This finally happend: novel tool for fusion discovery from RNA-seq data

There was a long and a bit crazy story, however the toolkit that I was working on has now a publication in PLOS OnE. In short, tool has some unique features including support of strand-specificity to detect anti-sense chimeras and discovery of intergenic fusions. It's open-source and available in bitbucket repo.

It took us more than 3 years to finish the publication and this was amazing experience, which allowed me to learn what really can happen in science. Main lesson: there can be serious competition in research area that results in multiple unexpected issues. The journals with high impact factor are complex systems. Imagine submitting a manuscript, waiting for review 4 months(!) and receiving a statement that the "manuscript should be rejected while tool ability X is not important", with some strange citations. And then, exactly one month after rejection of your manuscript, there is a publication in the same journal with main statement of "the importance of ability X" in their tool. In our case the "ability X" was fusion isoform discovery confirmed with experimental validation.

This was probably main project for me during PhD and a perfect lesson. Of course, I am super grateful to my supervisor Dr. Fernando Garcia-Alcalde, to the whole team from MPIIB and to Lexogen company for amazing support. Moreover, additional useful comments I received from Prof. Steven Salzberg and he doesn't need an introduction for those who are working in sequencing data analysis area (btw, there is also his awesome blog).

Despite the complexity and multiple factors, science remains to me the most exciting and interesting area, where critical revision and communication have high impact. I will be glad to any comments, fixes or suggestions about InFusion. And of course, wish everyone not to experience any strange "non-scientific" problems, but have honest and correct reviews. Stay in science ;)

BOSC 2015: amazing as always

I just returned from ISMB/ECCB 2015 conference that was in Dublin. However, I would like to describe my favorite pre-conference event. Of course, this is BOSC. I consider BOSC as one of the best conferences due to the importance of "open" activity in any science. As always, all the presentations were awesome. Hopefully the videos of the talks will be available soon, I look forward to it. Here I'll just mention some talks that were specially interesting for me.

Of course, both keynotes were amazing.

First one was from Holly Bik. As a biologist she turned to bioinformatics and described in detail this process and current results. Already from the name of the talk it's clear to understand the main point: "Bioinformatics: Still a scary world for biologists". As a bioinformatician in frequent contact with biologists I understand this status and totally agree with it. Biologists have a lot of work to do, and getting experience in bioinformatics is not so easy. However, it is great that there are already more and more biologists who are going deeper in this direction.

Second keynote was from Ewan Birney, a Joint Associate Director of EMBL-EBI and co-founder of Open Bioinformatics Foundation. He is a perfect example of bioinformatics super-specialist. Several topics were described in detail during this talk. The most interesting subject in my opinion - importance of open source code. Three basic reasons: transparency, efficiency and community. In the end of the talk there was a surprising block about storing of text information in DNA (more details here). In this case one room will be enough to keep encoded in DNA "all" written books. So, if you read "Fahrenheit 451" by Ray Bradbury, this looks like a perfect solution for the main problem.

Among other talks I was especially interested in RNA-seq analysis. "GO express" project presented by Kevin Rue-Albrecht is a nice example of a detailed clustering and group detection investigation from gene expression analysis.

One other project I would like to mention is a novel pipeline design toolkit called Nextflow (presented by Paolo Di Tommaso). Of course, there is a number of workflow managers. However the toolkit that can be applied only by creating small scripts to make runs parallel and with detailed reports is very useful for practical bioinformaticians.

The most surprising talk for me that was from Bastian Greshake about openSNP database. Basically this database allows to submit personal SNP data created by companies such as 23andme. In result it provides rather interesting statistics comparison from supplied datasets. This comparison might be useful for for future research projects and even just for users to find people rather similar to them. One cool point: disclaimer, totally recommend to read it!

I was also giving a small talk during the conference. It was about second version of Qualimap. The talk was rather quick (only 5 mintues, no questions afterwards) therefore very useful as practice. Additionally I got several interesting questions in the poster session. Moreover, I met people who are using Qualimap and additionally during the ISMB/ECCB conference there was a cool poster about Eager project from Alexander Peltzer that mentions Qualimap as a part of a pipeline.

Ok, that is enough about BOSC event, totally recommend to visit the next one during ISMB 2016!

BOSC-2013: my personal summary

ISMB/ECCB 2013 is over, and now I have some time to wrap up my thoughts and impressions.

Actually I would like to tell about one of the SIGs that was preceding ISMB: the Bioinformatics Open Source Conference or simply BOSC 2013. This conference is organized by the Open Bionformatics Foundation (guys responsible for Biopython, BioJava and other awesome projects) and devoted to all aspects of developing open source software for bioinformatics research. Starting from this year the scope of the conference was extended from open software to open science in general.

This was the second time I attended BOSC and once again I enjoyed greatly the people and the talks. Although BOSC is not the biggest SIG, it has this awesome atmosphere of a community of enthusiasts. For me it is an event where I can meet and talk to people who share my views on how the bioinformatics research should be conducted. A lot of things are being discussed: new open source tools and pipelines, visualization methods along with best practices to perform bioinformatics analysis and balance between being a software engineer and a researcher producing scientific results.

All talks were great, I highly recommend to check the presentation slides. Soon there will be video also. I would like to highlight several talks that I found especially interesting for myself.

Jug: Python-library that allows using decorators to easily launch multiple instances of your pipeline.

Ten simple rules of the open development of scientific software: based on a manuscript with the same name, which I missed somehow. This paper is a part of bigger PLOS "Ten simple rules of ..." collection.

DGE-Vis: an interesting interactive way to visualize RNA-seq expression studies

Unipro UGENE: a sequence analysis toolkit with sexy GUI. This is the project I've been involvled with for a long time, so I was very happy that it was presented at BOSC.

bcbbio: a community developed pipeline for SNP calling. Even if you are not interested in SNP discovery, this post by Brad Chapman is still worth looking at, because it contains many nice ideas on how to develop a reliable bioiformatics pipeline.

This time I was also giving a talk at BOSC. It was about Qualimap, a tool for next generation sequencing alignment data quality assesment. I have been working on it since I started my PhD at MPIIB in October 2011. We published the paper almost a year ago and since then Qualimap has become more mature and gathered a small community of users. We continue to maintain the tool and improve it based on the feedback from users. As I mentioned during the conference we are soon moving to a bitbucket repo. Subscribe to the Google group for updates.


Btw, one of the speakers was Sean Eddy. During his talk I felt somewhat similar to being at the concert of a favorite rock band \m/ I wish I had my copy of Sequence Analysis book with me to get an autograph :) One cool idea from his talk: sometimes reinventing the wheel and developing your own home-brewed set of tools for common tasks is actually normal. This activity should be considered as an exercise which allows to better understand things that you work on. After having enough time spent playing with the concept, it is still recommended to switch to the best instruments available ;)


The conference also included several panel discussions. An important discussion was devoted to the funding of open source scientific software development. It is commonly considered that main result of scientific research should be a manuscript. However for a computational biologist most often the software is true result of the research, while the paper is only "an advertisiment". Unfortunately the software usually is not considered by grant committees or lab bosses as a relevant result. The discussion demonstrated that bioinformatics community slowly moves away from this misconception, however a lot of work has to be done yet.

So, to sum up: BOSC is awesome, don't miss it next year in Boston.