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biox library (NGS, next-generation sequencing)

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biox library (NGS, next-generation sequencing)

Postby ademcan » Sun Mar 25, 2012 19:10

Dear all,

I am Adem Bilican PhD student at the University of Lausanne since January 2011.
My PhD project is about "the evolution of alternative splicing mechanisms in vertebrates".
Before my PhD I worked almost two years as a computer scientist at the University of Maastricht in the Netherlands.
I participated to the Google Summer Of Code 2009 with the GenMAPP group and worked on PathVisio ( a pathway visualization tool.

In our lab in Lausanne we generated a huge amount of RNA-sequencing data set comprising 11 species (great apes, macaque, mouse, opossum, platypus, chicken and xenopus) and 8 tissues (brain, cerebellum, heart, kidney, liver, testis, placenta and ovary).
We used the Illumina GAIIX sequencer to run the RNA-seq studies and generated about ~3.5 billion of 76 base pairs reads.
In my project, I am analyzing all these reads to study the evolution of alternative splicing regulatory mechanisms.
I am using self-made Python and R scripts to analyze fasta, fastq, Bed, sam, bam… formatted files.
I am also using tools such as Samtools, Bedtools, Bowtie, Tophat and Cufflinks to analyze all the reads.

I would be very interested in participating to the Google Summer Of Code 2012 with your organization.
I will put my knowledge about Next-Generation Sequencing and programming to develop a support for many different file formats, and also simple wrappers for existing tools. I can also perform some output graphics using R or matplotlib (basic knowledge about matplotlib as I already used it for a previous project).
One can find very interesting tools also on Galaxy ( and the UCSC genome browser (
It will be interesting to have a look also at these tools and integrate them on the project.

I would be very grateful if you can guide me for a starting point.
Thank you very much for your help.

Best regards,
Adem Bilican

Re: biox library (NGS, next-generation sequencing)

Postby ademcan » Tue Mar 27, 2012 10:33

Dear all,

I would like to discuss with Orange group members more into details about my project proposition.
To do so I tried to join the Skype conversation but it is not working.
I am using Mac OS. When I click the link, Skype opens and connect to the conversation but I cannot see anybody online and send any message.
Do you know how can I solve this problem ?
Thank you for your help.

Best, Adem

Re: biox library (NGS, next-generation sequencing)

Postby gregorr » Tue Apr 03, 2012 14:33

Dear Adem,

first, i am very sorry for the late reply. As usual, bioinformaticians are ultra-busy :)

Your current experience sounds ideal for our project (which is flexible). Our lab is currently working with lots of RNA-seq data, mostly from the Illumina platforms. Our current vision/challenge is developing different custom-made solutions (platforms) for data analytics in connection with different experimental settings (diff. gene expression, studies of protein-RNA interactions, also alternative splicing, data visualization etc).

Since in this process we are developing many custom-made tools, your task would be to help us construct a Python library (a tentative name is "biox").

There are two fields that we would like to cover:

a) script-wrapping the current state-of-the-art software (bowtie2, samtools, etc) in Python
b) support reading/writting/indexing/searching different formats (memory/speed efficient implementation)

If you are interested please take some time to write what would you try to implement (try to be realistic and estimate what is do-able in the given amount of time).

In case you need any additional information please don't hesitate to contact me directly or write on this forum.

Kind regards,
Gregor Rot

ps: regarding Skype, the provided link should work (you are added to a Skype group i think and somebody needs to accept you).

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