references.bib

% Reports
@Report{bayesiannetworks,
	title = {A Tutorial on Learning With Bayesian Networks},
	url = {http://research.microsoft.com/apps/pubs/default.aspx?id=69588},
	number = {{MSR}-{TR}-95-06},
	institution = {Microsoft Research},
	author = {Heckerman, David},
	date = {1995-03}
}

@Report{affinity-propagation,
    title = {Clustering by Passing Messages Between Data Points},
    url = {http://www.psi.toronto.edu/affinitypropagation/FreyDueckScience07.pdf},
    volume = {315},
    author = {Brendan J. Frey and Delbert Dueck},
    date = {2007-02-16}
}

@inproceedings{pagerank,
  added-at = {2008-01-09T21:02:24.000+0100},
  address = {Brisbane, Australia},
  author = {Page, L. and Brin, S. and Motwani, R. and Winograd, T.},
  biburl = {http://www.bibsonomy.org/bibtex/2ac49c33e114ca171db40cece6a0ae4d6/sac},
  booktitle = {Proceedings of the 7th International World Wide Web Conference},
  interhash = {ca10cf0b0dd668c64b1f378ff0775849},
  intrahash = {ac49c33e114ca171db40cece6a0ae4d6},
  keywords = {2007 kde pagerank seminar web},
  pages = {161--172},
  timestamp = {2008-01-09T21:02:24.000+0100},
  title = {The PageRank citation ranking: Bringing order to the Web},
  url = {citeseer.nj.nec.com/page98pagerank.html},
  year = 1998
}

@Article{iri,
    title="iRefIndex: A consolidated protein interaction database with
    provenance",
    author="Razick, Sabry and Magklaras, George and Donaldson, Ian M.",
    journal="BMC Bioinformatics",
    volume=9,
    number=1,
    year=2008,
    month=sep,
    url = {http://irefindex.org/wiki/index.php?title=iRefIndex},
    urldate = {2015-05-07}
}

@Article{irefweb,
    title="iRefWeb: interactive analysis of consolidated protein interaction
    data and their supporting evidence",
    author="Turner, Brian and Razick, Sabry and Turinsky, Andrei L. and
    Vlasblom, James and Crowdy, Edgar K. and Cho, Emerson and Morrison, Kyle and
    Donaldson, Ian M. and Wodak, Shoshana J.",
    journal="Database",
    volume=16,
    year=2010,
    month=sep,
    url = {http://wodaklab.org/iRefWeb/search/index},
    urldate = {2016-07-08}
}

@Phdthesis{mcl,
    title = {Graph clustering by flow simulation},
    school = {Utrecth of University},
    author = {Stijn Marinus van Dongen},
    year = {2000},
    url = {http://micans.org/mcl/}
}

@Article{galaxy,
    title="The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update",
    author="Afgan, Enis and Baker, Dannon and ven den Beek, Marius and
    Blankenberg, Danial and Bouvier, Dave and Cech, Martin and Chilton, John and
    Clements, Dave and Coraor, Nate and Eberhard, Carl and Grüning, Björn and
    Guerier, Aysam and Hillman-Jackson, Jennifer and Von Kuster, Greg and
    Rasche, Eric and Soranzo, Nicola and Turaga, Nitesh and Taylor, James and
    Nekrutenko, Anton and Goecks, Jeremy",
    journal="Nucleic Acids Research",
    year=2016,
    month=jul,
    url = {https://usegalaxy.org/},
    urldate = {2015-05-08}
}
    
@Article{biopython,
    title="Biopython: freely available Python tools for computational molecular
    biology and bioinformatics",
    author="Cock, Peter J.A. and Antao, Tiago and Chang, Jeffrey T. and Chapman,
    Brad A. and Cox, Cymon J. and Dalke, Andrew and Friedberg, Iddo and
    Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and de Hoon,
    Michiel J. L.",
    journal="Bioinformatics",
    year=2009,
    month=mar,
    volume=25,
    issue=11,
    url = {http://biopython.org/wiki/Main_Page},
    urldate = {2015-05-20}
}

@Article{hgnc-site,
    title="Genenames.org: the HGNC resources in 2015",
    author="Gray, KA and Yates, B and Seal, RL and Wright, MW and Bruford, EA",
    journal="Nucleic Acids Res.",
    year=2015,
    month=jan,
    url = {http://www.genenames.org},
    urldate = {2016-02-23}
}

@Article{sklearn,
    title={Scikit-learn: Machine Learning in {P}ython},
    author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
         and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
         and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
         Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
    journal={Journal of Machine Learning Research},
    volume={12},
    pages={2825--2830},
    year={2011}
}

@Article{panther,
    title="PANTHER: A Library of Protein Families and Subfamilies Indexed by
    Function",
    author="Thomas, Paul D. and Campbell, Michael J. and Kejariwal, Anish and
    Mi, Huaiyu and Karlak, Brian and Daverman, Robin and Diemer, Karen and
    Muruganujan, Anushya and Narechania, Apurva",
    journal="Genome Research",
    year=2003,
}

@Article{personalized2,
    title="Phosphoproteome Integration Reveals PatientSpecific
    Networks in Prostate Cancer",
    author="Drake, Justin M. and Paull, Evan O. and Graham, Nicholas A. and
    Graeber, Thomas G. and Witte, Owen N. and Stuart, Joshua M.",
    journal="Cell",
    volume="166",
    pages="1--14",
    year=2016,
    month=aug
}

@Article{disease-ppi,
    title="Pathway mapping and development of disease-specific biomarkers:
    protein-based network biomarkers",
    author="Chen, Hao and Zhu, Zhitu and Zhu, Yichun and Mei, Yunging and Cheng,
    Yunfeng",
    journal="Journal of Cellular and Molecular Medicine",
    year=2015,
    month=feb,
    pages="297--314"
}

@Article{psa-overtreatment,
    title="mRNA Expression Signature of Gleason Grade Predicts
    Lethal Prostate Cancer",
    author="Penney, Kathryn L. and Sinnott, Jennifer A. and Fall, Katja and
    Pawitan, Uidi and Hoshida, Yujin and Kraft, Peter and Stark, Jennifer R. and
    Fiorentino, Michelangelo and Perner, Sven and Finn, Stephen and Calza,
    Stefano and Flavin, Richard and Freedman, Matthew L. and Setlur, Sunita and
    Sesso, Howard D. and Andersson, Swen-Olof and Martin, Neil and Kantoff,
    Philip W. and Johansson, Jan-Erik and Adami, Hans-Olov and Rubin, Mark A.
    and Loda, Massimo and Golub, Todd R. and Andrén, Ove and Stampfer, Meir J.
    and Mucci, Lorelei A.",
    journal="Journal of Clinical Oncology",
    pages="2391--2396",
    volume="29",
    number="17",
    month=jun,
    year=2011
}

@Article{mcl-inflation,
    title="Evaluation of cluster algorithms for protein-protein interaction
        networks",
    author="Brohée, Sylvain and van Helden, Jacques",
    journal="BMC Informatics",
    year="2006",
    doi="10.1186/1471-2106-7-488"
}
@Article{disease-prwp,
    author="Chen, Jing
        and Aronow, Bruce J.
        and Jegga, Anil G.",
    title="Disease candidate gene identification and prioritization using
        protein interaction networks",
    journal="BMC Bioinformatics",
    year="2009",
    volume="10",
    number="1",
    pages="1--14",
    abstract="Although most of the current disease candidate gene
        identification and prioritization methods depend on functional
        annotations, the coverage of the gene functional annotations is a
        limiting factor. In the current study, we describe a candidate gene
        prioritization method that is entirely based on protein-protein
        interaction network (PPIN) analyses.",
    issn="1471-2105",
    doi="10.1186/1471-2105-10-73",
    url="http://dx.doi.org/10.1186/1471-2105-10-73"
}

@Article{jensen,
    title = {DISEASES: text mining and data integration of disease-gene
        associations},
    author = {Pletscher-Frankild, S and Pallejà, A and Tsafou, K and Binder, JX
        and Jensen, LJ},
    journal = {Methods},
    volume = 74,
    pages= {83--89},
    month = mar,
    year = 2015
}

@Article{dragon,
    title = {DDPC: Dragon Database of Genes associated with Prostate Cancer},
    author = {Magungo, M and Kaur, M and Kwofie, SK and Radovanovic, A and Schaefer, U and Schmeier, S and Oppon, E and
        Christoffels, A and Bajic, VB},
    journal = {Oxford Journals - Nucleic Acids Research},
    month = sep,
    year = 2010
}

@Article{disgenet,
    title = {DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.},
    author = {Piñero, J. and Queralt-Rosinach, N and Bravo, À and Bauer-Mehren, A and Baron, M and Sanz, F and Furlong,
    Li},
    journal = {Oxford University Press},
    month = apr,
    year = 2015
}

@Article{netrank,
    title = {Google Goes Cancer: Improving Outcome Prediction for Cancer
             Patients By Network-Based Ranking of Marker Genes},
    author = {Christof Winter and Glen Kristiansen and Stephan Kersting and
              Janine Roy and Daniela Aust and Thomas Knösel and Petra Rümmele
              and Beatrix Jahnke and Vera Hentrich and Felix Rückert and Marco
              Niedergethmann and Wilko Weichert and Marcus Bahra and Hans j:
              Schlitt and Utz Settmacher and Helmut Friess and Markus Büchler
              and Hans-Detlev Saeger and Michael Shcoreder and Christian
              Pilarsky and Robert Grützmann},
    journal = {PLoS Comput Biol.},
    month = may,
    year = 2012
}
@Article{generank,
    author={Morrison, Julie L.  and Breitling, Rainer and Higham, Desmond J.
            and Gilbert, David R.},
    title={GeneRank: Using search engine technology for the analysis of microarray experiments},
    journal={BMC Bioinformatics},
    year={2005},
    volume={6},
    number={1},
    pages={1--14},
    abstract={Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a ``treated'' sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method -- based on the PageRank algorithm employed by the popular search engine Google -- that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information.},
    issn={1471-2105},
    doi={10.1186/1471-2105-6-233},
    url={http://dx.doi.org/10.1186/1471-2105-6-233}
}

@Article{pr-bio,
    title = {When the web meets the cell: Using Personalized PageRank for
        Analyzing Protein Interaction Networks},
    author = {Ivn, Gbor and Grolmusz, Vince},
    date = {2010-12-12},
    journal = {Bioinformatics Advance Access}
}

@Article{random-walks1,
    title = {Walkin on a Graph with a Magnifying Glass},
    author = {Kurant, Maciej and Minas, Gjoka and Butts, Carter T. and
              Markopoulou, Athina},
    url = {http://arxiv.org/abs/1101.5463},
    year = {2011},
    month = jan
}


@Article{random-walks2,
   author = {{Pearson}, K.},
    title = "{The Problem of the Random Walk}",
  journal = {Nature},
     year = 1905,
    month = aug,
   volume = 72,
    pages = {342},
      doi = {10.1038/072342a0},
   adsurl = {http://adsabs.harvard.edu/abs/1905Natur..72..342P},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
%  Article references
@Article{sw-rwr,
    title = {Seed-weighted Random Walks Ranking Method and Its application to
        Leukemia Cancer Biomarker Prioritizations},
    author = {Tianxio Huan and Xiaogang Wu and Zengliang Bai and Jake Y. Chen},
    year = {2009},
    page = {220--225}
}

% not used
@Article{biomarkerproteomic,
	title = {Biomarker clustering to address correlations in proteomic data},
	volume = {7},
	issn = {16159853, 16159861},
	url = {http://doi.wiley.com/10.1002/pmic.200600514},
	doi = {10.1002/pmic.200600514},
	pages = {1037--1046},
	number = {7},
	journaltitle = {{PROTEOMICS}},
	author = {Carlson, Scott M. and Najmi, Amir and Cohen, Harvey J.},
	urldate = {2015-05-22},
	date = {2007-04},
	langid = {english},
}
% not used
@Article{newnetworkclustering,
    author = {Wu, Meng-Yun AND Dai, Dao-Qing AND Zhang, Xiao-Fei AND Zhu, Yuan},
    journal = {PLoS ONE},
    publisher = {Public Library of Science},
    title = {Cancer Subtype Discovery and Biomarker Identification via a New Robust Network Clustering Algorithm},
    year = {2013},
    month = jul,
    volume = {8},
    url = {http://dx.doi.org/10.1371%2Fjournal.pone.0066256},
    pages = {e66256},
    number = {6},
    doi = {10.1371/journal.pone.0066256}
}        

@Article{spici,
	title = {{SPICi}: a fast clustering algorithm for large biological networks},
	volume = {26},
	issn = {1367-4803, 1460-2059},
	url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btq078},
	doi = {10.1093/bioinformatics/btq078},
	shorttitle = {{SPICi}},
	pages = {1105--1111},
	number = {8},
	journaltitle = {Bioinformatics},
	author = {Jiang, P. and Singh, M.},
	urldate = {2015-05-22},
	date = {2010-04-15},
	langid = {english},
}

@Article{siri,
    author = {Anne-Ruxandra Carvunis and Trey Ideker},
    title = {Siri of the Cell: What biology Could Learn from the iPhone},
    journal = {CellPress},
    year = {2014},
    month = apr,
    volume = {157}
}
@Article{networkbigdata,
    author = {Hamid Bolouri},
    title = {Modeling genomic regulatory networks with big data},
    journal = {CellPress},
    year = {2014},
    month = may,
    volume = {30},
    number = {5}
}
@Article{networkmodels,
    author = {Dana Pe'er and Nir Hacohen},
    title = {Principles and Strategies for Developing Network Models in Cancer},
    journal = {CellPress},
    year = {2011},
    month = mar,
    volume = {144}
}
@Article{personalized,
    author = {Rebecca J. Leary and Isaac Kinde and Frank Diehl and Kerstin Schmidt and Chris Clouser and Cisilya Duncan
        and Alena Antipova and Clarence Lee and Kevin McKernan and Francisco M. De La Vega and Kenneth W. Kinzler and
        Bert Vogelstein and Luis A. Diaz Jr.  and Victor E. Velculesc },
    title = {Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing},
    journal = {Science Translational Medicine},
    year = {2010},
    volume = {2}
}

@Article{beyondpsa,
    author = {John R. Prensner and Mark A. Ruin and John T. Wei and Arul M. Chinnayiyan},
    title = {Beyond PSA: The next generation of prostate cancer biomarkers},
    journal = {Sci Transl Med},
    year = {2012},
    volume = {1}
}

@Article{psa-age, 
    author = {Michael F.Berger and Michael S. Lawrence and Francesca Demichelis and Yotam Drier and Kristian Cibulskis
        and Andrey Y. Sivachenko and Andrea Sboner and Raquel Esgueva and Lukas Habegger and Lauren Ambrogio and Timothy
    Fennell and Melissa Parkin and Gordon Saksena and Douglas Voet and Alex H. Ramos and Trevor J. Pugh and Jane
    Wilkinson and Sheila Fisher and Wendy Winckler and Scott Mahan and Kristin Ardlie and Jennifer
    Baldwin and Jonathan W. Simons and Naoki Kitabayashi and Theresa Y. MacDonald and Philip W. Kantoff and Lynda Chin
    and Stacey B. Gabriel and Mark B. Gerstein and Todd R. Golub and Matthew Meyerson and Ashutosh Tewari and Eric S.
    Lander and Gad Getz and Mark A. Rubin and Levi A. Garraway},
    title = {The genomic complexity of primary human prostate cancer},
    journal = {Nature},
    year = {2011},
    volume = {1}
}

@Article{pca3-size,
    author = {Alexander Haesea and Alexandre de la Tailleb and Hendrik van Poppelc and Michael Marbergerd and
        Arnulf Stenzle and Peter F.A. Muldersf and Hartwig Hulandg and Clément-Claude Abboub and Mesut Remzid and
        Martina Tinzld and Susan Feyerabende and Alexander B. Stillebroerf and Martijn P.M.Q. van Gilsf and
        Jack A. Schalkenf},
    title = {Clinical Utility of the PCA3 Urine Assay in European Men Scheduled for Repeat Biopsy},
    journal = {European Urology},
    year = {2008},
    volume = {54}
}

@Article{pathway-network,
    author = {Pau Creixell and Jüri Reimand and Syed Haider and Guanming Wu and Tatsuhiro Shibata and Miguel Vazquez and Ville Mustonen and
        Abel Gonzalez-Perez and John Pearson and Chris Sander and Benjamin J Raphael and Debora S Marks and B F Francis Oulette and
        Alfonso Valencia and Gary D Bader and Paul C Boutros and Joshua M Stuart and Rune Linding and Nuria Lopez-Bigas and Lincoln D
            Stein},
    title = {Pathway and network analysis of cancer genomes},
    journal = {Nature Methods},
    publisher = {Nature America Inc.},
    year = {2015},
    month = jul,
    volume = {12},
    number = {7}
}

% unused
@Article{biomarker-problem,
    author = {Charles L. Sawyers},
    title = {The biomarker problem},
    journal = {Nature},
    publisher = {Nature Publishing Group},
    year = {2008},
    volume = {452},
	date = {2008-04-03}
}

@Article{ap-vs-mcl,
    author = {James Vlasblom and Shoshana J Wodak},
    title = {Markov clustering versus affinity propagation for the partitioning of
protein interaction graphs},
    journal = {BMC Bioinformatics},
    date = {2009-03-30}
}

@Article{biomarker2,
    author = {Biomarkers Definitions Working Group},
    title = {Biomarkers and surrogate endpoints: Preferred definitions and
             conceptual framework},
    journal = {Clinical Pharmacology \& Therapeutics},
    volume = {69},
    number = {3},
    pages = {89--95},
    date = {2001-03-18}
}

@Article{biomarker3,
    title = {What are Biomarkers?},
    author = {Kyle Strimbu and Jorge A. Tavel},
    journal = {Current Opinion in HIV and AIDS},
    month = nov,
    year = 2010
}

@Article{cancerburden2,
    title = {The Global Burden of Cancer 2013},
    author = {Mohsen Naghavi},
    journal = {JAMA Oncology},
    month = jul,
    year = 2015
}

@Article{str,
    title="String v0.1: protein-protein interaction networks, with increased
    coverage and integration",
    author="Francheschini, A and Szklarczyk, D and Frankild, S and Kuhn, M and
    Simonovic, M and Roth, A and Lin, J and Minguez, P and Bork, P and von
    Mering, C and Jensen LJ",
    journal="Nucleic Acids Research (Database issue)",
    year=2013,
    month=jan,
    url = {http://string-db.org/},
    urldate = {2015-05-07}
}
@Article{iridb,
    title="iRefScape. A Cytoscape plug-in for visualizatoin and data mining of
    protein interaction data from iRefIndex",
    author="Razick, Sabry and Mora, Antonio and Boddie, Paul and Michalickova,
    Katerina and Donaldson, Ian M.",
    journal="BMC Bioinformatics",
    year=2011,
    month=oct,
    url = {http://apps.cytoscape.org/apps/irefscape},
    urldate = {2015-05-07}
}


% Conference references
@conference{osgi-peter-kriens,
    author = {opk},
    title = {OSGi Introductory Tutorial By Peter Kriens},
    booktitle = {Øredev, Øresund Developers Conference, OSGi Introductory Tutorial By Peter Kriens},
    publisher = {IBM, aQuote and OSGi Alliance},
    year = {2006},
    url = {http://archive.oredev.org/download/18.5bd7fa0510edb4a8ce4800019273/1385354018499/Peter_Kriens_-_Workshop_OSGi_Hands-on.pdf},
    urldate = {2015-05-08}
}

@online{gm,
    title="GeneMANIA",
    author="Warde-Farley, D and Donaldson, SL and Comes, O and Zuberi, K and
    Badrawi, R and Chao, P and Franz, M and Grouios, C and Kazi, F and Lopes, CT
    and Maitland, A and Mostafavi, S and Montojo, J and Shao, Q and Wright,
    G and Bader, GD and Morris, Q",
    journal="Nucleic Acids Research",
    year=2010,
    month=jul,
    url = {http://www.genemania.org/},
    urldate = {2015-05-07}
}

@online{gmdb,
    title="GeneMANIA",
    author="Montojo, Jason and GeneMANIA TEAM",
    url = {http://apps.cytoscape.org/apps/genemania},
    urldate = {2015-05-07}
}
@online{cytoscape-osgi,
    title="Cytoscape 3.0 App Development",
    author="Hull, Tim",
    url = {http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper},
    urldate = {2015-05-08}
}
@online{cancerfacts,
    title="Prostate-Specific Antigen (PSA) test",
    author="The National Cancer Institute",
    url = {http://www.cancer.gov/cancertopics/types/prostate/psa-fact-sheet},
    urldate = {2015-05-11}
}
@online{biomarker1,
    title="What is a Biomarker?",
    author = {Dr Ananya Mandal, MD},
    url = {http://www.news-medical.net/health/What-is-a-Biomarker.aspx},
    urldate = {2015-05-12}
}
@online{ngs1,
    title="Illumina",
    author="Illumina Inc.",
    url = {http://www.illumina.com/technology/next-generation-sequencing.html},
    urldate = {2015-05-11}
}
@online{modularization,
    title="Modularity in Java 9: Stacking up with Project Jigsaw, Penrose ans
    OSGi",
    author="Hanson, Jeff",
    url = {http://www.javaworld.com/article/2878952/java-platform/modularity-in-java-9.html},
    urldate = {2015-05-20}
}
@online{osgi,
    title="Architecture",
    author="OSGi Alliance",
    url = {http://www.osgi.org/Technology/WhatIsOSGi},
    urldate = {2015-05-20}
}
@online{cleancode,
    title="Clean Code: A Handbook of Agile Software Craftsmanship",
    author="Amazon.com",
    note="Cite for proof of existence of the book - author of the book is Robert
    C. Martin",
    url = {http://www.amazon.com/Clean-Code-Handbook-Software-Craftsmanship/dp/0132350882},
    urldate = {2015-05-20}
}
@online{designpattern,
    title="Design Pattern, Definition - What does Design Pattern mean?",
    author="Techopedia Inc.",
    url = {http://www.techopedia.com/definition/18822/design-pattern},
    urldate = {2015-05-20}
}
@online{cm2,
    title="clusterMaker2 - Multi-algorithm clustering app for Cytoscape",
    author="Morris, Scooter and Apeltsin, Leonard and Newman, Aaron and
    Baumbach, Jan and Wittkop, Tobias and Su, Gang and Bader, Gray and Tomar
    Abhiraj",
    url = {http://apps.cytoscape.org/apps/clustermaker2},
    urldate = {2015-05-22}
}
@online{graphml,
    title="The GraphML File Format",
    author="GraphML Team",
    url = {http://graphml.graphdrawing.org/},
    urldate = {2016-02-19}
}
@online{dna-methyl,
    title="What is DNA Methylation?",
    author="Robertson, Sally",
    url = {http://www.news-medical.net/life-sciences/What-is-DNA-Methylation.aspx},
    urldate = {2016-02-22}
}
@online{legacy-neo4j,
    title="The Neo4j Developer Manual v3.0",
    author="Neo Technology",
    url = {http://neo4j.com/docs/stable/rest-api-cypher.html},
    urldate = {2016-03-17}
}
@online{transactional-neo4j,
    title="The Neo4j Developer Manual v3.0",
    author="Neo Technology",
    url = {http://neo4j.com/docs/stable/rest-api-transactional.html},
    urldate = {2016-03-17}
}
@online{cyneo4j,
    title = {cyNeo4j - A Cytoscape app to connect to a Neo4J database and
             execute extensions of the Neo4j database},
    author = {Georg Summer},
    note = {Author name was found on the wordpress page of the app
            https://cyneo4j.wordpress.com/},
    url = {https://github.com/gsummer/cyNeo4j},
    urldate = {2016-03-17}
}
@online{color-blindness2,
    title="COLORRRS",
    author="Jamie Brittain",
    url = {http://hex.colorrrs.com/},
    urldate = {2016-06-09}
}
@online{color-blindness3,
    title = {Testing the colors of a web chart, (center), to ensure that no
        information is lost to the various forms of color-blindness.},
    author = {https://commons.wikimedia.org/wiki/User:Grolltech},
    note = {Grolltech is the username for the person responsible},
    url = {https://en.wikipedia.org/wiki/Color_blindness#/media/File:Safe_Chart_Colors-F99-FEC-ADD.jpg}, 
    urldate = {2016-07-24}
}
@online{hits,
    title="Authorative Sources in a Hyperlinked Environment",
    author="Kleinberg, Jon M.",
    url = {https://www.cs.cornell.edu/home/kleinber/auth.pdf},
    urldate = {2016-07-05}
}
@online{hits-origin,
    title="Lecture 4: HITS Algorithm",
    author="Tanase, Raluca and Radu, Remus",
    url="http://www.math.cornell.edu/~mec/Winter2009/RalucaRemus/Lecture4/lecture4.html",
    urldate="2016-07-05"
}

@online{jung,
    title="JUNG - Java Universal Network/Graph Framework",
    author="O'Madadhain, Joshua and Fisher, Danyel and Nelson, Tom",
    url = {http://jung.sourceforge.net/},
    urldate = {2016-07-07}
}
@online{pr-parameters,
    title = {How Google Finds Your Needle in the Web's Haystack},
    author = {Austin, David},
    url = {http://www.ams.org/samplings/feature-column/fcarc-pagerank},
    urldate = {2016-07-07}
}
@online{cm2-github,
    title="clusterMaker2 github repository",
    author="Morris, Scooter",
    url = {https://github.com/RBVI/clusterMaker2},
    urldate = {2016-07-08}
}
@online{factory-design,
    title = {Design Pattern - Factory Pattern},
    author = {tutorialspoint.com},
    url = {http://www.tutorialspoint.com/design_pattern/factory_pattern.htm},
    urldate = {2016-07-24}
}
@online{java-superclass,
    title = {Using the keyword super},
    author = {Oracle},
    url = {https://docs.oracle.com/javase/tutorial/java/IandI/super.html},
    urldate = {2016-07-24}
}
@online{cytoscape-cookbook,
    title = {CytoScape 3 App Cookbook},
    author = {TimHull},
    url = {http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook},
    urldate = {2016-07-24}
}
@online{java-swing,
    title = {Package javax.swing},
    author = {Orcale},
    url = {https://docs.oracle.com/javase/8/docs/api/javax/swing/package-summary.html},
    urldate = {2016-07-24}
}
@online{git-pull-request,
    title = {Using pull requests},
    author = {GitHub Inc.},
    url = {https://help.github.com/articles/using-pull-requests/},
    urldate = {2016-07-24}
}
@online{ranklust-accepted,
    title = {Merge in ranking algorithms from Henning-Lund-Hanssen},
    author = {scootermorris},
    url = {https://github.com/RBVI/clusterMaker2/commit/f055347df9af397b4f15866bc35db55b8bb5b357},
    urldate = {2016-07-24}
}
@online{pandas,
    title = {Python Data Analysis Libarary},
    author = {NumFOCUS},
    url = {http://pandas.pydata.org/},
    urldate = {2016-07-24}
}
@online{python,
    title = {Python},
    author = {Guido van Rossum},
    url = {https://www.python.org/},
    urldate = {2016-07-24}
}
@online{numpy,
    title = {Numerical Python},
    author = {Numpy Developers},
    url = {http://www.numpy.org/},
    urldate = {2016-07-24}
}
@online{jigsaw,
	title = {Project Jigsaw},
	author = {OpenJDK},
	url = {http://openjdk.java.net/projects/jigsaw/},
	urldate = {2016-07-24}
}
@online{cypher,
	title = {Intro to Cypher},
	author = {Neo Technology Inc.},
	url = {https://neo4j.com/developer/cypher-query-language/},
	urldate = {2016-07-24}
}
@online{neo4j,
	title = {Neo4J},
	author = {Neo Technology Inc.},
	url = {https://neo4j.com/},
	urldate = {2016-07-24}
}
@online{spark,
    title = {Apache Spark},
    author = {Apache},
    url = {http://spark.apache.org/},
	urldate = {2016-07-24}
}
@online{git-fork,
    title = {Fork A Repo},
    author = {GitHub Inc.},
    url = {https://help.github.com/articles/fork-a-repo/},
	urldate = {2016-07-25}
}
@online{cyneo4j-auth,
    title = {Copy of CyNeo4J plugin of Cytoscape - now with authorization!},
    author = {Henning Lund-Hanssen},
    url = {https://github.com/henninglh/CyNeo4J},
	urldate = {2016-07-25}
}
@online{osgi-felix,
    title = {Apache Felix Maven Bundle Plugin (BND)},
    author = {Apache},
    url = {http://felix.apache.org/documentation/subprojects/apache-felix-maven-bundle-plugin-bnd.html},
	urldate = {2016-07-25}
}
@online{itext,
    title = {IText},
    author = {iText Software Corp.},
    url = {http://developers.itextpdf.com/},
	urldate = {2016-07-25}
}
@online{lowagie-to-itext,
    title = {Fixed changed POM dependencies},
    author = {matthiaskoenig},
    note = {Author is a GitHub.com username},
    url = {https://github.com/RBVI/clusterMaker2/pull/3/commits/42d910b51cb6cae0511379346b8e0b8ac85a124b},
	urldate = {2016-07-25}
}
@online{cytoscape-api,
    title = {Cytoscape Swing App API (swing-app-api) 3.3.0 API},
    author = {Cytoscape Consortium},
    url = {http://chianti.ucsd.edu/cytoscape-3.3.0/API/},
	urldate = {2016-07-25}
}
@online{kegg,
    title = {KEGG PATHWAY Database},
    author = {Kanehisa Laboratories},
    url = {http://www.genome.jp/kegg/pathway.html},
	urldate = {2016-07-26}
}
@online{cosmic-download,
    title = {COSMIC - Catalogue of somatic mutations in cancer},
    author = {Wellcome Trust Sanger Institute},
    url = {http://cancer.sanger.ac.uk/cosmic/files?data=/files/grch38/cosmic/v77/CosmicHGNC.tsv.gz},
    urldate = {2016-08-07}
}
@online{plotly,
    title = {Plotly - Make charts and dashboards online},
    author = {Plotly},
    url = {https://plot.ly/plot},
    urldate = {2016-08-09}
}
@online{maven,
    title = {Apache Maven Project},
    author = {Apache},
    url = {https://maven.apache.org/},
    urldate = {2016-08-09}
}
@online{pom,
    title = {What is the POM?},
    author = {Apache},
    url = {https://maven.apache.org/pom.html#What_is_the_POM},
    urldate = {2016-08-09}
}
@online{jar,
    title = {What is JAR?},
    author = {Oracle},
    url = {https://docs.oracle.com/javase/8/docs/technotes/guides/jar/jarGuide.html},
    urldate = {2016-08-09}
}
@online{grep,
    title = {grep(1) - Linux man page},
    author = {Ken Thompson},
    url = {http://linux.die.net/man/1/grep},
    urldate = {2016-08-10}
}
@online{distild,
    title={DistiLD - Diseases and Traits in LD},
    author={Disease Systems Biology Group},
    url={http://distild.jensenlab.org/about.html},
    urldate={2016-08-13}
}
@online{pantherdb,
    title="Panther Classification System",
    author="Paul Thomas",
    url="http://pantherdb.org/",
    urldate={2016-08-13}
}