestDisk"
SECTION = "security"
LICENSE = "GPLv2+"

DEPENDS = "e2fsprogs zlib util-linux"

LIC_FILES_CHKSUM = "file://COPYING;beginline=1;endline=2;md5=1fbd81241fe252ec0f5658a521ab7dd8"

SRC_URI = "http://archive.ubuntu.com/ubuntu/pool/universe/t/${PN}/${PN}_${PV}.orig.tar.bz2"

SRC_URI[md5sum] = "b1f0edabc9035e9ec9c8e0a95059ff3f"
SRC_URI[sha256sum] = "a597c3ebc375acdf0ff60f44ed8935a301132aae78ec00f64f091637d055326c"

inherit autotools-brokensep  pkgconfig

PACKAGECONFIG ?= ""
PACKAGECONFIG[ncurses] = "--with-ncurses-lib=${STAGING_INCDIR} --with-ncurses-includes=${STAGING_LIBDIR}, --without-ncurses, ncurses,"

PACKAGECONFIG[jpeg] = "--with-jpeg-lib=${STAGING_INCDIR} --with-jpeg-includes=${STAGING_LIBDIR}, --without-jpeg, jpeg,"

RDEPENDS_${PN} = "libewf"

repository: akuster/meta-kali

repo_name: akuster/meta-kali