Webtool – WG4

Rationale

Many tools for BIAS are available. The information about these tools is non-uniform and often focuses on technicalities about the implemented methods, rather than the problems the tools can actually solve. Since BioImage Analysts in their daily work focus on applied problems, this information is often
inadequate. To overcome this issue, the WG4 “Webtool” will deliver a web-based platform
(BioImage Informatics Search Engine – BISE) that matches the problem to the relevant
tools.

Workplan

Learning from the success of community based projects (e.g Wikipedia), to achieve this goal, a crowdsourcing technique fostering exchanges and collaboration will be applied. In its initial phase WG4 will implement the first version of BISE with a web-based interface, after reviewing existing technological solutions. Once established, BISE will be incrementally updated. WG4 will deliver a proposal of ontology for the organisation of data and implement a search engine for the webtool. It provides a unification of views: problem based (e.g. “find nuclei in cells”), method based (e.g. “active contour based segmentation”) and tool based (e.g. “CellProfiler”). Additionally, the webtool will include i) a community-edited rating of tools; ii) discussion forums for both tools and problems; and iii) an interface to WG5-benchmarks’. The webpage will gather commented links on articles describing algorithms with high potential but without usable source code . “Calls for implementation” will be launched to plan their collaborative implementation through threads in the forum.
The database behind the search engine should be edited in a manner similar to Wikipedia: i.e. 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 (IA tools) is cured. These meetings, called “Taggathons”,  will be  events where Bioimage Analysts gather to boost the content (software, workflows, etc). They are also aimed at teaching consensus on future directions and making sure the webtool opening will meet the defined schedule. WG4 deliverables will be interconnected with other WGs.  BISE will be promoted (WG3) and will aggregate workflow information from other WGs (e.g. WG1). WG4 will utilize the datasets provided by WG5 when connecting tools with problems. Tools, workflows, and datasets from WG6 will be integrated in the BISE to make it an online companion for teaching.