finding the right wording, get list of existing tools, what is possible to do automatically, finding the right people to contact for collaborations/questions
A usual approach for biologists starting in bioimaging for a given application is to start with software state of the art and look for an existing tools exactly solving the targeted problem. It is likely that some tools may come close to that but also that other tools developed for other bioimaging question may also serve. Bise may help in such a situation. For instance a query on Microtubule will, with maximum relevance, point to
Microtubule Length Analysis,
Tracking of Microtububule Tips,
Microtubules Tool (3D), but also, with smaller relevance BISE will point toward tools developed for other biological communities such as
Simple Neurite Tracer. This illustrates the possibility to bridge biological communities through BISE by pointing tools of wide applicability.
Remark TODO: tools based on morphological similarity should also be included, e.g. tubeness and vesselness should also be pointed.= sghape based description
Now let’s imagine a biologist interested in extracting Micro vessels
Here also some tools developed for other biological communities (again S
imple Neurite Tracer). This further illustrates the possibility to address the Babel tower issue…. but with still long way to go. Interestingly in this case
Tubeness is in the set of answers.
Remark TODO : Concerning the possibility to find the right people. There is the possibility to contact the author of the tools but some of them are surely not in the game anymore. Would be important to point the user of BISE toward expert in the NEUBIAS network with interest in the biological problem and expertise in the bioimage analysis.
Remark : A snapshot on this could be reused with the filament tracing (6 Figures only are required for the Article).
5.3 Analysts
fill the gap between a technical/methods paper and its implementation (complements the information from the method paper), get standardized and quality information about the tools, find out what the needs of the biologists are (from comments and feedback left by those); diffuse his/her own unpublished tools/workflows; place to point biologists to when they ask for help
Examples:
- Publish & retrieve updated information about a tool (tool was published in a scientific article before)
- Publish & retrieve information about a tool that is not published in a scientific article (yet)
- Publish & retrieve a concrete implementation of a previously published method|algorithm
- Publish & retrieve details about a script or workflow (including details about certain steps mentioned in a methods section of a scientific article)
- Note: publishing & retrieving information|details includes links to documentation, source-code repositories, platform-specific repositories, download options, training materials, software dependencies, etc.
- In a simplified user model, the use cases above are publish for “developers”, and retrieve for “image analysts”
- Analysts: Add information about experience with a tool. Analysts, biologists, developers: Retrieve it.
- Analysts, developers, curators: Add links to a comparison (e.g. a benchmark test or a review) of a set of tools. Analysts, biologists, developers: Retrieve it.
- Analysts, developers, biologists, curators: Compare information (e.g. implementation details) about various tools. Fostered by standardising such information.
- example data
Could there be a table of information versus use cases?
information | developer | analyst | biologist | curator | investor | society |
updated information about a tool published in a scientific article before | Publish, Compare | Retrieve, Compare | Retrieve some data, Compare | Compare, Update some data | Retrieve some data | |
concrete implementation of a previously published method|algorithm |
etc. |
5.4 Stake holders
(‘a person with an interest or concern in something’) : 1) A single point of entry to the community from outside. A display of achievement/deliverable. Uses: bibliometry/tracking. 2) Toward reproducible science (aka FAIR, +dataset +containers) 3) image analysis from other field (satellite imaging, astronomy, materials etc....)
- editors/journals:
- a software repository. permanent ID/accession number/DOI? Question possible to generate IMPORTANCE of VERSIONING?
- toward live/active/interactive/augmented paper: workflow per paper/per figure
- host institution: find all the tools developed by an institute/author; tagging by affiliation/by orcid? Orgit? (for institution)
- funders: part of a ‘software management plan’: permanent ID/accession number/DOI
- teaching (cf Elixir-neubias hackathon 14th and 15th of May+WG5): link to datasets and workflow for a given topic
- extract some metrics on available tools given specific disciplines/fields (light sheet microscopy for instance) Number of tools /topic/operation?
- (Science outreach?) other fields
6. A central hub for documentation and discussion of and links to code