@article {Avocado,
journal = {Computer Graphics Forum},
title = {{AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research}},
author = {Stitz, Holger and Luger, Stefan and Streit, Marc and Gehlenborg, Nils},
year = {2016},
publisher = {The Eurographics Association and John Wiley & Sons Ltd.},
ISSN = {1467-8659},
DOI = {10.1111/cgf.12924}
}

@article{bioconductor,
    address = {Department of Biostatistical Science, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA. rgentlem@jimmy.harvard.edu},
    author = {Gentleman, Robert C. and Carey, Vincent J. and Bates, Douglas M. and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J. and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y. and Zhang, Jianhua},
    booktitle = {Genome Biology},
    doi = {10.1186/gb-2004-5-10-r80},
    issn = {1465-6914},
    journal = {Genome biology},
    keywords = {genomics, highly, metaadpd, microarray, mining, silico},
    number = {10},
    pages = {R80--16},
    pmcid = {PMC545600},
    pmid = {15461798},
    posted-at = {2008-12-01 14:31:17},
    priority = {2},
    publisher = {BioMed Central},
    title = {{Bioconductor: open software development for computational biology and bioinformatics.}},
    url = {http://dx.doi.org/10.1186/gb-2004-5-10-r80},
    volume = {5},
    year = {2004}
}


@Article{VizBi,
  author = {Gehlenborg, Nils 
  and O'Donoghue, Sean 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 Gavin, Anne-Claude},
  title = {Visualization of omics data for systems biology},
  year = {2010},
  journal = {Nat. Methods},
  volume = {7},
  pages = {S56-68},
  pmid = {20195258}
}

@Article{Partl,
author="Partl, Christian
and Lex, Alexander
and Streit, Marc
and Kalkofen, Denis
and Kashofer, Karl
and Schmalstieg, Dieter",
title="enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets",
journal="BMC Bioinformatics",
year="2013",
volume="14",
number="19",
pages="S3",
issn="1471-2105",
doi="10.1186/1471-2105-14-S19-S3",
url="http://dx.doi.org/10.1186/1471-2105-14-S19-S3"
}

@article{Kairam15,
  added-at = {2015-08-21T00:00:00.000+0200},
  author = {Kairam, Sanjay and Riche, Nathalie Henry and Drucker, Steven M. and Fernandez, Roland and Heer, Jeffrey},
  biburl = {http://www.bibsonomy.org/bibtex/2a2ae1501c8d7b4b9c4e0a70ad5507ca9/dblp},
  ee = {http://dx.doi.org/10.1111/cgf.12642},
  interhash = {f5749e1ea0a115fc82eec21e4f88990a},
  intrahash = {a2ae1501c8d7b4b9c4e0a70ad5507ca9},
  journal = {Comput. Graph. Forum},
  keywords = {dblp},
  number = 3,
  pages = {301-310},
  timestamp = {2015-08-22T11:33:19.000+0200},
  title = {Refinery: Visual Exploration of Large, Heterogeneous Networks through Associative Browsing.},
  url = {http://dblp.uni-trier.de/db/journals/cgf/cgf34.html#KairamRDFH15},
  volume = 34,
  year = 2015
}

@article{Partl16,
  author    = {Christian Partl and
               Samuel Gratzl and
               Marc Streit and
               Anne Mai Wassermann and
               Hanspeter Pfister and
               Dieter Schmalstieg and
               Alexander Lex},
  title     = {Pathfinder: Visual Analysis of Paths in Graphs},
  journal   = {Comput. Graph. Forum},
  volume    = {35},
  number    = {3},
  pages     = {71--80},
  year      = {2016},
  url       = {http://dx.doi.org/10.1111/cgf.12883},
  doi       = {10.1111/cgf.12883},
  timestamp = {Fri, 05 Aug 2016 20:46:31 +0200},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/cgf/PartlGSWPSL16},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}

@article{cytoscape,
    address = {Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.},
    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 L. 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.},
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    journal = {Nature protocols},
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    pmcid = {PMC3685583},
    pmid = {17947979},
    posted-at = {2010-04-30 08:46:19},
    priority = {2},
    publisher = {Nature Publishing Group},
    title = {{Integration of biological networks and gene expression data using Cytoscape.}},
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    year = {2007}
}

@paper{gephi,
author = {Mathieu Bastian and Sebastien Heymann and Mathieu Jacomy},
title = {Gephi: An Open Source Software for Exploring and Manipulating Networks},
conference = {International AAAI Conference on Weblogs and Social Media},
year = {2009},
keywords = {network;network science;visualization;graph exploration;open source;free software;dynamic network;interactive interface;graph;force vector;java;OpenGL;3-D visualization;user-centric;graph layout;complex graph rendering;network analysis;webatlas},
abstract = {Gephi is an open source software for graph and network analysis. It uses a 3D render engine to display large networks in real-time and to speed up the exploration. A flexible and multi-task architecture brings new possibilities to work with complex data sets and produce valuable visual results. We present several key features of Gephi in the context of interactive exploration and interpretation of networks. It provides easy and broad access to network data and allows for spatializing, filtering, navigating, manipulating and clustering. Finally, by presenting dynamic features of Gephi, we highlight key aspects of dynamic network visualization.},
url = {http://www.aaai.org/ocs/index.php/ICWSM/09/paper/view/154}
}

@Misc{scipy,
  author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
  title =     {{SciPy}: Open source scientific tools for {Python}},
  year =      {2001--},
  url = "http://www.scipy.org/",
  note = {[Online; accessed 2017-02-22]}
}

@article{scikit-learn,
 title={Scikit-learn: Machine Learning in {P}ython},
 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
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         and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
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@article{arrieta2015,
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  author={Arrieta-Ortiz, Mario L and Hafemeister, Christoph and Bate, Ashley Rose and Chu, Timothy and Greenfield, Alex and Shuster, Bentley and Barry, Samantha N and Gallitto, Matthew and Liu, Brian and Kacmarczyk, Thadeous and others},
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  publisher={EMBO Press}
}

@article{Blatti2015,
author = {Blatti, Charles and Kazemian, Majid and Wolfe, Scot and Brodsky, Michael and Sinha, Saurabh},
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pages = {3998},
year = {2015},
doi = {10.1093/nar/gkv195},
URL = { + http://dx.doi.org/10.1093/nar/gkv195},
eprint = {/oup/backfile/Content\_public/Journal/nar/43/8/10.1093\_nar\_gkv195/2/gkv195.pdf}
}

@article{karwacz2017,
  title={Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation},
  author={Karwacz, Katarzyna and Miraldi, Emily R and Pokrovskii, Maria and Madi, Asaf and Yosef, Nir and Wortman, Ivo and Chen, Xi and Watters, Aaron and Carriero, Nicholas and Awasthi, Amit and others},
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  year={2017},
  publisher={Nature Research}
}

@article{yosef2013,
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}

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  publisher={Elsevier}
}

@article{ipython,
  title={IPython: a system for interactive scientific computing},
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  number={3},
  year={2007},
  publisher={IEEE}
}

@article{wang2006,
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  pages={2413--2420},
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@article{genotet,
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  year={2014},
  publisher={IEEE}
}

@article{fruchterman1991graph,
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@article{csardi2006igraph,
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}

@article{inferelator,
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@misc{jpgeneviz,
  author = {Watters, Aaron and and Miraldi, Emily},
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  year = {2017},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/simonsfoundation/jp\_gene\_viz}},
  commit = {4effeff767a8384ce4dac4d0daae7e29da4e05c1}
}

@misc{binder,
  author = {Andrew Osheroff},
  title = {binder},
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  journal = {GitHub repository},
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}

@article{docker,
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 year = {2014},
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} 

@article{cytoscapejs,
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@book{highcharts,
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@article{motif,
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