{"id":226,"date":"2016-06-17T18:53:42","date_gmt":"2016-06-17T17:53:42","guid":{"rendered":"http:\/\/eubias.org\/NEUBIAS\/?page_id=226"},"modified":"2018-08-22T09:48:09","modified_gmt":"2018-08-22T08:48:09","slug":"what-is-taggathon","status":"publish","type":"page","link":"https:\/\/eubias.org\/NEUBIAS\/what-is-taggathon\/","title":{"rendered":"Taggathon"},"content":{"rendered":"
\n
\n\t

Taggathon<\/strong> is our original\u00a0concept and is an effort to bridge the life science world and the image processing world. As compared to hackathon where developers gather to code, here people gather to \"tag<\/strong>\" information in a database to create a searchable online repository for the community (the webtool<\/strong>*<\/a><\/em>). The aim is to manually annotate available implementations of image processing algorithms to offer easier\u00a0access to versatile bioimage analysis components<\/em><\/strong>*<\/a> and workflows<\/em><\/strong>* <\/a>\u00a0. Their mutual relationship accessible\u00a0in the webtool facilitates the customization of workflows. The webtool workgroup of the NEUBIAS action (Workgroup 4<\/a>; WG4) organizes\u00a0Taggathons<\/strong>\u00a0to construct and to deliver the webtool<\/em>.<\/p>\n

The first NEUBIAS Taggathon in September 2016<\/a>\u00a0will implement the basis of the webtool, that will be extended by new\u00a0features\u00a0based on the planning by\u00a0WG4. Fourteen taggers will be invited to participate to this taggathon. If you are interested in taking part, please contact Perrine and Chong<\/strong>.<\/p>\n

Information about the previous Taggathons<\/strong> and and the\u00a0target\u00a0webtool<\/em>\u00a0envisioned by our\u00a0network\u00a0can be found here<\/a> and\u00a0here<\/a>.\u00a0The result of previous Taggathons is our prototype webtool biii.info<\/a>, which we will try to upgrade in new\u00a0Taggathons<\/strong> starting from 2016.<\/p>\n

<\/p>\n

The Goal of NEUBIAS Taggathons - A Bioimage Analysis Webtool -<\/h3>\n

Many tools for BioImage Analysis are already readily available. Information about these tools is however non-uniform and often focuses on technicalities about the methods implemented rather than the biological problems the tools can actually solve. Since Bioimage Analysts*<\/a> focus on applied problems, this information is often inadequate.\u00a0To overcome this issue, a\u00a0workgroup\u00a0of NEUBIAS (workgroup 4, WG4) will deliver a web-based platform that matches specific bioimage analysis problems to the relevant tools.<\/p>\n

Learning from the success of community-based projects (e.g.<\/em> Wikipedia) to achieve this goal, a crowdsourcing technique fostering exchanges and collaboration will be applied.\u00a0In the initial phase and after reviewing existing technological solutions, WG4 will implement the first version of this web tool with a web-based interface\u00a0 Once established, the web tool will be incrementally updated. It will provide a unification of views: problem-based (e.g. \u201cfind nuclei in cells\u201d, or workflows<\/em>*<\/a>), algorithm\/method-based (e.g. \u201cactive contour based segmentation\u201d, components<\/em>*<\/a>) and tool-based (e.g. \u201cCellProfiler\u201d, or software\/libraries<\/em>*<\/a>).<\/p>\n

Additionally, the webtool will include:<\/p>\n

    \n
  1. a community-edited rating of tools;<\/li>\n
  2. discussion forums on both tools and problems;<\/li>\n
  3. an interface to WG5 benchmarking web application.<\/li>\n<\/ol>\n

    The webtool will also gather commented links on articles describing algorithms with high potential but currently without usable source code.\u00a0\"Calls for implementation<\/strong>\u201d will be launched to plan collaborative implementation through threads in the forum.\u00a0The database behind the search engine will be edited in a manner similar to Wikipedia: i.e.<\/em> the community provides content that is managed by curators. Crowd-sourced database editing will be reinforced by strategic meetings in order to ensure that a defined target number of entries is curated .<\/p>\n

    These meetings, which we call Taggathons<\/strong>, will be events where bioimage analysts gather to boost the content (software\/libraries, workflows, components<\/em>). They are also aimed at reaching consensus on future directions and making sure the launch of the webtool will meet the defined schedule.<\/p>\n

    The activity of WG4 to organize Taggathons<\/strong> and to deliver\u00a0the webtool\u00a0will be interconnected with other workgroups (WGs). The web tool will aggregate workflow information from other WGs. WG4 will use the datasets provided by the sample image and benchmark workgroup (WG5)<\/strong> when connecting tools to problems. Tools, workflows, and datasets will be integrated in the web tool to make it an online companion for teaching organized by the training workgroup (WG2)<\/strong>.<\/p>\n<\/div>\n<\/div><\/div><\/div>

    \n
    \n\t