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Guillaume Filion
Lives in Barcelona
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Guillaume Filion

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Very well put "I want developer parity so that I can spend my time improving code rather than debugging differences between environments."
#bioinformatics  
How I develop. Published Fri July 24 2015. I've been in the bioinformatics field for almost 10 years, originally coming from a molecular biology degree background, I deciding to move into computing after struggling to find a job doing lab work. This post is a general outline of how I now develop ...
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Guillaume Filion

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Updating the lab website with our publications. It's nice to keep it alive.
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Ever wanted to compute eigenvalues with sparse matrices? APRACK is the real deal. Surprisingly, it is not available in R by default, but the developers of the igraph package have written a nice port. So in case you look for it, there it is.

#computing  
#mathematics  
#statistics  
Arguments. func: The function to perform the matrix-vector multiplication. ARPACK requires to perform these by the user. The function gets the vector x as the first argument, and it should return Ax, where A is the “input matrix”. (The input matrix is never given explicitly.) ...
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Bayesian networks are claimed to transform correlations in cause-consequence relationships. However, in my post-doc I realized this not to be the case. In this blog post I explain why.

#bioinformatics  
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Quite a nice project to know a little bit better what lurks in our oceans.
#bioinformatics  
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Writing some C library code that needs graceful error handing? Here are a couple of suggestions.
#softwaredevelopment  
#C  
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Guillaume Filion

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The distribution of the largest fragment of a broken stick has been worked out a long time ago. But somehow this result is difficult to find on the Internet. With the help of the Cross Validated community, I found readable proofs for this distribution and its asymptotic limit.
#statistics  
#bioinformatics  
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"Time and energy spent on trying to increase internet clicks is time and energy we don't spend on the tedious administrative activities that are needed to actually affect change."
Throughout history, engineers, medical doctors and other applied scientists have helped convert basic science discoveries into products, public goods and policy that have greatly improved our quality of life. With rare exceptions, it has taken years if not decades to establish these discoveries.
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Lior Pachter recently offered a cash prize to answer a scientific question. He got over a million views and got several answers from distinguished biologists. Very neat.

#bioinformatics  
#evolution  
Two weeks ago in my post Pachter's P-value Prize I offered $latex {\bf \frac{\$100}{p}}$ for justifying a reasonable null model and a p-value (p) associated to the statement ""Strikingly, 95% of ca...
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Our sequence algorithm Starcode has finally been published after almost a year of delay. In the lab, we use barcodes to track our reporters by high throughput  sequencing. Unfortunately, the barcodes are sometimes mis-sequenced and we need to correct the mistakes, which is why we developed Starcode. We hope it can be useful for more people. The code is open source and available from Github.

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Who are bioinformaticians and what do they do?

"Obviously, bioinformatics is about data, mostly gene/protein sequences and expression. It is also good to know that bioinformatics likes genomes and networks, and that it has more affinities with structural biology than with evolution."

#bioinformatics
What is bioinformatics about? | Filed under information retrieval, PubMed, journals, bioinformatics.
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Have him in circles
115 people
Manuel Arbona's profile photo
Patrick Berger's profile photo
devlin tjoitang's profile photo
Dmitry Ivankov's profile photo
Leszek Pryszcz's profile photo
Sébastien Vigneau's profile photo
Patrick Berger's profile photo
Jean-Baptiste Bianquis's profile photo
David Gaudry's profile photo
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Team leader at the CRG, Barcelona
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Male
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Randomness is an attitude
Introduction

"Because I give a fuck!"

That's why I am doing what I do. I give a fuck that everbody gets a chance to learn. I give a fuck that knowledge be shared. I give a fuck that children will live in a better world than ours.

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Guillaume Filion's +1's are the things they like, agree with, or want to recommend.
Bioinformatics Zen - How I develop
www.bioinformaticszen.com

How I develop. Published Fri July 24 2015. I've been in the bioinformatics field for almost 10 years, originally coming from a molecular bio

arpack {igraph} | inside-R | A Community Site for R
www.inside-r.org

Arguments. func: The function to perform the matrix-vector multiplication. ARPACK requires to perform these by the user. The function gets t

I was wrong
liorpachter.wordpress.com

Two weeks ago in my post Pachter's P-value Prize I offered $latex {\bf \frac{\$100}{p}}$ for justifying a reasonable null model and a p-valu

Bayesian networks and causation
blog.thegrandlocus.com

Bayesian networks and causation | Filed under statistics, Bayesian networks, causes, correlation.

GigaScience | Full text | The ocean sampling day consortium
www.gigasciencejournal.com

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain

Starcode: sequence clustering based on all-pairs search
bioinformatics.oxfordjournals.org

Abstract Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology.

What is bioinformatics about?
blog.thegrandlocus.com

What is bioinformatics about? | Filed under information retrieval, PubMed, journals, bioinformatics.

Genome Biology | Full text | When will ‘open science’ become simply ‘sci...
genomebiology.com

Open science describes the practice of carrying out scientific research in a completely transparent manner, and making the results of that r

Why do bioinformatics?
blog.thegrandlocus.com

Why do bioinformatics? | Filed under software pollution, benchmark, bioinformatics.

Google+
plus.google.com

Google+ is a place to connect with friends and family, and explore all of your interests. Share photos, send messages, and stay in touch wit

borborygmi
nhoffman.github.io

Illumina provides a program for demultiplexing sequencing output called bcl2fastq . They get a gold star for releasing the source - the down

5 Steps to Develop a Basic AngularJS Application with Example
www.thegeekstuff.com

Angular.js is a client-side javascript framework developed and maintained by Google. It is a MVW ( Model View Whatever ) framework. It gives

Starcode: sequence clustering based on all-pairs search
bioinformatics.oxfordjournals.org

Abstract Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology.

The Extent and Consequences of P-Hacking in Science
journals.plos.org

Publication bias resulting from so-called "p-hacking" is pervasive throughout the life sciences; however, its effects on general conclusions

Emailing with Python and SPSS
andrewpwheeler.wordpress.com

Emailing automated messages using Python was on my bucket list for a few projects, so here I will illustrate how to do that within SPSS. Bas

"What then should we teach about hypothesis testing?" - Statistical Mode...
andrewgelman.com

Someone who wishes to remain anonymous writes in: Last week, I was looking forward to a blog post titled “Why continue to teach and use hypo

If cars were made by bioinformaticians...
blog.thegrandlocus.com

If cars were made by bioinformaticians... | Filed under cars, bioinformatics, software.

I found the service at ShBarcelona to be good, with high level of responsiveness. The personnel is committed, foreigner-friendly and amicable. Negative point, I found the repair services (plumbers, electricians etc.) they contract overpriced. But overall they left me a good impression.
Public - 10 months ago
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