PICRUSt - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

I think that my favourite talk from the 1st International Environmental ‘Omics Synthesis Conference was the Keynote address by Jack Gilbert on the Earth Microbiome Project and other cool microbial metagenomic/metagenetic stuff. It also featured an impressively contrived acronym:

PICRUSt - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Langille MGI et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology 31, 814–821.

GOBLET - Global Organisation for Bioinformatics Learning, Education & Training

I’m at the 1st International Environmental Omics Synthesis (iEOS) Conference conference in Cardiff, which means (a) very little time for posting, and (b) a wealth of acronyms on display. A particularly notable contribution from one of the earlier sessions was GOBLET: Global Organisation for Bioinformatics Learning, Education & Training.

GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation. Its mission is to:

1. Provide a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees (including a training portal for sharing materials, tools, tips and techniques; guidelines and best practice documents; facilities to help train the trainers; and offering different learning pathways for different types of learner)

2. Facilitate capacity development in bioinformatics in all countries

3. Develop standards and guidelines for bioinformatics education and training

4. Act as a hub for fund gathering

5. Reach out to, amongst others, teachers at high schools, to bridge the gap to the next generation of bioinformaticians, and

6. Foster the international community of B3CB trainers

As well as the natty acronym, it could be quite useful.

BEDASSLE - Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology

Courtesy of Graham Coop on Twitter comes BEDASSLE: Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology.

"This is a method [Gideon Bradburd] worked on in collaboration with Peter Ralph and Graham Coop. It allows users to quantify the relative contributions of geographic and environmental distance to patterns of genetic differentiation."

This is a very solid ad hoc contrived acronym - making a word that is easy to pronounce but also (thanks to the altered spelling) easy to Google whilst not sounding too contrived. Hats off to Gideon, Peter and Graham. (I'm not really sure that I understand the connection to the logo, though!)

PURRS - Personal Unconditional Rescue Rehabilitation Re-homing Satisfactorily

Posts are a bit thin on the ground at present due to moving house and travelling around, but here’s an acronym that I came across whilst packing up my worldly goods. It’s the motto of Barbara’s Cat Rescue and deserves a mention here firstly because of it’s clear pre hoc contrived nature and, (a more important) secondly, to give a bit of extra publicity to Barbara.

PURRS - Personal Unconditional Rescue Rehabilitation Re-homing Satisfactorily

If looking after homeless animals is your kind of thing, please visit (and “Like”) Barbara’s Facebook page. Better still, make a donation!