Metagenomics
COST training school: Bioinformatics for microbial community analysis
I will be helping teach one day of this course which is fully-funded if you are a student from a COST-participating country… see below for details: Deadline is next week, so hurry if you are interested. COST training school ES1103: Bioinformatics for microbial community analysis Dates: December 11th- 14th (the school will begin at 1pm [...]
Sequencing low diversity libraries on Illumina MiSeq
Research Fellow in Microbial Bioinformatics
Research Fellow Microbial Bioinformatics University of Birmingham - School of Biosciences Salary: from £27,428 to £37,990 a year Fixed term: until 31 July 2016 Closing date: 17 December 2011 Reference: 47410 Applications are invited for a Research Fellow position devoted to bioinformatics support and research in the field of high-throughput sequencing and the microbiology of trauma patients. This exciting opportunity [...]
Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Day 3
Here is a crude file dump of my live tweets from the third day of the Applying Advanced Molecular Techniques to Healthcare Infection. Same caveats as before: apologies for extraneous material, but something better than nothing. Also have created newspaper of links from the meeting here: http://paper.li/mjpallen/1319610603 #AAMTHI am signing off live tweeting and will start [...]
High-memory servers for bioinformatics / metagenome assemblies
I want to get a 512Gb RAM machine for bioinformatics, specifically for doing metagenome and large genome assemblies. For some good background on why a server like this is a good idea (as opposed to, say, a cluster) check out Jermdemo’s post on Big-Ass Servers(tm). 512Gb machines are now fairly easy to source, you just [...]
Are diagnostic and public health bacteriology ready to become branches of genomic medicine?
This article of ours has just appeared in Genome Medicine. Pallen and Loman Genome Medicine 2011, 3:53 http://genomemedicine.com/content/3/8/53 MUSINGS: Are diagnostic and public health bacteriology ready to become branches of genomic medicine? Mark J Pallen* and Nicholas J Loman Diagnostic medical bacteriology is a conservative discipline. When busy house officers scribble ‘M, C & S’ [...]
Exploring inner space: the chicken gut microbiome (and another job opportunity!)
Nick is going to post very soon on the application of high-throughput sequencing to microbial community profiling using 16S rDNA sequences and the insights he gained into this process from a recent workshop. In the meantime, allow me to wax lyrical on the contents of chicken shit…! More seriously, why should anyone be interested in [...]
Technical advances in bacterial metagenomics
I chanced upon this RFA from the NIH entitled Development of New Technologies Needed for Studying the Human Microbiome (R01) which struck me as a good summary of the necessary technical developments before we can get definitive answers on the composition of the human (and other) microbiomes. Development of methods to isolate single microbial cells. [...]