Commit f636eaa3 authored by Vidjil Team's avatar Vidjil Team Committed by Mathieu Giraud
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doc/roadmap.md: draft roadmap

This roadmap was discussed by the team for several months and takes care of several user requests.
It is focused on user-facing features, even if many items involve more backend changes.
We are glad to share this roadmap. It will be regularly updated.

See #4136, vdj#842
parent 402bb118
# Roadmap
The development of the Vidjil platform is tracked with [gitlab](http://gitlab.vidjil.org).
As of 2020, there are more than 1500 [open issues](http://gitlab.vidjil.org/issues),
but also more than 1500 closed issues.
Issues can be either in English or in French.
This roadmap is focused on user-facing features, even if many items involve more backend changes,
and links to actual issues in our gitlab with more technical content.
The roadmap is regularly updated and discussed with our users and collaborators,
in particular at each Vidjil Workshop.
Items generally go through the following stages:
- **Research**, **Planning**: discussion on the issues and on the strategy.
Take days, months... or years.
This is the default stage for all items that are not currently developed or scheduled for development.
- **Development**: software, test and documentation engineering.
Going to this stage (or schedule to going here) means that we identified enough time to work on it.
Take between weeks and months
- **Beta**: available for selected users, feedback with these users. Contact us if you are interested.
Usually 1 to 3 months
- **Availability**: available for everyone, with appropriate documentation
These stages can be
pending and not scheduled (no icon),
pending and scheduled (⏳),
in progress (🚧),
or finished (✅).
# Bioinformatics roadmap
The following points mix bioinformatics research, often in collaboration with hematologists or immunologists,
with software engineering.
## Better tools for full repertoire analysis
- Show distributions of the full repertoire #3902
+ Development: Q3-Q4 2019 ✅
+ Beta: Q1 2020 ✅
+ **Availability: Q2 2020**
+ Extensions: 2021
- Implement better repertoire comparisons #3857 #3855
- Build another dedicated tool for full repertoire comparison (app-stats)
+ **Development: since 2018, ongoing in 2020** 🚧 @flothoni
+ Beta: Q3-Q4 2020
## Better tools for MRD analysis
- Run custom scripts for MRD #3838 #3846
+ Development: since Q2 2019, ongoing in 2020 for #3846 🚧 @flothoni
+ **Beta: Q3 2020** 🚧
+ Availability: Q3 2020, contact us to set up your MRD scenarios
- Better display MRD data in the web platform
## Analysis of data with UMI, single-cell and/or paired chains
- Provide more tools to analyze UMI data (We now advise people to use external demultiplexing to handle UMI) #2309
- Provide specific tools to analyze single cell data and/or paired chains data #2344
## Better sequence analysis
- Show more sequence features (such as FR1...) in the sequence aligner #2135
+ Development: scheduled in Q4 2020 ⏳ @duez
- Improve links to third-service analyses: ArrestSubsets #3917 ✅, VDJdb #1880
- Improve the alignment between sequences #3332
## Server: statistics, including quality control, on a set of samples
- Provide statistics given a set on samples #3171
- Provide a quality control, for example on a run #2175
+ Development: since Q3 2019 🚧
## Improved and extended analysis of some recombinations
These points are not in the roadmap with fixed dates.
- Extend set of recombinations
- Find generalized recombinations, even unexpected #1400 #2818
- Work on clone phylogenies
- Work on noisy data, such as third-generation sequencers
Perspectives depends on collaboration.
These points are *ongoing research* 🚧 in the Bonsai team with selected collaborators.
For some of these points, we are open to new partners.
They often imply core algorithmic work on Vidjil-algo, often combined with updates on the web application.
Contact us if you are interested and/or if you have/plan to have such data.
# Technical roadmap
These software engineering tasks may of course influence biological studies.
They often require development or refactor work.
## User preferences and presets
- Allow the user to store preferences #878
+ Development: scheduled in Q3 2020 ⏳ @duez
- "My Account": Better view on a user samples, preferences
+ Development: scheduled in Q2-Q3 2020 ⏳ @duez
- Create presets for specific studies or diseases #2836
## Improved data import/export and interoperability
- Improve upload of multiple files #2878
+ Development: scheduled in Q2-Q3 2020 ⏳ @duez
- Improve AIRR support and AIRR integrations #3591 #morefields
- Export all clones #3842
+ Development: ✅
+ Beta: Q1 2020 ✅
+ **Availability: Q2 2020**
- More integration with IMGT/HighV-Quest
+ Ongoing collaboration with IMGT, since Q4 2019 🚧
## Server: statistics, including quality control, on a set of samples
- Provide statistics given a set on samples #3171
- Provide a quality control, for example on a run #2175
+ Development: since Q3 2019 🚧
+ Beta: Q2-3 2020 ?
## Speed
- Speed-up vidjil-algo, especially for full designation of every clone #920 #1169
+ 2018: 10x speed-up of V(D)J designation ✅
+ 2020: ongoing work on Aho-Corasick automaton 🚧
- Speed-up the web client, especially when 10+ samples and/or 1000+ clones are displayed #3903 #2196 #2462
+ Q4 2019, ... 🚧
- Speed-up the web server, especially when handling 1000+ samples #3169
+ Q4 2019, Q1 2020, ... 🚧
These points are always ongoing:
We often work on backend changes that eventually improve the efficiency on the platform.
## Improved ergonomy of the web platform
- Make the web client be fully responsive (works on tablet, and better work on various resolutions) #1740
+ Development: Q1-Q2 2020 🚧
- Develop new view(s) to browse large immune repertoires #1975
- Improve ergonomy with 10+ samples #3895 #4105
- Redesign the interface, improve the design #2245
+ Development (sequence analyzer): Q2-Q3 2020 🚧
+ Development (clone information): late 2020 ⏳
+ Other points: not before 2021-⏳
# Administrative roadmap
- Make the [VidjilNet Consortium](http://www.vidjil.net) grow
+ Expand the community, make more members join
+ Setup health-data (HDS, RGPD) provider: 2020 🚧
- Organize regularly Vidjil Workshops
+ Workshops organized in
[2016](http://www.vidjil.org/workshop-2016),
[17](http://www.vidjil.org/workshop-2017),
[19](http://www.vidjil.org/workshop-2019),
[20](http://vidjil.org/workshop-2020)
- Help the hospitals to get certification
+ First documents in Q4 2019 / Q1-Q2 2020 for french COFRAC 🚧
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