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Slides from DjangoCong 2013

On Github ComSource / MicroGeno-DjangoCong-2013

TailorDev - ComSource, DjangoCong 2013

Towards an advanced & open

web platform

for bacterial genotyping

DjangoCong 2013

September, 28th 2013 - UTMB, Belfort, France


Introduction to bacterial genotyping. People involved. The past, The present (demo), The future of MicroGeno.



Nucleic acids (DNA & RNA) ...

... could be cast to strings

>gi|176120924|ref|NC_001417.2| Enterobacterio phage MS2, complete genome

Tandem Repeat (TR)

Consecutive sequences of 1 to more than 200 nucleotides, perfectly identical or not.

  • TR are found in all genomes.
  • Intragenic & intergenic regions.

Variable Number of Tandem Repeat (VNTR)

A polymorphic TR is called VNTR

[...] variations in the repeat number contribute to adaption to environmental changes, through protein function [...] or through regulation of gene expression

Multiple Loci VNTR Analysis (MLVA)

  • Genotyping method
  • Intra-species comparison of strains
  • Analysis of several (multiple) VNTRs dispersed on the genome
  • Deduce the strain code corresponding to the number of repeats at each VNTR

e.g. for VNTRs A - B - C:

Strain_01 : 7 - 10 - 4 // Strain_02 : 8 - 4 - 7

Why do we need bacterial genotyping?

  • To compare large numbers of strains isolated from clinical and environmental sources
  • To perform outbreak investigations
  • To study bacterial population structure and emergence of clones
  • To invest the origin of a biological sample (biodefense, forensics)

The people

G. Vergnaud, PhD

  • Scientific head of MicroGeno
  • Searching for a lead developer
  • MLVABank code refactoring


{ TailorDev }

  • Web & print agency
  • Toulouse & Clermont-Ferrand, France
  • Julien Maupetit, PhD, Co-Founder (CTO)
  • Strong background in bio-informatics

The past


  • From 2007 to 2013
  • Originally developed & maintained by Paris Sud
  • PHP & JavaScript, no framework

MLVABank features

  • User-friendly
  • Cooperative databases
  • Contributors keep control of their data
  • MLVA data, but not only...

The present

  • MicroGeno is the new MLVABank
  • Development started in 2012
  • Completely rewrote from scratch
  • Python - Django web framework
  • Twitter Bootstrap

MicroGeno core features

  • Logical data storage (relational database schema)
  • in situ clusters analysis (dendrogram, MST)
  • Not dedicated to a particular species
  • Supports MLVA, MLST, SNP, SPOLIGO and CRISPR data
  • Cloud-ready (SaaS & PaaS)

Demo party!

The future

Ongoing directions (1)

  • Open Source
  • Docs, docs, docs (developers and end-users)
  • Tests, tests, tests (TDD)
  • Move front-end to a JS framework such as AngularJS

Ongoing directions (2)

  • Local analysis tools
  • Synchronize (selected) data to the/your cloud

Ongoing directions (3)

MicroGeno Chip

Thank you!


This presentation is available at https://github.com/ComSource/

Icons credit

Cassette designed by Pavel Andreev from The Noun Project

Cloud Download designed by P.J. Onori from The Noun Project

Rocket designed by Jean-Philippe Cabaroc from The Noun Project

VNTR figure: wikipedia

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.