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Announcing the Dr Motifs project

by A. Bretaudeau on April 14, 2010


Welcome to the inaugural post for the Dr Motifs project! I think this is the perfect place to present you the aim of this project.

What’s this?

So the first question you might ask is: what is this project?

The basic idea of Dr Motifs is to build a platform to ease the access to bioinformatics tools dedicated to pattern matching and pattern discovery.

Main targets are:

  • To propose most standard pattern matching and discovery tools
  • To propose innovative software developed by INRIA Symbiose team (or other teams worldwide)
  • To integrate all these tools into a common platform, allowing workflows creation
  • To create pre-designed workflows to be used by beginners for common analysis
  • To create a website to publish news and reviews from the patterns world (great, you’ve found this website!)
  • To provide some help to people wanting to learn more about patterns, but who don’t know how to start.

Why this project?

Dr Motifs is a response to a situation that we believe is problematic: in the last few years there has been more and more software developed in the field of pattern discovery and matching. However, this field of research is still quite obscure for many people, and most notably by potential users of these tools.

The usual questions are: “Which tool is adapted to find X type of motif?”, “Is tool A better than tool B?”, “Tool C was cool 5 years ago, is there anything better now?”, …

Even for a specialist, it is often difficult to have a complete vision of all the software and algorithms available. For a biologist, it is even more complicated to find his way in the world of patterns. This is becoming more sensible with the growth of high-throughput technologies where people have to run many analysis and choose software based on the quality of its results and its speed of execution.

We would like Dr Motifs to become a comprehensive website to help people:

  • to launch common analysis in a simple manner
  • to make choices when they want to do new analysis
  • to stay in touch with patterns actuality.

GenOuest and Symbiose team have been active in the field of pattern analysis these last few years, and we believe we can make such a website.

Who’s working on that?

The original idea for Dr Motifs has grown at the GenOuest bioinformatics platform in Rennes (France) led by Olivier Collin. The project is funded by IBiSA organism.

Development is done by Anthony Bretaudeau, developer at the GenOuest bioinformatics platform.

Other people from GenOuest or INRIA Symbiose team (which is the team associated to the GenOuest platform) will participate to this blog from time to time.

You are encouraged to participate to this project by commenting our work, sharing your thoughts on the projects, …

Why is it called “Dr Motifs”?

Choosing a good name is not the easiest part of a project. This name came up after a very long and intensive brainstorming a little thinking about the thematic of the project: “pattern discovery and matching”.

In french you write it: “D√©couverte et recherche de Motifs“. Tada! We found the perfect name: “Dr Motifs”.

Ok, what’s next?

At the time of writing, I’m doing an inventory of the tools already available on the platform. Most of them are currently available from our website, in the “Pattern discovery” and “Pattern matching and models” sections. It is also time to do some bibliography! Development will become soon, but we’ll discuss that later.

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