Commit 7501d30a authored by Mathieu Giraud's avatar Mathieu Giraud

README.org: update, appnote submission

parent d249e875
......@@ -26,18 +26,17 @@ to output all sequenced clones. The analysis is extremely fast
because, in the first phase, no alignment is performed with database
germline sequences.
The Vidjil *dynamic browser* is made for the visualization and
The Vidjil *web application* is made for the interactive visualization and
analysis of clones and their tracking along the time in a MRD setup or
in a immunological study. The browser can visualize data processed by
the Vidjil algorithm or by other V(D)J analysis pipelines.
The browser enables to explore further cluterings proposed
in a immunological study. The web application can visualize data processed by
the Vidjil algorithm or by other V(D)J analysis pipelines, and
enables to explore further cluterings proposed
by software and/or done manually done by the user.
Finally, a *patient database* with a server
is currently developed to link the browser and the
algorithmic part. The goal is that the clinicians will be able to
upload, manage and process their runs directly on the browser (with
authentication).
The web application can be linked to a *sample, experiment and patient database*
able to store sequencing data and metadata, to run RepSeq software
and to save annotations directly from the web application, with authentication.
Clinicians or researchers in immunology or hematology
can manage, upload, analyze and annotate their runs directly on the web applicaiton.
* Vidjil components
......@@ -47,9 +46,9 @@ authentication).
- Development code is under [[algo/]]
- Documentation: [[doc/algo.org]]
** The browser and the patient database
** The web application
- Access at http://rbx.vidjil.org/browser (demo login: demo@vidjil, password: vidjil)
- Access at http://app.vidjil.org/browser (demo login: demo@vidjil, password: vidjil)
- Please contact us if you would like to test your data and have a full account on the web server
- Development code is under [[browser/]] and [[server/]]
- Documentation (in progress): [[doc/browser.org]] and [[doc/server.org]]
......@@ -78,7 +77,11 @@ The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), by R
* References
If you use Vidjil for your research, please cite the following reference:
If you use Vidjil for your research, please cite the following references:
Marc Duez et al.,
“Vidjil: High-throughput analysis of immune repertoire”,
submitted
Mathieu Giraud, Mikaël Salson, et al.,
“Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing”,
......
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