Forum: Pablo Cingolani of snpEff uses this
gravatar for Istvan Albert
6.2 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Pablo Cingolani is an independent bioinformatics consultant working with various institutions such as Genome Quebec, Wayne State University and McGill University.

He graduated in 1997 with a degree in Electrical Engineering from the University of Buenos Aires, Argentina, then went on and received an MBA degree in Business Administration from Universidad del CEMA, Argentina followed by  a Masters of Science in Computer Science (with a bioinformatics focus) in 2008 from McGill University, Canada.

He is the author of snpEff and snpSift toolsets for genetic variant annotation and effect prediction. These tools, published in 2012, have been widely adopted and have produced results that support  discoveries in hundreds of scientific publications. Mr Cingolani is also the lead developer of BigDataScript a programming language for computational pipeline management.

What hardware do you use?
MacBook and Linux Desktop for programming.

A couple of clusters (~1,200 and ~25,000 CPUs) both of them shared with way too many users

What is your text editor?
For scripts: vi (Sublime, on rare occasions)

For programs: Eclipse (Dark theme, so my eyes don't melt by the end of the day)

What software do you use for your work? 

  • Scripting: Python and Perl
  • Programming: Mostly Java (sometimes Go)
  • Pipelines: I wasn't happy with any of the options, so I created my own programming language "bds" (BigDataScript: ). Now I can programm and debug a pipeline/script on my laptop, when it's ready I just deploy it to a cluster with thousands of CPUs (no need to change a single line of code). And yes, the name "BigDataScript" is supposed to sound lame (it was a joke).  
  • Analysis: BWA, SamTools and BcfTools Tuxedo suite tools (Bowtie, TopHat, Cufflinks, etc.) GATK, Picard PLINK, Mantra, SKAT/SKAT-O SnpEff, SnpSift

What do you use to create plots and charts?
I use R for stats, plots and charts. Although I openly hate R because I think it's one of the least intuitive programming languages in the planet (followed closely by Malbolge and BrainF***)

What do you consider the best language to do bioinformatics with?
Due to laziness, I try to avoid languages that are not garbage collected (for instance, nowadays I only use C/C++ when speed is paramount) I'm happy with my language choices at script, programming and pipeline levels (Python/Perl, Java and bds). But this is a matter of personal taste.

What bioinformatics tools/software do not get enough recognition?
If we are talking about "user recognition", probably most tools are somehow recognized.

On the other hand, "official recognition" seems to be hard. When I talk to people who created very popular bioinformatics tools, most seem to have problems getting resources or grants to maintain and improve their software.

See all post in this series

To be notified of new post in the series follow the first post: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this

uses-this forum • 3.8k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Istvan Albert ♦♦ 86k

"I openly hate R" <--- Too funny.

BDS seems interesting. Enjoying this whole series.

ADD REPLYlink written 6.2 years ago by Madelaine Gogol5.2k

Seriously, I openly hate R, too.

ADD REPLYlink written 6.2 years ago by lh332k

Pablo is also a Biostars member

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Jeremy Leipzig19k
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