Directed Panspermia Doesn't Belong In Schools (and Probably Never Will)
Opening to the Ideas section of the Boston Globe this past Sunday, I was immediately faced with a grotesque site. Nothing to do with the appalling terrorism of fifteen years ago, but instead the Globe putting front-and-center in the section a truly awful idea,which the subhead trumpeted"Creationism can have a basis in science - if aliens are involved".Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - September 12, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Playing with #magicblast, the #NCBI Short read mapper. My notebook
NCBI MAGIC Blast was recently mentioned by BioMickWatson on twitter.
Looks pretty cool. Perhaps once again the answer to all bfx questions will be BLAST RE https://t.co/4D5e9QQnrb pic.twitter.com/bwW3y0yl2n- Mick Watson (@BioMickWatson) September 9, 2016
Here, I'll be playing with magicblast and I'll compare its output with bwa (Makefile below).
First, here is an extract of the manual for (Source: YOKOFAKUN)
Source: YOKOFAKUN - September 8, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
Portrait Of A Genomics Instrumentation Impresario
Veteran biotech reporterLuke Timmerman's new book,Hood: A Trailblazer of the Genomics Age, is a valuable exploration of one of the leading figures in the early development of genomics and proteomics. This in depth look at a key scientist covers not only his achievements and glories, but also his less than stellar moments and tendencies. Timmerman has combined his own interviews and research with nuggets pulled from prior news articles and oral histories of scientists who crossed paths (and som etimes figurative swords) with Hood. While the book has issues, I would recommend it to anyone interested in the history of...
Source: Omics! Omics! - September 7, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Wikipedia, and other non-evil things
Tommorrow, TNG will head off for his penultimate first day of grade school. And unfortunately, that almost certainly means another attempt to indoctrinate him in a catechism I find both depressing and infuriating. It goes something like this:"Wikipedia is not a reliable source. Wikipedia is not citable. Don't use Wikipedia".Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 29, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Data corruption using Excel: 12+ years and counting
This study examined 35 175 supplementary Excel data files from 3 597 published articles. Simple yet clever, isn’t it. I bet you wish you’d thought of doing that. I do. The conclusion: about 20% of articles have associated data files in which gene names have been corrupted by Excel.
What if there is no tomorrow? There wasn’t one today.
We tell you not to use Excel. You counter with a host of reasons why you have to use Excel. None of them are good reasons. I don’t know what else to say. Except to reiterate that probably 80% or more of the data analyst’s time is spent on data cleaning and a good...
Source: What You're Doing Is Rather Desperate - August 25, 2016 Category: Bioinformatics Authors: nsaunders Tags: bioinformatics publications software excel genes Source Type: blogs
Math Toys, Much Enjoyed!
Last week, I attended a free public talk at the Society for Industrial and Applied Mathematics (SIAM) here in Boston. This is a wonderful public outreach concept which too few conferences sport. The speaker, Tadashi Tokieda of University of Cambridge, illustrated a number of fascinating phenomena which can be demonstrated with simple toys or household objects. Tokieda didn't lecture from a bunch of slides; most of the talk was in the form of live demonstrations -- and demonstrations made with overt glee! There's a Storify of the entire meeting, in which mine and others of the Tokieda talk can be found.Read ...
Source: Omics! Omics! - July 18, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Infinity's Sad RUD
Almost five years ago, < a href= " http://omicsomics.blogspot.com/2011/09/transitions.html " > I wrote of voluntarily leaving Infinity Pharmaceuticals < /a > . Particularly due to the novelty (for me) of the voluntary part, at times I & #39;ve wondered how long I would have stayed there. Indeed, the offspring asked just that question just over a week ago. I do know now when I couldn & #39;t have stayed any longer, as to my great dismay Infinity announced last week it was discontinuing its Discovery operations due to a disappointing drug trial result. < br > < br > < a href= " http://omicsomics.blogspot.com/2016/06/infi...
Source: Omics! Omics! - June 20, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Group member profile - Romain Studer
Next up on this series of group member profiles is Romain Studer (blog, scholar profile, twitter), a postdoc in the group that is very interested in protein evolution combining sequence and structural information.What was the path the brought you to the group? Where are you from and what did you work on before arriving in the group?My main interest in biology is the study of proteins in a broad diversity of organisms. My PhD work, as well as my postdoctoral research, was focused on protein evolution, at the primary sequence level and at the tertiary structure level.I did my undergraduate studies and PhD work at University ...
Source: Evolution of Cellular Networks - June 17, 2016 Category: Cytology Tags: group Source Type: blogs
London Calling 2016: Further Thoughts
London Calling was two weeks ago, and I still haven't written anything beyond the write-up of Clive Brown's talk (note that many of the talks are now view-able via Oxford Nanopore's website). I did finally make some headway on Storifying the tweets. After several self-inflicted wounds (starting with failing to read my write-up of the previous experience of trying to post to Storify from the command line, but also from failing to record the details of that final critical command), I did succeed. This time I decided to group the tweets into several broad categories -- with tweets potentially showing up in m...
Source: Omics! Omics! - June 9, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling: Notes on Brownian Commotion
I'm behind on writing up London Calling. I can partly blame a failing computer -- though rebooting it seems to have righted it for the moment. A bigger challenge is that I had the luxury of staying in London thru the weekend, and have been trying to pack as much in of England as I can. To really do justice to everything, I need to scan all the tweets -- and that will take some time. But I have dug into everything around Clive Brown's talk (kudos to NextGenSeek for Storifying that portion of the meeting's tweets!_ about the current and future state of the Oxford Nanopore platform, so I will focus on that...
Source: Omics! Omics! - May 28, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
pubmed: extracting the 1st authors' gender and location who published in the Bioinformatics journal.
In this post I'll get some statistics about the 1st authors in the "Bioinformatics" journal from pubmed. I'll extract their genders and locations.
I'll use some tools I've already described some years ago but I've re-written them.
Downloading the dataTo download the paper published in Bioinformatics, the pubmed/entrez query is '"Bioinformatics"[jour]'.
I use pubmeddump to download all those (Source: YOKOFAKUN)
Source: YOKOFAKUN - May 26, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
London Calling Preview
ON Thursday and Friday this week Oxford Nanopore will be holding their second annual London Calling meeting. I successfully defended my schedule this year, so I'll be on the ground there. If you follow me on Twitter and don't want to be buried in nanopore tweets, mute the hashtag #nanoporeconf (a rather large hashtag for talking about nano stuff!) LC is OxNano's premier event, so what might we see from the company?Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 24, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Inconstant lines
If you order chemicals, then the supplier provides a certificate of analysis, which shows the amounts of impurities or their limit of detection. Fir physics experiments, one can purchase components which have been carefully cast or machined to precise dimensions. Barring errors by the manufacturers, these reagents and components can be relied upon, as their consistency is known. Alas, for biological systems, such constancy is often a mirage.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 23, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Sickle Cell Anemia: An underprioritized disease?
The Sunday Boston Globe today had a front page piece by STAT's Sharon Begley that asks some challenging questions about prioritization of disease research. Poking around the STAT site, I found that the original article was even longer and better, but between the important issues it raises, some interesting peripheral stuff and at least one gaping hole, there's plenty to discuss.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 21, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Playing with the @ORCID_Org / @ncbi_pubmed graph. My notebook.
"ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized. "I've recently discovered that pubmed now integrates ORCID identfiers.
and so it begins ! :-D @ (Source: YOKOFAKUN)
Source: YOKOFAKUN - May 20, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
