Blogs I follow, for those who are now addicted to Science-y blogs...

So it was requested of me to post what blogs I personally follow so I will list them below.

As I said in the first blog for the series in Cesky Krumlov...I most likely will let this blog go dormant until I have something useful to say, but for those of you who would love to get daily musings from other scientists in the field who post of a semi-regular/daily basis let me wett your appetite for what's out there and you can search on your own too.

Normally I subscribe via RSS/Google reader. If you have google reader and there isn't an RSS subscribe button on the blog simply copy/paste the URL into google reader and it'll subscribe to what's posted at the URL.

Happy Reading!

1. Aetiology: discussing causes, origins, evolution and implications in human disease (Tara Smith)
2. Avian Flu Diary: infectious disease hobbyist, influenza and disaster preparedness
3. Xkcd: comic on physics, math, science--pretty much geeky fun.
4. What If: same guy as xkcd but answers questions using math, science, physics etc...in the most awesome geeky way possible.
5. The tree of Life: Jonathan Eisen's blog about microbes, genomes, omics, UCDavis and the tree of life
6. BacPathGenomics: genomics and evolution of bacterial pathogens
7. coastalpathogens: blog about coastal pathogens among other things.
8. This is NOT Junk: Michael Eisen's blog (equally great) about DNA, evolution, open science, genomes etc.
9. Daniel Wilson's blog: evolutionary biologist and researcher in genetics
10. Download the Universe: book reviews that include science books, focused on e-books
11. DrugMonkey: US biomedical research industry blogger
12. iMicroBham: Science teaching blog
13. microBEnet: microbiology of the built environment
14. Microbiology Bytes: latest news about microbiology
15. Omics! Omics!: A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.
16. Outbreak News: news on outbreaks all over the world
17. Pathogens: Genes and Genomes: A heady mix of bacterial pathogenomics, next-generation sequencing, type-III secretion, bioinformatics and evolution!
18. PLoS Blogs Network
19. Rob Dunn: Wildlife of our bodies writer/biologist
20. Science Professor: life of a science professor
21. Science-Based Medicine: Issues and controversies between science and medicine
22. Science Hubb: A blog about interesting science
23. SEQAnswers.com
24. Seqonomics: economics of personalized medicine from a Sanger Inst. researcher
25. Small Things Considered: Amer Soc of Micro blog on microbiology, virology and parasites
26. The febrile muse: portrayal of infectious disease in literature and arts
27. The medicine show: Forbes blog from Matthew Herper on Science, politics, education etc.
28. The molecular ecologist: blog on molecular ecology (all organisms)
29. Twisted Bacteria: science communicator who focuses on actinomycetes
30. Virology blog: Vincent Racaniello's excellent virology blog and podcasts
31. What's up doc?: Blog for postgraduate researchers with resources, links and advice
32. zoonotica: blog that focuses on the viral/pathogen human/animal interface
33. All creatures great and small: Preaching microbial supremecy: Science teaching blog from professor at primarily undergraduate teaching institution

That ought to get you started...

Workshop on Genomics 2013: Final musings, anecdotes, mutterings and OCD tendencies garnered...

Greetings bioinformatic campers!

Last blog from ever so idyllic Prague, Czech Republic.

It has been a long two weeks, jam packed with beer, wine, sequencing, programs like RAD and programs like CRAP--mmm, haha; fun-guys, snow ball fights, genomics, scary math, more oddly named software, tutorials galore, unix ninjas and sequencing gurus, enough 'considerations' to have us spinning for years to come...so lets rehash the glory a little bit shall we?

Of life, love, linux and latent twitching... Highlights from 2013 Workshop on Genomics, Cesky Krumlov, Czech Republic in no particular order--most of the below is in good fun, a lot intellectually was learned, see all the previous blogs! But in reflection there were some truly golden moments both scientifically and personally as those that attended and those that ran the workshop were indeed awesome like that:

Blog Series: WoG, Cesky Krumlov: Day 12: Evolutionary genomics, Sake and a program called CRAP (you can't make this stuff up...)

Well I hope everyone has been enjoying reading about the various topics discussed at this workshop. Hopefully you have some new ideas, new programs and new considerations to fuel your OCD tendencies and make you twitch at night...

And with that...our last speaker for the workshop:

Antonis Rokas
Vanderbilt University
Nashville, TN

Topic Evolutionary Genomics

So, given we've been on high octane genomics using NGS for 11 days straight Antonis was merciful to us for this last talk and after a brief introduction to evolutionary genomics gave us some 'vignettes from the field' on the topics of comparative functional genomics, populations genomics and phylogenomics.

The progress of our understanding and study of genomics is no different than other fields historically. In geography old maps would have you falling off the end of the world (cause you know it's flat right?). Then as we became more informed about our world (and it helps that explorers didn't fall off the end) our maps evolved and today we have google maps, google view, google directions...yes, be comforted in knowing....google is always there...watching....you.

During our infantile understanding of chemistry--it was alchemy and you can imagine all the shenanigans that must've taken place as people desperately attempted to heal in a time of limited medicine, limited understanding of the human body and of disease in general--so they turn to herbs and 'potions' and did many things that ended up more harmful than helpful. Now there's a pill for everything...and then some!

When the first genomes were sequenced it was much the same thing...ok, we have a genome--now what. Some people though that discovering the genome and putting it together would decode the 'language' of life...not so much. In our process of understanding a genome, we conduct assembly, gene/ORF finding, assignation of motifs and regulatory areas if possible. Understanding genomes also requires theory just as differences in anatomy suggest adaptation in animals and similarity suggesting common origins; so is it with genomes. Similarity suggesting common origins and differences in sequence suggesting adaptation. Genomes provide a common 'yardstick'.

Blog Series: WoG, Cesky Krumlov: Day 11: Functional metagenomic modeling with some Drosophila sperm thrown in for good measure...

Joseph Bielawski
Dalhousie University
Halifax, Nova Scotia, Canada

Topic: Searching for functional divergence in genomes and metagenomes

We are going to start off with the metagenomic portion of the talk first then at the bottom we'll hash out the genomic portion of his talk...

So in conducting research in metagenomics, as we learned from Rob Beiko's talk it's about who is there and what are they doing. Today we focused on how to infer function from metagenomic data. How to tack on phenotype to a metagenome 'genotype' if you will.

So you have two approaches in metagenomics: targeted analysis (ala PCR amplification from the environment using universal primers to catch all the organisms with your gene of interest) and random analysis which is a catch-all for everything you got within your sample. Now it's always great to have apriori knowledge and you are highly encouraged to collect as much metadata as possible about your sample...but inferring function from metagenomics is quite daunting especially if you have little to go on so it helps to have a model.

Now models are by no means going to fully explain exactly what's going on in the actual environment but they allow you to make inferences based on your data that you can explore in further detail and corroborate.

The model we will discuss actually doesn't have a name that I could find within his slides! So I will call it MetaG-MetaP-Modeling (MMM)...metagenomic metabolic pathway modeling. Bear in mind when the publication comes out it'll have most likely a cooler name.

Blog Series: WoG, Cesky Krumlov: Day 10: How beavers and black queens teach us about Metagenomics...

Robert Beiko
Dalhousie University
Halifax, Nova Scotia, Canada

Topic: Metagenomics

So the term 'metagenomics' was coined by Jo Handelsman in 1998. Metagenomics describes the functional and sequence based analysis of the collective microbial genomes contained in an environmental sample.

• This rather 'pure' definition excludes PCR based metagenomic studies as they only provide information about one gene.

The beaver gut is an example of a microbial community hard at work digesting the wood the beaver eats. Unfortunately, as I learned anew today...that microbial community is apparently also nom-i-licious and also gets digested at some point. Sucks to be them. But given turnover the cycle continues, the wood is digested and the balance of nature maintained. Still sucks to be a bacterium in the beaver gut...I gotta say.

Metagenomics asks two essential questions:

1. Who is there?
2. What are they doing?

TANGENT!: Comparison Charts for NGS Platforms 2013

If you are thinking about buying an NGS platform...

Travis Glenn has released the 2013 tables comparing NGS platforms seven ways from Sunday, so you can make an informed decision.

I found them on a blog I follow: www.molecularecologist.com

Table 1a-c: de novo, resequencing and other applications. NGS Platform grades.

Table 2a: Runtime, reads and yield

Table 2b: Costs/run, Costs/MB, minimum costs

Table 3a: Instrument Costs

Table 3b: Computation Resources

Table 3c: Error Rates

Table 4: Advantages and disadvantages of each instrument

Citation: Glenn, TC. 2011. Field Guide to Next Generation DNA Sequencers. Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2011.03024.x

Blog Series: WoG, Cesky Krumlov; Day 9: A Tale of RAD-taggin Sea Drag-ins

Dr. Bill Cresko
University of Oregon
Sensei of the Unix Ninja

Topic: Genomic analysis of non-model organisms, RAD-tags and STACKS

Greetings!

So today we launch into how to analyze critters that do not contain a reference genome or have relatively few annotations associated with their genome, the proverbial black box we bang our heads against.

What is a non-model versus model organism anyway?

Model organisms have 'an entire community trying to dissect one species usually in an effort to understand humans better.' The mouse is a model organism, E. coli K12 is a model organism.

Non-model organisms are studied by relatively few, don't contain good references usually and have no correlation to research going on in humans; meaning they don't necessarily further our knowledge of processes in humans.

However, despite not having the breadth of knowledge that model organisms have--the literal arsenal of annotations--we still have the same questions about non-model organisms as we do with model organisms!

1. How do major differences among lineages evolve
2. What is the relatedness between organisms?
3. What is adaptation like in these organisms?

There are fundamental processes in evolution:

1. Origin of genetic variation: via mutation and migration
2. Sorting of that variation: variation can be affected by genetic drift and natural selection for instance. For those drawing a blank on 'genetic drift'...it is the change in allele frequency over generations...for those of you drawing a blank on 'allele'...an allele is essentially a gene or better yet a specific 'version' of the gene. So one gene can have more than one 'flavor'. An allele is a particular flavor of that gene as determined by it's sequence data.  For those of you drawing a blank on gene...click over to the nyan cat you tube video--be entertained and don't come back to this blog until you know what a gene is.
3. Simultaneous genotyping of neutral and adaptive loci (for population genomics): neutral loci provide a genome wide background that gives you estimates of effective population size and can be used for phylogeography. Adaptive loci are outliers from the neutral background and can lend insight into selective sweeps or local adaptation.

So the naive solution when approaching a project with a non-model organisms is to just 'sequence everything'. Why? Because sequencing is still quite expensive and for many studies is pretty much a waste.

Genomes are generally organized as linkage blocks so essentially as long as you have well spaced markers that will work just as well for genotype for a fraction of the cost. Having genetic maps are very useful in genome studies and often times a great first step to guide you in whether full genome sequencing really needs to be done to answer the scientific question you have.

So the Cresko lab is heavily involved in an alternative approach that exploits these linkage blocks in the genome. It bypasses the need for a full genome and still provides tons of data about the genome in addition to building a genetic map and doing genotyping that can guide further studies/hypotheses.

The technique is called RAD-tags, the program/pipeline is called STACKS and the 'grand architect' our resident Unix Ninja--Julian Catchen.