New OncodriveFM release 0.3.2

//New OncodriveFM release 0.3.2

New OncodriveFM release 0.3.2

Some time ago Abel wrote about how to identify cancer drivers from tumor somatic mutations, and presented OncodriveFM. Nuria also posted a nice poster explaining it together with TransFIC.
Initially, OncodriveFM was written by Abel as a Perl script and distributed through our web. Later on I had to implement the analysis workflows of IntOGen SM, which required to use it intensively. However,
we realized that the code of OncodriveFM could be significantly improved in terms of performance, as there is a part of the analysis that  may take quite a lot of time depending on the input data. This is why I decided to implement it again, starting from a prototype written by Abel, using Python.

This new release 0.3.2 has been extensively validated to check that the results match those of the original implementation, and includes some important optimizations. The first is the use of NumPy for internal data representation and calculations, and the second is the possibility to use multi-core processors to run the most expensive part in parallel. Moreover, the command line interface has been improved, and now is quite flexible and easy to use.

This new OncodriveFM depends on numerical Python libraries (numpy, scipy, statsmodels) that have to be installed previously in order to work. There is a detailed documentation in the Bitbucket repository that specifies how to install the dependencies, how to download and install OncodriveFM, and how to run the included example.

We encourage you to use the Bitbucket issue system to ask for features or report errors.


Related posts

New IntOGen somatic mutations analysis version available

How to identify cancer drivers from tumors somatic mutations?



By | 2013-03-26T21:58:58+00:00 March 26th, 2013|Categories: BG News|Tags: |2 Comments

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  1. Keegan Korthauer March 27, 2013 at 8:47 pm - Reply

    Is this new version of OncodriveFM already implemented in IntOGen SM version 2.0.0? If not, will it be updated soon?

    • Christian Perez-Llamas April 3, 2013 at 8:07 am - Reply

      IntOGen SM 2.0.0 uses OncodriveFM version 0.2. There have been some bug fixes and performance improvements since that version of OncodriveFM. We are about to release a new version of OncodriveFM that includes the possibility to use the mean as test estimator. We are also about to release a new version of IntOGen SM (2.1.0) that uses the latest OncodriveFM version using the mean estimator, fixes some installation problems, and implements new features (most probably during this week or the next one).

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