Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Programming

Dobrý večer! from Cesky Krumlov, Czech Republic! Ok that's enough Czech from me...

Section 8: Programming

So BioPerl and (I'm going to plug BioPython in here too--see below, PyCogent) are basically what they sound like, perl codes/scripts/modules (however is easier for you to think about it) and python code (Perl and Python being programming languages) geared toward applications in biological analysis.

Now my husband is a programmer turned bioinformatic programmer and his best advice is to jump right in and just keep using it. My main concern with that...aside from my inability to manifest a 36 hour day that would allow me to take on learning a computer langauge...is I don't use it every day in my job. This makes it difficult to say the least to retain all the commands in your head and even then--when in doubt 'Google!' The links above, the BioPerl one being suggested in the preparation materials for the workshop and the BioPython will give you an idea of the modules/programs that have been constructed using those languages and provide more links if you want to get further into the mire and meld programming with biological analysis. You will have to learn some basics of the language itself before jumping into the biological application of it just for functionality's sake.

Now that's all I'm going to say for the moment, but we'll come back to this...my husband who was trained as a computer scientist and is a programmer who just recently got thrown into the world of biology head first and is now programming (using Python) for bioinformatic analysis has a python tutorial and some advice to dispense to you all who aspire to move in that direction...but he has to write it up.

In the meantime, one thing you absolutely need to get comfortable with is the ominous black box called command-line. You simply have to learn how to navigate around your computer in command-line interface. The conference organizers have provided a helpful tutorial so we are going to go through that and I'll add as we go based on my own trial and error experiences.

Blog Series: Workshop on Genomics; Cesky Krumlov; Preparation--Metagenomics

Section 7: Metagenomics

Metagenomics is a massive topic! My first encounter with metagenomics was in my Ph.D. work; metagenomics of a hot spring microbial community (we focused on two hot springs in Yellowstone National Park).

For the purposes of this workshop 2 readings and a PubMed search are suggested:

1. Wooley, JC; A Godzik and I Friedberg. 2010. A primer on metagenomics. PLoS Computational Biology 6:e1000667. (open access and a good read)
2. QIIME PubMed Search
3. Knights, D; EK Costello and R Knight. 2011. Supervised classification of human microbiota. FEMS Microbiology Reviews. 35:343-359. (not open access, subscription required).

Essentially, metagenomics focuses on all, or as many as can be detected using todays methods, of the organisms within an environment (usually unculturable organisms are the 'target'). That's not to say you can't 'create' an environment in the lab that hosts several known or culturable organisms and do a metagenomics study on that, but most of the research has been done on 'in vivo' environments such as hot springs, the ocean, acid drainage sites, and humans...to name a few. Dr. Rob Knight's lab at UC Boulder, CO for instance has been involved in quite a bit of work in metagenomics as it pertains to humans and environmental bacteria. One of the papers, aside from the one above, which alas is not freely available either is quite nice and focuses on human gut microbiota (Lozupone, CA et al., 2012. Nature).

Looking for more open access pubs with a focus on microbiomes/metagenomics?

• Tito, RY et al., 2012. Insights from characterizing extinct human gut microbiomes. PLoS One. 7:e51146.
• Zupancic, ML et al., 2012. Analysis of the gut microbiota in the older order Amish and its relation to the metabolic syndrome. PLoS One. 7:e43052.
• Gevers, D et al., 2012. The human microbiome project: a community resource for the healthy human microbiome. PLoS Biology. 10:e1001377 .
• Harris, K et al., 2013. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 7:50-60 
• Yatsunenko, T et al., 2012. Human gut microbiome viewed across age and geography. Nature. 486:222-227.

Nature Reviews also has a focus on metagenomics that might be useful in finding more studies across fields in this subject, though I cannot guarantee what's open access and what's not.

QIIME = Quantitative Insights into Microbial Ecology. It's a software package (refer to disclaimer about software!) that assists in the analysis of microbial communities and focuses on data generated via high throughput sequencing methods.

Personal Opinion...it's pretty cool. Unfortunately it's not approved at WRAIR...yet.

Jesse Stombaugh from the Biofrontiers Institute (UC Boulder, CO) has some nice slides that show some of QIIME's analysis. Slides 14-19 show you the QIIME workflow. Additionally if you find microBEnet a group that focuses on microbiology of the Built Environment on youtube, they have several videos detailing how to use QIIME.

Or if you're the type of bioinformatic cowboy to just jump into the program itself, check out the QIIME website. If you're a programmer, python is useful to know but not totally necessary if you end up getting into the nuts and bolts of the software. For those of you going python-wha??? See next section on programming which will talk about BioPerl and some Python.

Alright fellow aspiring bioinformaticians...my last prep blog will probably come in the Czech Republic as I head out tonight, then we'll be jumping right into the workshop!

Next Up: Preparation--Programming