text:
@article{biovisPaduano1,
title={{Extended LineSets}: A Visualization Technique for the Interactive Inspection of Biological Pathways},
author={Francesco Paduano and Angus G. Forbes},
journal = {BMC Proceedings},
volume = {9},
number={6},
pages={S4},
address={Dublin, Ireland},
//month = {August},
year = {2015},
}

@article{biovisDang1,
title={{PathwayMatrix: V}isualizing Binary Relationships between Proteins in Biological Pathways},
author={Tuan Nhon Dang and Paul Murray and Angus G. Forbes},
address={Dublin, Ireland},
journal = {BMC Proceedings},
volume = {9},
number={6},
pages={S3},
year = {2015},
//month = {August},
//note = {\doi{10.1186/1753-6561-9-S6-S3}}
}

@article{biovisDang2,
title={{ReactionFlow}: An interactive visualization tool for
causality analysis in biological pathways},
author={Tuan Nhon Dang and Paul Murray and Jillian Aurisano and A. G. Forbes},
journal = {BMC Proceedings},
address={Dublin, Ireland},
volume = {9},
number={6},
pages={S6},
year = {2015},
//month = {August},
//note = {\doi{10.1186/1753-6561-9-S6-S6}}
}

@inproceedings{Ma_EuroVis_SP,
author = {Chihua Ma and Robert V. Kenyon and Angus G. Forbes and Tanya Berger-Wolf and Bernard J. Slater and Daniel A. Llano},
title= {Visualizing Dynamic Brain Networks Using an Animated Dual-Representation},
booktitle = {Proc. Eurographics Conf. on Visualization},
pages={73--77},
//address={Cagliari, Italy},
//month = {May},
year = {2015},
//note = {\doi{10.2312/eurovisshort.20151128}}
}

@inproceedings{tagriver2011,
  author = {Angus G. Forbes and Basak Alper and Tobias H{\"o}llerer and George Legrady},
  booktitle = {IEEE Workshop on Interactive Visual Text Analytics},
  title = {Interactive Folksonomic Analytics with the {Tag River} Visualization},
  year = {2011},
}

@ARTICLE{ThemeRiver,
author={Havre, S. and Hetzler, E. and Whitney, P. and Nowell, L.},
journal={{IEEE} Trans. Vis. Comput. Graph.},
title={{ThemeRiver: V}isualizing thematic changes in large document collections},
year={2002},
//month={Jan},
volume={8},
number={1},
pages={9-20},
doi={10.1109/2945.981848},
ISSN={1077-2626},}

@ARTICLE{Cui-et-al-2014,
author={Cui, W. and Liu, S. and Wu, Z. and Wei, H.},
journal={{IEEE} Trans. Vis. Comput. Graph.},
title={How Hierarchical Topics Evolve in Large Text Corpora},
year={2014},
//month={Dec},
volume={20},
number={12},
pages={2281-2290},
keywords={Algorithm design and analysis;Context awareness;Data visualization;Document handling;Text analysis;Text mining;Hierarchical topic visualization;data transformation;evolutionary tree clustering},
doi={10.1109/TVCG.2014.2346433},
ISSN={1077-2626},}

@article {Kochtchi2014,
author = {Kochtchi, Artjom and von Landesberger, Tatiana and Biemann, Chris},
title = {Networks of Names: Visual Exploration and Semi-Automatic Tagging of Social Networks from Newspaper Articles},
journal = {Comput. Graph. Forum},
volume = {33},
number = {3},
publisher = {Blackwell Publishing Ltd},
issn = {1467-8659},
//url = {http://dx.doi.org/10.1111/cgf.12377},
doi = {10.1111/cgf.12377},
pages = {211--220},
year = {2014},
}

@INPROCEEDINGS{Krstajic-et-al-2010,
author={Krstajic, M. and Mansmann, F. and Stoffel, A. and Atkinson, M. and Keim, D.A.},
booktitle={Data Engineering Workshops (ICDEW), 2010 IEEE 26th International Conf. on},
title={Processing online news streams for large-scale semantic analysis},
year={2010},
//month={March},
pages={215-220},
keywords={Internet;information filtering;Europe media monitor;Internet;information filtering;large-scale semantic analysis;online news stream processing;publishing industry;semantic news analysis system;Data security;Humans;Information filtering;Information filters;Internet;Large-scale systems;Law;Legal factors;Monitoring;Streaming media},
doi={10.1109/ICDEW.2010.5452710},}

@inproceedings{Forbes2011interactive,
  title={Interactive Folksonomic Analytics with the {Tag R}iver Visualization},
  author={Forbes, Angus Graeme and Alper, Basak and H{\"o}llerer, Tobias and Legrady, George},
  booktitle={Proc. IEEE Workshop on Interactive Visual Text Analytics (TextVis)},
  address={Providence, Rhode Island},
  year={2011},
  //month={October}
}

@INPROCEEDINGS{Eler-et-al-2009,
author={Eler, D.M. and Paulovich, F.V. and de Oliveira, M.C.F. and Minghim, R.},
booktitle={Information Visualisation, 2009 13th International Conference},
title={Topic-Based Coordination for Visual Analysis of Evolving Document Collections},
year={2009},
month={July},
pages={149-155},
keywords={text analysis;document interpretation;document maps;multiple coordinated views;textual files;time varying document collection analysis;topic detection;topic extraction;topic-based coordination;visual analysis;Availability;Clouds;Data mining;Data visualization;Information analysis;Multidimensional systems;Ontologies;Principal component analysis;Text analysis;Visual analytics;coordination;corpus visualization;text visualization;topic extraction},
doi={10.1109/IV.2009.31},
ISSN={1550-6037},}

@INPROCEEDINGS{Kucher-Kerren-2015,
author={Kucher, K. and Kerren, A.},
booktitle={Visualization Symp. (PacificVis), 2015 IEEE Pacific},
title={Text visualization techniques: Taxonomy, visual survey, and community insights},
year={2015},
pages={117-121},
keywords={data analysis;data visualisation;interactive systems;pattern classification;text analysis;categorization taxonomy;community insight;data analysis;interactive visual survey;text visualization technique;Browsers;Data visualization;Market research;Media;Taxonomy;Visualization;Visualization;community analysis;interaction;survey;taxonomy;text visualization;web-based systems},
doi={10.1109/PACIFICVIS.2015.7156366},
month={April},}

@INPROCEEDINGS{Heimerl-et-al-2014,
author={Heimerl, F. and Lohmann, S. and Lange, S. and Ertl, T.},
booktitle={System Sciences (HICSS), 2014 47th Hawaii International Conference on},
title={Word Cloud Explorer: Text Analytics Based on Word Clouds},
year={2014},
pages={1833-1842},
keywords={data visualisation;natural language processing;text analysis;context information;natural language processing;sophisticated interaction techniques;text analysis tasks;text analytics;text summarization;visualization method;visualization paradigm;word cloud explorer;word clouds;Context;Layout;Pragmatics;Tag clouds;Text analysis;User interfaces;Visualization;interaction;natural language processing;tag clouds;text analytics;visualization;word cloud explorer;word clouds}, doi={10.1109/HICSS.2014.231},
month={Jan},}

@inproceedings{Kuo-et-al:2007,
 author = {Kuo, Byron Y-L and Hentrich, Thomas and Good, Benjamin M . and Wilkinson, Mark D.},
 title = {Tag Clouds for Summarizing Web Search Results},
 booktitle = {Proc. 16th International Conference on World Wide Web},
 series = {WWW '07},
 year = {2007},
 isbn = {978-1-59593-654-7},
 location = {Banff, Alberta, Canada},
 pages = {1203--1204},
 numpages = {2},
 //url = {http://doi.acm.org/10.1145/1242572.1242766},
 doi = {10.1145/1242572.1242766},
 acmid = {1242766},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {PubMed, content summarization, literature search, natural language processing, tag cloud, tagging, text mining, visualization},
}

@inproceedings{beck2014generalized,
  title={Generalized Pythagoras trees for visualizing hierarchies},
  author={Beck, Fabian and Burch, Michael and Munz, Tanja and Di Silvestro, Lorenzo and Weiskopf, Daniel},
  booktitle={Proc. International Conf. on Information Visualization Theory and Application},
  pages={17--28},
  year={2014}
}

@article{shneiderman1992tree,
  title={Tree visualization with tree-maps: 2-d space-filling approach},
  author={Shneiderman, Ben},
  journal={ACM Trans. Graph.},
  volume={11},
  number={1},
  pages={92--99},
  year={1992},
  publisher={ACM}
}

@ARTICLE{TreeVisSchulz,
author={Schulz, H.-J.},
journal={IEEE Comput. Graph. Appl.},
title={{Treevis.net: A} Tree Visualization Reference},
year={2011},
volume={31},
number={6},
pages={11-15},
}

@inproceedings{viegas2013google,
  title={Google+ ripples: A native visualization of information flow},
  author={Vi{\'e}gas, Fernanda and Wattenberg, Martin and Hebert, Jack and Borggaard, Geoffrey and Cichowlas, Alison and Feinberg, Jonathan and Orwant, Jon and Wren, Christopher},
  booktitle={Proc. 22nd international conference on World Wide Web},
  pages={1389--1398},
  year={2013},
  organization={International World Wide Web Conferences Steering Committee}
}

@article{pourdehnad2013myc,
  title={Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers},
  author={Pourdehnad, Michael and Truitt, Morgan L and Siddiqi, Imran N and Ducker, Gregory S and Shokat, Kevan M and Ruggero, Davide},
  journal={Proc. National Academy of Sciences},
  volume={110},
  number={29},
  pages={11988--11993},
  year={2013},
  publisher={National Acad Sciences}
}

@article{shahbazian2006mtor,
  title={The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity},
  author={Shahbazian, David and Roux, Philippe P and Mieulet, Virginie and Cohen, Michael S and Raught, Brian and Taunton, Jack and Hershey, John WB and Blenis, John and Pende, Mario and Sonenberg, Nahum},
  journal={The EMBO journal},
  volume={25},
  number={12},
  pages={2781--2791},
  year={2006},
  }

@incollection{wilkinson2008tumor,
  title={Tumor Suppressors p53 and TGF$\beta$ Converge to Regulate the Alpha-Fetoprotein Oncodevelopmental Tumor Marker},
  author={Wilkinson, Deepti S and Barton, Michelle Craig},
  booktitle={Transforming Growth Factor-$\beta$ in Cancer Therapy, Volume II},
  pages={309--320},
  year={2008},
  publisher={Springer}
}

@inproceedings{zheng2008pten,
  title={Pten and p53 converge on c-Myc to control differentiation, self-renewal, and transformation of normal and neoplastic stem cells in glioblastoma},
  author={Zheng, H and Ying, H and Yan, H and Kimmelman, AC and Hiller, DJ and Chen, A-J and Perry, SR and Tonon, G and Chu, GC and Ding, Z and others},
  booktitle={Cold Spring Harbor symposia on quantitative biology},
  pages={sqb--2008},
  year={2008},
  organization={Cold Spring Harbor Laboratory Press}
}

@incollection{keggonline,
year={2013},
isbn={978-1-4419-9862-0},
booktitle={Encyclopedia of Systems Biology},
editor={Dubitzky, Werner and Wolkenhauer, Olaf and Cho, Kwang-Hyun and Yokota, Hiroki},
title={KEGG Pathway Database},
url={http://dx.doi.org/10.1007/978-1-4419-9863-7_472},
publisher={Springer New York},
author={Qiu, Yu-Qing},
pages={1068-1069},
language={English}
}

@article{croft2014reactome,
  title={The Reactome pathway knowledgebase},
  author={Croft, David and Mundo, Antonio Fabregat and Haw, Robin and Milacic, Marija and Weiser, Joel and Wu, Guanming and Caudy, Michael and Garapati, Phani and Gillespie, Marc and Kamdar, Maulik R and others},
  journal={Nucleic acids research},
  volume={42},
  number={D1},
  pages={D472--D477},
  year={2014},
  publisher={Oxford Univ Press}
}

@article{hanahan2011hallmarks,
  title={Hallmarks of cancer: the next generation},
  author={Hanahan, Douglas and Weinberg, Robert A},
  journal={cell},
  volume={144},
  number={5},
  pages={646--674},
  year={2011},
  publisher={Elsevier}
}

@article{cairns2011regulation,
  title={Regulation of cancer cell metabolism},
  author={Cairns, Rob A and Harris, Isaac S and Mak, Tak W},
  journal={Nature Reviews Cancer},
  volume={11},
  number={2},
  pages={85--95},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{luo2003targeting,
  title={Targeting the PI3K-Akt pathway in human cancer-Rationale and promise},
  author={Luo, Ji and Manning, Brendan D and Cantley, Lewis C},
  journal={Cancer cell},
  volume={4},
  number={4},
  pages={257--262},
  year={2003},
  publisher={Elsevier Science}
}

@article{reya2001stem,
  title={Stem cells, cancer, and cancer stem cells},
  author={Reya, Tannishtha and Morrison, Sean J and Clarke, Michael F and Weissman, Irving L},
  journal={nature},
  volume={414},
  number={6859},
  pages={105--111},
  year={2001},
  publisher={Nature Publishing Group}
}

@article{PathwayCommons2011,
author = {Cerami, Ethan G. and Gross, Benjamin E. and Demir, Emek and Rodchenkov, Igor and Babur, Ã and Anwar, Nadia and Schultz, Nikolaus and Bader, Gary D. and Sander, Chris},
title = {{Pathway C}ommons, a web resource for biological pathway data},
volume = {39},
number = {suppl 1},
pages = {D685-D690},
year = {2011},
journal = {Nucleic Acids Research}
}

@article{Ethan2010Automatic,
author = {Ethan Cerami and Emek Demir and Nikolaus Schultz and Barry S. Taylor and Chris Sander},
title = {{Automated Network Analysis Identifies Core Pathways in Glioblastoma}},
journal = {PLOS One},
volume = {5},
year = {2010},
issue = {2},
doi = {10.1371/journal.pone.0008918.g005},
masid = {33784621}
}

@article{VisANT2009,
author = {Hu, Zhenjun and Hung, Jui-Hung and Wang, Yan and Chang, Yi-Chien and Huang, Chia-Ling and Huyck, Matt and DeLisi, Charles},
title = {VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology},
volume = {37},
number = {suppl 2},
pages = {W115-W121},
year = {2009},
doi = {10.1093/nar/gkp406},
abstract ={Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on correlations ignored. Here, we report on new capabilities of VisANT?an integrative software platform for the visualization, mining, analysis and modeling of the biological networks?which extend the application of GO in network visualization, analysis and inference. The new VisANT functions can be classified into three categories. (i) Visualization: a new tree-based browser allows visualization of GO hierarchies. GO terms can be easily dropped into the network to group genes annotated under the term, thereby integrating the hierarchical ontology with the network. This facilitates multi-scale visualization and analysis. (ii) Flexible annotation schema: in addition to conventional methods for annotating network nodes with the most specific functional descriptions available, VisANT also provides functions to annotate genes at any customized level of abstraction. (iii) Finding over-represented GO terms and expression-enriched GO modules: two new algorithms have been implemented as VisANT plugins. One detects over-represented GO annotations in any given sub-network and the other finds the GO categories that are enriched in a specified phenotype or perturbed dataset. Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu.},
//url = {http://nar.oxfordjournals.org/content/37/suppl_2/W115.abstract},
eprint = {http://nar.oxfordjournals.org/content/37/suppl_2/W115.full.pdf+html},
journal = {Nucleic Acids Research}
}

@inproceedings{GridBasedVisualization2010,
 author = {Rohrschneider, Markus and Heine, Christian and Reichenbach, Andr{\'e} and Kerren, Andreas and Scheuermann, Gerik},
 title = {A Novel Grid-based Visualization Approach for Metabolic Networks with Advanced Focus\&Context View},
 booktitle = {Proc. 17th International Conf. on Graph Drawing},
 series = {GD'09},
 year = {2010},
 isbn = {3-642-11804-6, 978-3-642-11804-3},
 location = {Chicago, IL},
 pages = {268--279},
 numpages = {12},
 //url = {http://dx.doi.org/10.1007/978-3-642-11805-0_26},
 doi = {10.1007/978-3-642-11805-0_26},
 acmid = {2174385},
 publisher = {Springer-Verlag},
 address = {Berlin, Heidelberg}
}

@Article{TVNViewer2012,
AUTHOR = {Curtis, Ross and Xiang, Jing and Parikh, Ankur and Kinnaird, Peter and Xing, Eric},
TITLE = {Enabling dynamic network analysis through visualization in TVNViewer},
JOURNAL = {BMC Bioinformatics},
VOLUME = {13},
YEAR = {2012},
NUMBER = {1},
PAGES = {204},
//url = {http://www.biomedcentral.com/1471-2105/13/204},
DOI = {10.1186/1471-2105-13-204},
PubMedID = {22897913},
ISSN = {1471-2105},
ABSTRACT = {BACKGROUND:Many biological processes are context-dependent or temporally specific. As a result, relationships between molecular constituents evolve across time and environments. While cutting-edge machine learning techniques can recover these networks, exploring and interpreting the rewiring behavior is challenging. Information visualization shines in this type of exploratory analysis, motivating the development ofTVNViewer (http://sailing.cs.cmu.edu/tvnviewer webcite), a visualization tool for dynamic network analysis.RESULTS:In this paper, we demonstrate visualization techniques for dynamic network analysis by using TVNViewer to analyze yeast cell cycle and breast cancer progression datasets.CONCLUSIONS:TVNViewer is a powerful new visualization tool for the analysis of biological networks that change across time or space.}
}

@Article{ChiBE2_2014,
AUTHOR = {Babur, Ozgun and Dogrusoz, Ugur and Cakir, Merve and Aksoy, Bulent and Schultz, Nikolaus and Sander, Chris and Demir, Emek},
TITLE = {Integrating biological pathways and genomic profiles with ChiBE 2},
JOURNAL = {BMC Genomics},
VOLUME = {15},
YEAR = {2014},
NUMBER = {1},
PAGES = {642},
}

@Article{BioFabric2012,
AUTHOR = {Longabaugh, William},
TITLE = {Combing the hairball with BioFabric: a new approach for visualization of large networks},
JOURNAL = {BMC Bioinformatics},
VOLUME = {13},
YEAR = {2012},
NUMBER = {1},
PAGES = {275},
//url = {http://www.biomedcentral.com/1471-2105/13/275},
DOI = {10.1186/1471-2105-13-275},
PubMedID = {23102059},
ISSN = {1471-2105},
ABSTRACT = {BACKGROUND:The analysis of large, complex networks is an important aspect of ongoing biological research. Yet there is a need for entirely new, scalable approaches for network visualization that can provide more insight into the structure and function of these complex networks.RESULTS:To address this need, we have developed a software tool named BioFabric, which uses a novel network visualization technique that depicts nodes as one-dimensional horizontal lines arranged in unique rows. This is in distinct contrast to the traditional approach that represents nodes as discrete symbols that behave essentially as zero-dimensional points. BioFabric then depicts each edge in the network using a vertical line assigned to its own unique column, which spans between the source and target rows, i.e. nodes. This method of displaying the network allows a full-scale view to be organized in a rational fashion; interesting network structures, such as sets of nodes with similar connectivity, can be quickly scanned and visually identified in the full network view, even in networks with well over 100,000 edges. This approach means that the network is being represented as a fundamentally linear, sequential entity, where the horizontal scroll bar provides the basic navigation tool for browsing the entire network.CONCLUSIONS:BioFabric provides a novel and powerful way of looking at any size of network, including very large networks, using horizontal lines to represent nodes and vertical lines to represent edges. It is freely available as an open-source Java application.}
}

@article{Paxtools2013,
    author = {Demir, , Emek AND Babur, , Özgün AND Rodchenkov, , Igor AND Aksoy, , Bülent Arman AND Fukuda, , Ken I. AND Gross, , Benjamin AND Sümer, , Onur Selçuk AND Bader, , Gary D. AND Sander, , Chris},
    journal = {PLoS Comput Biol},
    publisher = {Public Library of Science},
    title = {Using Biological Pathway Data with Paxtools},
    year = {2013},
    month = {09},
    volume = {9},
    //url = {http://dx.doi.org/10.1371\%2Fjournal.pcbi.1003194},
    pages = {e1003194},
    abstract = {<p>A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.</p>},
    number = {9},
    doi = {10.1371/journal.pcbi.1003194}
}

@article {cBioPortal2013,
	author = {Gao, Jianjiong and Aksoy, B{\"u}lent Arman and Dogrusoz, Ugur and Dresdner, Gideon and Gross, Benjamin and Sumer, S. Onur and Sun, Yichao and Jacobsen, Anders and Sinha, Rileen and Larsson, Erik and Cerami, Ethan and Sander, Chris and Schultz, Nikolaus},
	title = {Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal},
	volume = {6},
	number = {269},
	pages = {pl1--pl1},
	year = {2013},
	journal = {Science Signaling}
}

@article{GEO2011,
author = {Barrett, Tanya and Troup, Dennis B. and Wilhite, Stephen E. and Ledoux, Pierre and Evangelista, Carlos and Kim, Irene F. and Tomashevsky, Maxim and Marshall, Kimberly A. and Phillippy, Katherine H. and Sherman, Patti M. and Muertter, Rolf N. and Holko, Michelle and Ayanbule, Oluwabukunmi and Yefanov, Andrey and Soboleva, Alexandra},
title = {NCBI GEO: archive for functional genomics data sets?10 years on},
volume = {39},
number = {suppl 1},
pages = {D1005-D1010},
year = {2011},
journal = {Nucleic Acids Research}
}

@book{ClusteringAlgorithms,
 author = {J.A. Hartigan},
 title = {Clustering Algorithms},
 year = {1975},
 publisher = {John Wiley \& Sons},
 address = {New York},
 }

@inproceedings{ScagExplorer2014,
 author = {Dang, Tuan Nhon and Wilkinson, Leland},
 title = {{ScagExplorer: E}xploring Scatterplots by Their Scagnostics},
 booktitle = {Proc. IEEE Pacific Visualization Symp.},
 year = {2014},
 pages = {73--80},
}

@article{Entourage2013,
 author = {Lex, Alexander and Partl, Christian and Kalkofen, Denis and Streit, Marc and Gratzl, Samuel and Wassermann, Anne Mai and Schmalstieg, Dieter and Pfister, Hanspeter},
 title = {Entourage: Visualizing Relationships Between Biological Pathways Using Contextual Subsets},
 journal = {{IEEE} Trans. Vis. Comput. Graph.},
 issue_date = {December 2013},
 volume = {19},
 number = {12},
 month = dec,
 year = {2013},
 issn = {1077-2626},
 pages = {2536--2545},
 numpages = {10},
 //url = {http://dx.doi.org/10.1109/TVCG.2013.154},
 doi = {10.1109/TVCG.2013.154},
 acmid = {2553766},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {Pathway visualization, biological networks, subsets, graphs, biomolecular data},
}

@ARTICLE{CompressedAdjacencyMatrices2012,
author={Dinkla, K. and Westenberg, M.A. and van Wijk, J.J.},
journal={{IEEE} Trans. Vis. Comput. Graph.},
title={Compressed Adjacency Matrices: Untangling Gene Regulatory Networks},
year={2012},
month={Dec},
volume={18},
number={12},
pages={2457-2466},
keywords={biology computing;data visualisation;genetics;matrix algebra;network theory (graphs);compressed adjacency matrices;directed networks;gene regulatory networks;motifs;neatly-arranged visualization;network characteristics;node-link diagrams;rearrangement clustering;scale-free distribution;sparse network;standard adjacency matrix;standard visualization;structural characteristics;visualization domain;Bismuth;Computer aided manufacturing;Layout;Proteins;Sparse matrices;Standards;Visualization;Network;adjacency matrix;gene regulation;scale-free},
doi={10.1109/TVCG.2012.208},
ISSN={1077-2626},}

@article{Cytoscape_2007,
	Annote = {10.1038/nprot.2007.324},
	Author = {Cline, Melissa S and Smoot, Michael and Cerami, Ethan and Kuchinsky, Allan and Landys, Nerius and Workman, Chris and Christmas, Rowan and Avila-Campilo, Iliana and Creech, Michael and Gross, Benjamin and Hanspers, Kristina and Isserlin, Ruth and Kelley, Ryan and Killcoyne, Sarah and Lotia, Samad and Maere, Steven and Morris, John and Ono, Keiichiro and Pavlovic, Vuk and Pico, Alexander R and Vailaya, Aditya and Wang, Peng-Liang and Adler, Annette and Conklin, Bruce R and Hood, Leroy and Kuiper, Martin and Sander, Chris and Schmulevich, Ilya and Schwikowski, Benno and Warner, Guy J and Ideker, Trey and Bader, Gary D},
	Date = {2007/10//print},
	Date-Added = {2014-12-04 19:29:20 +0000},
	Date-Modified = {2014-12-04 19:29:20 +0000},
	Isbn = {1754-2189},
	Journal = {Nat. Protocols},
	L3 = {http://www.nature.com/nprot/journal/v2/n10/suppinfo/nprot.2007.324_S1.html},
	M3 = {10.1038/nprot.2007.324},
	Month = {10},
	Number = {10},
	Pages = {2366--2382},
	Publisher = {Nature Publishing Group},
	Title = {Integration of biological networks and gene expression data using Cytoscape},
	Ty = {JOUR},
	//url = {http://dx.doi.org/10.1038/nprot.2007.324},
	Volume = {2},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nprot.2007.324}
}

@article{charbonnier2008social,
  title={The social network of a cell: recent advances in interactome mapping},
  author={Charbonnier, Sebastian and Gallego, Oriol and Gavin, Anne-Claude},
  journal={Biotechnology annual review},
  volume={14},
  pages={1--28},
  year={2008},
  publisher={Elsevier}
}

@article{mathivanan2006evaluation,
  title={An evaluation of human protein-protein interaction data in the public domain},
  author={Mathivanan, Suresh and Periaswamy, Balamurugan and Gandhi, TKB and Kandasamy, Kumaran and Suresh, Shubha and Mohmood, Riaz and Ramachandra, YL and Pandey, Akhilesh},
  journal={BMC bioinformatics},
  volume={7},
  number={Suppl 5},
  pages={S19},
  year={2006},
  publisher={BioMed Central Ltd}
}

@article{von2002comparative,
  title={Comparative assessment of large-scale data sets of protein--protein interactions},
  author={Von Mering, Christian and Krause, Roland and Snel, Berend and Cornell, Michael and Oliver, Stephen G and Fields, Stanley and Bork, Peer},
  journal={Nature},
  volume={417},
  number={6887},
  pages={399--403},
  year={2002},
  publisher={Nature Publishing Group}
}

@article{bader2006pathguide,
  title={Pathguide: a pathway resource list},
  author={Bader, Gary D and Cary, Michael P and Sander, Chris},
  journal={Nucleic acids research},
  volume={34},
  number={suppl 1},
  pages={D504--D506},
  year={2006},
  publisher={Oxford Univ Press}
}

@article{kanehisa2008kegg,
  title={KEGG for linking genomes to life and the environment},
  author={Kanehisa, Minoru and Araki, Michihiro and Goto, Susumu and Hattori, Masahiro and Hirakawa, Mika and Itoh, Masumi and Katayama, Toshiaki and Kawashima, Shuichi and Okuda, Shujiro and Tokimatsu, Toshiaki and others},
  journal={Nucleic acids research},
  volume={36},
  number={suppl 1},
  pages={D480--D484},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{matthews2009reactome,
  title={Reactome knowledgebase of human biological pathways and processes},
  author={Matthews, Lisa and Gopinath, Gopal and Gillespie, Marc and Caudy, Michael and Croft, David and de Bono, Bernard and Garapati, Phani and Hemish, Jill and Hermjakob, Henning and Jassal, Bijay and others},
  journal={Nucleic acids research},
  volume={37},
  number={suppl 1},
  pages={D619--D622},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{suderman2007tools,
  title={Tools for visually exploring biological networks},
  author={Suderman, Matthew and Hallett, Michael},
  journal={Bioinformatics},
  volume={23},
  number={20},
  pages={2651--2659},
  year={2007},
  publisher={Oxford Univ Press}
}

@article{pavlopoulos2008survey,
  title={A survey of visualization tools for biological network analysis},
  author={Pavlopoulos, Georgios A and Wegener, Anna-Lynn and Schneider, Reinhard},
  journal={Biodata mining},
  volume={1},
  number={1},
  pages={1--11},
  year={2008},
  publisher={Springer}
}

@article{gehlenborg2010visualization,
  title={Visualization of omics data for systems biology},
  author={Gehlenborg, Nils and O'Donoghue, Se{\'a}n I and Baliga, Nitin S and Goesmann, Alexander and Hibbs, Matthew A and Kitano, Hiroaki and Kohlbacher, Oliver and Neuweger, Heiko and Schneider, Reinhard and Tenenbaum, Dan and others},
  journal={Nature methods},
  volume={7},
  pages={S56--S68},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{saraiya2005visualizing,
  title={Visualizing biological pathways: requirements analysis, systems evaluation and research agenda},
  author={Saraiya, Purvi and North, Chris and Duca, Karen},
  journal={Information Visualization},
  volume={4},
  number={3},
  pages={191--205},
  year={2005},
  publisher={SAGE Publications}
}

@article{barsky2007cerebral,
  title={Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation},
  author={Barsky, Aaron and Gardy, Jennifer L and Hancock, Robert EW and Munzner, Tamara},
  journal={Bioinformatics},
  volume={23},
  number={8},
  pages={1040--1042},
  year={2007},
  publisher={Oxford Univ Press}
}

@article{shannon2003cytoscape,
  title={Cytoscape: a software environment for integrated models of biomolecular interaction networks},
  author={Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin S and Wang, Jonathan T and Ramage, Daniel and Amin, Nada and Schwikowski, Benno and Ideker, Trey},
  journal={Genome research},
  volume={13},
  number={11},
  pages={2498--2504},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

@article{hu2009visant,
  title={VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology},
  author={Hu, Zhenjun and Hung, Jui-Hung and Wang, Yan and Chang, Yi-Chien and Huang, Chia-Ling and Huyck, Matt and DeLisi, Charles},
  journal={Nucleic acids research},
  pages={gkp406},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{kitano2002systems,
  title={Systems biology: a brief overview},
  author={Kitano, Hiroaki},
  journal={Science},
  volume={295},
  number={5560},
  pages={1662--1664},
  year={2002},
  publisher={American Association for the Advancement of Science}
}

@article{lex2013entourage,
  title={Entourage: Visualizing relationships between biological pathways using contextual subsets},
  author={Lex, Alexander and Partl, Christian and Kalkofen, Denis and Streit, Marc and Gratzl, Samuel and Wassermann, Anne Mai and Schmalstieg, Dieter and Pfister, Hanspeter},
  journal={Visualization and Computer Graphics, IEEE Transactions on},
  volume={19},
  number={12},
  pages={2536--2545},
  year={2013},
  publisher={IEEE}
}

@article{babur2010chibe,
  title={ChiBE: interactive visualization and manipulation of BioPAX pathway models},
  author={Babur, Ozgun and Dogrusoz, Ugur and Demir, Emek and Sander, Chris},
  journal={Bioinformatics},
  volume={26},
  number={3},
  pages={429--431},
  year={2010},
  publisher={Oxford Univ Press}
}

@article{demir2010biopax,
  title={The BioPAX community standard for pathway data sharing},
  author={Demir, Emek and Cary, Michael P and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming and D'Eustachio, Peter and Schaefer, Carl and Luciano, Joanne and others},
  journal={Nature biotechnology},
  volume={28},
  number={9},
  pages={935--942},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{cerami2011pathway,
  title={Pathway Commons, a web resource for biological pathway data},
  author={Cerami, Ethan G and Gross, Benjamin E and Demir, Emek and Rodchenkov, Igor and Babur, {\"O}zg{\"u}n and Anwar, Nadia and Schultz, Nikolaus and Bader, Gary D and Sander, Chris},
  journal={Nucleic acids research},
  volume={39},
  number={suppl 1},
  pages={D685--D690},
  year={2011},
  publisher={Oxford Univ Press}
}

@article{longabaugh2012combing,
  title={Combing the hairball with BioFabric: a new approach for visualization of large networks},
  author={Longabaugh, William JR},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={275},
  year={2012},
  publisher={BioMed Central Ltd}
}

@article{dinkla2012compressed,
  title={Compressed adjacency matrices: untangling gene regulatory networks},
  author={Dinkla, Kasper and Westenberg, Michel A and van Wijk, Jarke J},
  journal={Visualization and Computer Graphics, IEEE Transactions on},
  volume={18},
  number={12},
  pages={2457--2466},
  year={2012},
  publisher={IEEE}
}

@article{Fredriksson2003GProteinCoupledReceptors,
author = {Fredriksson, Robert and Lagerstrom, Malin C. and Lundin, Lars-Gustav and Schioth, Helgi B.},
title = {The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints},
volume = {63},
number = {6},
pages = {1256-1272},
year = {2003},
abstract ={The superfamily of G-protein-coupled receptors (GPCRs) is very diverse in  structure and function and its members are among the most pursued targets for  drug development. We identified more than 800 human GPCR sequences and  simultaneously analyzed 342 unique functional nonolfactory human GPCR  sequences with phylogenetic analyses. Our results show, with high bootstrap  support, five main families, named glutamate, rhodopsin, adhesion,  frizzled/taste2, and secretin, forming the GRAFS classification system. The  rhodopsin family is the largest and forms four main groups with 13  sub-branches. Positions of the GPCRs in chromosomal paralogons regions  indicate the importance of tetraploidizations or local gene duplication events  for their creation. We also searched for ?fingerprint? motifs  using Hidden Markov Models delineating the putative inter-relationship of the  GRAFS families. We show several common structural features indicating that the  human GPCRs in the GRAFS families share a common ancestor. This study  represents the first overall map of the GPCRs in a single mammalian genome.  Our novel approach of analyzing such large and diverse sequence sets may be  useful for studies on GPCRs in other genomes and divergent protein  families.},
//url = {http://molpharm.aspetjournals.org/content/63/6/1256.abstract},
journal = {Molecular Pharmacology}
}

@article {Gether2002ProteinCoupledReceptors,
author = {Gether, Ulrik and Asmar, Fazila and Meinild, Anne Kristine and Rasmussen, Soren G. F.},
title = {Structural Basis for Activation of G-Protein-Coupled Receptors},
journal = {Pharmacology and Toxicology},
volume = {91},
number = {6},
publisher = {Munksgaard International Publishers},
issn = {1600-0773},
//url = {http://dx.doi.org/10.1034/j.1600-0773.2002.910607.x},
pages = {304--312},
year = {2002},
}

@article{HierarchicalEdgeBundles2006,
 author = {Holten, Danny},
 title = {Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data},
 journal = {IEEE Transactions on Visualization and Computer Graphics},
 issue_date = {September 2006},
 volume = {12},
 number = {5},
 month = sep,
 year = {2006},
 issn = {1077-2626},
 pages = {741--748},
 numpages = {8},
 //url = {http://dx.doi.org/10.1109/TVCG.2006.147},
 doi = {10.1109/TVCG.2006.147},
 acmid = {1187772},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {Network visualization, Network visualization, edge bundling, edge aggregation, edge concentration, curves, graph visualization, tree visualization, node-link diagrams, hierarchies, treemaps., curves, edge aggregation, edge bundling, edge concentration, graph visualization, hierarchies, node-link diagrams, tree visualization, treemaps.},
}

@inproceedings{Lee:2006TaskTaxonomy,
 author = {Lee, Bongshin and Plaisant, Catherine and Parr, Cynthia Sims and Fekete, Jean-Daniel and Henry, Nathalie},
 title = {Task Taxonomy for Graph Visualization},
 booktitle = {Proc. 2006 AVI Workshop on BEyond Time and Errors: Novel Evaluation Methods for Information Visualization},
 series = {BELIV '06},
 year = {2006},
 isbn = {1-59593-562-2},
 location = {Venice, Italy},
 pages = {1--5},
 numpages = {5},
 //url = {http://doi.acm.org/10.1145/1168149.1168168},
 doi = {10.1145/1168149.1168168},
 acmid = {1168168},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {evaluation, graph visualization, task taxonomy},
}

@inproceedings{Wang:2006EvaluatingTree,
 author = {Wang, Yue and Teoh, Soon Tee and Ma, Kwan-Liu},
 title = {Evaluating the Effectiveness of Tree Visualization Systems for Knowledge Discovery},
 booktitle = {Proc. Eurographics Conf. on Visualization},
 year = {2006},
 isbn = {3-905673-31-2},
 location = {Lisbon, Portugal},
 pages = {67--74},
 numpages = {8},
 //url = {http://dx.doi.org/10.2312/VisSym/EuroVis06/067-074},
 doi = {10.2312/VisSym/EuroVis06/067-074},
 acmid = {2384806},
}

@inproceedings{Kobsa:2004UserExperimentsWithTree,
 author = {Kobsa, Alfred},
 title = {User Experiments with Tree Visualization Systems},
 booktitle = {Proc. IEEE Symp. on Information Visualization},
 series = {INFOVIS '04},
 year = {2004},
 isbn = {0-7803-8779-3},
 pages = {9--16},
 numpages = {8},
 //url = {http://dx.doi.org/10.1109/INFOVIS.2004.70},
 doi = {10.1109/INFOVIS.2004.70},
 acmid = {1038776},
 publisher = {IEEE Computer Society},
  }

@article {Von:2011LargeGraphs,
author = {von Landesberger, T. and Kuijper, A. and Schreck, T. and Kohlhammer, J. and van Wijk, J.J. and Fekete, J.-D. and Fellner, D.W.},
title = {Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges},
journal = {Comput. Graph. Forum},
volume = {30},
number = {6},
publisher = {Blackwell Publishing Ltd},
issn = {1467-8659},
//url = {http://dx.doi.org/10.1111/j.1467-8659.2011.01898.x},
doi = {10.1111/j.1467-8659.2011.01898.x},
pages = {1719--1749},
keywords = {visual graph analysis, graph visualization, graph interaction, visual analytics},
year = {2011},
}

@incollection{Henry:2007MatLink,
year={2007},
isbn={978-3-540-74799-4},
booktitle={Human-Computer Interaction – INTERACT 2007},
volume={4663},
series={Lecture Notes in Computer Science},
editor={Baranauskas, Cécilia and Palanque, Philippe and Abascal, Julio and Barbosa, SimoneDinizJunqueira},
doi={10.1007/978-3-540-74800-7_24},
title={MatLink: Enhanced Matrix Visualization for Analyzing Social Networks},
url={http://dx.doi.org/10.1007/978-3-540-74800-7_24},
publisher={Springer Berlin Heidelberg},
keywords={Node-Link Diagram; Matrix Visualization; Social Network},
author={Henry, Nathalie and Fekete, Jean-Daniel},
pages={288-302},
language={English}
}

@article{OneZoom2012,
	Address = {San Francisco, USA},
	An = {PMC3472976},
	Author = {Rosindell, J and Harmon, L J},
	Date = {2012/10/},
	Date-Added = {2015-03-31 17:02:12 +0000},
	Date-Modified = {2015-03-31 17:02:12 +0000},
	Db = {PMC},
	Doi = {10.1371/journal.pbio.1001406},
	Isbn = {1544-9173; 1545-7885},
	J1 = {PLoS Biol},
	Journal = {PLoS Biology},
	Month = {10},
	Number = {10},
	Pages = {e1001406},
	Publisher = {Public Library of Science},
	Title = {OneZoom: A Fractal Explorer for the Tree of Life},
	Ty = {JOUR},
	U1 = {PBIOLOGY-D-12-02473{$[$}PII{$]$}; 23091419{$[$}pmid{$]$}},
	//url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472976/},
	Volume = {10},
	Year = {2012},
	Year1 = {2012/10/16},
	Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472976/},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pbio.1001406}}

	@inproceedings{Wattenberg1999TreeMaps,
 author = {Wattenberg, Martin},
 title = {Visualizing the Stock Market},
 booktitle = {CHI '99 Extended Abstracts on Human Factors in Computing Systems},
 series = {CHI EA '99},
 year = {1999},
 isbn = {1-58113-158-5},
 location = {Pittsburgh, Pennsylvania},
 pages = {188--189},
 numpages = {2},
 //url = {http://doi.acm.org/10.1145/632716.632834},
 doi = {10.1145/632716.632834},
 acmid = {632834},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {interactive graphics, investing, treemap, visualization},
}

@INPROCEEDINGS{Bruls99squarifiedtreemaps,
    author = {Mark Bruls and Kees Huizing and Jarke van Wijk},
    title = {Squarified Treemaps},
    booktitle = {In Proc. Eurographics Symp. on Visualization},
    year = {1999},
    pages = {33--42},
    publisher = {Press}
}

@inproceedings{VanWijk1999CushionTreemaps,
 author = {Van Wijk, Jarke J. and van de Wetering, Huub},
 title = {Cushion Treemaps: Visualization of Hierarchical Information},
 booktitle = {Proc. 1999 IEEE Symp. on Information Visualization},
 series = {INFOVIS '99},
 year = {1999},
 isbn = {0-7695-0431-0},
 pages = {73--},
 //url = {http://dl.acm.org/citation.cfm?id=857189.857663},
 acmid = {857663},
 publisher = {IEEE Computer Society},
 address = {Washington, DC, USA},
 keywords = {Information Visualization, Tree Visualization, Treemaps},
}

@inproceedings{Balzer2005VoronoiTreemaps,
 author = {Balzer, Michael and Deussen, Oliver and Lewerentz, Claus},
 title = {Voronoi Treemaps for the Visualization of Software Metrics},
 booktitle = {Proc. 2005 ACM Symp. on Software Visualization},
 series = {SoftVis '05},
 year = {2005},
 isbn = {1-59593-073-6},
 location = {St. Louis, Missouri},
 pages = {165--172},
 numpages = {8},
 //url = {http://doi.acm.org/10.1145/1056018.1056041},
 doi = {10.1145/1056018.1056041},
 acmid = {1056041},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {software metrics, treemaps, voronoi diagrams},
}

@inproceedings {MiriahMeyer2012ClockMap,
booktitle = {EuroVis - Short Papers},
editor = {Miriah Meyer and Tino Weinkaufs},
title = {{ClockMap: Enhancing Circular Treemaps with Temporal Glyphs for Time-Series Data}},
author = {Fischer, Fabian and Fuchs, Johannes and Mansmann, Florian},
year = {2012},
DOI = {10.2312/PE/EuroVisShort/EuroVisShort2012/097-101}
}

@article{Kruskal1983IciclePlots,
     jstor_articletype = {research-article},
     title = {Icicle Plots: Better Displays for Hierarchical Clustering},
     author = {Kruskal, J. B. and Landwehr, J. M.},
     journal = {The American Statistician},
     jstor_issuetitle = {},
     volume = {37},
     number = {2},
     jstor_formatteddate = {May, 1983},
     pages = {pp. 162-168},
     //url = {http://www.jstor.org/stable/2685881},
     ISSN = {00031305},
     abstract = {An icicle plot is a method for presenting a hierarchical clustering. Compared with other methods of presentation, it is far easier in an icicle plot to read off which objects belong to which clusters, and which objects join or drop out from a cluster as we move up and down the levels of the hierarchy, though these benefits only appear when enough objects are being clustered. Icicle plots are described, and their benefits are illustrated using a clustering of 48 objects.},
     language = {English},
     year = {1983},
     publisher = {Taylor & Francis, Ltd. on behalf of the American Statistical Association},
     copyright = {Copyright © 1983 American Statistical Association},
    }

    @inproceedings{Plaisant2002SpaceTree,
 author = {Plaisant, Catherine and Grosjean, Jesse and Bederson, Benjamin B.},
 title = {SpaceTree: Supporting Exploration in Large Node Link Tree, Design Evolution and Empirical Evaluation},
 booktitle = {Proc. IEEE Symp. on Information Visualization (InfoVis'02)},
 series = {INFOVIS '02},
 year = {2002},
 isbn = {0-7695-1751-X},
 pages = {57--},
 //url = {http://dl.acm.org/citation.cfm?id=857191.857752},
 acmid = {857752},
 publisher = {IEEE Computer Society},
 address = {Washington, DC, USA},
}

@inproceedings{Lamping1995HyperbolicTrees,
 author = {Lamping, John and Rao, Ramana and Pirolli, Peter},
 title = {A Focus+Context Technique Based on Hyperbolic Geometry for Visualizing Large Hierarchies},
 booktitle = {Proc. ACM Conf. on Human Factors in Computing Systems},
 series = {CHI '95},
 year = {1995},
 isbn = {0-201-84705-1},
 location = {Denver, Colorado, USA},
 pages = {401--408},
 numpages = {8},
 //url = {http://dx.doi.org/10.1145/223904.223956},
 doi = {10.1145/223904.223956},
 acmid = {223956},
 publisher = {ACM Press/Addison-Wesley Publishing Co.},
 address = {New York, NY, USA},
}

@inproceedings{Card2002DOITrees,
 author = {Card, Stuart K. and Nation, David},
 title = {Degree-of-interest Trees: A Component of an Attention-reactive User Interface},
 booktitle = {Proc. Working Conf. on Advanced Visual Interfaces},
 series = {AVI '02},
 year = {2002},
 isbn = {1-58113-537-8},
 location = {Trento, Italy},
 pages = {231--245},
 numpages = {15},
 //url = {http://doi.acm.org/10.1145/1556262.1556300},
 doi = {10.1145/1556262.1556300},
 acmid = {1556300},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {DOI trees, attention-reactive user interfaces, degree-of-interest trees, fisheye displays, focus+context, hierarchical display, information visualization, tree},
}

@Article{Junker2006VANTED,
AUTHOR = {Junker, Bjorn and Klukas, Christian and Schreiber, Falk},
TITLE = {VANTED: A system for advanced data analysis and visualization in the context of biological networks},
JOURNAL = {BMC Bioinformatics},
VOLUME = {7},
YEAR = {2006},
NUMBER = {1},
PAGES = {109},
PubMedID = {16519817},
ISSN = {1471-2105},
}

@Article{Dang2015ReactionFlow,
AUTHOR = {Dang, Tuan and Murray, Paul and Aurisano, Jillian and Forbes, Angus G.},
TITLE = {ReactionFlow: An Interactive Visualization Tool for Causality Analysis in Biological Pathways.},
JOURNAL = {BioVis 2015},
VOLUME = {In press},
YEAR = {2015},
NUMBER = {},
PAGES = {},
PubMedID = {},
ISSN = {},
}

@article{Stef2014FromDetailToOverview,
  author    = {Stef van den Elzen and
               Jarke J. van Wijk},
  title     = {Multivariate Network Exploration and Presentation: From Detail to Overview via Selections and Aggregations},
  journal   = {{IEEE} Trans. Vis. Comput. Graph.},
  volume    = {20},
  number    = {12},
  pages     = {2310--2319},
  year      = {2014},
  url       = {http://dx.doi.org/10.1109/TVCG.2014.2346441},
  doi       = {10.1109/TVCG.2014.2346441},
  timestamp = {Thu, 13 Nov 2014 15:38:05 +0100},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/tvcg/ElzenW14},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}

@article{HenryNodeTrix2007,
 author = {Henry, Nathalie and Fekete, Jean-Daniel and McGuffin, Michael J.},
 title = {NodeTrix: A Hybrid Visualization of Social Networks},
 journal = {{IEEE} Trans. Vis. Comput. Graph.},
 issue_date = {November 2007},
 volume = {13},
 number = {6},
 month = nov,
 year = {2007},
 issn = {1077-2626},
 pages = {1302--1309},
 numpages = {8},
 //url = {http://dx.doi.org/10.1109/TVCG.2007.70582},
 doi = {10.1109/TVCG.2007.70582},
 acmid = {1313161},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {Aggregation, Hybrid visualization, Interaction., Matrix visualization, Network visualization, Network visualization, Matrix visualization, Hybrid visualization, Aggregation, Interaction.},
}
@INPROCEEDINGS{Elmqvist2008ZAME,
author={Elmqvist, N. and Thanh-Nghi Do and Goodell, H. and Henry, N. and Fekete, J.},
booktitle={Visualization Symp., 2008. PacificVIS '08. IEEE Pacific},
title={ZAME: Interactive Large-Scale Graph Visualization},
year={2008},
month={March},
pages={215-222},
keywords={data visualisation;matrix algebra;GPU shader programs;ZAME;adjacency matrix graph representation;higher-order meta- representations;interactive large-scale graph visualization;matrix ordering algorithms;smooth multiscale browsing;zoomable adjacency matrix explorer;Aggregates;Biology computing;Computer displays;Data visualization;Electronic mail;Information systems;Large-scale systems;Navigation;Performance analysis;Proteins;H.5.1 [Information Systems]: Multimedia Information SystemsÂ¿Animations;H.5.2 [Information Systems]: User Interfaces;I.3 [Computer Methodologies]: Computer Graphics},
doi={10.1109/PACIFICVIS.2008.4475479},}

@inproceedings{Kornaropoulos2012DAGView,
 author = {Kornaropoulos, Evgenios M. and Tollis, Ioannis G.},
 title = {DAGView: An Approach for Visualizing Large Graphs},
 booktitle = {Proc. 20th International Conference on Graph Drawing},
 series = {GD'12},
 year = {2013},
 isbn = {978-3-642-36762-5},
 location = {Redmond, WA},
 pages = {499--510},
 numpages = {12},
 //url = {http://dx.doi.org/10.1007/978-3-642-36763-2_44},
 doi = {10.1007/978-3-642-36763-2_44},
 acmid = {2449809},
 publisher = {Springer-Verlag},
 address = {Berlin, Heidelberg},
}

@inproceedings{Wattenberg2005BabyNames,
 author = {Wattenberg, Martin},
 title = {Baby Names, Visualization, and Social Data Analysis},
 booktitle = {Proc. IEEE Symp. on Information Visualization},
 year = {2005},
 pages = {1--7},
 }

 @article{Dork2010BackChannel,
 author = {Dork, Marian and Gruen, Daniel and Williamson, Carey and Carpendale, Sheelagh},
 title = {A Visual Backchannel for Large-Scale Events},
 journal = {{IEEE} Trans. Vis. Comput. Graph.},
 issue_date = {November 2010},
 volume = {16},
 number = {6},
 year = {2010},
 issn = {1077-2626},
 pages = {1129--1138},
 numpages = {10},
 //url = {http://dx.doi.org/10.1109/TVCG.2010.129},
 doi = {10.1109/TVCG.2010.129},
 acmid = {1907999},
 }

@article{EvoRiver2014,
  author    = {Guodao Sun and
               Yingcai Wu and
               Shixia Liu and
               Tai{-}Quan Peng and
               Jonathan J. H. Zhu and
               Ronghua Liang},
  title     = {{EvoRiver: V}isual Analysis of Topic Competition on Social Media},
  journal   = {{IEEE} Trans. Vis. Comput. Graph.},
  volume    = {20},
  number    = {12},
  pages     = {1753--1762},
  year      = {2014},
  url       = {http://dx.doi.org/10.1109/TVCG.2014.2346919},
  doi       = {10.1109/TVCG.2014.2346919},
  timestamp = {Thu, 13 Nov 2014 15:38:05 +0100},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/tvcg/SunWLPZL14},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}
@article{Curtis2011TVNViewer,
author = {Curtis, Ross E. and Yuen, Amos and Song, Le and Goyal, Anuj and Xing, Eric P.},
title = {TVNViewer: An interactive visualization tool for exploring networks that change over time or space},
volume = {27},
number = {13},
pages = {1880-1881},
year = {2011},
doi = {10.1093/bioinformatics/btr273},
abstract ={Summary: The relationship between genes and proteins is a dynamic relationship that changes across time and differs in different cells. The study of these differences can reveal various insights into biological processes and disease progression, especially with the aid of proper tools for network visualization. Toward this purpose, we have developed TVNViewer, a novel visualization tool, which is specifically designed to aid in the exploration and analysis of dynamic networks.Availability: TVNViewer is freely available with documentation and tutorials on the web at http://sailing.cs.cmu.edu/tvnviewer.Contact: epxing@cs.cmu.edu},
//url = {http://bioinformatics.oxfordjournals.org/content/27/13/1880.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/27/13/1880.full.pdf+html},
journal = {Bioinformatics}
}

@article{Cui2011TextFlow,
 author = {Cui, Weiwei and Liu, Shixia and Tan, Li and Shi, Conglei and Song, Yangqiu and Gao, Zekai and Qu, Huamin and Tong, Xin},
 title = {{TextFlow: T}owards Better Understanding of Evolving Topics in Text},
 journal = {{IEEE} Trans. Vis. Comput. Graph.},
 issue_date = {December 2011},
 volume = {17},
 number = {12},
 year = {2011},
 issn = {1077-2626},
 pages = {2412--2421},
 numpages = {10},
 //url = {http://dx.doi.org/10.1109/TVCG.2011.239},
 doi = {10.1109/TVCG.2011.239},
 acmid = {2068654},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {Text visualization, Topic evolution, Hierarchical Dirichlet process, Critical event.},
}

@article{Xu2013TopicCompetition,
 author = {Xu, Panpan and Wu, Yingcai and Wei, Enxun and Peng, Tai-Quan and Liu, Shixia and Zhu, Jonathan J. H. and Qu, Huamin},
 title = {Visual Analysis of Topic Competition on Social Media},
 journal = {{IEEE} Trans. Vis. Comput. Graph.},
 volume = {19},
 number = {12},
 year = {2013},
 pages = {2012--2021},
 numpages = {10},
 //url = {http://dx.doi.org/10.1109/TVCG.2013.221},
 doi = {10.1109/TVCG.2013.221},
 acmid = {2553800},
 }

@INPROCEEDINGS{Liu2014TopicPanorama,
author={Shixia Liu and Xiting Wang and Jianfei Chen and Jun Zhu and Baining Guo},
booktitle={Visual Analytics Science and Technology (VAST), 2014 IEEE Conference on},
title={TopicPanorama: A full picture of relevant topics},
year={2014},
pages={183-192},
keywords={data visualisation;graph theory;LOD-based visualization;TopicPanorama;density-based graph visualization;distinctive topics;graph matching method;radially stacked tree visualization;relevant topics;topic graph;visual analytics;Algorithm design and analysis;Correlation;Google;Government;Internet;Layout;Visualization;Topic graph;graph matching;graph visualization;level-of-detail;user interactions},
doi={10.1109/VAST.2014.7042494},
month={Oct},}

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 acmid = {1477421},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 }

 @ARTICLE{TopicCompetition2013Xu,
author={Panpan Xu and Yingcai Wu and Enxun Wei and Tai-Quan Peng and Shixia Liu and Zhu, J.J.H. and Huamin Qu},
journal={{IEEE} Trans. Vis. Comput. Graph.},
title={Visual Analysis of Topic Competition on Social Media},
year={2013},
volume={19},
number={12},
pages={2012--2021},
doi={10.1109/TVCG.2013.221},
ISSN={1077-2626},
}

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}

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  howpublished = {\url{http://similardiversity.net/}},
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journal={{IEEE} Trans. Vis. Comput. Graph.},
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year={2012},
volume={18},
number={12},
pages={2679-2688},
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ISSN={1077-2626},
month={Dec},}

@article{Liu2013StoryFlow,
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@inproceedings{dang2012fmfinder,
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@article{arias2011rdf,
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year={2013},
volume={19},
number={3},
pages={470-483},
doi={10.1109/TVCG.2012.128},
ISSN={1077-2626},
month={March},}

@inproceedings{Purchase1997Aesthetic,
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@article{Javed2010BradedGraph,
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@inproceedings{dang2013timeexplorer,
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@article{Shmueli2006TimeSearcher,
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@inproceedings{buono2005interactive,
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@inproceedings{periodic98,
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@online{Gellman2013EdwardSnowden,
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}

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@INPROCEEDINGS{Elzen2013ReorderingMSV,
author={van den Elzen, S. and Holten, D. and Blaas, J. and van Wijk, J.J.},
booktitle={Proc. IEEE Pacific Visualization Symp.},
title={Reordering Massive Sequence Views: {E}nabling temporal and structural analysis of dynamic networks},
year={2013},
pages={33--40},
doi={10.1109/PacificVis.2013.6596125},
ISSN={2165-8765},
}

@inproceedings{Greilich2009TimeArcTrees,
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 acmid = {2421941},
}

@ARTICLE{Burch2011ParallelEdge,
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title={Parallel Edge Splatting for Scalable Dynamic Graph Visualization},
year={2011},
volume={17},
number={12},
pages={2344-2353},
doi={10.1109/TVCG.2011.226},
ISSN={1077-2626},
}

@inproceedings{Garey1974NPcomplete,
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}

@ARTICLE{Kirkpatrick83optimizationby,
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@INPROCEEDINGS{Beck2012RSVP,
author={Beck, F. and Burch, M. and Vehlow, C. and Diehl, S. and Weiskopf, D.},
booktitle={Proc. IEEE Symp. on Visual Languages and Human-Centric Computing},
title={Rapid Serial Visual Presentation in dynamic graph visualization},
year={2012},
pages={185-192},
}

@inproceedings{McGee2012StudyHEB,
 author = {McGee, Fintan and Dingliana, John},
 title = {An Empirical Study on the Impact of Edge Bundling on User Comprehension of Graphs},
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 year = {2012},
 pages = {620--627},
}

@ARTICLE{Krstajic2011CloudLines,
author={Krstajic, M. and Bertini, E. and Keim, D.A.},
journal={{IEEE} Trans. Vis. Comput. Graph.},
title={{CloudLines: C}ompact Display of Event Episodes in Multiple Time-Series},
year={2011},
volume={17},
number={12},
pages={2432-2439},
}

@article{luo2012eventriver,
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  publisher={IEEE}
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@inproceedings{Reas2005Processing,
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@article{Bostock2011D3,
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@article {beck2016taxonomy,
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@inproceedings{Burch2012RadialEdgeSplatting,
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@INPROCEEDINGS{Vehlow2013RadialLayeredMatrix,
author={C. Vehlow and M. Burch and H. Schmauder and D. Weiskopf},
booktitle={Proc. Int. Conf. on Information Visualisation},
title={Radial Layered Matrix Visualization of Dynamic Graphs},
year={2013},
pages={51-58},
}

@inproceedings{Bach2014MatrixCubes,
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 title = {Visualizing Dynamic Networks with Matrix Cubes},
 booktitle = {Proc. ACM Conf. on Human Factors in Computing Systems},
 year = {2014},
 pages = {877--886},
 acmid = {2557010},
 keywords = {dynamic networks, information visualization, interaction, metaphors, multiple views},
}

@INPROCEEDINGS{Brandes2002VisualUnrolling,
author={U. Brandes and S. R. Corman},
booktitle={IEEE Symp. on Information Visualization},
title={Visual unrolling of network evolution and the analysis of dynamic discourse},
year={2002},
pages={145-151},
}

@ARTICLE {Yi2010Timematrix,
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    JOURNAL = { Int. J. Hum. Comput. Int. },
    AUTHOR = { Yi, Ji Soo and Elmqvist, Niklas and Seungyoon, Lee},
    YEAR = { 2010 },
    PAGES = { 1031--1051 },
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@article{Ghoniem2005Readability,
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@ARTICLE{Henry2006MatrixExplorer,
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year={2006},
volume={12},
number={5},
pages={677-684},
keywords={data visualisation;diagrams;graph theory;matrix algebra;pattern clustering;social sciences computing;MatrixExplorer;clustering functions;dual-representation system;interactive filtering;matrix-based representations;network visualization system;node-link diagrams;social networks;consensus.;exploratory process;interactive clustering;matrix ordering;matrix-based representations;node-link diagrams;social networks visualization;Algorithms;Cluster Analysis;Computer Graphics;Computer Simulation;Information Storage and Retrieval;Models, Biological;Population Dynamics;Social Behavior;Social Support;Software;User-Computer Interface},
doi={10.1109/TVCG.2006.160},
ISSN={1077-2626},
//month={Sept},
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@inproceedings{Bach2015multipiles,
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@inproceedings{Reda2011Community,
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@inproceedings{Kim2010TimeNets,
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@article{Ahn2014TaxonomyEvolution,
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%References for  BioLinker submitted to BioVis 2016
@InProceedings{Valenzuela:16,
  author    = {Valenzuela-Esc\'{a}rcega, Marco A. and Gustave Hahn-Powell  and Mihai Surdeanu},
  title     = {Odin's Runes: A Rule Language for Information Extraction},
  booktitle = {Proceedings of the 10th edition of the Language Resources and Evaluation Conference (LREC)},
  year      = {2016},
}

@InProceedings{Valenzuela:15,
  author    = {Valenzuela-Esc\'{a}rcega, Marco A. and Gustave Hahn-Powell and Thomas Hicks and Mihai Surdeanu},
  title     = {A Domain-independent Rule-based Framework for Event Extraction},
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  year      = {2015},
}

@article{Valenzuela2015DBLP,
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  journal   = {CoRR},
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  year      = {2015},
  url       = {http://arxiv.org/abs/1509.07513},
  timestamp = {Thu, 01 Oct 2015 14:28:48 +0200},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/corr/Valenzuela-Escarcega15},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}

@article{Kutmon2016WikiPathways,
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year = {2016},
journal = {Nucleic Acids Research}
}

@article{Dang2016TimeArcs,
 author = {Tuan Dang and Nick Pendar and Angus Graeme Forbes},
 title = {TimeArcs: Visualizing fluctuations in dynamic networks},
 journal = {IEEE Conference on Visualization (EuroVis)},
 year = {2016},
}

@article{Dang2010Stacking,
    author = {Dang, Tuan N. and Wilkinson, Leland and Anand, Anushka},
    citeulike-article-id = {9416572},
    journal = {IEEE Transactions On Visualization And Computer Graphics},
    number = {6},
    posted-at = {2011-06-15 16:00:59},
    priority = {2},
    title = {{Stacking graphic elements to avoid over-plotting}},
    volume = {16},
    year = {2010}
}

@INPROCEEDINGS{Wilkinson2005scagnostics,
author={L. Wilkinson and A. Anand and R. Grossman},
booktitle={Proceedings of the IEEE Symposium on Information Visualization},
title={Graph-theoretic scagnostics},
year={2005},
pages={157-164},
keywords={data visualisation;graph theory;Tukey scagnostics;data visualization;graph-theoretic scagnostics;statistical graphics;Area measurement;Computer interfaces;Covariance matrix;Density measurement;Displays;Kernel;Length measurement;Scattering;Symmetric matrices;Visualization},
ISSN={1522-404X}}

@ARTICLE{Dang2014Transforming,
author={T. N. Dang and L. Wilkinson},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Transforming Scagnostics to Reveal Hidden Features},
year={2014},
volume={20},
number={12},
pages={1624-1632},
keywords={data mining;data visualisation;statistical analysis;data visualization;hidden structure discovery;scagnostics;scale transformation;scatterplot collection;scatterplot diagnostics;scatterplot matrices;statistical transformations;Data visualization;Feature extraction;Shape analysis;Visual analytics;High-Dimensional Visual Analytics;Scagnostics;Scatterplot matrix;Transformation},
ISSN={1077-2626},
month={Dec},}

@Article{Huang2009Bioinformatics,
AUTHOR = {	Huang, da W and 	Sherman, BT and 	Lempicki, RA	},
TITLE = {Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.},
JOURNAL = {Nucleic Acids Research},
VOLUME = {37},
YEAR = {2009-01-01 00:00:00.001},
NUMBER = {5},
PAGES = {1-13},
DOI = {10.1093/nar/gkn923},
ISSN = {1362-4962},
}

@article{Suderman2007Tools,
 author = {Suderman, Matthew and Hallett, Michael},
 title = {Tools for Visually Exploring Biological Networks},
 journal = {Bioinformatics},
 issue_date = {September 2007},
 volume = {23},
 number = {20},
 month = sep,
 year = {2007},
 issn = {1367-4803},
 pages = {2651--2659},
 numpages = {9},
 url = {http://dx.doi.org/10.1093/bioinformatics/btm401},
 doi = {10.1093/bioinformatics/btm401},
 acmid = {1349188},
 publisher = {Oxford University Press},
 address = {Oxford, UK},
}

@Article{Pavlopoulos2008Survey,
author="Pavlopoulos, Georgios A.
and Wegener, Anna-Lynn
and Schneider, Reinhard",
title="A survey of visualization tools for biological network analysis",
journal="BioData Mining",
year="2008",
volume="1",
number="1",
pages="12",
abstract="The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing.",
issn="1756-0381",
doi="10.1186/1756-0381-1-12",
url="http://dx.doi.org/10.1186/1756-0381-1-12"
}

repository: iDataVisualizationLab/BioLinker

repo_name: iDataVisualizationLab/BioLinker


text:
package service

import (
	"encoding/json"
	"fmt"
	"path"
	"testing"
	"time"

	etcd "github.com/coreos/etcd/client"
	. "github.com/smartystreets/goconvey/convey"
	"golang.org/x/net/context"
)

func TestRegister(t *testing.T) {
	Convey("After registering service test", t, func() {
		host := genHost("test-register")
		Convey("It should be available with etcd", func() {
			r, err := Register("test_register", host, make(chan struct{}))
			So(err, ShouldBeNil)
			<-r

			res, err := KAPI().Get(context.Background(), "/services/test_register/"+host.Name, &etcd.GetOptions{})
			So(err, ShouldBeNil)

			h := &Host{}
			json.Unmarshal([]byte(res.Node.Value), &h)

			So(path.Base(res.Node.Key), ShouldEqual, host.Name)
			So(h, ShouldResemble, host)
		})

		Convey(fmt.Sprintf("And the ttl must be < %d", HEARTBEAT_DURATION), func() {
			r, _ := Register("test2_register", host, make(chan struct{}))
			<-r
			res, err := KAPI().Get(context.Background(), "/services/test2_register/"+host.Name, &etcd.GetOptions{})
			So(err, ShouldBeNil)
			now := time.Now()
			duration := res.Node.Expiration.Sub(now)
			So(duration, ShouldBeLessThanOrEqualTo, HEARTBEAT_DURATION*time.Second)
		})

		Convey("After sending stop, the service should disappear", func() {
			stop := make(chan struct{})
			host := genHost("test-disappear")
			r, _ := Register("test3_register", host, stop)
			<-r
			close(stop)
			time.Sleep(100 * time.Millisecond)
			_, err := KAPI().Get(context.Background(), "/services/test3_register/"+host.Name, &etcd.GetOptions{})
			So(etcd.IsKeyNotFound(err), ShouldBeTrue)
		})
	})
}

repository: neoduan/etcd-discovery

license_type: permissive

repo_name: neoduan/etcd-discovery

branch_name: refs/heads/master

extension: go


text:
@CONFERENCE{hoffer1996,
  author = {R. Hoffer and D. Dean},
  title = {Geomatics at Colorado State University},
  booktitle = {6th Forest Service Remote Sensing Applications Conference},
  year = {1996},
  month = {April 29--May 3},
  owner = {tbhartman},
  timestamp = {2012.07.13}
}

@ARTICLE{ikegami1990,
  author = {R. Ikegami and D.G. Wilson and J.R. Anderson and G.J. Julien},
  title = {Active Vibration Control Using NiTiNOL and Piezoelectric Ceramics,},
  journal = {Journal of Intelligent Material Systems and Structures},
  year = {1990},
  volume = {20},
  pages = {189--206},
  number = {2},
  owner = {tbhartman},
  timestamp = {2012.07.13}
}

@INBOOK{inman1998,
  chapter = {Smart Structures Solutions to Vibration Problems},
  pages = {79--83},
  title = {International Conference on Noise and Vibration Engineering},
  publisher = {Elsevier},
  year = {1998},
  editor = {C.W. Jefford and K.L. Reinhart and L.S. Shield},
  author = {D.J. Inman},
  address = {Amsterdam},
  owner = {tbhartman},
  timestamp = {2012.07.13}
}

@TECHREPORT{margarit1993,
  author = {K.L. Margarit and F.Y. Samnford},
  title = {Basic Technology of Intelligent Systems},
  institution = {Department of Smart Materials, Virginia Polytechnic Institute and
	State University},
  year = {1993},
  number = {Fourth Progress Report},
  address = {Blacksburg},
  month = {March},
  owner = {tbhartman},
  timestamp = {2012.07.13}
}

@BOOK{mitsiti1996,
  title = {Wavelet Toolbox},
  publisher = {The Math Works, Inc.},
  year = {1996},
  author = {M. Mitsiti},
  pages = {111--117},
  owner = {tbhartman},
  timestamp = {2012.07.13}
}

repository: tbhartman/asc-cls

repo_name: tbhartman/asc-cls

extension: bib


text:
module.exports = query_2_json
query_2_json.query2json = query2json
query_2_json.query2json = query2json
query_2_json.json2tree = json2tree
query_2_json.rule2tree = rule2tree
query_2_json.tree2json = tree2json
query_2_json.tree2rule = tree2rule

function json2query(input) {

    var OperatorsFns = {
        equal: function (v) {
            return v[0] + " == " + v[1];
        },
        not_equal: function (v) {
            return v[0] + " != " + v[1];
        },
        less: function (v) {
            return v[0] + " < " + v[1];
        },
        less_or_equal: function (v) {
            return v[0] + " <= " + v[1];
        },
        greater: function (v) {
            return v[0] + " > " + v[1];
        },
        greater_or_equal: function (v) {
            return v[0] + " >= " + v[1];
        }
    }

    if (!input) {
        return null;
    }

    var self = this;

    return (function parse(group, level = 0) {

        if (['AND', 'OR'].indexOf(group.condition.toUpperCase()) === -1) {
            throw new Error('Unable to build rule with condition ' + group.condition);
        }

        if (!group.rules) {
            return {};
        }

        var parts = [];

        group.rules.forEach(function (rule) {
            if (rule.rules && rule.rules.length > 0) {
                parts.push(parse(rule, level + 1));
            } else if (rule.rules && rule.rules.length == 0) {
                return
            } else {
                let op = ""
                switch (rule.operator.toLowerCase()) {
                    case "=":
                    case "==":
                    case "eq":
                    case "eqeq":
                    case "equal":
                        op = "equal"
                        break;
                    case "!=":
                    case "not_eq":
                    case "not_equal":
                        op = "not_equal";
                        break;
                    case "<":
                    case "less":
                        op = "less";
                        break;
                    case ">":
                    case "greater":
                        op = "greater";
                        break;
                    case "<=":
                    case "less_or_equal":
                        op = "less_or_equal";
                        break;
                    case ">=":
                    case "greater_or_equal":
                        op = "greater_or_equal";
                        break;
                }
                var expFunction = OperatorsFns[op];
                var ruleExpression = {};
                if (expFunction === undefined) {
                    ruleExpression = ""
                } else {
                    ruleExpression = expFunction.call(self, [rule.field, rule.value]);
                }
                parts.push(ruleExpression);
            }
        });

        var output = '';
        for (var i = 0; i < parts.length; i++) {
            if (typeof parts[i + 1] != 'undefined') {
                if (parts[i] != "") {
                    let joiner = group.condition.toLowerCase() == 'and' ? ' && ' : ' || '
                    output += parts[i] + joiner
                }
            } else {
                if (parts[i] != "") {
                    output += parts[i];
                }
            }
        }
        if (level == 0) return output
        output = '(' + output + ')';

        return (output);

    })(input);
}

function query2json(str, opts) {
    if (typeof str !== 'string') return [str]
    var res = [str]

    if (typeof opts === 'string' || Array.isArray(opts)) {
        opts = { brackets: opts }
    }
    else if (!opts) opts = {}

    var brackets = opts.brackets ? (Array.isArray(opts.brackets) ? opts.brackets : [opts.brackets]) : ['{}', '[]', '()']

    var escape = opts.escape || '___'

    brackets.forEach(function (bracket) {
        // create parenthesis regex
        var pRE = new RegExp(['\\', bracket[0], '[^\\', bracket[0], '\\', bracket[1], ']*\\', bracket[1]].join(''))

        var ids = []

        function replaceToken(token, idx, str) {
            // save token to res
            var refId = res.push(token.slice(bracket[0].length, -bracket[1].length)) - 1

            ids.push(refId)

            return escape + refId + escape
        }

        res.forEach(function (str, i) {
            var prevStr

            // replace paren tokens till there’s none
            var a = 0
            while (str != prevStr) {
                prevStr = str
                str = str.replace(pRE, replaceToken)
                if (a++ > 10e3) throw Error('References have circular dependency. Please, check them.')
            }

            res[i] = str
        })

        // wrap found refs to brackets

        ids = ids.reverse()
        res = res.map(function (str) {
            ids.forEach(function (id) {
                str = str.replace(new RegExp('(\\' + escape + id + '\\' + escape + ')', 'g'), bracket[0] + '$1' + bracket[1])
            })
            return str
        })
    })

    var re = new RegExp('\\' + escape + '([0-9]+)' + '\\' + escape)
    return function nest({ str, refs, level = 0 }) {
        var res = [], match
        let condition = "and"
        let rules = str.trim().replace(" ", "").split(/[\|\&]{2}/g)//split by ||, &&
        if (str.trim().replace(" ", "").indexOf("||") != -1) condition = "or"
        var a = 0
        rules.forEach(r => {
            while (match = re.exec(r)) {
                if (a++ > 10e3) throw Error('Circular references in parenthesis')
                let s = refs[match[1]]
                if (s != '') {
                    let OR = s.trim().replace(" ", "").split("||")
                    let AND = s.trim().replace(" ", "").split("&&")
                    OR = OR.filter((i) => i.indexOf("&&") == -1 && i != "")
                    AND = AND.filter((i) => i.indexOf("||") == -1 && i != "")
                    OR = OR.map(o => o.trim())
                    AND = AND.map(a => a.trim())
                    if (AND.length > 0 || OR.length > 0) {
                        res.push({ ...nest({ str: s, refs, level: level + 1 }) })
                    }
                }
                r = r.slice(match.index + (match[0].length + 1))//skips the next bracket
            }
            if (r != '') {
                let rules = r.trim().replace(" ", "");
                let fields = rules.trim().split(/(?!\])(?<!\[)[\*\=\!\/\%\<\>]{1,3}/g)//split into left and right
                let operator = rules.trim().replace(fields[0], "").replace(fields[1], "").trim()
                let obj = {
                    id: "r-" + Math.random().toString(36).substr(2, 9),
                    field: fields[0] ? fields[0].trim() : "",
                    operator,
                    value: fields[1] ? fields[1].trim() : ""
                }
                res.push(obj)
            }
        })
        return { id: "g-" + Math.random().toString(36).substr(2, 9), condition, rules: res }
    }({ str: res[0], refs: res })
}
function json2tree(obj) {
    let treeObj = {
        key: "",
        title: "",
        children: []
    }
    if (obj.id !== "" && obj.id !== undefined) {
        if (obj.id.indexOf("g-") != -1) {
            treeObj.key = obj.id
            treeObj.title = obj.condition.toUpperCase()
            obj.rules.forEach(r => {
                let ch = json2tree(r)
                if (ch != null) {
                    ch.ParentKey = treeObj.key
                    treeObj.children.push(ch)
                }
            })

        } else if (obj.id.indexOf("r-") != -1) {
            treeObj.key = obj.id
            treeObj.title = (obj.field || "") + " " + (obj.operator || "") + " " + (obj.value || "")
            delete treeObj.children
        }
        return treeObj
    }
    return
}

function tree2json(obj) {
    let treeObj = {
        id: "",
        condition: "",
        rules: []
    }
    if (obj.key !== "" && obj.key !== undefined) {
        if (obj.key.indexOf("g-") != -1) {
            treeObj.id = obj.key
            treeObj.condition = obj.title.trim().toLowerCase()
            obj.children.forEach(r => {
                let ch = tree2json(r)
                if (ch != null) {
                    ch.ParentId = treeObj.id
                    treeObj.rules.push(ch)
                }
            })

        } else if (obj.key.indexOf("r-") != -1) {
            treeObj.id = obj.key
            let rules = obj.title.trim().replace(" ", "");
            let fields = rules.trim().split(/(?!\])(?<!\[)[\*\=\!\/\%\<\>]{1,3}/g)//split into left and right
            let operator = rules.trim().replace(fields[0], "").replace(fields[1], "").trim()
            treeObj.field = fields[0] ? fields[0].trim() : ""
            treeObj.operator = operator
            treeObj.value = fields[1] ? fields[1].trim() : ""
            delete treeObj.condition
            delete treeObj.rules
        }
        return treeObj
    }
    return
}

function rule2tree(str) {
    return json2tree(query_2_json(str, { brackets: ['()'] }))
}
function tree2rule(tree) {
    let json = tree2json(tree)
    return json2query(json)
}

function query_2_json(arg, opts) {
    isObject = function (a) {
        return (!!a) && (a.constructor === Object);
    };
    if (typeof arg === "string") {
        return query2json(arg, opts)
    } else if (isObject(arg)) {
        return json2query(arg)
    } else {
        return -1
    }
}

license: MIT

extension: js


text:
// Code generated by the Pulumi SDK Generator DO NOT EDIT.
// *** WARNING: Do not edit by hand unless you're certain you know what you are doing! ***

package servicecatalogappregistry

import (
	"context"
	"reflect"

	"errors"
	"github.com/pulumi/pulumi-aws-native/sdk/go/aws/internal"
	"github.com/pulumi/pulumi/sdk/v3/go/pulumi"
)

// Resource Schema for AWS::ServiceCatalogAppRegistry::ResourceAssociation
type ResourceAssociation struct {
	pulumi.CustomResourceState

	// The name or the Id of the Application.
	Application    pulumi.StringOutput `pulumi:"application"`
	ApplicationArn pulumi.StringOutput `pulumi:"applicationArn"`
	// The name or the Id of the Resource.
	Resource    pulumi.StringOutput `pulumi:"resource"`
	ResourceArn pulumi.StringOutput `pulumi:"resourceArn"`
	// The type of the CFN Resource for now it's enum CFN_STACK.
	ResourceType ResourceAssociationResourceTypeOutput `pulumi:"resourceType"`
}

// NewResourceAssociation registers a new resource with the given unique name, arguments, and options.
func NewResourceAssociation(ctx *pulumi.Context,
	name string, args *ResourceAssociationArgs, opts ...pulumi.ResourceOption) (*ResourceAssociation, error) {
	if args == nil {
		return nil, errors.New("missing one or more required arguments")
	}

	if args.Application == nil {
		return nil, errors.New("invalid value for required argument 'Application'")
	}
	if args.Resource == nil {
		return nil, errors.New("invalid value for required argument 'Resource'")
	}
	if args.ResourceType == nil {
		return nil, errors.New("invalid value for required argument 'ResourceType'")
	}
	opts = internal.PkgResourceDefaultOpts(opts)
	var resource ResourceAssociation
	err := ctx.RegisterResource("aws-native:servicecatalogappregistry:ResourceAssociation", name, args, &resource, opts...)
	if err != nil {
		return nil, err
	}
	return &resource, nil
}

// GetResourceAssociation gets an existing ResourceAssociation resource's state with the given name, ID, and optional
// state properties that are used to uniquely qualify the lookup (nil if not required).
func GetResourceAssociation(ctx *pulumi.Context,
	name string, id pulumi.IDInput, state *ResourceAssociationState, opts ...pulumi.ResourceOption) (*ResourceAssociation, error) {
	var resource ResourceAssociation
	err := ctx.ReadResource("aws-native:servicecatalogappregistry:ResourceAssociation", name, id, state, &resource, opts...)
	if err != nil {
		return nil, err
	}
	return &resource, nil
}

// Input properties used for looking up and filtering ResourceAssociation resources.
type resourceAssociationState struct {
}

type ResourceAssociationState struct {
}

func (ResourceAssociationState) ElementType() reflect.Type {
	return reflect.TypeOf((*resourceAssociationState)(nil)).Elem()
}

type resourceAssociationArgs struct {
	// The name or the Id of the Application.
	Application string `pulumi:"application"`
	// The name or the Id of the Resource.
	Resource string `pulumi:"resource"`
	// The type of the CFN Resource for now it's enum CFN_STACK.
	ResourceType ResourceAssociationResourceType `pulumi:"resourceType"`
}

// The set of arguments for constructing a ResourceAssociation resource.
type ResourceAssociationArgs struct {
	// The name or the Id of the Application.
	Application pulumi.StringInput
	// The name or the Id of the Resource.
	Resource pulumi.StringInput
	// The type of the CFN Resource for now it's enum CFN_STACK.
	ResourceType ResourceAssociationResourceTypeInput
}

func (ResourceAssociationArgs) ElementType() reflect.Type {
	return reflect.TypeOf((*resourceAssociationArgs)(nil)).Elem()
}

type ResourceAssociationInput interface {
	pulumi.Input

	ToResourceAssociationOutput() ResourceAssociationOutput
	ToResourceAssociationOutputWithContext(ctx context.Context) ResourceAssociationOutput
}

func (*ResourceAssociation) ElementType() reflect.Type {
	return reflect.TypeOf((**ResourceAssociation)(nil)).Elem()
}

func (i *ResourceAssociation) ToResourceAssociationOutput() ResourceAssociationOutput {
	return i.ToResourceAssociationOutputWithContext(context.Background())
}

func (i *ResourceAssociation) ToResourceAssociationOutputWithContext(ctx context.Context) ResourceAssociationOutput {
	return pulumi.ToOutputWithContext(ctx, i).(ResourceAssociationOutput)
}

type ResourceAssociationOutput struct{ *pulumi.OutputState }

func (ResourceAssociationOutput) ElementType() reflect.Type {
	return reflect.TypeOf((**ResourceAssociation)(nil)).Elem()
}

func (o ResourceAssociationOutput) ToResourceAssociationOutput() ResourceAssociationOutput {
	return o
}

func (o ResourceAssociationOutput) ToResourceAssociationOutputWithContext(ctx context.Context) ResourceAssociationOutput {
	return o
}

// The name or the Id of the Application.
func (o ResourceAssociationOutput) Application() pulumi.StringOutput {
	return o.ApplyT(func(v *ResourceAssociation) pulumi.StringOutput { return v.Application }).(pulumi.StringOutput)
}

func (o ResourceAssociationOutput) ApplicationArn() pulumi.StringOutput {
	return o.ApplyT(func(v *ResourceAssociation) pulumi.StringOutput { return v.ApplicationArn }).(pulumi.StringOutput)
}

// The name or the Id of the Resource.
func (o ResourceAssociationOutput) Resource() pulumi.StringOutput {
	return o.ApplyT(func(v *ResourceAssociation) pulumi.StringOutput { return v.Resource }).(pulumi.StringOutput)
}

func (o ResourceAssociationOutput) ResourceArn() pulumi.StringOutput {
	return o.ApplyT(func(v *ResourceAssociation) pulumi.StringOutput { return v.ResourceArn }).(pulumi.StringOutput)
}

// The type of the CFN Resource for now it's enum CFN_STACK.
func (o ResourceAssociationOutput) ResourceType() ResourceAssociationResourceTypeOutput {
	return o.ApplyT(func(v *ResourceAssociation) ResourceAssociationResourceTypeOutput { return v.ResourceType }).(ResourceAssociationResourceTypeOutput)
}

func init() {
	pulumi.RegisterInputType(reflect.TypeOf((*ResourceAssociationInput)(nil)).Elem(), &ResourceAssociation{})
	pulumi.RegisterOutputType(ResourceAssociationOutput{})
}

repository: pulumi/pulumi-aws-native

repo_name: pulumi/pulumi-aws-native

gha_language: Go


text:
DESCRIPTION = "A handy tool to manipulate and read memory mapped registers"
HOMEPAGE = "https://github.com/pengutronix/memtool"

LICENSE = "GPL-2.0-only"
LIC_FILES_CHKSUM = "file://COPYING;md5=b234ee4d69f5fce4486a80fdaf4a4263"

SRC_URI = "http://www.pengutronix.de/software/memtool/downloads/memtool-${PV}.tar.xz"
SRC_URI[md5sum] = "b3b16018cda270fa1d375ea09b67d6ae"
SRC_URI[sha256sum] = "87cb7175266ff3a00a9c1f541c4c6c93693ffbe8dcc0d97a60d13c45ff860900"

PACKAGECONFIG ??= "mdio"
PACKAGECONFIG[mdio] = "--enable-mdio,--disable-mdio"

inherit autotools

repository: pengutronix/meta-ptx

repo_name: pengutronix/meta-ptx

gha_license_id: MIT

gha_language: BitBake

extension: bb


text:
// resources
package nap

import "testing"

func TestEndpointTemplate(t *testing.T) {
	res := &RestResource{
		Endpoint: "/user/{{.user}}",
		Method:   "GET",
		Router:   NewRouter(),
	}
	renderedEndpoint := res.RenderEndpoint(map[string]string{
		"user": "matt",
	})
	if renderedEndpoint != "/user/matt" {
		t.Fail()
	}
}

repository: davidlares/nap

repo_name: davidlares/nap


text:
@article{Schaefer_2017,
	doi = {10.1093/cercor/bhx179},
	url = {https://doi.org/10.1093%2Fcercor%2Fbhx179},
	year = 2017,
	month = {jul},
	publisher = {Oxford University Press ({OUP})},
	pages = {1--20},
	author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo},
	title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}},
	journal = {Cerebral Cortex}
}
@article{Thomas_Yeo_2011,
	doi = {10.1152/jn.00338.2011},
	url = {https://doi.org/10.1152%2Fjn.00338.2011},
	year = 2011,
	month = {jun},
	publisher = {American Physiological Society},
	volume = {106},
	number = {3},
	pages = {1125--1165},
	author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner},
	title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity},
	journal = {Journal of Neurophysiology}
}

repository: PennLINC/xcpEngine

repo_name: PennLINC/xcpEngine

gha_language: Shell


text:
SUMMARY = "HTML::Tagset - data tables useful in parsing HTML"
AUTHOR = "Andy Lester <andy@petdance.com>"
HOMEPAGE = "https://metacpan.org/module/HTML::Tagset"
SECTION = "libs"
LICENSE = "Artistic-1.0 | GPL-1.0+"
LIC_FILES_CHKSUM = "file://README;md5=1c7e012ab7d1e1944084310d6a48a32f"

SRC_URI = "http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/HTML-Tagset-${PV}.tar.gz"
SRC_URI[md5sum] = "d2bfa18fe1904df7f683e96611e87437"
SRC_URI[sha256sum] = "adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2"

S = "${WORKDIR}/HTML-Tagset-${PV}"

inherit cpan

BBCLASSEXTEND = "native"


text:
# Locate CoreServices
# This module defines
# CORESERVICES_LIBRARY
# CORESERVICES_FOUND

IF(APPLE)
  SET(CORESERVICES_FOUND "YES")
  SET(CORESERVICES_LIBRARY "-framework CoreServices")
ELSE(APPLE)
  SET(CORESERVICES_FOUND "NO")
ENDIF(APPLE)

repository: jdpipe/libcamiface

repo_name: jdpipe/libcamiface

extension: cmake


text:
@book{DymMckean,
    author    = {{H. Dym and H.P McKean}},
    title     = {{Fourier Series and Integrals}},
    publisher = {{Academic Press}},
    address  = {{New York}},
    year      = {{1972}},
}

@misc{Weier,
title = {{Teorema de Weierstrass}},
howpublished = {\url{https://en.wikipedia.org/wiki/Extreme_value_theorem}},
note = {Visitado: 23-05-2016},
}

@misc{Squeeze,
title = {{Teorema del Acotamiento}},
howpublished = {\url{https://en.wikipedia.org/wiki/Squeeze_theorem}},
note = {Visitado: 23-05-2016},
}

@misc{Leibniz,
title = {{Regla Generalizada de Leibniz}},
howpublished = {\url{https://en.wikipedia.org/wiki/General_Leibniz_rule}},
note = {Visitado: 23-05-2016},
}

repository: mavillan/EACI

repo_name: mavillan/EACI


text:
package tcpspray

import (
	"net"
	"time"

	"github.com/pkg/errors"
)

type connector struct {
	target string
	conn   net.Conn
}

func connect(remote string, timeout time.Duration) (*connector, error) {
	conn, err := net.DialTimeout("tcp", remote, timeout)
	if err != nil {
		return nil, errors.Wrapf(err, "Coudn't connect to %s.", remote)
	}
	return &connector{target: remote, conn: conn}, nil
}

repository: mbobakov/spray-rabbit

repo_name: mbobakov/spray-rabbit