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Welcome to The Pipeline

...a blog for members of AustralianBioinformatics.net to share ideas, insights, questions...

Entries in Bioinformatics (4)

Thursday
Jan152015

Potential Publications in Fish Phylogeography Project

Are you

  •       Interested in evolution?
  •       Experienced in bioinformatics, computational biology or statistics?
  •       Free to focus on the phylogeographic analysis of sequence data for 3-4 weeks?
  •       Keen to get a high-impact publication?

…then read on

We are looking for a collaborator to work with on our interesting, novel, well-funded evolutionary biology project with high publication expectations (at Monash University). Specifically we are seeking someone to assist us with the analysis of genetic sequencing data. This is an excellent opportunity for a recent PhD graduate, or an early career researcher with experience in bioinformatics, computational biology or statistics. 

The crater lakes in Nicaragua’s Pacific Basin region are proving to be one of the most fertile areas in the world for novel biological research. In addition to the rugged beauty of the surrounding terrain and the lush tropical forest, underneath the lake’s surfaces evolutionary processes are occurring that many once considered incredibly implausible and that still remain highly controversial today. Specifically, several species of closely related cichlid fish (Amphilophus sp.) are co-existing in sympatry, with speciation events having occurred despite a lack of geographical barriers to prevent gene flow. Despite more than 150 years passing since the publication of The Origin of Species, the relative importance of the mechanisms generating and shaping organismal diversity still continue to be debated vigorously. Understanding these mechanisms that maintain and promote variation in traits under natural selection is therefore a major challenge for evolutionary theory.

Cichlid fishes are a diverse group that are well known for their ability to rapidly evolve and diversify. Closely related species often only vary conspicuously in regard to body colour and trophic characteristics, with differences also occurring within species. We travelled to Nicaragua earlier last year to sample Amphilophus cichlids from Nicaragua’s two great lakes, Lake Nicaragua and Managua. We specifically targeted two species, Amphilophus labiatus and Amphilophus citrinellus. These two species are closely related, however they differ in their diet and key aspects of their trophic morphology. In particular A. labiatus has large fleshy lips, a trait that pops up in several cichlid species across their range (mainly Africa and South/Central America).

Amphilophus labiatus has a patchy distribution, with populations often isolated by tens of kilometres. Elsewhere in Nicaragua, phenotypically similar forms of thick-lipped Amphilophus cichlid (found in different small crater lakes) appear to have occurred due to independent parallel adaptation, within a remarkable short time period. Which leads to the question did the thick-lipped phenotype arise once in the Nicaraguan great lakes or multiple times (in parallel) across the lakes in response to local environmental conditions? Amphilophus citrinellus lives in sympatry with A. labiatus, however it does not possess thick lips, it also has a significantly different diet and a much wider distribution. Importantly, A. citrinellus has two distinct forms that coexist together across much of the lakes. These forms differ in their general body colour, diet and also in the shape and size of the lower pharyngeal jaw, which is thought to be a fundamental cause of phenotypic differentiation and ecological speciation in cichlids via divergent evolution.

We (PhD Candidate Will Sowersby and Assoc. Prof. Bob Wong) have collected samples across the lakes for diet, morphometric and genetic analysis. This work is begin conducted as part of an international collaboration with Dr. Marta Barluenga (Museo Nacional de Ciencias Naturales, Spain), Prof. Walter Salzburger (University of Basel, Switzerland) and Dr. Topi Lehtonen (University of Turku, Finland), who all have multiple publications on Amphilophus cichlids in high impact factor journals. The genetic samples have been prepared for RAD tag sequencing analysis in Europe and the data will be available for analysis shortly.

Specifically we are looking for someone to generate the phylogeography of the two species from multiple locations in both lakes and at the level of gene flow between and within locations.

All samples have been collected and are currently being analysed, we estimate that this will be a short-term commitment. We are looking for a collaborator to work with us for a matter of weeks, starting in March, however we are somewhat flexible with dates at this stage.  You should have a PhD in a relevant subject area (e.g. computational biology, bioinformatics, statistics and genomics).

If you are interested please contact Will Sowersby for any further information: william.sowersby@monash.edu

Tuesday
Oct282014

The killer ninja skill in bioinformatics

"Hmmm... sed -n '1~4s/^@/>/p;2~4p' file.fq > file.fa
...while invisible..."
As usual, it was after the event that the deeper insights emerged...

Following a mind-expanding day of bioinformtics at InCoB 2014 earlier this year, we had repaired to a nearby restaurant for the conference dinner.

After discussing

  • (with Asif M Khan) how the major histocompatibility complex helps our immune system adapt in response to new diseases
  • (with Tin Wee Tan) how the Infiniband system used for high-speed data transfer inside supercomputers can be co-opted to provide insanely fast data transfer over tens of kilometres (e.g., across a city)
  • (with Asif and Tin Wee after some beers) plans for a pre-emptive intervention system for world peace

...talk turned to bioinformatics learning, education and training, following a lively discussion session (which I will be writing about soon) involving Vicky Schneider (TGAC, GOBLET), Michelle Brazas (bioinformatics.ca, GOBLET), a quartet of COMBINErs, and a roomful of enthusiasts.

So, what did we regard as the truly killer ninja skill in bioinformatics?

Was it

No.

We figured that the absolute killer ninja skill for bioinformaticians was:

the ability to learn stuff fast, and apply it well.

(OK, we may have to work on the phrasing a bit there, but it is still catchier than "metalearning".)

Like gene and protein expression, these sorts of opinions are time- and environment-dependent. However, on reflection, it speaks of one of the defining features of bioinformatics and bioscience these days: things change... fast.

...not so sure what is says about ninjas though.

Tuesday
Apr082014

Forensics, bioinformatics, and the back-of-the-briefcase effect

Professor James Curran gave a cracking seminar at the ANU Department of Statistics last week on his Adventures in Forensic Statistics.

James' talk reminded me of many things including

...that last point can be described as the "back-of-the-briefcase effect", a term coined by Mike Brown at CVAB 2013 as he recounted dialogue from some spy movie along the lines of "OK, zoom in on that briefcase... increase image resolution... close in on that some more... right, now show me the back of the briefcase."

...which makes me think of the dual-edged sword of biomolecular visualisation (though "back-of-the-nucleosome" is a little less catchy).

And as this train of thought pulls into the station for lunch, I return to the beginning by commending another of James Curran's presentations to you: Is Forensic Science the last bastion of resistance against Statistics?

Cheers,
David

Wednesday
Feb262014

Explicit is better than implicit

A warning on the issues which can come up when you're not aware of the implicit design decisions present in programming languages and libraries.

Click to read more ...