EBI-Sanger postdoctoral fellowship on Plasmodium kinase regulatory networks
I am happy to announce a call for applications for a EBI-Sanger postdoctoral fellowship to study the kinase regulatory networks in Plasmodium. This is one of four currently open calls in the the EBI–Sanger Postdoctoral (ESPOD) Programme and the call closes on the 26th of July. This interdisciplinary programme is meant to foster collaborations between the EBI and the Wellcome Trust Sanger Institute, both at the Genome Campus near Cambridge UK. Our project is a collaboration between myself (EBI), Jyoti Choudhary (mass-spectrometry group leader at Sanger) and Oliver Billker (group leader a...
Source: Public Rambling - May 13, 2013 Category: Bioinformaticians Tags: positions Source Type: blogs
Inserting the result of a BLAST into a Database using XSLT.
Here is the XML output of a BLAST:
tblastn
TBLASTN 2.2.27+
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Z
hang, Zheng Zhang, Webb (Source: YOKOFAKUN)
Source: YOKOFAKUN - May 1, 2013 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs
Java JNI bindings for BWA(mem-lite)
Motivation
BWA 7.4(http://bio-bwa.sourceforge.net/) contains a small C example(https://github.com/lh3/bwa/blob/master/example.c) for running bwa-mem as a library (bwamem-lite). I created some JNI bindings to see if I can bind the C bwa library to java and get the same output than bwamem-lite. I put the code on github at https://github.com/lindenb/jbwa.
Example
(compare to https://github.com/lh3 (Source: YOKOFAKUN)
Source: YOKOFAKUN - April 26, 2013 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs
Installing TPP 4.6.2 on Mountain Lion Mac OSX
This is for the open-source proteomics folks out there who run Macs. I finally figured out how to install the latest Transatlantic-Proteomics-Pipeline package (TPP 4.6.2) on my Mountain Lion Macbook Air. It was not fun, and involved debugging make and configure files.
Basically the workflow of the TPP build process is that src/Makefile contains the commands to build the TPP, but it will call several children Makefiles dotted all over the package. For instance, src/Makefile.incl contains the commands to build all the external dependencies (found in extern/) that are included in the TPP package.
To make TPP 4.6.2 work wi...
Source: Trapped in the USA - April 24, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
How to: remember that you once knew how to parse KEGG
Recently, someone asked me if I could generate a list of genes associated with a particular pathway. Sure, I said and hacked together some rather nasty code in R which, given a KEGG pathway identifier, used a combination of the KEGG REST API, DBGET and biomaRt to return HGNC symbols.
Coincidentally, someone asked the same question at Biostar. Pierre recommended the TogoWS REST service, which provides an API to multiple biological data sources. An article describing TogoWS was published in 2010.
An excellent suggestion – and one which, I later discovered, I had bookmarked. Twice. As long ago as 2008. This “redis...
Source: What You're Doing Is Rather Desperate - April 22, 2013 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics programming ruby biostar how to kegg pathways rest Source Type: blogs
The case for article submission fees
For scientific journal articles the cost of publishing is almost exclusively covered by the articles that are accepted for publication. Either by the published authors or by the libraries. Advertisement and other items like the organization of conferences are probably not a very significant source of income. I don't want to argue here again the value of publishers and how we should be decoupling the costs of publishing (close to zero) from peer-review, accreditation and filtering. Instead I just want to explore the idea for a very obvious form a income that is not used - submission fees. Why don't journ...
Source: Public Rambling - April 7, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
A brief note: R 3.0.0 and bioinformatics
Today marks the release of R 3.0.0. There will be plenty of commentary and useful information at sites such as R-bloggers (for example, Tal’s post).
Version 3.0.0 is great news for bioinformaticians, due to the introduction of long vectors. What does that mean? Well, several months ago, I was using the simpleaffy package from Bioconductor to normalize Affymetrix exon microarrays. I began as usual by reading the CEL files:
f <- list.files(path = "data/affyexon", pattern = ".CEL.gz", full.names = T, recursive = T)
cel <- ReadAffy(filenames = f)
When this happened:
Error in read.affybatch(fi...
Source: What You're Doing Is Rather Desperate - April 3, 2013 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics programming statistics 3.0.0 affymetrix bioconductor microarray Source Type: blogs
Benchmark the experimental data not just the integration
There was a paper out today in Molecular Systems Biology with a resource of kinase-substrate interactions obtained from in-vitro kinase assays using protein micro-arrays. It is clear that there is a significant difference between what a kinase regulates inside a cell and what it could phosphorylate in-vitro given appropriate conditions. In fact, reviewer number 1 in the attached comments (PDF), explains at length why these protein-array based kinase interactions may be problematic. The authors are aware of this and integrate the protein-array data with additional data sources to derive a higher confidence dataset of kinase...
Source: Public Rambling - April 2, 2013 Category: Bioinformaticians Tags: bioinformatics Source Type: blogs
The glacial pace of innovation in scientific publishing
Nature made available today a collection of articles about the future of publishing. One of these is a comment by Jason Priem on "Scholarship: Beyond the paper". It is beautifully written and inspirational. It is clear that Jason has a finger on the pulse of the scientific publishing world and is passionate about it. He sees a future of a "decoupled" journal, where modular distributed data streams can be built into stories openly and in real time. Where certification and filtering are not tied to the act of publishing and can happen on the fly by aggregating social peer review. While I wa...
Source: Public Rambling - March 28, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
Git for bioinformaticians at the Bioinformatics FOAM meeting
Last week, I attended the annual Computational and Simulation Sciences and eResearch Conference, hosted by CSIRO in Melbourne. The meeting includes a workshop that we call Bioinformatics FOAM (Focus On Analytical Methods). This year it was run over 2.5 days (up from the previous 1.5 by popular request); one day for internal CSIRO stuff and the rest open to external participants.
I had the pleasure of giving a brief presentation on the use of Git in bioinformatics. Nothing startling; aimed squarely at bioinformaticians who may have heard of version control in general and Git in particular but who are yet to employ either. I...
Source: What You're Doing Is Rather Desperate - March 26, 2013 Category: Bioinformaticians Authors: nsaunders Tags: australia bioinformatics computing meetings csiro eresearch foam git ict slideshare version control Source Type: blogs
Embedding Pubmed, Graphiviz and a remote image in #LaTeX. My notebook. .
I'm learning LaTeX. Today I learned how to create a new command in LaTeX.
\newcommand{name}[num]{definition}"Basically the command requires two arguments: the name of the command you want to create, and the definition of the command" . I played with LaTeX and wrote the following three commands:
Embedding a remote pictureThe following LaTeX document defines a new command "\remoteimage". It takes 3 (Source: YOKOFAKUN)
Source: YOKOFAKUN - March 25, 2013 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs
The end of Google Reader: a scientist’s perspective
Since 2005, I have started almost every working day by using one Web application – an application that occupies a permanent browser tab on my work and home desktop machines. That application is Google Reader.
If you’re reading this, you’re probably aware that Google Reader will cease to exist from July 1 2013. Others have ranted, railed against the corporate machine and expressed their sadness. I thought I’d try to explain why, for this working scientist at least, RSS and feed readers are incredibly useful tools which I think should be valued highly.
Some feeds, yesterday
RSS: a primer
When I first...
Source: What You're Doing Is Rather Desperate - March 18, 2013 Category: Bioinformaticians Authors: nsaunders Tags: google web resources google reader rss Source Type: blogs
Post AGBT: A Longish Item on Long Sequencing
As others have noted, a significant theme at AGBT this year was sequencing at length. While this year lacked true bombshells, PacBio impressed many with their making single-contig bacterial genome assemblies look easy. Moleculo had been the object of much pre-meeting excitement, and while very few additional details emerged about their process, several talks showed what could be done. As I have discussed previously, Nabsys demonstrated their “positional sequencing” system to select invitees in a hotel suite. Optical mapping from OpGen and BioNano Genomics featured in a few posters, but did not attract much atte...
Source: Omics! Omics! - February 26, 2013 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
