Reproducibility: releasing code is just part of the solution
This week in Retraction Watch: Hypertension retracts paper over data glitch.
The retraction notice describes the “data glitch” in question (bold emphasis added by me):
…the authors discovered an error in the code for analyzing the data. The National Health and Nutrition
Examination Survey (NHANES) medication data file had multiple observations per participant and
was merged incorrectly with the demographic and other data files. Consequently, the sample size was
twice as large as it should have been (24989 instead of 10198). Therefore, the corrected estimates of
the total number of US adults with hyperten...
Source: What You're Doing Is Rather Desperate - August 21, 2012 Category: Bioinformaticians Authors: nsaunders Tags: open science publications reproducibility retraction Source Type: blogs
Twitter coverage of the ISMB 2012 meeting: some statistics
OK, let’s do this: some statistics and visualization of the tweets for ISMB 2012.
First, thanks to Stephen Turner who got things started in this post at his excellent blog, Getting Genetics Done. Subscribe to his feed if you don’t already do so.
I’ve created a Github repository for this project (and future Twitter-related work). If you’d like to reproduce the analyses (or skip reading this post), there’s a Sweave file and the resulting PDF. The Sweave file contains a relative path to the data file, so to run the analysis you’ll need to clone the repository, cd to ismb/code/sweave and ru...
Source: What You're Doing Is Rather Desperate - August 16, 2012 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics meetings statistics ismb ismb2012 Source Type: blogs
I am starting a group at the EMBL-EBI
I signed the contract this week to start a
research group at the European Bioinformatics Institute (EBI) in Cambridge, an
outstation of the European Molecular Biology Laboratory (EMBL). After blogging
my way through a PhD and postdoc it is a pleasure to be able to write
this blog post. In January, I will be joining an amazing group of people
working in bioinformatics services and basic research where I plan to continue studying
the evolution of cellular interaction networks. I am currently interested in
the broad problem of understanding how genetic variability gets propagated
through molecules and interaction networks to ...
Source: Public Rambling - July 19, 2012 Category: Bioinformaticians Source Type: blogs
Evolution and Function of Post-translational Modifications
In this study we have tried to assign a function to post-translational modifications (PTMs) that are derived from mass-spectrometry (MS). This follows directly from previous work where we looked at the evolution of phosphorylation in three fungal species (paper, blog post). We (and other groups) have seen that phosphorylation sites diverge rapidly but we don't really know if this divergence of phosphosites results in meaningful functional consequences. In order to address this we need to know the function of post-translational modifications (if they have any). Since these MS studies now routinely report several t...
Source: Public Rambling - July 19, 2012 Category: Bioinformaticians Tags: PTMs academia evolution phosphorylation P1 Source Type: blogs
The Minimal Publishable Unit
What constitutes a minimal publishable unit in scientific publishing ? The transition to online publishing and the proliferation of journals is creating a setting where anything can be published. Every week spam emails almost beg us to submit our next research to some journal. Yes, I am looking at you Bentham and Hindawi. At the same time, the idea of a post-publication peer review system also promotes an increase in number of publications. With the success of PLoS ONE and its many clones we are in for another large increase in the rate of scientific publishing. Publish-then-sort as they say.
With...
Source: Public Rambling - May 9, 2012 Category: Bioinformaticians Tags: publishing Source Type: blogs
Individual genomics of yeast
Nature Genetics used to be one of my favorite science journals. It consistently had papers that I found exciting. That changed about 5 years ago or so when they had a very clear editorial shift into genome-wide association studies (GWAS). Don't take me wrong, I think GWAS are important and useful but I don't find it very exciting to have lists of regions of DNA that might be associated with a phenotype. I want to understand how variation at the level of DNA gets propagated through structures and interaction networks to cause these differences in phenotype. I mostly stayed out of GWAS since I was focusing on the e...
Source: Public Rambling - March 28, 2012 Category: Bioinformaticians Tags: personal genome original research Source Type: blogs
Book Review - The Filter Bubble
Following my previous post I thought it was on topic to mention a book I read recently called “The Filter Bubble”. The book, authored by Eli Pariser, discusses the several applications of personalization filters in the digital world. As several books I have read in the past couple of years, I found it via a TED talk where the author neatly summarizes the most important points. Even if you are not too interested in technology it is worth watching it. I am usually very optimistic about the impact of technology on our lives but Pariser raises some interesting potential negative consequences of personalization fi...
Source: Public Rambling - February 29, 2012 Category: Bioinformaticians Tags: books review Source Type: blogs
Academic value, jobs and PLoS ONE's mission
Becky Ward from the blog "It Takes 30" just posted a thoughtful comment regarding the Elsevier boycott. I like the fact that she adds some perspective as a former editor contributing to the ongoing discussion. This follows also from a recent blog post from Michael Eisen regarding academic jobs and impact factors. The tittle very much summarizes his position: "The widely held notion that high-impact publications determine who gets academic jobs, grants and tenure is wrong". Eisen is trying to play down the value of the "glamour" high impact factor magazines and fighting for the success of open access journal...
Source: Public Rambling - February 23, 2012 Category: Bioinformaticians Tags: publishing Source Type: blogs
The 2012 Bioinformatics Survey
I am interrupting my current blogging hiatus to point to a great initiative by Michael Barton. He is collecting some information regarding those working in the fields of bioinformatics / computational biology in this survey. This is a repeat from a similar analysis done in 2008 and I think is it is really worth getting a felling for how things have been changing. We can all benefit from the end result. So far, after 2 weeks, there have been close to 400 entries to the survey but the rate of new entries is slowing down. So, if you have not done so already, go and fill it out or bug some colleague to do so.&nb...
Source: Public Rambling - February 22, 2012 Category: Bioinformaticians Source Type: blogs
Predicting kinase specificity from phosphorylation data
Over the past few years, improvements in mass-spectrometry methods have resulted in a big increase in throughput for the identification of post-translational modifications (PTMs). It is even hard to keep up with all the phosphoproteomics papers and the accumulation of phosphorylation data. Most often, improvements in methods result in interesting challenges and opportunities. In this case, how can we make use of this explosion in PTM data ? I will try to explore a fairly straightforward idea, on how to use phosphorylation data to predict kinase substrate specificity. I'll describe here the general idea and j...
Source: Public Rambling - May 25, 2011 Category: Bioinformaticians Tags: P2 phosphorylation Source Type: blogs
