This blog in 2013
In something of an end-of-year tradition, WordPress provides users with an effort-free blog post in the form of an annual report. Here is mine.
My ambitious plan at the start of 2013 was to aim for 4 posts a month. I managed 28 and I’m happy with that; about one every two weeks.
Looking forward to a new year of blogging. All the best to you and yours for 2014.Filed under: personal, this blog (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - January 3, 2014 Category: Bioinformaticians Authors: nsaunders Tags: personal this blog Source Type: blogs
Peering Through the Flowcell Glass, Darkly
As 2013 draws to a close, I've decided to stick my neck out and make some predictions for 2014. Perhaps I'll get lucky and a few will even come true! After several mental experimentations on the structure, I'll settle for stepping roughly past each major player.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 31, 2013 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
State of the lab, year 1 – setting up
I have used this blog in the past to keep track of my academic life where I can give a less formal perspective on papers I have published or ideas I am working on. Starting a group has made me think a bit about what I blog about. I have more responsibilities towards the people that have decided to work with me, towards the institution that has hired me (EMBL-EBI) and funding sources that support our work. At least for now I have decided to keep on sharing my personal view and in that context I though it could be interesting to write down my path as group leader in academia. This might become a yearly “thing”.I started ...
Source: Public Rambling - December 18, 2013 Category: Bioinformaticians Tags: academia Source Type: blogs
Career advice: switching to computational research
Laboratory work, of the “wet” kind, not working out for you? Or perhaps you just need new challenges. Think you have some aptitude with data analysis, computers, mathematics, statistics? Maybe a switch to computational biology is what you need.
That’s the topic of the Nature Careers feature “Computing: Out of the hood“. With thoughts and advice from (on Twitter) @caseybergman, @sarahmhird, @kcranstn, @PavelTomancak, @ctitusbrown and myself.
I enjoyed talking with Roberta and she did a good job of capturing our thoughts for the article. One of these days, I might even write here about my own jo...
Source: What You're Doing Is Rather Desperate - December 18, 2013 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics career computing journals nature Source Type: blogs
Submission time again
Four years since my last post, just pretending nothing happened since then …
Just trying to submit a manuscript online and struggling with the online submission system at Cell press – probably the same kind of problems at other places. I can understand that the final paper must not exceed a certain length, but is it really necessary to count letters (including spaces, for sure) for every stupid free-text input field? Oh well, it is probably not called ‘online submission’ for nothing. Here is a definition from the Longman Dictionary of Contemporary English:
sub‧mis‧sion
the state of being comple...
Source: Suicyte Notes - December 15, 2013 Category: Bioinformaticians Authors: Kay at Suicyte Tags: language publishing silliness Uncategorized Source Type: blogs
Assembling a Review of a Review of Assembling
A review on short-read de novo genome assembly appeared recently in PLoS Computational Biology, titled "Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges". I think the review has a number of merits, but I also find a number of frustrating flaws. I'm going to write this entry much as I would have written a referee report on it. Unfortunately, that will mean I'll dwell a bit more on the flaws than the assets, but if you are interested in the fieldRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 15, 2013 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs...
Here are a few tools I recently wrote (and reinvented) for Jvarkit.
BamViewGui
a simple java-Swing-based BAM viewer.
VcfShuffle
Shuffle a VCF.
GroupByGene
Group VCF data by Gene
$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\
java -jar dist/groupbygene.jar |\
head | column -t
#chrom min.POS max.POS gene.name gene.type samples.affected (Source: YOKOFAKUN)
Source: YOKOFAKUN - December 12, 2013 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs
R: how not to use savehistory() and source()
Admitting to stupidity is part of the learning process. So in the interests of public education, here’s something stupid that I did today.
You’re working in the R console. Happy with your exploratory code, you decide to save it to a file.
savehistory(file = "myCode.R")
Then, you type something else, for example:
ls()
# more lines here
And then, decide that you should save again:
savehistory(file = "myCode.R")
You quit the console. Returning to it later, you recall that you saved your code and so can simply run source() to get back to the same point:
source("myCode.R")
Unfor...
Source: What You're Doing Is Rather Desperate - December 3, 2013 Category: Bioinformaticians Authors: nsaunders Tags: programming research diary statistics stupidity Source Type: blogs
Did The Biochemists of Yore Know Morse Code?
So, this piece is going to be mostly asking questions. In one of the corners of my dream world I have a scientific historian on retainer, but in the real world my substitute is to throw some questions out and hope some knowledgeable people leave comments. If someone I spark someone’s term paper or thesis topic, I ask only that I get an electronic draft!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 15, 2013 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
Why bioinformaticians hate the “traditional journal article”
This article is no exception. That said, it does at least describe the computational methods used in reasonable detail.
I struggle with the entire notion of data as “supplemental”. Presumably, it still means “not considered sufficiently important to occupy page space.” To a bioinformatician of course, the data are far more important than the prosaic description in the journal article. As for page space – hello? The Web? Anyone?
Problem 2: the arbitrary nature of what data are included
Proteins identified using mass spectrometry are listed in table S2 of the supplementary data. Except where the...
Source: What You're Doing Is Rather Desperate - November 5, 2013 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics genomics journals pandoravirus publishing Source Type: blogs
Introducing BMC MicroPub – fast, granular and revolutionary
I am happy to be able to share some exciting science publishing news with you. As you know, in the past few years, there has been a tremendous progress in open access publishing. The author-paying model has been shown to be viable in large part thanks to the pioneering efforts of BMC and PLOS. In particular PLOS One has been an incredible scientific and business success story that many others are trying to copy. Although these efforts are a great step forward they don't do enough to set all of the scientific knowledge free in a timely fashion. Sure you can publish almost anything today such as metadata, datasets, negative ...
Source: Public Rambling - November 1, 2013 Category: Bioinformaticians Tags: fiction publishing Source Type: blogs
We’re only 10% human. According to…who?
Reading an interesting post at Genomes Unzipped, “Human genetics is microbial genomics“, which states:
Only 10% of cells on your “human” body are human anyway, the rest are microbial.
Have you read a sentence like that before? So have I. So has a reader who left a comment:
I was wondering if you have a source for “Only 10% of cells on your “human” body are human anyway, the rest are microbial”
It’s a good question. Everyone quotes this figure, almost no-one provides a reference. Let’s go in search of one.
Wikipedia. Don’t make it your primary source. However, it’s often ...
Source: What You're Doing Is Rather Desperate - October 30, 2013 Category: Bioinformaticians Authors: nsaunders Tags: publications gut human microbiology microbiome microbiota Source Type: blogs
Bacteria and Alzheimer’s disease: I just need to know if ten patients are enough
You can guarantee that when scientists publish a study titled:
Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue
a newspaper will publish a story titled:
Poor dental health and gum disease may cause Alzheimer’s
Without access to the paper, it’s difficult to assess the evidence. I suggest you read Jonathan Eisen’s analysis of the abstract. Essentially, it makes two claims:
that cultured astrocytes (a type of brain cell) can adsorb and internalize lipopolysaccharide (LPS) from Porphyromonas gingivalis, a bacterium found in the mou...
Source: What You're Doing Is Rather Desperate - October 30, 2013 Category: Bioinformaticians Authors: nsaunders Tags: publications R science news statistics alzheimers bacteria lps power significance Source Type: blogs
Sysbio postdoc fellowship: spatio-temporal control of cell-cycle regulation
Funding is available for a 3 year postdoctoral fellowship to study spatio-temporal control in cell-cycle regulation. This is a join project between our group at the EMBL-EBI and the Quantitative Cell Biology group headed by Silvia Santos at the MRC Clinical Sciences Centre in London. More information about the groups interests can be found in the respective webpages.
The main objective of this project will be to study how the spatial and temporal control of key cell-cycle proteins change in different biological contexts. Examples of these different contexts include different differentiation states and/or differe...
Source: Public Rambling - October 29, 2013 Category: Bioinformaticians Tags: positions systems biology Source Type: blogs
Spanish Prisoner, ZX-81 or Turbo Pascal?
In the movie The Spanish Prisoner, a brilliant inventor possesses a paranoia that "The Process" he has invented will be stolen by deceitful competitors, and everyone speaks with a highly distinctive cadence. The entire movie is suffused with deceit, starting with the title which is a notorious con scheme akin to the modern Nigerian scam. I spent last evening in some of the space in which the movie was filmed listening to a scientist in that mold (& distinctive speech) describe a process his group has invented (indeed, by lucky chance I helped him find the venue). But many remain unconvinced that Clive Brown...
Source: Omics! Omics! - October 25, 2013 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
