We’re pleased to announce another incremental release of Gitools, version 2.2. Amongst the many improvements (listed at the bottom of this post) we’d like to highlight the effort that we put into improving performance, specifically with genomic data: mutual exclusion and co-occurrence statistics coupled with a new feature called “data events” – which helps to get a quick grasp of the data.
Three years ago, Abel developed and published in the American Journal of Human Genetics an approach to combine the results of several tools aimed at identifying disease-related single nucleotide variants (SNVs). He called the strategy a Consensus Deleteriousness score of SNVs, or Condel. It consisted in computing a weighted average of the scores of five of these tools (SIFT, PolyPhen2, MutationAssessor, LogRE and MAPP). The weights were extracted from the complementary cumulative distributions of the scores of sets of known disease-related and neutral SNVs. He showed that the Consensus score of the five tools outperformed the five individual methods, as well as other approaches to combine them. He presented the Condel of these five tools in one of the first posts of this blog, The making of Condel (CONsensus DELeteriousness Score), published on April 1, 2011.
We’d like to communicate two things: We have released a new version of Gitools which brings new capabilities. With these the new Gitools 2.1.0 in the suitcase, Nuria and myself are traveling to Heidelberg, to give a tutorial session at the Vizualizing Biological data conference (VIZBI).
Since last year I am participating in the COST Action BM1204 titled “An integrated European platform for pancreas cancer research: from basic science to clinical and public health interventions for a rare disease”, and in particular in its Work Group focus on “Omics Data Integration”.
As part of this Work Group, we have prepared a training workshop that will take place in Heidelberg, Germany on February 14, from 1-5pm. The covered topics fit into a series of workshops that will be organized within this COST Action.
Two years ago I attended the VIZBI 2012 to present our latest work on and with Gitools, a tool we use to explore interactive heatmaps of genomics data. The days spent in Heidelberg were fruitful and refreshing and after all also were an inspiration to write the review about Visualizing multidimensional cancer genomics data.
We are very honored to announce that we have received funds for a 3-year project from the money raised in the last telethon broadcast La Marató de TV3.
This is an annual television program broadcasted in Catalonia since 1996 which is devoted to diseases that are currently incurable. La Marató has a big repercussion in our country, not only for its ability to raise funds but also because it fulfills the task of informing the public about these diseases, the state of the art of the treatment and the importance of the research to advance in their prevention and cure.
The University Pompeu Fabra has produced a video in which we explain in brief our research. We recorded three versions of the video, one in Catalan, one in Spanish and one in English. The videos are distributed through the UPF youtube channel.
Yesterday I gave a talk at the PRBB Computational Genomics Seminars Series. In that talk I summarized our work of this year in the lab. Basically, we have developed methods to identify cancer driver genes and we have applied them to thousands of tumor resequenced genomes. Here, I leave you the slides, and I summarize the talk below.