diff --git a/browser/js/model.js b/browser/js/model.js index 484092a34e5f2dd898a9c17c33b0d7658fe9b7ca..210054a7d844f45c26393dfe9e99332e7b6d81da 100644 --- a/browser/js/model.js +++ b/browser/js/model.js @@ -32,6 +32,8 @@ * */ VIDJIL_JSON_VERSION = '2014.09'; + +// See also docker/ci/Dockerfile BROWSER_COMPATIBILITY = { "Firefox": { "legacy": 32, diff --git a/doc/roadmap.md b/doc/roadmap.md index 0d9e53d0876880ab57f37ac56ff02ea52401dec3..7bc7128b9837d2c3d74f18eaaf45882f71fdaad5 100644 --- a/doc/roadmap.md +++ b/doc/roadmap.md @@ -12,7 +12,7 @@ in particular at each Vidjil Workshop. Items generally go through the following stages: - - **Research**, **Planning**: discussion on the issues and on the strategy. + - **Research**, **Evaluation**: 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. @@ -63,7 +63,7 @@ with software engineering. + Beta: 2021 - Provide specific tools to analyze single cell data and/or paired chains data #2344 -## Better sequence analysis +## Better sequence and recombination analysis - Show more sequence features (such as FR1...) in the sequence aligner #2135 + **Available since Q2 2021**, ✅ @@ -74,30 +74,46 @@ with software engineering. - Estimate clone lengths according to different primer sets #2043 + **Available since Q2 2021**, ✅ + + - Improve alignment of D genes #2002 + + - Get longer consensus sequence #4686 + + **Available since Q4 2021**, ✅ + +Moreover, we always try to improve and extend the analysis of some recombinations: + + - Extend set of recombinations + - Find generalized recombinations, even unexpected #1400 #2818 + - Work on clone phylogenies + - Work on noisy data, such as third-generation sequencers -## Server: statistics, including quality control, on a set of samples +These points are *ongoing research* 🚧 in the Bonsai team with selected collaborators and are not in the roadmap with fixed dates. +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 analysis needs. + + +## Better tools for quality assesment and massification of analyses + +Routine, and sometimes even 100+ samples. - Provide statistics given a set on samples #3171 - Provide a quality control, for example on a run #2175 + **Development ongoing** 🚧 @mikael-s @duez + Beta: Q2 2022 + + - Provide contamination information #1744 + - Develop new view(s) to browse large sets of immune repertoires #1975 (see also app-stats) -## Improved and extended analysis of some recombinations + - Improve batch creation/upload of data and metadata + + **Availibility : 2020** ✅ (creation with `.csv`) + + Batch upload -These points are not in the roadmap with fixed dates. + - Provide batch generation of reports - - 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 @@ -105,6 +121,23 @@ Contact us if you are interested and/or if you have/plan to have such data. These software engineering tasks may of course influence biological studies. They often require development or refactor work. +## Improved technical foundations + +State-of-the-art technical foundations help agile development +These point + + - Improve test framework (new Cypress framework #xxxx, drop Watir framework #4908, improve reproducibility) + + **Development: Q2-Q4 2021** + + - Improve packaging: improve Docker containers, toward 100% dockerisation #4320 + + **Development: Q4 2021** + + - Migrate the web2py server and task scheduler #3691 #4832 + + Evaluation: Q1 2022 ⏳ + + - Use a Javascript framework #4511 #4883 + + Evaluation: Q1 2022 ⏳ + ## User preferences and presets - Allow the user to store preferences #878 @@ -114,6 +147,9 @@ They often require development or refactor work. + **Availability: Q4 2020** ✅ - Create presets for specific studies or diseases #2836 + + - Allow more colors for clonotypes #1547 + + Development: 2022 ⏳ @duez ## Improved data import/export and interoperability @@ -156,8 +192,6 @@ We often work on backend changes that eventually improve the efficiency on the p - Make the web client be fully responsive (works on tablet, and better work on various resolutions) #1740 + Development: since 2020 🚧 @magiraud - - Develop new view(s) to browse large immune repertoires #1975 - - Comparing 10+ samples + Improve ergonomy with the current view #4105: Q2 2020 ✅ + New view(s) for comparing many samples #3895 @@ -178,7 +212,7 @@ We often work on backend changes that eventually improve the efficiency on the p # Human and administrative roadmap - Make the [VidjilNet Consortium](http://www.vidjil.net) grow - + Expand the community, make more members join + + Expand the community, make more members join (first General Assembly in December 2021 ⏳) + Setup [healthcare data hosting](http://www.vidjil.org/healthcare) (HDS, RGPD): Q3 2020 ✅ + Regularly take into account user requests diff --git a/docker/ci/Dockerfile b/docker/ci/Dockerfile index d4c58ebb66262d5e5c9f08887a179725d5654c75..293efe6804dbb8e7ee9738d48f707297a91747d3 100644 --- a/docker/ci/Dockerfile +++ b/docker/ci/Dockerfile @@ -1,6 +1,8 @@ FROM ubuntu:20.04 LABEL version="0.2" + +### See also BROWSER_COMPATIBILITY browser/js/model.js LABEL description="An Cypress based docker image which comes with cypress pipeline and various browsers version.\ Versions: \ Firefox: 62 (legacy), 78 (supported), 89 (latest) \