{"ID":78031,"post_author":"2","post_date":"2018-12-14 12:20:14","post_date_gmt":"0000-00-00 00:00:00","post_content":"","post_title":"LIMSjournal - Winter 2016: Volume 2, Issue 4","post_excerpt":"","post_status":"draft","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"","to_ping":"","pinged":"","post_modified":"2018-12-14 12:20:14","post_modified_gmt":"2018-12-14 17:20:14","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.limsforum.com\/?post_type=ebook&p=78031","menu_order":0,"post_type":"ebook","post_mime_type":"","comment_count":"0","filter":"","_ebook_metadata":{"enabled":"on","private":"0","guid":"748E04E4-C053-4D7D-B433-0191645FDCF1","title":"LIMSjournal - Winter 2016: Volume 2, Issue 4","subtitle":"","cover_theme":"nico_6","cover_image":"https:\/\/www.limsforum.com\/wp-content\/plugins\/rdp-ebook-builder\/pl\/cover.php?cover_style=nico_6&subtitle=&editor=John+Jones&title=LIMSjournal+-+Winter+2016%3A+Volume+2%2C+Issue+4&title_image=https%3A%2F%2Fwww.limswiki.org%2Fimages%2Fe%2Fef%2FFig2_Lam_BMCBioinformatics2016_17.gif&publisher=Laboratory+Informatics+Institute","editor":"John Jones","publisher":"Laboratory Informatics Institute","author_id":"2","image_url":"","items":{"3c37748e91f98bf94197cc33a06161b1_type":"article","3c37748e91f98bf94197cc33a06161b1_title":"Critical questions for community informatics in practice from an ethical perspective (Wolske and Rhinesmith 2016)","3c37748e91f98bf94197cc33a06161b1_url":"https:\/\/www.limswiki.org\/index.php\/Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective","3c37748e91f98bf94197cc33a06161b1_plaintext":"\n\n\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\n\t\t\t\tJournal:Critical questions for community informatics in practice from an ethical perspective\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\tFrom LIMSWiki\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\tJump to: navigation, search\n\n\t\t\t\t\t\n\t\t\t\t\tFull article title\n \nCritical questions for community informatics in practice from an ethical perspectiveJournal\n \nThe Journal of Community InformaticsAuthor(s)\n \nWolske, Martin; Rhinesmith, ColinAuthor affiliation(s)\n \nUniversity of Illinois at Urbana-Champaign, Simmons CollegePrimary contact\n \ncrhinesmith at simmons dot eduYear published\n \n2016Volume and issue\n \n12(3)Page(s)\n \n236\u2014242DOI\n \nNoneISSN\n \n1721-4441Distribution license\n \nCreative Commons Attribution-NonCommercial-ShareAlike 2.5Website\n \nhttp:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/1325Download\n \nhttp:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/1325\/1236 (PDF)\n\nContents\n\n1 Preamble \n2 Method \n3 Critical questions \n\n3.1 Maximizing benefit, minimizing harm \n3.2 Participation and pluralism \n3.3 Philosophy of technology \n\n\n4 Acknowledgments \n5 Footnotes \n6 References \n7 Notes \n\n\n\nPreamble \nCommunity informatics (CI) in practice informs and equips individuals and groups in geographic communities to advance the agency of constituents.[a] Information and communication technologies (ICT) are selected, designed, and implemented in ways that are consistent with constituents\u2019 own values and goals. This approach includes recognition that ICT non-use may also be appropriate, particularly when the use of ICTs would contradict constituents\u2019 values and goals. Community informatics practice seeks to make \u201ceffective use\u201d of technology[2] to support community development projects in ways that advance a sustainable approach to community enrichment and power.[3] CI practice integrates participatory design of information technology resources, popular education, and asset-based development to enhance quality of life.[4] However, without its own set of ethical guidelines and practice standards, CI remains underdeveloped as a field of practice.[3]\nCollaboratively developed through three years of conference workshops, this set of guiding critical questions seeks to further promote ethical practice in CI. This document serves as a complement to the researcher-focused \"Code of Ethics for Community Informatics Researchers\"[5] and expands upon the \"Ethics of Community Informatics Research and Practice\" pattern card.[6] While there often is overlap between research and practice, community informatics is increasingly informing projects undertaken by those who do not primarily identify as academic or career researchers but who do important work at the intersection of information, technology, and society at the community level. Therefore, this document also serves as a complement to the codes of ethics and standards of practice for community-centered professions such as social work, urban planning, public health, and library, archival, and information science.\nThese guiding critical questions affirm the need to state social justice principles more explicitly in community informatics. Unequal power relations will always be a factor, and CI practice can benefit from guidelines to ensure these relationships are more equitable. The groups that comprise communities are not homogeneous, nor singular[7], and include nonhuman residents.[8][9] On the other hand, individuals belong to multiple, intersecting communities[7][10]; this includes those with leadership roles in CI projects. Power relations exist within and between communities, and they are ever changing. Further, knowledge of the world is socially constructed within specific historical and social contexts that are fundamentally mediated by power relations. Facts are always determined by some degree of ideological inscription.[11] Power inequalities and other injustices in practices, relationships, and social systems can only be confronted by leveraging group difference as a resource for dialogue comprised of both shared action and reflection.[7]\nWhile CI projects focus on effective use of technologies, we acknowledge technologies do not solve, revolutionize, transform, or otherwise serve as independent agents acting upon humans as objects. Rather, as sociotechnical artifacts, technologies are shaped by a diverse set of social, cultural, economic, political, and historical factors that become embedded within the artifacts themselves. These technological developments consequently influence the appropriation, use, and limitations of artifacts as well as their impact and eventual disposition or sustainability. In this way, technologies amplify the human forces involved in design, production, distribution, and consumption \u2014 forces for justice and oppression, forces for mutual benefit and greed.\nCI practitioners must challenge themselves in ongoing and systematic ways to identify how they invite participation while withholding the truth \u2014 potentially from themselves, as well from their partners \u2014 with regard to how CI projects can sometimes be forced to fit within established governmental, educational, cultural, economic, and other social systems in ways that reify unjust aspects of such systems. Indeed, it is only through dialogue and the building of equitable relationships across group differences[7] that our partnerships can expose the truth and create change to those portions of our engagement that are oppressive to others and ourselves.\nThese efforts to decolonize CI practice are not an end themselves, but a continuous process embedded within praxis. We stand with Freire[12], who states \"to exist, humanly, is to name the world, to change it. Once named, the world in its turn reappears to the namers as a problem and requires of them a new naming.\" As such, this reflective document serves as a waypoint to guide further dialogue toward a continuously evolving set of practices. The evolution of CI as praxis is intended to advance CI practitioners\u2019 abilities to work, whenever relevant, as allies in support of a community\u2019s own liberatory efforts. This evolution must be guided by deep and mutually respectful dialogue between the diverse constituencies involved in CI projects. Such dialogue should contribute to a popular education initiative in which all participants jointly and continually construct, deconstruct, and reconstruct understandings of core concepts, such as community, self-determination, engagement, social justice, power, and social change to increase awareness of the interlocking social systems within which CI practice happens.\nIn sum, then, this document seeks to outline a set of critical questions that not only guide ethical CI practice, but also guide the personal transformation of practitioners to embrace all as experts in their own right.\n\nMethod \nWorkshops held at the Community Informatics Research Network (CIRN) conferences in 2013, 2014, and 2015 were used to guide development of this framework. During the 2013 conference, the need for such a framework was affirmed and the work of a cohort from the Pluralizing the Archival Curriculum Group[13] was identified as a model for establishing this statement.\nAt the 2014 workshop, a range of model principles were reviewed individually and discussed in small groups. During the first part of the workshop, participants reviewed posters and\nprintouts of various model principles. Participants were provided with sticky notes and large blank sheets of paper on which to provide comments. Recommendations for alternative sets of principles were also solicited from participants. The second half of the workshop consisted of open small- and large-group discussion to further refine ideas. After the 2014 conference, a page was created on the community CIRN Wiki[14] listing the results of the 2014 process, with the goal of encouraging community informatics practitioners to discuss this framework with community partners and reflect on their practices in light of these guidelines.\nAt the 2015 CIRN conference, the preliminary version of this document was prominently posted throughout the conference, with sticky notes provided to enable ongoing feedback. A World Caf\u00e9 approach[15] was then used within a workshop to gather participant feedback on the proposed statement, while considering how the statement might be applicable to community informatics research, teaching, and practice. The authors gathered the feedback and created a new draft for publication as a means to widen the audience reviewing and commenting on this document.\nIt should be noted that as two white, cisgender, heterosexual male scholars working at higher education institutions in the United States, we recognize the ethical dilemmas involved in publishing this document. These dilemmas include privileging lineal written language as well as calling attention to imperialist, patriarchal, and racist ideologies embedded within Western academic culture and practices. We welcome further consideration of how to address this grand challenge to promote an active community practice in, and not just discussions about, pluralism. We also recognize the following pressing questions are yet unaddressed in this document:\n\n Can these ethical guidelines even be carried out within a university research environment? When funding, tenure, and advancement dictate relatively narrow research, teaching, and service activities, other epistemologies, ontologies, and methods that embrace justice and mutual benefit are often set aside.\n Is CI a practice that requires an advanced degree within a Western academic culture or is it open to epistemological pluralism and alternative educational traditions?\n What other barriers prevent CI practitioners from embracing guidelines that promote ethics, diversity, and inclusion in CI practice? How can these obstacles be overcome?\nCritical questions \nIn order to guide the evolution of ethical community informatics in practice, as well as the personal transformation of CI practitioners who seek to embrace all as equals and experts, we put forward this initial set of critical questions to inform CI praxis. In addressing each question in ongoing and systematic ways, it is important to determine whether the right people are at the table to inform dialogue and negotiate decisions guiding action. Further, for each question, we should ask \u201cHow do we know?\u201d so as to challenge our personal histories, cultures, and ways of knowing and what we value as truth.\n\nMaximizing benefit, minimizing harm \n What individual and social benefits will result through this CI project, and for whom? What individual and social harms will result through this project, and to whom? What will be the benefits and harm to nonhuman residents through this CI project? Is any one segment unfairly burdened with the costs of, or any harm resulting from, this CI project?\n In what ways do my racial and cultural heritage and historical background influence how I understand the potential benefits and harms that may result from this CI project? In what ways do the racial and cultural heritage and historical background of others engaged in the project influence how they understand benefits and harms?\n What are the objectives of the constituents, and how do they align with, or come in conflict with, the objectives of those initiating and\/or informing the community informatics project?\n What methods and rules of conduct are appropriate (and inappropriate) in the design, development, implementation, and evaluation of the CI project? Who has ownership of, and credit for, the created works and data, and who determines the means by which products may be disseminated and under what conditions?\n How can we use the CI project to move beyond addressing an immediate opportunity or need in order to foster agency and knowledge power on the part of the constituencies with which we ally? In what ways are we reducing the agency of others by doing that which others have the expertise and opportunity to do?\n Have checkpoints been built into project timelines to assess and compare anticipated versus actual benefits and harms and to allow for renegotiation of decisions guiding action?\n Are we bringing false assumptions and overgeneralizations into a project based on our experiences in past CI projects?\n Are we making promises that we cannot keep in CI projects by using language that translates differently within different contexts?\nParticipation and pluralism \n What does it mean to be inclusive in this context? What does it mean to have self-determination?\n Which individuals and communities are engaged in the CI project, and why? Which individuals and communities are not engaged in the project, and why not?\n Are we taking all necessary steps to ensure that constituents are free to participate in CI projects and are informed about their roles in such projects? Are we allowing participants to freely choose the nature and length of the partnership as their right?\n Are we privileging the input, values, belief systems, and cultural expressions of those directly impacted by CI projects, especially those historically excluded from full participation in society?\n Are we seeking to understand the distinct situations, perspectives, lived experiences, and knowledge of those involved in CI projects, especially attending to group differences?\n Are we entering into engagement as allies in a spirit of mutual trust, respect, genuineness, and commitment? Are we appropriately ceding control as a symbol of trust and a component of trust building?\n Are we allotting sufficient time for relationship building at the start and throughout the CI project? What happens when funding and institutional timelines come into conflict with the time needed for effective dialogue and relationship building?\nPhilosophy of technology \n What everyday technologies might be unseen and displaced because of an overly narrow definition of what should be considered an appropriate technology? Who are the local innovators whose technologies might be championed as part of a CI project?\n Are people with the needed skill sets engaged in the design and implementation of the CI project to maximize the likelihood that it is a community building project and not solely a technology-focused initiative?\n How can we seek to understand and leverage constituencies\u2019 everyday experiences with technology as an essential gateway for understanding (a) how oppressive systems in society reinforce existing inequalities and (b) the role that different technologies, as applied in context, play in amplifying these social processes?\n Have the impacts on all stakeholders \u2014 including future generations, nonhuman residents, those who intersect with the participants and beneficiaries of CI projects, and those involved in the mining of minerals, in the production of technologies, and in end-of-life recycling \u2014 been considered in the selection and implementation of specific technologies?\n How might the voices of technology skeptics and traditionalists inform adoption, or non-adoption, of a CI project? What important insights regarding culture, values, and history are these perspectives bringing to the engagement?\n How do we balance considerations of ease of implementation, purchase costs, operational costs, human costs, sustainability, and end-of-life effects when choosing between different technologies?\n How should we proceed when there isn\u2019t alignment amongst various stakeholders regarding important aspects of technology implementation? Is this an opportunity to embrace difference as a resource for community building and the construction of new knowledge in CI projects?\n How do we proceed when ethical and legal aspects come into conflict, especially in the global context when the ethics and laws of one culture come into conflict with those of another? Do complex situations like these present opportunities to embrace group differences as resources for community building and the construction of new knowledge in CI projects?\n How do we balance our relationships with members of the community with the requirements of our places of employment and project funders when a constituency determines adoption or acquisition would be counter to their interests, values, belief systems, and\/or cultural ways of being and doing?\n How can we develop new definitions of success in CI projects that do not require adoption of digital technologies or acquisition of data and artifacts?\n How do we introduce technology opportunities without encouraging technological utopianism?\nAcknowledgments \nWe gratefully acknowledge Anne Gilliland and Kelvin White, who co-led the 2014 and 2015 workshops with the two authors. We also extend a sincere thank you to all the participants of each of the three workshops.\n\nFootnotes \n\n\n\u2191 Throughout this document, we use Stoecker\u2019s[1] distinction between constituency (that is, \u201cpeople who have important life experience in common\u201d) and community (that is, \u201ca collectivity in a local setting whose members interact in many different ways that results in the mutual enhancement and sustainability of the collectivity and its constituents\u201d). \n\n\nReferences \n\n\n\u2191 Stoecker, R. (2014). \"What if?\". All Ireland Journal of Teaching and Learning in Higher Education 6 (1). http:\/\/www.aishe-j.org\/?page_id=137 .   \n\n\u2191 Gurstein, M. (2003). \"Effective use: A community informatics strategy beyond the digital divide\". First Monday 8 (12). http:\/\/firstmonday.org\/article\/view\/1107\/1027 .   \n\n\u2191 3.0 3.1 Stoecker, R. (2005). \"Is community informatics good for communities? Questions confronting an emerging field\". The Journal of Community Informatics 1 (3). http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/183\/129 .   \n\n\u2191 Campbell, N.D.; Eubanks, V. (2004). \"Community Informatics as a Pathway to Social Change\". Brillo Magazine. Archived from the original on 17 March 2005. https:\/\/web.archive.org\/web\/20050317102659\/http:\/\/www.brillomag.net\/COPC\/CI\/index.html .   \n\n\u2191 Averweg, U.; O'Donnell, S. (2007). \"Code of ethics for community informatics researchers\". The Journal of Community Informatics 3 (1). http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/441\/307 .   \n\n\u2191 Stoecker, R.. \"Ethics of community informatics research and practice\". Public Sphere Project. http:\/\/www.publicsphereproject.org\/node\/266 .   \n\n\u2191 7.0 7.1 7.2 7.3 Young, I.M. (1997). \"Difference as a resource for democratic communication\". In Bohman, J.; Rehg, W.. Deliberative Democracy: Essays in Reason and Politics. MIT Press. pp. 383\u2013406. ISBN 9780262522410.   \n\n\u2191 Leopold, A. (1949). \"The Land Ethic\". A Sand County Almanac. Ballantine Books.   \n\n\u2191 Kimmerer, R.W. (2013). \"Learning the Grammar of Animacy\". Braiding Sweetgrass. Milkweed Editions. ISBN 9781571313355.   \n\n\u2191 \"Introduction\". Pilgrimages\/Peregrinajes: Theorizing Coalition Against Multiple Oppressions. Rowman & Littlefield Publishers. 2003. pp. 1\u201339. ISBN 9780742514591.   \n\n\u2191 Kincheloe, J.L.; McLaren, P. (2005). \"Rethinking critical theory and qualitative research\". In Denzin, N.K.; Lincoln, Y.S.. The SAGE Handbook of Qualitative Research. SAGE Publications. pp. 303\u2013342. ISBN 9780761927570.   \n\n\u2191 Freire, P. (2000). Pedagogy of the Oppressed. Continuum International Publishing Group. p. 81. ISBN 0826412769.   \n\n\u2191 Pluralizing the Archival Curriculum Group (2011). \"Educating for the archival multiverse\". The American Archivist 74 (1): 69\u2013101. doi:10.17723\/aarc.74.1.hv339647l2745684.   \n\n\u2191 \"Towards a CIRN Framework for Ethics, Diversity, and Inclusion\". CIRN Commons. Community Informatics Research Network. 2014. http:\/\/cirn.wikispaces.com\/Towards+a+CIRN+Framework+for+Ethics,+Diversity,+and+Inclusion .   \n\n\u2191 \"World Cafe Method\". The World Caf\u00e9 Community Foundation. http:\/\/www.theworldcafe.com\/key-concepts-resources\/world-cafe-method\/ .   \n\n\nNotes \nThis presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. A few minor capitalization and punctuation changes were also made. In a case or two, the original URL no longer works, and an alternative or archived version was used. Original references were alphabetical, but they are organized in order of appearance here, by design.\n\n\n\n\n\n\nSource: <a rel=\"external_link\" class=\"external\" href=\"https:\/\/www.limswiki.org\/index.php\/Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\">https:\/\/www.limswiki.org\/index.php\/Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective<\/a>\n\t\t\t\t\tCategories: LIMSwiki journal articles (added in 2016)LIMSwiki journal articles (all)LIMSwiki journal articles on community informatics\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\n\t\t\n\t\t\tNavigation menu\n\t\t\t\t\t\n\t\t\tViews\n\n\t\t\t\n\t\t\t\t\n\t\t\t\tJournal\n\t\t\t\tDiscussion\n\t\t\t\tView source\n\t\t\t\tHistory\n\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\n\t\t\t\t\n\t\t\t\tPersonal tools\n\n\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\t\t\tLog in\n\t\t\t\t\t\t\t\t\t\t\t\t\tRequest account\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\t\t\n\t\tNavigation\n\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tMain page\n\t\t\t\t\t\t\t\t\t\t\tRecent changes\n\t\t\t\t\t\t\t\t\t\t\tRandom page\n\t\t\t\t\t\t\t\t\t\t\tHelp\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\n\t\t\t\n\t\t\tSearch\n\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t \n\t\t\t\t\t\t\n\t\t\t\t\n\n\t\t\t\t\t\t\t\n\t\t\n\t\t\t\n\t\t\tTools\n\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tWhat links here\n\t\t\t\t\t\t\t\t\t\t\tRelated changes\n\t\t\t\t\t\t\t\t\t\t\tSpecial pages\n\t\t\t\t\t\t\t\t\t\t\tPermanent link\n\t\t\t\t\t\t\t\t\t\t\tPage information\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\n\t\t\n\t\tPrint\/export\n\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tCreate a book\n\t\t\t\t\t\t\t\t\t\t\tDownload as PDF\n\t\t\t\t\t\t\t\t\t\t\tDownload as Plain text\n\t\t\t\t\t\t\t\t\t\t\tPrintable version\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\n\t\t\n\t\tSponsors\n\t\t\n\t\t\t \r\n\n\t\r\n\n\t\r\n\n\t\r\n\n\t\n\t\r\n\n \r\n\n\t\n\t\r\n\n \r\n\n\t\n\t\r\n\n\t\n\t\r\n\n\t\r\n\n\t\r\n\n\t\r\n\t\t\n\t\t\n\t\t\t\n\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t This page was last modified on 12 December 2016, at 22:26.\n\t\t\t\t\t\t\t\t\tThis page has been accessed 362 times.\n\t\t\t\t\t\t\t\t\tContent is available under a Creative Commons Attribution-ShareAlike 4.0 International License unless otherwise noted.\n\t\t\t\t\t\t\t\t\tPrivacy policy\n\t\t\t\t\t\t\t\t\tAbout LIMSWiki\n\t\t\t\t\t\t\t\t\tDisclaimers\n\t\t\t\t\t\t\t\n\t\t\n\t\t\n\t\t\n\n","3c37748e91f98bf94197cc33a06161b1_html":"<body class=\"mediawiki ltr sitedir-ltr ns-206 ns-subject page-Journal_Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective skin-monobook action-view\">\n<div id=\"rdp-ebb-globalWrapper\">\n\t\t<div id=\"rdp-ebb-column-content\">\n\t\t\t<div id=\"rdp-ebb-content\" class=\"mw-body\" role=\"main\">\n\t\t\t\t<a id=\"rdp-ebb-top\"><\/a>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<h1 id=\"rdp-ebb-firstHeading\" class=\"firstHeading\" lang=\"en\">Journal:Critical questions for community informatics in practice from an ethical perspective<\/h1>\n\t\t\t\t\n\t\t\t\t<div id=\"rdp-ebb-bodyContent\" class=\"mw-body-content\">\n\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\n\t\t\t\t\t<!-- start content -->\n\t\t\t\t\t<div id=\"rdp-ebb-mw-content-text\" lang=\"en\" dir=\"ltr\" class=\"mw-content-ltr\">\n\n\n<h2><span class=\"mw-headline\" id=\"Preamble\">Preamble<\/span><\/h2>\n<p>Community informatics (CI) in practice informs and equips individuals and groups in geographic communities to advance the agency of constituents.<sup id=\"rdp-ebb-cite_ref-2\" class=\"reference\"><a href=\"#cite_note-2\" rel=\"external_link\">[a]<\/a><\/sup> Information and communication technologies (ICT) are selected, designed, and implemented in ways that are consistent with constituents\u2019 own values and goals. This approach includes recognition that ICT non-use may also be appropriate, particularly when the use of ICTs would contradict constituents\u2019 values and goals. Community informatics practice seeks to make \u201ceffective use\u201d of technology<sup id=\"rdp-ebb-cite_ref-3\" class=\"reference\"><a href=\"#cite_note-3\" rel=\"external_link\">[2]<\/a><\/sup> to support community development projects in ways that advance a sustainable approach to community enrichment and power.<sup id=\"rdp-ebb-cite_ref-StoeckerIsComm05_4-0\" class=\"reference\"><a href=\"#cite_note-StoeckerIsComm05-4\" rel=\"external_link\">[3]<\/a><\/sup> CI practice integrates participatory design of information technology resources, popular education, and asset-based development to enhance quality of life.<sup id=\"rdp-ebb-cite_ref-5\" class=\"reference\"><a href=\"#cite_note-5\" rel=\"external_link\">[4]<\/a><\/sup> However, without its own set of ethical guidelines and practice standards, CI remains underdeveloped as a field of practice.<sup id=\"rdp-ebb-cite_ref-StoeckerIsComm05_4-1\" class=\"reference\"><a href=\"#cite_note-StoeckerIsComm05-4\" rel=\"external_link\">[3]<\/a><\/sup>\n<\/p><p>Collaboratively developed through three years of conference workshops, this set of guiding critical questions seeks to further promote ethical practice in CI. This document serves as a complement to the researcher-focused \"Code of Ethics for Community Informatics Researchers\"<sup id=\"rdp-ebb-cite_ref-AverwegCode07_6-0\" class=\"reference\"><a href=\"#cite_note-AverwegCode07-6\" rel=\"external_link\">[5]<\/a><\/sup> and expands upon the \"Ethics of Community Informatics Research and Practice\" pattern card.<sup id=\"rdp-ebb-cite_ref-StoeckerEthics_7-0\" class=\"reference\"><a href=\"#cite_note-StoeckerEthics-7\" rel=\"external_link\">[6]<\/a><\/sup> While there often is overlap between research and practice, community informatics is increasingly informing projects undertaken by those who do not primarily identify as academic or career researchers but who do important work at the intersection of <a href=\"https:\/\/www.limswiki.org\/index.php\/Information\" title=\"Information\" target=\"_blank\" class=\"wiki-link\" data-key=\"6300a14d9c2776dcca0999b5ed940e7d\">information<\/a>, technology, and society at the community level. Therefore, this document also serves as a complement to the codes of ethics and standards of practice for community-centered professions such as social work, urban planning, <a href=\"https:\/\/www.limswiki.org\/index.php\/Public_health_informatics\" title=\"Public health informatics\" target=\"_blank\" class=\"wiki-link\" data-key=\"f0372a80f101e9f6fd00490dc1ebcedd\">public health<\/a>, and library, archival, and information science.\n<\/p><p>These guiding critical questions affirm the need to state social justice principles more explicitly in community informatics. Unequal power relations will always be a factor, and CI practice can benefit from guidelines to ensure these relationships are more equitable. The groups that comprise communities are not homogeneous, nor singular<sup id=\"rdp-ebb-cite_ref-YoungDiff97_8-0\" class=\"reference\"><a href=\"#cite_note-YoungDiff97-8\" rel=\"external_link\">[7]<\/a><\/sup>, and include nonhuman residents.<sup id=\"rdp-ebb-cite_ref-LeopoldTheLand49_9-0\" class=\"reference\"><a href=\"#cite_note-LeopoldTheLand49-9\" rel=\"external_link\">[8]<\/a><\/sup><sup id=\"rdp-ebb-cite_ref-KimmererLearning13_10-0\" class=\"reference\"><a href=\"#cite_note-KimmererLearning13-10\" rel=\"external_link\">[9]<\/a><\/sup> On the other hand, individuals belong to multiple, intersecting communities<sup id=\"rdp-ebb-cite_ref-YoungDiff97_8-1\" class=\"reference\"><a href=\"#cite_note-YoungDiff97-8\" rel=\"external_link\">[7]<\/a><\/sup><sup id=\"rdp-ebb-cite_ref-LugonesIntro03_11-0\" class=\"reference\"><a href=\"#cite_note-LugonesIntro03-11\" rel=\"external_link\">[10]<\/a><\/sup>; this includes those with leadership roles in CI projects. Power relations exist within and between communities, and they are ever changing. Further, knowledge of the world is socially constructed within specific historical and social contexts that are fundamentally mediated by power relations. Facts are always determined by some degree of ideological inscription.<sup id=\"rdp-ebb-cite_ref-KincheloeRethink05_12-0\" class=\"reference\"><a href=\"#cite_note-KincheloeRethink05-12\" rel=\"external_link\">[11]<\/a><\/sup> Power inequalities and other injustices in practices, relationships, and social systems can only be confronted by leveraging group difference as a resource for dialogue comprised of both shared action and reflection.<sup id=\"rdp-ebb-cite_ref-YoungDiff97_8-2\" class=\"reference\"><a href=\"#cite_note-YoungDiff97-8\" rel=\"external_link\">[7]<\/a><\/sup>\n<\/p><p>While CI projects focus on effective use of technologies, we acknowledge technologies do not solve, revolutionize, transform, or otherwise serve as independent agents acting upon humans as objects. Rather, as sociotechnical artifacts, technologies are shaped by a diverse set of social, cultural, economic, political, and historical factors that become embedded within the artifacts themselves. These technological developments consequently influence the appropriation, use, and limitations of artifacts as well as their impact and eventual disposition or sustainability. In this way, technologies amplify the human forces involved in design, production, distribution, and consumption \u2014 forces for justice and oppression, forces for mutual benefit and greed.\n<\/p><p>CI practitioners must challenge themselves in ongoing and systematic ways to identify how they invite participation while withholding the truth \u2014 potentially from themselves, as well from their partners \u2014 with regard to how CI projects can sometimes be forced to fit within established governmental, educational, cultural, economic, and other social systems in ways that reify unjust aspects of such systems. Indeed, it is only through dialogue and the building of equitable relationships across group differences<sup id=\"rdp-ebb-cite_ref-YoungDiff97_8-3\" class=\"reference\"><a href=\"#cite_note-YoungDiff97-8\" rel=\"external_link\">[7]<\/a><\/sup> that our partnerships can expose the truth and create change to those portions of our engagement that are oppressive to others and ourselves.\n<\/p><p>These efforts to decolonize CI practice are not an end themselves, but a continuous process embedded within praxis. We stand with Freire<sup id=\"rdp-ebb-cite_ref-FreirePedag00_13-0\" class=\"reference\"><a href=\"#cite_note-FreirePedag00-13\" rel=\"external_link\">[12]<\/a><\/sup>, who states \"to exist, humanly, is to name the world, to change it. Once named, the world in its turn reappears to the namers as a problem and requires of them a new naming.\" As such, this reflective document serves as a waypoint to guide further dialogue toward a continuously evolving set of practices. The evolution of CI as praxis is intended to advance CI practitioners\u2019 abilities to work, whenever relevant, as allies in support of a community\u2019s own liberatory efforts. This evolution must be guided by deep and mutually respectful dialogue between the diverse constituencies involved in CI projects. Such dialogue should contribute to a popular education initiative in which all participants jointly and continually construct, deconstruct, and reconstruct understandings of core concepts, such as community, self-determination, engagement, social justice, power, and social change to increase awareness of the interlocking social systems within which CI practice happens.\n<\/p><p>In sum, then, this document seeks to outline a set of critical questions that not only guide ethical CI practice, but also guide the personal transformation of practitioners to embrace all as experts in their own right.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Method\">Method<\/span><\/h2>\n<p>Workshops held at the Community Informatics Research Network (CIRN) conferences in 2013, 2014, and 2015 were used to guide development of this framework. During the 2013 conference, the need for such a framework was affirmed and the work of a cohort from the Pluralizing the Archival Curriculum Group<sup id=\"rdp-ebb-cite_ref-PluralizingEduc11_14-0\" class=\"reference\"><a href=\"#cite_note-PluralizingEduc11-14\" rel=\"external_link\">[13]<\/a><\/sup> was identified as a model for establishing this statement.\n<\/p><p>At the 2014 workshop, a range of model principles were reviewed individually and discussed in small groups. During the first part of the workshop, participants reviewed posters and\nprintouts of various model principles. Participants were provided with sticky notes and large blank sheets of paper on which to provide comments. Recommendations for alternative sets of principles were also solicited from participants. The second half of the workshop consisted of open small- and large-group discussion to further refine ideas. After the 2014 conference, a page was created on the community CIRN Wiki<sup id=\"rdp-ebb-cite_ref-CIRNTowards14_15-0\" class=\"reference\"><a href=\"#cite_note-CIRNTowards14-15\" rel=\"external_link\">[14]<\/a><\/sup> listing the results of the 2014 process, with the goal of encouraging community informatics practitioners to discuss this framework with community partners and reflect on their practices in light of these guidelines.\n<\/p><p>At the 2015 CIRN conference, the preliminary version of this document was prominently posted throughout the conference, with sticky notes provided to enable ongoing feedback. A World Caf\u00e9 approach<sup id=\"rdp-ebb-cite_ref-WCMethod_16-0\" class=\"reference\"><a href=\"#cite_note-WCMethod-16\" rel=\"external_link\">[15]<\/a><\/sup> was then used within a workshop to gather participant feedback on the proposed statement, while considering how the statement might be applicable to community informatics research, teaching, and practice. The authors gathered the feedback and created a new draft for publication as a means to widen the audience reviewing and commenting on this document.\n<\/p><p>It should be noted that as two white, cisgender, heterosexual male scholars working at higher education institutions in the United States, we recognize the ethical dilemmas involved in publishing this document. These dilemmas include privileging lineal written language as well as calling attention to imperialist, patriarchal, and racist ideologies embedded within Western academic culture and practices. We welcome further consideration of how to address this grand challenge to promote an active community practice in, and not just discussions about, pluralism. We also recognize the following pressing questions are yet unaddressed in this document:\n<\/p>\n<ul><li> Can these ethical guidelines even be carried out within a university research environment? When funding, tenure, and advancement dictate relatively narrow research, teaching, and service activities, other epistemologies, ontologies, and methods that embrace justice and mutual benefit are often set aside.<\/li>\n<li> Is CI a practice that requires an advanced degree within a Western academic culture or is it open to epistemological pluralism and alternative educational traditions?<\/li>\n<li> What other barriers prevent CI practitioners from embracing guidelines that promote ethics, diversity, and inclusion in CI practice? How can these obstacles be overcome?<\/li><\/ul>\n<h2><span class=\"mw-headline\" id=\"Critical_questions\">Critical questions<\/span><\/h2>\n<p>In order to guide the evolution of ethical community informatics in practice, as well as the personal transformation of CI practitioners who seek to embrace all as equals and experts, we put forward this initial set of critical questions to inform CI praxis. In addressing each question in ongoing and systematic ways, it is important to determine whether the right people are at the table to inform dialogue and negotiate decisions guiding action. Further, for each question, we should ask \u201cHow do we know?\u201d so as to challenge our personal histories, cultures, and ways of knowing and what we value as truth.\n<\/p>\n<h3><span class=\"mw-headline\" id=\"Maximizing_benefit.2C_minimizing_harm\">Maximizing benefit, minimizing harm<\/span><\/h3>\n<ul><li> What individual and social benefits will result through this CI project, and for whom? What individual and social harms will result through this project, and to whom? What will be the benefits and harm to nonhuman residents through this CI project? Is any one segment unfairly burdened with the costs of, or any harm resulting from, this CI project?<\/li><\/ul>\n<ul><li> In what ways do my racial and cultural heritage and historical background influence how I understand the potential benefits and harms that may result from this CI project? In what ways do the racial and cultural heritage and historical background of others engaged in the project influence how they understand benefits and harms?<\/li><\/ul>\n<ul><li> What are the objectives of the constituents, and how do they align with, or come in conflict with, the objectives of those initiating and\/or informing the community informatics project?<\/li><\/ul>\n<ul><li> What methods and rules of conduct are appropriate (and inappropriate) in the design, development, implementation, and evaluation of the CI project? Who has ownership of, and credit for, the created works and data, and who determines the means by which products may be disseminated and under what conditions?<\/li><\/ul>\n<ul><li> How can we use the CI project to move beyond addressing an immediate opportunity or need in order to foster agency and knowledge power on the part of the constituencies with which we ally? In what ways are we reducing the agency of others by doing that which others have the expertise and opportunity to do?<\/li><\/ul>\n<ul><li> Have checkpoints been built into project timelines to assess and compare anticipated versus actual benefits and harms and to allow for renegotiation of decisions guiding action?<\/li><\/ul>\n<ul><li> Are we bringing false assumptions and overgeneralizations into a project based on our experiences in past CI projects?<\/li><\/ul>\n<ul><li> Are we making promises that we cannot keep in CI projects by using language that translates differently within different contexts?<\/li><\/ul>\n<h3><span class=\"mw-headline\" id=\"Participation_and_pluralism\">Participation and pluralism<\/span><\/h3>\n<ul><li> What does it mean to be inclusive in this context? What does it mean to have self-determination?<\/li><\/ul>\n<ul><li> Which individuals and communities are engaged in the CI project, and why? Which individuals and communities are not engaged in the project, and why not?<\/li><\/ul>\n<ul><li> Are we taking all necessary steps to ensure that constituents are free to participate in CI projects and are informed about their roles in such projects? Are we allowing participants to freely choose the nature and length of the partnership as their right?<\/li><\/ul>\n<ul><li> Are we privileging the input, values, belief systems, and cultural expressions of those directly impacted by CI projects, especially those historically excluded from full participation in society?<\/li><\/ul>\n<ul><li> Are we seeking to understand the distinct situations, perspectives, lived experiences, and knowledge of those involved in CI projects, especially attending to group differences?<\/li><\/ul>\n<ul><li> Are we entering into engagement as allies in a spirit of mutual trust, respect, genuineness, and commitment? Are we appropriately ceding control as a symbol of trust and a component of trust building?<\/li><\/ul>\n<ul><li> Are we allotting sufficient time for relationship building at the start and throughout the CI project? What happens when funding and institutional timelines come into conflict with the time needed for effective dialogue and relationship building?<\/li><\/ul>\n<h3><span class=\"mw-headline\" id=\"Philosophy_of_technology\">Philosophy of technology<\/span><\/h3>\n<ul><li> What everyday technologies might be unseen and displaced because of an overly narrow definition of what should be considered an appropriate technology? Who are the local innovators whose technologies might be championed as part of a CI project?<\/li><\/ul>\n<ul><li> Are people with the needed skill sets engaged in the design and implementation of the CI project to maximize the likelihood that it is a community building project and not solely a technology-focused initiative?<\/li><\/ul>\n<ul><li> How can we seek to understand and leverage constituencies\u2019 everyday experiences with technology as an essential gateway for understanding (a) how oppressive systems in society reinforce existing inequalities and (b) the role that different technologies, as applied in context, play in amplifying these social processes?<\/li><\/ul>\n<ul><li> Have the impacts on all stakeholders \u2014 including future generations, nonhuman residents, those who intersect with the participants and beneficiaries of CI projects, and those involved in the mining of minerals, in the production of technologies, and in end-of-life recycling \u2014 been considered in the selection and implementation of specific technologies?<\/li><\/ul>\n<ul><li> How might the voices of technology skeptics and traditionalists inform adoption, or non-adoption, of a CI project? What important insights regarding culture, values, and history are these perspectives bringing to the engagement?<\/li><\/ul>\n<ul><li> How do we balance considerations of ease of implementation, purchase costs, operational costs, human costs, sustainability, and end-of-life effects when choosing between different technologies?<\/li><\/ul>\n<ul><li> How should we proceed when there isn\u2019t alignment amongst various stakeholders regarding important aspects of technology implementation? Is this an opportunity to embrace difference as a resource for community building and the construction of new knowledge in CI projects?<\/li><\/ul>\n<ul><li> How do we proceed when ethical and legal aspects come into conflict, especially in the global context when the ethics and laws of one culture come into conflict with those of another? Do complex situations like these present opportunities to embrace group differences as resources for community building and the construction of new knowledge in CI projects?<\/li><\/ul>\n<ul><li> How do we balance our relationships with members of the community with the requirements of our places of employment and project funders when a constituency determines adoption or acquisition would be counter to their interests, values, belief systems, and\/or cultural ways of being and doing?<\/li><\/ul>\n<ul><li> How can we develop new definitions of success in CI projects that do not require adoption of digital technologies or acquisition of data and artifacts?<\/li><\/ul>\n<ul><li> How do we introduce technology opportunities without encouraging technological utopianism?<\/li><\/ul>\n<h2><span class=\"mw-headline\" id=\"Acknowledgments\">Acknowledgments<\/span><\/h2>\n<p>We gratefully acknowledge Anne Gilliland and Kelvin White, who co-led the 2014 and 2015 workshops with the two authors. We also extend a sincere thank you to all the participants of each of the three workshops.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Footnotes\">Footnotes<\/span><\/h2>\n<div class=\"reflist\" style=\"list-style-type: lower-alpha;\">\n<ol class=\"references\">\n<li id=\"cite_note-2\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-2\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\">Throughout this document, we use Stoecker\u2019s<sup id=\"rdp-ebb-cite_ref-StoeckerWhat14_1-0\" class=\"reference\"><a href=\"#cite_note-StoeckerWhat14-1\" rel=\"external_link\">[1]<\/a><\/sup> distinction between constituency (that is, \u201cpeople who have important life experience in common\u201d) and community (that is, \u201ca collectivity in a local setting whose members interact in many different ways that results in the mutual enhancement and sustainability of the collectivity and its constituents\u201d).<\/span>\n<\/li>\n<\/ol><\/div>\n<h2><span class=\"mw-headline\" id=\"References\">References<\/span><\/h2>\n<div class=\"reflist references-column-width\" style=\"-moz-column-width: 30em; -webkit-column-width: 30em; column-width: 30em; list-style-type: decimal;\">\n<ol class=\"references\">\n<li id=\"cite_note-StoeckerWhat14-1\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-StoeckerWhat14_1-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation Journal\">Stoecker, R. (2014). <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/www.aishe-j.org\/?page_id=137\" target=\"_blank\">\"What if?\"<\/a>. <i>All Ireland Journal of Teaching and Learning in Higher Education<\/i> <b>6<\/b> (1)<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/www.aishe-j.org\/?page_id=137\" target=\"_blank\">http:\/\/www.aishe-j.org\/?page_id=137<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=What+if%3F&rft.jtitle=All+Ireland+Journal+of+Teaching+and+Learning+in+Higher+Education&rft.aulast=Stoecker%2C+R.&rft.au=Stoecker%2C+R.&rft.date=2014&rft.volume=6&rft.issue=1&rft_id=http%3A%2F%2Fwww.aishe-j.org%2F%3Fpage_id%3D137&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-3\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-3\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation Journal\">Gurstein, M. (2003). <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/firstmonday.org\/article\/view\/1107\/1027\" target=\"_blank\">\"Effective use: A community informatics strategy beyond the digital divide\"<\/a>. <i>First Monday<\/i> <b>8<\/b> (12)<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/firstmonday.org\/article\/view\/1107\/1027\" target=\"_blank\">http:\/\/firstmonday.org\/article\/view\/1107\/1027<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Effective+use%3A+A+community+informatics+strategy+beyond+the+digital+divide&rft.jtitle=First+Monday&rft.aulast=Gurstein%2C+M.&rft.au=Gurstein%2C+M.&rft.date=2003&rft.volume=8&rft.issue=12&rft_id=http%3A%2F%2Ffirstmonday.org%2Farticle%2Fview%2F1107%2F1027&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-StoeckerIsComm05-4\"><span class=\"mw-cite-backlink\">\u2191 <sup><a href=\"#cite_ref-StoeckerIsComm05_4-0\" rel=\"external_link\">3.0<\/a><\/sup> <sup><a href=\"#cite_ref-StoeckerIsComm05_4-1\" rel=\"external_link\">3.1<\/a><\/sup><\/span> <span class=\"reference-text\"><span class=\"citation Journal\">Stoecker, R. (2005). <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/183\/129\" target=\"_blank\">\"Is community informatics good for communities? Questions confronting an emerging field\"<\/a>. <i>The Journal of Community Informatics<\/i> <b>1<\/b> (3)<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/183\/129\" target=\"_blank\">http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/183\/129<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Is+community+informatics+good+for+communities%3F+Questions+confronting+an+emerging+field&rft.jtitle=The+Journal+of+Community+Informatics&rft.aulast=Stoecker%2C+R.&rft.au=Stoecker%2C+R.&rft.date=2005&rft.volume=1&rft.issue=3&rft_id=http%3A%2F%2Fci-journal.net%2Findex.php%2Fciej%2Farticle%2Fview%2F183%2F129&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-5\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-5\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation web\">Campbell, N.D.; Eubanks, V. (2004). <a rel=\"external_link\" class=\"external text\" href=\"https:\/\/web.archive.org\/web\/20050317102659\/http:\/\/www.brillomag.net\/COPC\/CI\/index.html\" target=\"_blank\">\"Community Informatics as a Pathway to Social Change\"<\/a>. <i>Brillo Magazine<\/i>. Archived from <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/www.brillomag.net\/COPC\/CI\/index.html\" target=\"_blank\">the original<\/a> on 17 March 2005<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"https:\/\/web.archive.org\/web\/20050317102659\/http:\/\/www.brillomag.net\/COPC\/CI\/index.html\" target=\"_blank\">https:\/\/web.archive.org\/web\/20050317102659\/http:\/\/www.brillomag.net\/COPC\/CI\/index.html<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Community+Informatics+as+a+Pathway+to+Social+Change&rft.atitle=Brillo+Magazine&rft.aulast=Campbell%2C+N.D.%3B+Eubanks%2C+V.&rft.au=Campbell%2C+N.D.%3B+Eubanks%2C+V.&rft.date=2004&rft_id=https%3A%2F%2Fweb.archive.org%2Fweb%2F20050317102659%2Fhttp%3A%2F%2Fwww.brillomag.net%2FCOPC%2FCI%2Findex.html&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-AverwegCode07-6\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-AverwegCode07_6-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation Journal\">Averweg, U.; O'Donnell, S. (2007). <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/441\/307\" target=\"_blank\">\"Code of ethics for community informatics researchers\"<\/a>. <i>The Journal of Community Informatics<\/i> <b>3<\/b> (1)<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/441\/307\" target=\"_blank\">http:\/\/ci-journal.net\/index.php\/ciej\/article\/view\/441\/307<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Code+of+ethics+for+community+informatics+researchers&rft.jtitle=The+Journal+of+Community+Informatics&rft.aulast=Averweg%2C+U.%3B+O%27Donnell%2C+S.&rft.au=Averweg%2C+U.%3B+O%27Donnell%2C+S.&rft.date=2007&rft.volume=3&rft.issue=1&rft_id=http%3A%2F%2Fci-journal.net%2Findex.php%2Fciej%2Farticle%2Fview%2F441%2F307&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-StoeckerEthics-7\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-StoeckerEthics_7-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation web\">Stoecker, R.. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/www.publicsphereproject.org\/node\/266\" target=\"_blank\">\"Ethics of community informatics research and practice\"<\/a>. <i>Public Sphere Project<\/i><span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/www.publicsphereproject.org\/node\/266\" target=\"_blank\">http:\/\/www.publicsphereproject.org\/node\/266<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Ethics+of+community+informatics+research+and+practice&rft.atitle=Public+Sphere+Project&rft.aulast=Stoecker%2C+R.&rft.au=Stoecker%2C+R.&rft_id=http%3A%2F%2Fwww.publicsphereproject.org%2Fnode%2F266&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-YoungDiff97-8\"><span class=\"mw-cite-backlink\">\u2191 <sup><a href=\"#cite_ref-YoungDiff97_8-0\" rel=\"external_link\">7.0<\/a><\/sup> <sup><a href=\"#cite_ref-YoungDiff97_8-1\" rel=\"external_link\">7.1<\/a><\/sup> <sup><a href=\"#cite_ref-YoungDiff97_8-2\" rel=\"external_link\">7.2<\/a><\/sup> <sup><a href=\"#cite_ref-YoungDiff97_8-3\" rel=\"external_link\">7.3<\/a><\/sup><\/span> <span class=\"reference-text\"><span class=\"citation book\">Young, I.M. (1997). \"Difference as a resource for democratic communication\". In Bohman, J.; Rehg, W.. <i>Deliberative Democracy: Essays in Reason and Politics<\/i>. MIT Press. pp. 383\u2013406. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/International_Standard_Book_Number\" target=\"_blank\">ISBN<\/a> 9780262522410.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Difference+as+a+resource+for+democratic+communication&rft.atitle=Deliberative+Democracy%3A+Essays+in+Reason+and+Politics&rft.aulast=Young%2C+I.M.&rft.au=Young%2C+I.M.&rft.date=1997&rft.pages=pp.%26nbsp%3B383%E2%80%93406&rft.pub=MIT+Press&rft.isbn=9780262522410&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-LeopoldTheLand49-9\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-LeopoldTheLand49_9-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation book\">Leopold, A. (1949). \"The Land Ethic\". <i>A Sand County Almanac<\/i>. Ballantine Books.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=The+Land+Ethic&rft.atitle=A+Sand+County+Almanac&rft.aulast=Leopold%2C+A.&rft.au=Leopold%2C+A.&rft.date=1949&rft.pub=Ballantine+Books&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-KimmererLearning13-10\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-KimmererLearning13_10-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation book\">Kimmerer, R.W. (2013). \"Learning the Grammar of Animacy\". <i>Braiding Sweetgrass<\/i>. Milkweed Editions. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/International_Standard_Book_Number\" target=\"_blank\">ISBN<\/a> 9781571313355.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Learning+the+Grammar+of+Animacy&rft.atitle=Braiding+Sweetgrass&rft.aulast=Kimmerer%2C+R.W.&rft.au=Kimmerer%2C+R.W.&rft.date=2013&rft.pub=Milkweed+Editions&rft.isbn=9781571313355&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-LugonesIntro03-11\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-LugonesIntro03_11-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation book\">\"Introduction\". <i>Pilgrimages\/Peregrinajes: Theorizing Coalition Against Multiple Oppressions<\/i>. Rowman & Littlefield Publishers. 2003. pp. 1\u201339. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/International_Standard_Book_Number\" target=\"_blank\">ISBN<\/a> 9780742514591.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Introduction&rft.atitle=Pilgrimages%2FPeregrinajes%3A+Theorizing+Coalition+Against+Multiple+Oppressions&rft.date=2003&rft.pages=pp.%26nbsp%3B1%E2%80%9339&rft.pub=Rowman+%26+Littlefield+Publishers&rft.isbn=9780742514591&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-KincheloeRethink05-12\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-KincheloeRethink05_12-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation book\">Kincheloe, J.L.; McLaren, P. (2005). \"Rethinking critical theory and qualitative research\". In Denzin, N.K.; Lincoln, Y.S.. <i>The SAGE Handbook of Qualitative Research<\/i>. SAGE Publications. pp. 303\u2013342. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/International_Standard_Book_Number\" target=\"_blank\">ISBN<\/a> 9780761927570.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Rethinking+critical+theory+and+qualitative+research&rft.atitle=The+SAGE+Handbook+of+Qualitative+Research&rft.aulast=Kincheloe%2C+J.L.%3B+McLaren%2C+P.&rft.au=Kincheloe%2C+J.L.%3B+McLaren%2C+P.&rft.date=2005&rft.pages=pp.%26nbsp%3B303%E2%80%93342&rft.pub=SAGE+Publications&rft.isbn=9780761927570&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-FreirePedag00-13\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-FreirePedag00_13-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation book\">Freire, P. (2000). <i>Pedagogy of the Oppressed<\/i>. Continuum International Publishing Group. p. 81. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/International_Standard_Book_Number\" target=\"_blank\">ISBN<\/a> 0826412769.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Pedagogy+of+the+Oppressed&rft.aulast=Freire%2C+P.&rft.au=Freire%2C+P.&rft.date=2000&rft.pages=p.%26nbsp%3B81&rft.pub=Continuum+International+Publishing+Group&rft.isbn=0826412769&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-PluralizingEduc11-14\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-PluralizingEduc11_14-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation Journal\">Pluralizing the Archival Curriculum Group (2011). \"Educating for the archival multiverse\". <i>The American Archivist<\/i> <b>74<\/b> (1): 69\u2013101. <a rel=\"external_link\" class=\"external text\" href=\"http:\/\/en.wikipedia.org\/wiki\/Digital_object_identifier\" target=\"_blank\">doi<\/a>:<a rel=\"external_link\" class=\"external text\" href=\"http:\/\/dx.doi.org\/10.17723%2Faarc.74.1.hv339647l2745684\" target=\"_blank\">10.17723\/aarc.74.1.hv339647l2745684<\/a>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Educating+for+the+archival+multiverse&rft.jtitle=The+American+Archivist&rft.aulast=Pluralizing+the+Archival+Curriculum+Group&rft.au=Pluralizing+the+Archival+Curriculum+Group&rft.date=2011&rft.volume=74&rft.issue=1&rft.pages=69%E2%80%93101&rft_id=info:doi\/10.17723%2Faarc.74.1.hv339647l2745684&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-CIRNTowards14-15\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-CIRNTowards14_15-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation web\"><a rel=\"external_link\" class=\"external text\" href=\"http:\/\/cirn.wikispaces.com\/Towards+a+CIRN+Framework+for+Ethics,+Diversity,+and+Inclusion\" target=\"_blank\">\"Towards a CIRN Framework for Ethics, Diversity, and Inclusion\"<\/a>. <i>CIRN Commons<\/i>. Community Informatics Research Network. 2014<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/cirn.wikispaces.com\/Towards+a+CIRN+Framework+for+Ethics,+Diversity,+and+Inclusion\" target=\"_blank\">http:\/\/cirn.wikispaces.com\/Towards+a+CIRN+Framework+for+Ethics,+Diversity,+and+Inclusion<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=Towards+a+CIRN+Framework+for+Ethics%2C+Diversity%2C+and+Inclusion&rft.atitle=CIRN+Commons&rft.date=2014&rft.pub=Community+Informatics+Research+Network&rft_id=http%3A%2F%2Fcirn.wikispaces.com%2FTowards%2Ba%2BCIRN%2BFramework%2Bfor%2BEthics%2C%2BDiversity%2C%2Band%2BInclusion&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<li id=\"cite_note-WCMethod-16\"><span class=\"mw-cite-backlink\"><a href=\"#cite_ref-WCMethod_16-0\" rel=\"external_link\">\u2191<\/a><\/span> <span class=\"reference-text\"><span class=\"citation web\"><a rel=\"external_link\" class=\"external text\" href=\"http:\/\/www.theworldcafe.com\/key-concepts-resources\/world-cafe-method\/\" target=\"_blank\">\"World Cafe Method\"<\/a>. The World Caf\u00e9 Community Foundation<span class=\"printonly\">. <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/www.theworldcafe.com\/key-concepts-resources\/world-cafe-method\/\" target=\"_blank\">http:\/\/www.theworldcafe.com\/key-concepts-resources\/world-cafe-method\/<\/a><\/span>.<\/span><span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=World+Cafe+Method&rft.atitle=&rft.pub=The+World+Caf%C3%A9+Community+Foundation&rft_id=http%3A%2F%2Fwww.theworldcafe.com%2Fkey-concepts-resources%2Fworld-cafe-method%2F&rfr_id=info:sid\/en.wikipedia.org:Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\"><span style=\"display: none;\"> <\/span><\/span><\/span>\n<\/li>\n<\/ol><\/div>\n<h2><span class=\"mw-headline\" id=\"Notes\">Notes<\/span><\/h2>\n<p>This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. A few minor capitalization and punctuation changes were also made. In a case or two, the original URL no longer works, and an alternative or archived version was used. Original references were alphabetical, but they are organized in order of appearance here, by design.\n<\/p>\n<!-- \nNewPP limit report\nCached time: 20181214172026\nCache expiry: 86400\nDynamic content: false\nCPU time usage: 0.379 seconds\nReal time usage: 0.405 seconds\nPreprocessor visited node count: 12158\/1000000\nPreprocessor generated node count: 34050\/1000000\nPost\u2010expand include size: 69636\/2097152 bytes\nTemplate argument size: 24487\/2097152 bytes\nHighest expansion depth: 15\/40\nExpensive parser function count: 0\/100\n-->\n\n<!-- \nTransclusion expansion time report (%,ms,calls,template)\n100.00% 391.257 1 - -total\n 78.17% 305.828 2 - Template:Reflist\n 65.32% 255.582 15 - Template:Citation\/core\n 28.07% 109.820 6 - Template:Cite_book\n 26.86% 105.083 5 - Template:Cite_journal\n 16.26% 63.612 4 - Template:Cite_web\n 15.46% 60.487 1 - Template:Infobox_journal_article\n 14.90% 58.294 1 - Template:Infobox\n 8.94% 34.995 80 - Template:Infobox\/row\n 4.25% 16.616 24 - Template:Citation\/make_link\n-->\n\n<!-- Saved in parser cache with key limswiki:pcache:idhash:9844-0!*!0!!en!*!* and timestamp 20181214172025 and revision id 28730\n -->\n<\/div><div class=\"printfooter\">Source: <a rel=\"external_link\" class=\"external\" href=\"https:\/\/www.limswiki.org\/index.php\/Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective\">https:\/\/www.limswiki.org\/index.php\/Journal:Critical_questions_for_community_informatics_in_practice_from_an_ethical_perspective<\/a><\/div>\n\t\t\t\t\t\t\t\t\t\t<!-- end content -->\n\t\t\t\t\t\t\t\t\t\t<div class=\"visualClear\"><\/div>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/div>\n\t\t<!-- end of the left (by default at least) column -->\n\t\t<div class=\"visualClear\"><\/div>\n\t\t\t\t\t\n\t\t<\/div>\n\t\t\n\n<\/body>","3c37748e91f98bf94197cc33a06161b1_images":[],"3c37748e91f98bf94197cc33a06161b1_timestamp":1544808025,"93ffd2dd01fba825e2b243a1047f5239_type":"article","93ffd2dd01fba825e2b243a1047f5239_title":"VennDiagramWeb: A web application for the generation of highly customizable Venn and Euler diagrams (Lam et al. 2016)","93ffd2dd01fba825e2b243a1047f5239_url":"https:\/\/www.limswiki.org\/index.php\/Journal:VennDiagramWeb:_A_web_application_for_the_generation_of_highly_customizable_Venn_and_Euler_diagrams","93ffd2dd01fba825e2b243a1047f5239_plaintext":"\n\n\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\n\t\t\t\tJournal:VennDiagramWeb: A web application for the generation of highly customizable Venn and Euler diagrams\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\tFrom LIMSWiki\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\tJump to: navigation, search\n\n\t\t\t\t\t\n\t\t\t\t\tFull article title\n \nVennDiagramWeb: A web application for the generation of highly customizable Venn and Euler diagramsJournal\n \nBMC BioinformaticsAuthor(s)\n \nLam, F.; Lalansingh, C.M.; Babaran, H.E.; Wang, Z.; Prokepec, S.D.; Fox, N.S.; Boutros, P.C.Author affiliation(s)\n \nOntario Institute for Cancer Research, University of TorontoPrimary contact\n \nEmail: Paul dot Boutros at oicr dot on dot caYear published\n \n2016Volume and issue\n \n17Page(s)\n \n401DOI\n \n10.1186\/s12859-016-1281-5ISSN\n \n1471-2105Distribution license\n \nCreative Commons Attribution 4.0 InternationalWebsite\n \nhttp:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1281-5Download\n \nhttp:\/\/bmcbioinformatics.biomedcentral.com\/track\/pdf\/10.1186\/s12859-016-1281-5 (PDF)\n\nContents\n\n1 Abstract \n\n1.1 Background \n1.2 Results \n1.3 Conclusions \n\n\n2 Background \n3 Implementation \n4 Results \n\n4.1 User interface \n4.2 Features \n\n4.2.1 Data file uploads \n4.2.2 R code access \n4.2.3 Image downloads \n4.2.4 Multiple workspaces \n\n\n\n\n5 Discussion \n\n5.1 Benefits \n5.2 Comparison to existing tools \n\n\n6 Conclusions \n7 Abbreviations \n8 Declarations \n\n8.1 Acknowledgements \n\n8.1.1 Funding \n8.1.2 Availability of data and materials \n8.1.3 Authors\u2019 contributions \n8.1.4 Competing interests \n8.1.5 Consent for publication \n8.1.6 Ethics approval and consent to participate \n\n\n\n\n9 Additional files \n10 References \n11 Notes \n\n\n\nAbstract \nBackground \nVisualization of data generated by high-throughput, high-dimensionality experiments is rapidly becoming a rate-limiting step in computational biology. There is an ongoing need to quickly develop high-quality visualizations that can be easily customized or incorporated into automated pipelines. This often requires an interface for manual plot modification, rapid cycles of tweaking visualization parameters, and the generation of graphics code. To facilitate this process for the generation of highly-customizable, high-resolution Venn and Euler diagrams, we introduce VennDiagramWeb: a web application for the widely used VennDiagram R package. VennDiagramWeb is hosted at http:\/\/venndiagram.res.oicr.on.ca\/.\n\nResults \nVennDiagramWeb allows real-time modification of Venn and Euler diagrams, with parameter setting through a web interface and immediate visualization of results. It allows customization of essentially all aspects of figures, but also supports integration into computational pipelines via download of R code. Users can upload data and download figures in a range of formats, and there is exhaustive support documentation.\n\nConclusions \nVennDiagramWeb allows the easy creation of Venn and Euler diagrams for computational biologists, and indeed many other fields. Its ability to support real-time graphics changes that are linked to downloadable code that can be integrated into automated pipelines will greatly facilitate the improved visualization of complex datasets. For application support please contact PPaul dot Boutros at oicr dot on dot ca.\n\nBackground \nData visualization is a growing and important area of computational biology that demands high quality images which highlight the critical aspects of data. To elucidate all essential features of the data, one must perform a wide range of adjustments to various aspects of the plot, which can be a time-consuming process. Having fine-grained control over the parameters which define colors, fonts, label placements, element sizes, overall resolution, etc. leads to more effective plots which can convey necessary details in a publication-ready manner.\nPipelines facilitate automated, robust and reproducible data generation and analysis. Plotting is an important tool for both validation and reporting of results. Incorporating effective plots into these pipelines requires code that has been written specifically for each plot, as there is no single approach which can be applied to varied datasets. As a result, bioinformaticians often engage in long cycles of sequentially modifying plotting code, executing it, and observing the ultimate figure, until an optimum is reached. This process is inefficient and time-consuming.\nVenn and Euler diagrams are used frequently in computational biology to visualize the interactions between multiple sets of data. In genomics especially, a common assay is to compare gene lists occurring from separate analyses[1], such as contrasting lists of differentially abundant RNAs following drug treatments or lists of mutated genes across disease types. Venn diagrams are typically depicted as partially intersecting circles or other closed curves such that there are 2n separated regions as depicted by overlapping closed curves.[2] While Venn diagrams always depict all 2n possible regions, Euler diagrams can omit regions under which there are zero values in that region\u2019s subset. This allows Euler diagrams to be less visually complex, by depicting only a subset of all possible regions.[3] VennDiagramWeb facilitates the creation of both Venn and Euler diagrams, using the argument euler.d and scaled (both default TRUE). By default, VennDiagramWeb will create an Euler diagram where possible, displaying only regions containing one or more values. Users can force Venn diagrams only by setting both euler.d\u2009=\u2009FALSE and scaled\u2009=\u2009FALSE (Fig. 1).\n\r\n\n\n\n\n\n\n\n\n\n\n Figure 1. Euler and Venn diagrams produced by VennDiagramWeb each depicting three sets: x1\u2009=\u2009{7,8}, x2\u2009=\u2009{4,6,7}, x3\u2009=\u2009{4,7,8,10}. a. An Euler diagram, produced with euler.d\u2009=\u2009TRUE and scaled\u2009=\u2009TRUE. b. A Venn diagram, produced with euler.d\u2009=\u2009FALSE and scaled\u2009=\u2009FALSE.\n\n\n\nThe R statistical programming language has widespread use in the bioinformatics field, and so we developed VennDiagram to generate plots in this language.[4] The initial release has proven to be robust and useful, and has garnered 186 citations. As of June 8, 2016 the package has been downloaded from the Comprehensive R Archive Network (CRAN) over 75,000 times since its release in March 2011. Over half of these (>40,000) occurred in 2015 alone, highlighting growing popularity.[5]\nWe believe a graphic user interface for VennDiagram could bring the package to a wider audience and enhance workflows for pipeline developers by providing a real-time framework for plotting optimization. There are many existing web interfaces for creating Venn diagrams, including Venny[6], BioVenn[7], GeneVenn[8], and those from the CRP-Sante Microarray Centre[9] and the Universiteit Gent.[10] These tools perform the necessities of creating a Venn diagram, but are missing many features required to create completely customized publication-quality plots, and have no means of exporting code for integration in large scale analysis pipelines.\n\nImplementation \nOur first step was to improve upon the existing VennDiagram R package.[4] A series of changes were made to enhance code quality, including significant refactoring and documentation and exposure of several helper functions. Major feature additions included the ability to create quintuple Venn diagrams. These are highly complex figures, but maintain symmetry and are still easily interpretable (Fig. 2). A parameter to allow users to set a scale by which the areas and labels of the categories will be adjusted to was added. The ability to display proportions of the total population contained within the areas as percentages was also introduced. Many users requested a feature to display a text table of the partitions of the Venn diagram, which is now supported by the package. Users can also now specify an argument which will force the Venn diagram to only consider unique elements in each category when tabulating the sets. In order to have more comprehensive logging which can be integrated with other pipelines which may wrap the Venn diagram code, we now use Futile Logger to log the parameters and sets of the Venn diagrams that are generated at runtime.[11] Finally, users can now choose file types of tiff, png or svg, and can alternatively choose to not output a file, but instead output a list of R graphical objects which compose the entirety of the plot. The user can then modify and re-render the plot as desired.\n\r\n\n\n\n\n\n\n\n\n\n\n Figure 2. A quintuple set Venn diagram\n\n\n\nVennDiagramWeb was written using the R statistical programming language and leverages the VennDiagram R package.[4] It uses the web application server Shiny to create a robust graphical user interface which can execute R code on data and parameters dynamically as they change.[12] Using the Shiny web application server enabled us to create a solution that is composed nearly purely of R from end to end. Using a single language allows for very tight integration of security and error handling functionality. We are able to parse any inputs provided by the user and, using functionality built into the language, inspect those inputs to ensure there is no attempt to inject malicious code. The architecture of the web application is based around the code for the user interface and the code for the server. The user interface is defined by a series of widgets which accept the parameters and data files from the user, and display the rendered plot reactively as elements are changed. The server handles all arguments and data, ensures that they are safe and valid, and performs generation of figures.\n\nResults \nUser interface \nVennDiagramWeb is a graphical user interface for the venn.diagram function.[13] The application starts with a simple example loaded (Fig. 3). Users can also choose to load an example configuration using the drop-down menu in the top right area of the sidebar. Users can modify the parameters of the venn.diagram function using the sidebar, and the resultant plot is generated instantly in the center panel (Fig. 4). The parameters for venn.diagram are divided into eleven sections, allowing the user to quickly find parameters of interest. If the user is familiar with the R package VennDiagram, they can also search for a parameter by name. At the bottom of the sidebar, the user can download the plot displayed as an image. On the bottom bar, the user can choose the datasets plotted, preview the datasets and data partitions, view the R code used to generate the plot, and access proper citation information for VennDiagramWeb.\n\r\n\n\n\n\n\n\n\n\n\n\n Figure 3. The VennDiagramWeb user interface\n\n\n\n\r\n\n\n\n\n\n\n\n\n\n\n Figure 4. A Venn diagram generated using VennDiagramWeb, annotated to indicate the parameters corresponding to features of the plot. The panels in green highlight the parameters of the tool, showing with arrows what elements of the Venn diagram are directly affected. All green elements are not generated as part of the Venn diagram.\n\n\n\nFeatures \nVennDiagramWeb is meant to integrate seamlessly into scientific plot generation workflows. To this end we have included several key features: data file uploads, access to underlying R code, image downloads, and multiple workspaces.\n\nData file uploads \nUsers can upload up to five data files, up to two megabytes each, for use in generating their diagrams, which is quite large for Venn diagrams. These datasets are made available to the editor as dataframes titled data1, data2, etc. through to data5. This feature is found in the first tab on the bottom bar. The file uploading system is designed to accept tables output by R using the write.table function, but can accept any simple text table format, such as csv, tsv, and txt. Some options are available for file format customization, generally pertaining to the options of write.table. These options allow the user to specify the column separator, the presence of headers and\/or row names, and whether or not values are contained in quotes. The user is able to preview the first four lines of the datasets available. As an example, we have provided sample data for the reader to upload (Additional file 1) and visualize (Additional file 2).[14]\n\nR code access \nAs VennDiagramWeb is a graphic overlay for the R package VennDiagram, the user can access the generated R code to reproduce the plot as it appears on screen. This is useful because it allows the user to rapidly prototype the appearance of their desired Venn diagram, and then download the corresponding code for integration into their own pipelines. It is also a necessary feature because though a web application is user-friendly, many users may wish to avoid uploading their data to an external website, or may be restricted from doing so by privacy laws.[15] For this reason, users can experiment with VennDiagramWeb for diagram formatting and customization on toy datasets, and then download the resulting code for use with their real data.\n\nImage downloads \nVennDiagramWeb allows users to download publication-quality images of the Venn diagram displayed on screen. Users can choose the image format as tiff, png or svg, as well as resolution and physical size in inches.\n\nMultiple workspaces \nThe web application has an interface for creating and switching between tabs. This allows users to create several different plots simultaneously. Each workspace tab is distinct and does not share data or parameters to avoid unintentional effects on diagrams which are being generated concurrently.\n\nDiscussion \nBenefits \nThe datasets analyzed in biology and particularly in genomics can be enormous in scope and complexity, and we can only expect them to grow.[16] The rise of big data has lead to increasing attention to the field of data visualization.[17] As our datasets increase in size and our analyses increase in complexity, data visualization becomes crucial in allowing us to gain insight, see patterns and elucidate further areas of study in our experiments.[17][18][19] These visualizations have to be meaningful representations of the data.[18] Unsurprisingly, the figures we use to communicate our insights can become more convoluted with bigger and more complex data and, if poorly designed, risk confusing what they were meant to make clear. Indeed, the difficulty of achieving visual clarity in a diagram often increases in tandem with the necessity to do so.\nDespite the growing importance of data visualization, the scientific community faces technical challenges in creating figures that are meaningful and clear. Complex analyses and their visualizations can represent significant time and effort, and require programming skills the scientific community often lacks.[20] A paper with poorly designed figures could be significantly hampered: if a reader cannot grasp the key insights a figure is meant to convey, then the significance of the paper might be lost, or it may not be published at all, with obvious detriments to the field. There is a clear incentive to generate useful plots, and there is also a clear need for easier and more time-efficient methods to generate them. To this end, we are creating tools that improve both the quality of plots and the speed at which they can be created.\nIn genomics, a common analysis performed in experiments is list comparison. The Venn Diagram is a popular plot type for list comparison, providing a simple visualization of several possibly unrelated lists.[1] The manual generation of these plots can be difficult. Spatial organization and color choice of the groups and their overlapping sections such that they are both clear and aesthetically pleasing is important but nontrivial.[21] The VennDiagram R package addresses this issue. It is commonly in use[5], but we believe a simple graphical user interface for the package will bring it to an even wider audience, particularly to scientists who do not have strong skills in R.\n\nComparison to existing tools \nAs with VennDiagram, VennDiagramWeb offers many features that existing tools lack (Table 1). In addition to the advantages VennDiagram holds over other methods[4], VennDiagramWeb is the only web application we found that allows for tiff downloads, R code download, and multiple workspaces.\n\n\n\n\n\n\n\nTable 1. A comparison of features of VennDiagramWeb to other popular web applications used to generate Venn Diagrams\r\n\na Euler diagrams only; 3-set scaling only when mathematically possible\r\n\nb Uses inaccurate 3-set scaling with circles\n\n\n\nCategory\n\nParameter\n\nVennDiagram (Initial Release)\n\nVennDiagramWeb\n\nVenny\n\nBioVenn\n\nGeneVenn\n\nCRP-Sante Microarray Centre Venn Diagram\n\n\nGeneral\n\nInteractive interface\n\n\n\nX\n\nX\n\nX\n\nX\n\nX\n\n\nData file upload\n\nN\/A\n\nX\n\n\n\nX\n\nX\n\n\n\n\nMultiple workspaces\n\nN\/A\n\nX\n\n\n\n\n\n\n\n\n\n\nR code generation\n\nN\/A\n\nX\n\n\n\n\n\n\n\n\n\n\nCircle Options\n\nColor\n\nX\n\nX\n\n\n\nX\n\nX\n\n\n\n\nFill alpha\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nBorder style\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nBorder width\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nBorder color\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nCategory Labels\n\nContent\n\nX\n\nX\n\n\n\n\n\nX\n\n\n\n\nColor\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nFont\n\nX\n\nX\n\n\n\nX\n\nX\n\n\n\n\nSize\n\nX\n\nX\n\n\n\nX\n\nX\n\n\n\n\nStyle\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nLocation\n\nX\n\nX\n\n\n\nX (SVG only)\n\n\n\n\n\n\nPosition\n\nX\n\nX\n\n\n\nX (SVG only)\n\n\n\n\n\n\nDistance\n\nX\n\nX\n\n\n\nX (SVG only)\n\n\n\n\n\n\nJustification\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nArea Labels\n\nColor\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nFont\n\nX\n\nX\n\nX\n\nX\n\nX\n\n\n\n\nSize\n\nX\n\nX\n\nX\n\nX\n\nX\n\n\n\n\nStyle\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nTitles\n\nMain title\n\nX\n\nX\n\n\n\nX\n\nX\n\n\n\n\nSubtitle\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nPosition\n\nX\n\nX\n\n\n\nX (SVG only)\n\n\n\n\n\n\nColor\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nFont\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nSize\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nStyle\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nJustification\n\nX\n\nX\n\n\n\n\n\n\n\n\n\n\nFile Options\n\nOutput type\n\nTIFF\n\nTIFF\/SVG\/PNG\n\nPNG\n\nSVG\/PNG\n\nPNG\n\nPNG\n\n\nFigure resolution\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nBuilt-in gene ID recognition\n\n\n\n\n\n\n\nX\n\n\n\n\n\n\nMiscellaneous\n\nMaximum sets\n\n4\n\n5\n\n4\n\n3\n\n3\n\n3\n\n\nShapes used\n\nCircles\/Ellipses\n\nCircles\/Ellipses\n\nCircles\/Ellipses\n\nCircles\n\nCircles\n\nCircles\n\n\nScaling\n\n\n\nXa\n\n\n\nXb\n\n\n\n\n\n\nEuler diagrams\n\nX\n\nX\n\n\n\nX\n\n\n\n\n\n\nMargin size\n\n\n\nX\n\n\n\n\n\n\n\n\n\n\nRotation\n\n\n\nX\n\n\n\n\n\n\n\n\n\n\nTwo-set external lines\n\n\n\nX\n\n\n\n\n\n\n\n\n\n\nOther set-specific parameters\n\n\n\nX\n\n\n\n\n\n\n\n\n\n\nPartition display\n\n\n\nX\n\nX\n\nX\n\nX\n\nX\n\n\n\nConclusions \nVennDiagramWeb provides a unique way to integrate and optimize R code for data-visualization with web-based real-time manual optimization with computational pipelines. It will be a key resource for the field. For application support please contact PPaul dot Boutros at oicr dot on dot ca.\n\nAbbreviations \nCRAN: Comprehensive R Archive Network\n\nDeclarations \nAcknowledgements \nThe authors thank all members of the Boutros Lab for excellent technical assistance and support, as well as Hanbo Chen for developing the original VennDiagram package.\n\nFunding \nThis study was conducted with the support of the Ontario Institute for Cancer Research to PCB through funding provided by the Government of Ontario. Dr. Boutros was supported by a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award. This work was supported by Prostate Cancer Canada and is proudly funded by the Movember Foundation - Grant #RS2014-01. This work was supported by an NSERC Discovery Grant to PCB. NSF was supported by the CIHR Canadian Graduate Scholarship \u2013 Master\u2019s, the Medical Biophysics Excellence University of Toronto Fund Scholarship and the University of Toronto Geoff Lockwood and Kevin Graham Medical Biophysics Graduate Scholarship.\n\nAvailability of data and materials \nVennDiagramWeb can be accessed with the internet browsers Firefox and Chrome at http:\/\/venndiagram.oicr.on.ca. The base package VennDiagram can be downloaded from https:\/\/cran.r-project.org\/web\/packages\/VennDiagram\/index.html. No datasets were generated or used during the development of VennDiagramWeb.\n\nAuthors\u2019 contributions \nFL implemented the first version of the Shiny web application. CML and HEB iterated on that code to make the software more stable and robust. ZW refactored the original VennDiagram package, fixed bugs and added features. SDP wrote proof-of-concept code that led to significant changes in the method of rendering diagrams reactively. NSF tested and provided bug reports and feature requests which resulted in a more user-friendly interface. PCB supervised the development of the web application. All authors read and approved the final manuscript.\n\nCompeting interests \nThe authors declare that they have no competing interests.\n\nConsent for publication \nNot applicable.\n\nEthics approval and consent to participate \nNot applicable.\n\nAdditional files \nAdditional file 1: Table S1: Sample data for the user to upload. Hypergeometric testing was conducted on samples of rat and mouse liver tissue to identify similar transcriptomic profiles [14]. (XLS 189 kb)\nAdditional file 2: Figure S1: Venn Diagram created in VennDiagramWeb using Supplemental Table 1 [14] uploaded as data1, with x1\u2009=\u2009data1[data1$Mouse.Liver.Q\u2009<\u20090.05,]$HomologeneID. x2\u2009=\u2009data1[data1$Rat.Liver.Q\u2009<\u20090.05,]$HomologeneID. x3\u2009=\u2009NULL. category.names\u2009=\u2009Mouse,Rat. cat.pos\u2009=\u2009180. cat.dist\u2009=\u20090.02 and all other arguments default. (TIFF 758 kb)\n\nReferences \n\n\n\u2191 1.0 1.1 Bardou, P.; Mariette, J.; Escudi\u00e9, F. et al. (2014). \"jvenn: An interactive Venn diagram viewer\". BMC Bioinformatics 15: 293. doi:10.1186\/1471-2105-15-293. PMC PMC4261873. PMID 25176396. http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?tool=pmcentrez&artid=PMC4261873 .   \n\n\u2191 \"Venn Diagram\". MathWorld. Wolfram Research, Inc. http:\/\/mathworld.wolfram.com\/VennDiagram.html . Retrieved 22 August 2016 .   \n\n\u2191 Rodger, P. (22 September 2004). \"Venn Diagrams, Euler Diagrams and Leibniz\". 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PMID 26151137. http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?tool=pmcentrez&artid=PMC4494865 .   \n\n\u2191 17.0 17.1 Sridharan, M. (20 April 2015). \"Data Visualization - The Rosetta Stone of Data Science\". iCrunchData. REDN Enterprises, LLC. https:\/\/icrunchdata.com\/data-visualization-rosetta-stone-data-science\/ . Retrieved 08 June 2016 .   \n\n\u2191 18.0 18.1 Wong, B.. \"Data Visualization Initiative\". Broad Institute. Archived from the original on 06 September 2015. https:\/\/web.archive.org\/web\/20150906045214\/http:\/\/www.broadinstitute.org\/vis . Retrieved 08 June 2016 .   \n\n\u2191 \"Why you should start by learning data visualization and manipulation\". Sharp Sight Labs. 10 February 2015. http:\/\/sharpsightlabs.com\/blog\/2015\/02\/10\/start-with-data-visualization-manipulation\/ . Retrieved 08 June 2016 .   \n\n\u2191 Merali, Z. (2010). \"Computational science: ...Error\". Nature 467 (7317): 775\u20137. doi:10.1038\/467775a. PMID 20944712.   \n\n\u2191 Ruskey, F.; Savage, C.D.; Wagon, S. (2006). \"The Search for Simple Symmetric Venn Diagrams\" (PDF). Notices of the AMS 53 (11): 1304\u20131311. http:\/\/www.ams.org\/notices\/200611\/ea-wagon.pdf .   \n\n\nNotes \nThis presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. In one case, a URL was dead and an archived version of the page was included. In another, the live URL had changed and was updated in the text.\n\n\n\n\n\n\nSource: <a rel=\"external_link\" class=\"external\" href=\"https:\/\/www.limswiki.org\/index.php\/Journal:VennDiagramWeb:_A_web_application_for_the_generation_of_highly_customizable_Venn_and_Euler_diagrams\">https:\/\/www.limswiki.org\/index.php\/Journal:VennDiagramWeb:_A_web_application_for_the_generation_of_highly_customizable_Venn_and_Euler_diagrams<\/a>\n\t\t\t\t\tCategories: LIMSwiki journal articles (added in 2016)LIMSwiki journal articles (all)LIMSwiki journal articles on bioinformaticsLIMSwiki journal articles on data visualizationLIMSwiki journal articles on software\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\n\t\t\n\t\t\tNavigation menu\n\t\t\t\t\t\n\t\t\tViews\n\n\t\t\t\n\t\t\t\t\n\t\t\t\tJournal\n\t\t\t\tDiscussion\n\t\t\t\tView source\n\t\t\t\tHistory\n\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\n\t\t\t\t\n\t\t\t\tPersonal tools\n\n\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\t\t\tLog in\n\t\t\t\t\t\t\t\t\t\t\t\t\tRequest account\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\n\t\t\t\t\n\t\tNavigation\n\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tMain page\n\t\t\t\t\t\t\t\t\t\t\tRecent changes\n\t\t\t\t\t\t\t\t\t\t\tRandom page\n\t\t\t\t\t\t\t\t\t\t\tHelp\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\n\t\t\t\n\t\t\tSearch\n\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t \n\t\t\t\t\t\t\n\t\t\t\t\n\n\t\t\t\t\t\t\t\n\t\t\n\t\t\t\n\t\t\tTools\n\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tWhat links here\n\t\t\t\t\t\t\t\t\t\t\tRelated changes\n\t\t\t\t\t\t\t\t\t\t\tSpecial pages\n\t\t\t\t\t\t\t\t\t\t\tPermanent link\n\t\t\t\t\t\t\t\t\t\t\tPage information\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\n\t\t\n\t\tPrint\/export\n\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\tCreate a book\n\t\t\t\t\t\t\t\t\t\t\tDownload as PDF\n\t\t\t\t\t\t\t\t\t\t\tDownload as Plain text\n\t\t\t\t\t\t\t\t\t\t\tPrintable version\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\n\t\t\n\t\tSponsors\n\t\t\n\t\t\t \r\n\n\t\r\n\n\t\r\n\n\t\r\n\n\t\n\t\r\n\n \r\n\n\t\n\t\r\n\n \r\n\n\t\n\t\r\n\n\t\n\t\r\n\n\t\r\n\n\t\r\n\n\t\r\n\t\t\n\t\t\n\t\t\t\n\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t This page was last modified on 12 December 2016, at 17:30.\n\t\t\t\t\t\t\t\t\tThis page has been accessed 2,070 times.\n\t\t\t\t\t\t\t\t\tContent is available under a Creative Commons Attribution-ShareAlike 4.0 International License unless otherwise noted.\n\t\t\t\t\t\t\t\t\tPrivacy policy\n\t\t\t\t\t\t\t\t\tAbout LIMSWiki\n\t\t\t\t\t\t\t\t\tDisclaimers\n\t\t\t\t\t\t\t\n\t\t\n\t\t\n\t\t\n\n","93ffd2dd01fba825e2b243a1047f5239_html":"<body class=\"mediawiki ltr sitedir-ltr ns-206 ns-subject page-Journal_VennDiagramWeb_A_web_application_for_the_generation_of_highly_customizable_Venn_and_Euler_diagrams skin-monobook action-view\">\n<div id=\"rdp-ebb-globalWrapper\">\n\t\t<div id=\"rdp-ebb-column-content\">\n\t\t\t<div id=\"rdp-ebb-content\" class=\"mw-body\" role=\"main\">\n\t\t\t\t<a id=\"rdp-ebb-top\"><\/a>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<h1 id=\"rdp-ebb-firstHeading\" class=\"firstHeading\" lang=\"en\">Journal:VennDiagramWeb: A web application for the generation of highly customizable Venn and Euler diagrams<\/h1>\n\t\t\t\t\n\t\t\t\t<div id=\"rdp-ebb-bodyContent\" class=\"mw-body-content\">\n\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\n\t\t\t\t\t<!-- start content -->\n\t\t\t\t\t<div id=\"rdp-ebb-mw-content-text\" lang=\"en\" dir=\"ltr\" class=\"mw-content-ltr\">\n\n\n<h2><span class=\"mw-headline\" id=\"Abstract\">Abstract<\/span><\/h2>\n<h3><span class=\"mw-headline\" id=\"Background\">Background<\/span><\/h3>\n<p>Visualization of data generated by high-throughput, high-dimensionality experiments is rapidly becoming a rate-limiting step in <a href=\"https:\/\/www.limswiki.org\/index.php\/Computational_informatics\" title=\"Computational informatics\" target=\"_blank\" class=\"wiki-link\" data-key=\"80a08446a8f94f903e2d70e83e86c8ff\">computational biology<\/a>. There is an ongoing need to quickly develop high-quality visualizations that can be easily customized or incorporated into automated pipelines. This often requires an interface for manual plot modification, rapid cycles of tweaking visualization parameters, and the generation of graphics code. To facilitate this process for the generation of highly-customizable, high-resolution Venn and Euler diagrams, we introduce <i>VennDiagramWeb<\/i>: a web application for the widely used VennDiagram R package. <i>VennDiagramWeb<\/i> is hosted at <a rel=\"external_link\" class=\"external free\" href=\"http:\/\/venndiagram.res.oicr.on.ca\/\" target=\"_blank\">http:\/\/venndiagram.res.oicr.on.ca\/<\/a>.\n<\/p>\n<h3><span class=\"mw-headline\" id=\"Results\">Results<\/span><\/h3>\n<p><i>VennDiagramWeb<\/i> allows real-time modification of Venn and Euler diagrams, with parameter setting through a web interface and immediate visualization of results. It allows customization of essentially all aspects of figures, but also supports integration into computational pipelines via download of <a href=\"https:\/\/www.limswiki.org\/index.php\/R_(programming_language)\" title=\"R (programming language)\" target=\"_blank\" class=\"wiki-link\" data-key=\"1b0aa598f071aca4c5b4ee08d8bb2bde\">R code<\/a>. Users can upload data and download figures in a range of formats, and there is exhaustive support documentation.\n<\/p>\n<h3><span class=\"mw-headline\" id=\"Conclusions\">Conclusions<\/span><\/h3>\n<p><i>VennDiagramWeb<\/i> allows the easy creation of Venn and Euler diagrams for computational biologists, and indeed many other fields. Its ability to support real-time graphics changes that are linked to downloadable code that can be integrated into automated pipelines will greatly facilitate the improved visualization of complex datasets. For application support please contact PPaul dot Boutros at oicr dot on dot ca.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Background_2\">Background<\/span><\/h2>\n<p>Data visualization is a growing and important area of computational biology that demands high quality images which highlight the critical aspects of data. To elucidate all essential features of the data, one must perform a wide range of adjustments to various aspects of the plot, which can be a time-consuming process. Having fine-grained control over the parameters which define colors, fonts, label placements, element sizes, overall resolution, etc. leads to more effective plots which can convey necessary details in a publication-ready manner.\n<\/p><p>Pipelines facilitate automated, robust and reproducible data generation and analysis. Plotting is an important tool for both validation and reporting of results. Incorporating effective plots into these pipelines requires code that has been written specifically for each plot, as there is no single approach which can be applied to varied datasets. As a result, <a href=\"https:\/\/www.limswiki.org\/index.php\/Bioinformatics\" title=\"Bioinformatics\" target=\"_blank\" class=\"wiki-link\" data-key=\"8f506695fdbb26e3f314da308f8c053b\">bioinformaticians<\/a> often engage in long cycles of sequentially modifying plotting code, executing it, and observing the ultimate figure, until an optimum is reached. This process is inefficient and time-consuming.\n<\/p><p>Venn and Euler diagrams are used frequently in computational biology to visualize the interactions between multiple sets of data. In <a href=\"https:\/\/www.limswiki.org\/index.php\/Genomics\" title=\"Genomics\" target=\"_blank\" class=\"wiki-link\" data-key=\"96a82dabf51cf9510dd00c5a03396c44\">genomics<\/a> especially, a common assay is to compare gene lists occurring from separate analyses<sup id=\"rdp-ebb-cite_ref-Bardou_jvenn14_1-0\" class=\"reference\"><a href=\"#cite_note-Bardou_jvenn14-1\" rel=\"external_link\">[1]<\/a><\/sup>, such as contrasting lists of differentially abundant RNAs following drug treatments or lists of mutated genes across disease types. Venn diagrams are typically depicted as partially intersecting circles or other closed curves such that there are 2<sup>n<\/sup> separated regions as depicted by overlapping closed curves.<sup id=\"rdp-ebb-cite_ref-WeissteinVenn_2-0\" class=\"reference\"><a href=\"#cite_note-WeissteinVenn-2\" rel=\"external_link\">[2]<\/a><\/sup> While Venn diagrams always depict all 2<sup>n<\/sup> possible regions, Euler diagrams can omit regions under which there are zero values in that region\u2019s subset. This allows Euler diagrams to be less visually complex, by depicting only a subset of all possible regions.<sup id=\"rdp-ebb-cite_ref-RodgerEuler04_3-0\" class=\"reference\"><a href=\"#cite_note-RodgerEuler04-3\" rel=\"external_link\">[3]<\/a><\/sup> <i>VennDiagramWeb<\/i> facilitates the creation of both Venn and Euler diagrams, using the argument euler.d and scaled (both default TRUE). By default, <i>VennDiagramWeb<\/i> will create an Euler diagram where possible, displaying only regions containing one or more values. Users can force Venn diagrams only by setting both euler.d\u2009=\u2009FALSE and scaled\u2009=\u2009FALSE (Fig. 1).\n<\/p><p><br \/>\n<a href=\"https:\/\/www.limswiki.org\/index.php\/File:Fig1_Lam_BMCBioinformatics2016_17.gif\" class=\"image wiki-link\" target=\"_blank\" data-key=\"645d2d7b1f7fc5a31c18a27407bc5f58\"><img alt=\"Fig1 Lam BMCBioinformatics2016 17.gif\" src=\"https:\/\/www.limswiki.org\/images\/d\/d7\/Fig1_Lam_BMCBioinformatics2016_17.gif\" style=\"width: 100%;max-width: 400px;height: auto;\" \/><\/a>\n<\/p>\n<div style=\"clear:both;\"><\/div>\n<table style=\"\">\n<tr>\n<td style=\"vertical-align:top;\">\n<table border=\"0\" cellpadding=\"5\" cellspacing=\"0\" style=\"\">\n\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\"> <blockquote><b>Figure 1.<\/b> Euler and Venn diagrams produced by <i>VennDiagramWeb<\/i> each depicting three sets: x1\u2009=\u2009{7,8}, x2\u2009=\u2009{4,6,7}, x3\u2009=\u2009{4,7,8,10}. <b>a<\/b>. An Euler diagram, produced with euler.d\u2009=\u2009TRUE and scaled\u2009=\u2009TRUE. <b>b<\/b>. A Venn diagram, produced with euler.d\u2009=\u2009FALSE and scaled\u2009=\u2009FALSE.<\/blockquote>\n<\/td><\/tr>\n<\/table>\n<\/td><\/tr><\/table>\n<p>The R statistical programming language has widespread use in the bioinformatics field, and so we developed VennDiagram to generate plots in this language.<sup id=\"rdp-ebb-cite_ref-ChenVenn11_4-0\" class=\"reference\"><a href=\"#cite_note-ChenVenn11-4\" rel=\"external_link\">[4]<\/a><\/sup> The initial release has proven to be robust and useful, and has garnered 186 citations. As of June 8, 2016 the package has been downloaded from the Comprehensive R Archive Network (CRAN) over 75,000 times since its release in March 2011. Over half of these (>40,000) occurred in 2015 alone, highlighting growing popularity.<sup id=\"rdp-ebb-cite_ref-Cs.C3.A1rdi_cranlogs_5-0\" class=\"reference\"><a href=\"#cite_note-Cs.C3.A1rdi_cranlogs-5\" rel=\"external_link\">[5]<\/a><\/sup>\n<\/p><p>We believe a graphic user interface for VennDiagram could bring the package to a wider audience and enhance workflows for pipeline developers by providing a real-time framework for plotting optimization. There are many existing web interfaces for creating Venn diagrams, including Venny<sup id=\"rdp-ebb-cite_ref-OliverosVenny_6-0\" class=\"reference\"><a href=\"#cite_note-OliverosVenny-6\" rel=\"external_link\">[6]<\/a><\/sup>, BioVenn<sup id=\"rdp-ebb-cite_ref-HulsenBioVenn_7-0\" class=\"reference\"><a href=\"#cite_note-HulsenBioVenn-7\" rel=\"external_link\">[7]<\/a><\/sup>, GeneVenn<sup id=\"rdp-ebb-cite_ref-PiroozniaGeneVenn_8-0\" class=\"reference\"><a href=\"#cite_note-PiroozniaGeneVenn-8\" rel=\"external_link\">[8]<\/a><\/sup>, and those from the CRP-Sante Microarray Centre<sup id=\"rdp-ebb-cite_ref-MicroVenn_9-0\" class=\"reference\"><a href=\"#cite_note-MicroVenn-9\" rel=\"external_link\">[9]<\/a><\/sup> and the Universiteit Gent.<sup id=\"rdp-ebb-cite_ref-VIBCalculate_10-0\" class=\"reference\"><a href=\"#cite_note-VIBCalculate-10\" rel=\"external_link\">[10]<\/a><\/sup> These tools perform the necessities of creating a Venn diagram, but are missing many features required to create completely customized publication-quality plots, and have no means of exporting code for integration in large scale analysis pipelines.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Implementation\">Implementation<\/span><\/h2>\n<p>Our first step was to improve upon the existing VennDiagram R package.<sup id=\"rdp-ebb-cite_ref-ChenVenn11_4-1\" class=\"reference\"><a href=\"#cite_note-ChenVenn11-4\" rel=\"external_link\">[4]<\/a><\/sup> A series of changes were made to enhance code quality, including significant refactoring and documentation and exposure of several helper functions. Major feature additions included the ability to create quintuple Venn diagrams. These are highly complex figures, but maintain symmetry and are still easily interpretable (Fig. 2). A parameter to allow users to set a scale by which the areas and labels of the categories will be adjusted to was added. The ability to display proportions of the total population contained within the areas as percentages was also introduced. Many users requested a feature to display a text table of the partitions of the Venn diagram, which is now supported by the package. Users can also now specify an argument which will force the Venn diagram to only consider unique elements in each category when tabulating the sets. In order to have more comprehensive logging which can be integrated with other pipelines which may wrap the Venn diagram code, we now use Futile Logger to log the parameters and sets of the Venn diagrams that are generated at runtime.<sup id=\"rdp-ebb-cite_ref-RoweFutile_11-0\" class=\"reference\"><a href=\"#cite_note-RoweFutile-11\" rel=\"external_link\">[11]<\/a><\/sup> Finally, users can now choose file types of tiff, png or svg, and can alternatively choose to not output a file, but instead output a list of R graphical objects which compose the entirety of the plot. The user can then modify and re-render the plot as desired.\n<\/p><p><br \/>\n<a href=\"https:\/\/www.limswiki.org\/index.php\/File:Fig2_Lam_BMCBioinformatics2016_17.gif\" class=\"image wiki-link\" target=\"_blank\" data-key=\"d03976f95003d56a4a6fe2099ff2800c\"><img alt=\"Fig2 Lam BMCBioinformatics2016 17.gif\" src=\"https:\/\/www.limswiki.org\/images\/e\/ef\/Fig2_Lam_BMCBioinformatics2016_17.gif\" style=\"width: 100%;max-width: 400px;height: auto;\" \/><\/a>\n<\/p>\n<div style=\"clear:both;\"><\/div>\n<table style=\"\">\n<tr>\n<td style=\"vertical-align:top;\">\n<table border=\"0\" cellpadding=\"5\" cellspacing=\"0\" style=\"\">\n\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\"> <blockquote><b>Figure 2.<\/b> A quintuple set Venn diagram<\/blockquote>\n<\/td><\/tr>\n<\/table>\n<\/td><\/tr><\/table>\n<p><i>VennDiagramWeb<\/i> was written using the R statistical programming language and leverages the VennDiagram R package.<sup id=\"rdp-ebb-cite_ref-ChenVenn11_4-2\" class=\"reference\"><a href=\"#cite_note-ChenVenn11-4\" rel=\"external_link\">[4]<\/a><\/sup> It uses the web application server Shiny to create a robust graphical user interface which can execute R code on data and parameters dynamically as they change.<sup id=\"rdp-ebb-cite_ref-RStudioShiny_12-0\" class=\"reference\"><a href=\"#cite_note-RStudioShiny-12\" rel=\"external_link\">[12]<\/a><\/sup> Using the Shiny web application server enabled us to create a solution that is composed nearly purely of R from end to end. Using a single language allows for very tight integration of security and error handling functionality. We are able to parse any inputs provided by the user and, using functionality built into the language, inspect those inputs to ensure there is no attempt to inject malicious code. The architecture of the web application is based around the code for the user interface and the code for the server. The user interface is defined by a series of widgets which accept the parameters and data files from the user, and display the rendered plot reactively as elements are changed. The server handles all arguments and data, ensures that they are safe and valid, and performs generation of figures.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Results_2\">Results<\/span><\/h2>\n<h3><span class=\"mw-headline\" id=\"User_interface\">User interface<\/span><\/h3>\n<p><i>VennDiagramWeb<\/i> is a graphical user interface for the venn.diagram function.<sup id=\"rdp-ebb-cite_ref-ChenPackage16_13-0\" class=\"reference\"><a href=\"#cite_note-ChenPackage16-13\" rel=\"external_link\">[13]<\/a><\/sup> The application starts with a simple example loaded (Fig. 3). Users can also choose to load an example configuration using the drop-down menu in the top right area of the sidebar. Users can modify the parameters of the venn.diagram function using the sidebar, and the resultant plot is generated instantly in the center panel (Fig. 4). The parameters for venn.diagram are divided into eleven sections, allowing the user to quickly find parameters of interest. If the user is familiar with the R package VennDiagram, they can also search for a parameter by name. At the bottom of the sidebar, the user can download the plot displayed as an image. On the bottom bar, the user can choose the datasets plotted, preview the datasets and data partitions, view the R code used to generate the plot, and access proper citation information for VennDiagramWeb.\n<\/p><p><br \/>\n<a href=\"https:\/\/www.limswiki.org\/index.php\/File:Fig3_Lam_BMCBioinformatics2016_17.gif\" class=\"image wiki-link\" target=\"_blank\" data-key=\"4b9afb4ac8a1abc91960707f6c1e75b8\"><img alt=\"Fig3 Lam BMCBioinformatics2016 17.gif\" src=\"https:\/\/www.limswiki.org\/images\/1\/14\/Fig3_Lam_BMCBioinformatics2016_17.gif\" style=\"width: 100%;max-width: 400px;height: auto;\" \/><\/a>\n<\/p>\n<div style=\"clear:both;\"><\/div>\n<table style=\"\">\n<tr>\n<td style=\"vertical-align:top;\">\n<table border=\"0\" cellpadding=\"5\" cellspacing=\"0\" style=\"\">\n\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\"> <blockquote><b>Figure 3.<\/b> The <i>VennDiagramWeb<\/i> user interface<\/blockquote>\n<\/td><\/tr>\n<\/table>\n<\/td><\/tr><\/table>\n<p><br \/>\n<a href=\"https:\/\/www.limswiki.org\/index.php\/File:Fig4_Lam_BMCBioinformatics2016_17.gif\" class=\"image wiki-link\" target=\"_blank\" data-key=\"6425a21e5f2fff7eadc78c243e7f34ae\"><img alt=\"Fig4 Lam BMCBioinformatics2016 17.gif\" src=\"https:\/\/www.limswiki.org\/images\/b\/b2\/Fig4_Lam_BMCBioinformatics2016_17.gif\" style=\"width: 100%;max-width: 400px;height: auto;\" \/><\/a>\n<\/p>\n<div style=\"clear:both;\"><\/div>\n<table style=\"\">\n<tr>\n<td style=\"vertical-align:top;\">\n<table border=\"0\" cellpadding=\"5\" cellspacing=\"0\" style=\"\">\n\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\"> <blockquote><b>Figure 4.<\/b> A Venn diagram generated using <i>VennDiagramWeb<\/i>, annotated to indicate the parameters corresponding to features of the plot. The panels in green highlight the parameters of the tool, showing with arrows what elements of the Venn diagram are directly affected. All green elements are not generated as part of the Venn diagram.<\/blockquote>\n<\/td><\/tr>\n<\/table>\n<\/td><\/tr><\/table>\n<h3><span class=\"mw-headline\" id=\"Features\">Features<\/span><\/h3>\n<p><i>VennDiagramWeb<\/i> is meant to integrate seamlessly into scientific plot generation workflows. To this end we have included several key features: data file uploads, access to underlying R code, image downloads, and multiple workspaces.\n<\/p>\n<h4><span class=\"mw-headline\" id=\"Data_file_uploads\">Data file uploads<\/span><\/h4>\n<p>Users can upload up to five data files, up to two megabytes each, for use in generating their diagrams, which is quite large for Venn diagrams. These datasets are made available to the editor as dataframes titled data1, data2, etc. through to data5. This feature is found in the first tab on the bottom bar. The file uploading system is designed to accept tables output by R using the write.table function, but can accept any simple text table format, such as csv, tsv, and txt. Some options are available for file format customization, generally pertaining to the options of write.table. These options allow the user to specify the column separator, the presence of headers and\/or row names, and whether or not values are contained in quotes. The user is able to preview the first four lines of the datasets available. As an example, we have provided sample data for the reader to upload (Additional file 1) and visualize (Additional file 2).<sup id=\"rdp-ebb-cite_ref-SunCross14_14-0\" class=\"reference\"><a href=\"#cite_note-SunCross14-14\" rel=\"external_link\">[14]<\/a><\/sup>\n<\/p>\n<h4><span class=\"mw-headline\" id=\"R_code_access\">R code access<\/span><\/h4>\n<p>As <i>VennDiagramWeb<\/i> is a graphic overlay for the R package VennDiagram, the user can access the generated R code to reproduce the plot as it appears on screen. This is useful because it allows the user to rapidly prototype the appearance of their desired Venn diagram, and then download the corresponding code for integration into their own pipelines. It is also a necessary feature because though a web application is user-friendly, many users may wish to avoid uploading their data to an external website, or may be restricted from doing so by privacy laws.<sup id=\"rdp-ebb-cite_ref-GPOpubl191_15-0\" class=\"reference\"><a href=\"#cite_note-GPOpubl191-15\" rel=\"external_link\">[15]<\/a><\/sup> For this reason, users can experiment with <i>VennDiagramWeb<\/i> for diagram formatting and customization on toy datasets, and then download the resulting code for use with their real data.\n<\/p>\n<h4><span class=\"mw-headline\" id=\"Image_downloads\">Image downloads<\/span><\/h4>\n<p><i>VennDiagramWeb<\/i> allows users to download publication-quality images of the Venn diagram displayed on screen. Users can choose the image format as tiff, png or svg, as well as resolution and physical size in inches.\n<\/p>\n<h4><span class=\"mw-headline\" id=\"Multiple_workspaces\">Multiple workspaces<\/span><\/h4>\n<p>The web application has an interface for creating and switching between tabs. This allows users to create several different plots simultaneously. Each workspace tab is distinct and does not share data or parameters to avoid unintentional effects on diagrams which are being generated concurrently.\n<\/p>\n<h2><span class=\"mw-headline\" id=\"Discussion\">Discussion<\/span><\/h2>\n<h3><span class=\"mw-headline\" id=\"Benefits\">Benefits<\/span><\/h3>\n<p>The datasets analyzed in biology and particularly in genomics can be enormous in scope and complexity, and we can only expect them to grow.<sup id=\"rdp-ebb-cite_ref-StephensBig15_16-0\" class=\"reference\"><a href=\"#cite_note-StephensBig15-16\" rel=\"external_link\">[16]<\/a><\/sup> The rise of big data has lead to increasing attention to the field of data visualization.<sup id=\"rdp-ebb-cite_ref-SridharanData15_17-0\" class=\"reference\"><a href=\"#cite_note-SridharanData15-17\" rel=\"external_link\">[17]<\/a><\/sup> As our datasets increase in size and our analyses increase in complexity, data visualization becomes crucial in allowing us to gain insight, see patterns and elucidate further areas of study in our experiments.<sup id=\"rdp-ebb-cite_ref-SridharanData15_17-1\" class=\"reference\"><a href=\"#cite_note-SridharanData15-17\" rel=\"external_link\">[17]<\/a><\/sup><sup id=\"rdp-ebb-cite_ref-WongData_18-0\" class=\"reference\"><a href=\"#cite_note-WongData-18\" rel=\"external_link\">[18]<\/a><\/sup><sup id=\"rdp-ebb-cite_ref-SharpWhy_19-0\" class=\"reference\"><a href=\"#cite_note-SharpWhy-19\" rel=\"external_link\">[19]<\/a><\/sup> These visualizations have to be meaningful representations of the data.<sup id=\"rdp-ebb-cite_ref-WongData_18-1\" class=\"reference\"><a href=\"#cite_note-WongData-18\" rel=\"external_link\">[18]<\/a><\/sup> Unsurprisingly, the figures we use to communicate our insights can become more convoluted with bigger and more complex data and, if poorly designed, risk confusing what they were meant to make clear. Indeed, the difficulty of achieving visual clarity in a diagram often increases in tandem with the necessity to do so.\n<\/p><p>Despite the growing importance of data visualization, the scientific community faces technical challenges in creating figures that are meaningful and clear. Complex analyses and their visualizations can represent significant time and effort, and require programming skills the scientific community often lacks.<sup id=\"rdp-ebb-cite_ref-MeraliCompu10_20-0\" class=\"reference\"><a href=\"#cite_note-MeraliCompu10-20\" rel=\"external_link\">[20]<\/a><\/sup> A paper with poorly designed figures could be significantly hampered: if a reader cannot grasp the key insights a figure is meant to convey, then the significance of the paper might be lost, or it may not be published at all, with obvious detriments to the field. There is a clear incentive to generate useful plots, and there is also a clear need for easier and more time-efficient methods to generate them. To this end, we are creating tools that improve both the quality of plots and the speed at which they can be created.\n<\/p><p>In genomics, a common analysis performed in experiments is list comparison. The Venn Diagram is a popular plot type for list comparison, providing a simple visualization of several possibly unrelated lists.<sup id=\"rdp-ebb-cite_ref-Bardou_jvenn14_1-1\" class=\"reference\"><a href=\"#cite_note-Bardou_jvenn14-1\" rel=\"external_link\">[1]<\/a><\/sup> The manual generation of these plots can be difficult. Spatial organization and color choice of the groups and their overlapping sections such that they are both clear and aesthetically pleasing is important but nontrivial.<sup id=\"rdp-ebb-cite_ref-RuskeyTheSearch06_21-0\" class=\"reference\"><a href=\"#cite_note-RuskeyTheSearch06-21\" rel=\"external_link\">[21]<\/a><\/sup> The VennDiagram R package addresses this issue. It is commonly in use<sup id=\"rdp-ebb-cite_ref-Cs.C3.A1rdi_cranlogs_5-1\" class=\"reference\"><a href=\"#cite_note-Cs.C3.A1rdi_cranlogs-5\" rel=\"external_link\">[5]<\/a><\/sup>, but we believe a simple graphical user interface for the package will bring it to an even wider audience, particularly to scientists who do not have strong skills in R.\n<\/p>\n<h3><span class=\"mw-headline\" id=\"Comparison_to_existing_tools\">Comparison to existing tools<\/span><\/h3>\n<p>As with VennDiagram, <i>VennDiagramWeb<\/i> offers many features that existing tools lack (Table 1). In addition to the advantages VennDiagram holds over other methods<sup id=\"rdp-ebb-cite_ref-ChenVenn11_4-3\" class=\"reference\"><a href=\"#cite_note-ChenVenn11-4\" rel=\"external_link\">[4]<\/a><\/sup>, <i>VennDiagramWeb<\/i> is the only web application we found that allows for tiff downloads, R code download, and multiple workspaces.\n<\/p>\n<table style=\"\">\n<tr>\n<td style=\"vertical-align:top;\">\n<table class=\"wikitable\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\" style=\"\">\n\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" colspan=\"8\"><b>Table 1.<\/b> A comparison of features of VennDiagramWeb to other popular web applications used to generate Venn Diagrams<br \/>\n<p><sup>a<\/sup> Euler diagrams only; 3-set scaling only when mathematically possible<br \/>\n<sup>b<\/sup> Uses inaccurate 3-set scaling with circles\n<\/p>\n<\/td><\/tr>\n<tr>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">Category\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">Parameter\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">VennDiagram (Initial Release)\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">VennDiagramWeb\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">Venny\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">BioVenn\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">GeneVenn\n<\/th>\n<th style=\"background-color:#dddddd; padding-left:10px; padding-right:10px;\">CRP-Sante Microarray Centre Venn Diagram\n<\/th><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"4\">General\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Interactive interface\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Data file upload\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">N\/A\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Multiple workspaces\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">N\/A\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">R code generation\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">N\/A\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"5\">Circle Options\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Color\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Fill alpha\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Border style\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Border width\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Border color\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"9\">Category Labels\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Content\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Color\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Font\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Size\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Style\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Location\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X (SVG only)\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Position\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X (SVG only)\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Distance\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X (SVG only)\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Justification\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"4\">Area Labels\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Color\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Font\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Size\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Style\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"8\">Titles\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Main title\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Subtitle\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Position\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X (SVG only)\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Color\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Font\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Size\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Style\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Justification\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"3\">File Options\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Output type\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">TIFF\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">TIFF\/SVG\/PNG\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">PNG\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">SVG\/PNG\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">PNG\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">PNG\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Figure resolution\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Built-in gene ID recognition\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">X\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\" rowspan=\"9\">Miscellaneous\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Maximum sets\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">4\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">5\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">4\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">3\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">3\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">3\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Shapes used\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\/Ellipses\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\/Ellipses\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\/Ellipses\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\n<\/td>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Circles\n<\/td><\/tr>\n<tr>\n<td style=\"background-color:white; padding-left:10px; padding-right:10px;\">Scaling\n<\/td>\n<td style=\"background-color:wh
