Oxford's " No thanks, I've already got one "
< div class= " separator " style= " clear: both; text-align: center; " > < a href= " https://3.bp.blogspot.com/-UdpovECdYoY/VtmBWKsnnvI/AAAAAAAAAAA/TThQqS1bWgY/w1200-h300/event_theme.jpg " imageanchor= " 1 " style= " margin-left: 1em; margin-right: 1em; " > < img border= " 0 " height= " 100 " src= " https://3.bp.blogspot.com/-UdpovECdYoY/VtmBWKsnnvI/AAAAAAAAAAA/TThQqS1bWgY/w1200-h300/event_theme.jpg " width= " 400 " > < /a > < /div > Oxford Nanopore today hosted a Google hangout titled & quot; < a href= " https://plus.google.com/events/cuk2eofrekvogeam12klluivqts " > No thanks, I & #39;ve already got one < /a > & quo...
Source: Omics! Omics! - March 7, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Digging into the Illumina Lawsuit vs. Oxford Nanopore
Illumina's and University of Washington's filing of a patent lawsuit and related trade complaint against Oxford Nanopore made big news yesterday, with nice coverage from Mick Watson, GenomeWeb, Nature's Erika Check Hayden, Technology Reviews' Antonio Regalado, BioIT World's Aaron Krol, and venture capitalist Vishal Gulati. Each of these covers the onetime partnership between the two companies and their acrimonious parting of ways. Oxford Nanopore released a short and pithy response. Having failed to get an early jump on things, the ground is already well plowed. So my sloth and inertia have forc...
Source: Omics! Omics! - February 24, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Amplification-free, library-free sequencing? NanoString wants to be It
Perhaps the most unusual new technology to be unveiled at AGBT16 is NanoString's new approach to sequencing, which is in very early stages of development. Called Hyb And Seq the process is remarkable in being a purely hybridization-based single molecule method -- absolutely no enzymes are harmed during the operation of the system. That's remarkable -- the only enzyme-free (or nearly so) sequencing approaches to deliver serious amounts of data into Genbank are Maxam and Gilbert approaches (including Church's genomic sequencing and multiplex sequencing), and even those typically required restriction digestion...
Source: Omics! Omics! - February 23, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT16 Storify Completion & Rate Limits
< div > < br > < /div > < div > AGBT16 ended a week ago, but for various reasons I & #39;m just now catching up on my Storify project. A vacation was in there but also some tool building. As I was griping about the pains of organizing the tweets manually, Brian Krueger suggested what was already dawning on me (but it helps to be poked -- professional embarrassment is often a stronger motivator than pure annoyance) -- I needed t o stop doing this purely manually. So, off to deal with pulling in Tweets automatically and at least doing some organization programatically. < br > < /div > < a href= " http://omicsomics.blog...
Source: Omics! Omics! - February 19, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
10X Launches Chromium (#agbt16)
10X Genomics launched their approach to obtaining long-range genomic information last year with a big financing and some exciting preliminary data at AGBT15. Now they are back at AGBT16 with an upgraded instrument, improved biochemistry, new software and new applications, along with a trio of major co-marketing agreements and a splashy hire and a raft of both published and unpublished data from academic collaborators.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 11, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
State of lab, year 3 - the first group outcomes
This report marks the end of the third year of the lab. I have to stop thinking of how quickly a year goes by. We will have a review in March 2017 that will likely dictate our extension after the first 5 years and if extended the group has then an additional 4 years before having to leave the EMBL-EBI (after a maximum of 9 years). During the third year we said goodbye to Juan A Cordero Varela (master student, linkedIn). Marta Strumillo, that was doing an internship, stayed on to do her PhD in the group. Towards the very end of last year we were joined by two additional postdoctoral fellows, Bede Busby and Cristina Vie...
Source: Evolution of Cellular Networks - January 11, 2016 Category: Cytology Tags: academia state of the lab Source Type: blogs
This blog in 2015
It must be time for the annual report, kindly generated by the people from WordPress at the end of each year.
I’m pleased to see that I still averaged almost 2 posts a month, given that it was a difficult year in many ways (more on that later). Visitors from 202 countries! And if I never blogged again, it seems that people will want to learn about R’s apply functions for a long time to come.
2016 is going to be a bit “different”. Look out for the blog post which explains how and why, coming soon… Filed under: statistics, this blog Tagged: annual report, wordpress (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - December 29, 2015 Category: Bioinformatics Authors: nsaunders Tags: statistics this blog annual report wordpress Source Type: blogs
Variants + Spark = VariantSpark
Just a short note to alert you to a publication with my name on it. Great work by lead author and former colleague Aidan; I just did “the Gephi stuff”. If you’re interested in bioinformatics applications of Apache Spark, take a look at:
VariantSpark: population scale clustering of genotype information
Happy to report it is open access.Filed under: bioinformatics, publications Tagged: 1000 genomes, apache, machine learning, spark, variant (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - December 29, 2015 Category: Bioinformatics Authors: nsaunders Tags: bioinformatics publications 1000 genomes apache machine learning spark variant Source Type: blogs
Group member profile - Haruna Imamura
Here is the second entry into what I hope will be a very long series where I introduce our lab's members. Next up is Haruna Imamura (pubmed), an interdisciplinary postdoc with experience in mass-spectrometry and informatics.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? I first joined the biological network analysis group in my undergraduate course in the lab of Masaru Tomita at Keio University (Japan). I launched a project, which applied the concept of network analysis to a dataset of phosphorylation dynamics. Because of this experience, I gre...
Source: Evolution of Cellular Networks - December 15, 2015 Category: Cytology Tags: group Source Type: blogs
Replace journals with recommendation engines
There was another round of interesting discussions on twitter after Mike Eisen decided to scrub all journal tittles from his lab's publication list. Part of the discussion was summarized in this Nature news story. The general idea is that our science should not be evaluated by where it is published but should stand by its own merit. We all want this to happen but unfortunately we don't have infinite time to read papers. Megajournal and open access advocates often dismiss this problem. They will often say that journal rankings are not adequate filters and that we should be able to make our own opinions and to search for wha...
Source: Evolution of Cellular Networks - December 14, 2015 Category: Cytology Tags: publishing Source Type: blogs
Happy birthday my blog. You are now ten-year-old.
Happy birthday my blog. You are now 10-year-old. (Source: YOKOFAKUN)
Source: YOKOFAKUN - December 4, 2015 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
Predicting PTM specificities from MS data and interaction networks
Around four years ago I wrote this blog post where I suggested that it might be possible to combine protein interaction data with phosphosites from mass-spectrometry (MS) data to infer the specificity of protein kinases. I did a very simple pilot test and invited others to contribute to the idea. Nobody really picked up on it until Omar Wagih, a PhD student in the group, decided to test the limits of the approach. To his credit I didn't even ask him to do it, his main project was supposed to be on individual genomics. I am glad that he deviated long enough to get some interesting results that have now been published.A...
Source: Evolution of Cellular Networks - November 27, 2015 Category: Cytology Tags: academia open science P2 phosphorylation specificity Source Type: blogs
Novelty: an update
A recent tweet:
@neilfws I enjoyed this: https://t.co/ynyHRbgpLN Have you published (or are you thinking about publishing) this analysis anywhere?
— Marcus Munafo (@MarcusMunafo) October 7, 2015
PubMed articles containing “novel” in title or abstract 1845 – 2014made me think (1) has it really been 5 years, (2) gee, my ggplot skills were dreadful back then and (3) did I really not know how to correct for the increase in total publications?
So here is the update, at Github and a document at RPubs.
“Novel” findings, as judged by the usage of that word in titles and abstracts really have ...
Source: What You're Doing Is Rather Desperate - October 21, 2015 Category: Bioinformatics Authors: nsaunders Tags: publications R ruby statistics literature ncbi pubmed rstats Source Type: blogs
R and the Nobel Prize API
The Nobel Prizes. Love them? Hate them? Are they still relevant, meaningful? Go on admit it, you always imagined you would win one day.
Whatever you think of them, the 2015 results are in. What’s more, the good people of the Nobel Foundation offer us free access to data via an API. I’ve published a document over at RPubs, showing some of the ways to access and analyse their data using R. Just to get you started:
library(jsonlite)
u <- "http://api.nobelprize.org/v1/laureate.json"
nobel <- fromJSON(u)
In this post, just the highlights. Click the images for larger versions.
1. Gender
The...
Source: What You're Doing Is Rather Desperate - October 20, 2015 Category: Bioinformatics Authors: nsaunders Tags: R statistics api ggplot2 laureates nobel prizes rest rstats Source Type: blogs
Searching for duplicate resource names in PMC article titles
I enjoyed this article by Keith Bradnam, and the associated tweets, on the problem of duplicated names for bioinformatics software.
I figured that to some degree at least, we should be able to search for such instances, since the titles of published articles that describe software often follow a particular pattern. There may even be a grammatical term for it, but I’ll call it the announcement colon:
eDuS: Segmental Duplication Simulator
Reveel: large-scale population genotyping using low-coverage sequencing data
RNF: a general framework to evaluate NGS read mappers
Hammock: A Hidden Markov model-based peptide cluste...
Source: What You're Doing Is Rather Desperate - September 16, 2015 Category: Bioinformatics Authors: nsaunders Tags: open access programming ruby statistics duplicates pmc Source Type: blogs
