MICROBE 2018 recap - Bioinformatics - Comparison of Metaproteomics Tools

So Dr. Pratik Jagtap is from my current stomping grounds...Minnesota. He's a research assistant professor at the University of Minnesota, Minnesota Supercomputing Institute (MSI). His work focuses on tool development for proteomic analysis specifically for Galaxy-P and he has an impressive array of publications in the field. His latest 2018 offering:

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

Stalking his twitter account it is chock full of great links to studies and research being conducted in the are of proteomics so if that's a field of interest to you I recommend you follow his account.

In this particular presentation he was investigating the latest metaproteomic software offerings and evaluating their performance with an oral microbiome set courtesy of Rudney and colleagues 2015. He wasn't specific as to which Rudney 2015 article but I'm guessing it's this one - which appears to have links to fastq datasets from an oral microcosm study. Or it could be this publication from 2015 which Rudney is on, but not first or last author which talks about an oral microbiome dataset used specifically for Galaxy P, though I cannot be sure because the article is paywalled.

Comparison studies in bioinformatics are always informative because it sets down metrics by which we can start using to interrogate these programs and evaluate which ones are best for our experimental design, which are potentially flawed, what are the pros and cons for each such that we can justify their use or exclusion in our studies.

Want more Training in Bioinformatics?

More Training Opportunities, courtesy of Dr. Stephen Turner...

Dr. Stephen Turner runs the Getting Genetics Done Blog which has a lot of great posts regarding bioinformatics; general news, software developments and training. It's linked also over to the left as one of the blogs I follow.

He has compiled an extensive listing of Bioinformatics Workshops and Trainings which includes training programs, MOOCs (online courses/modules), workshops, short courses, literature, recommended reading and useful blogs.

It's worth a look.

Cheers,
Mel

---

Melanie Melendrez, Ph.D.

Contractor--CNTS

Chief, Bioinformatics, Lead Scientist

Walter Reed Army Institute of Research

Viral Diseases Branch

Silver Spring, MD 20910

melanie.c.melendrez.ctr@us.army.mil

Still Here...new series of blog posts coming

Greetings to my 6 followers and many others who peruse this blog via google, facebook or other link.

Rest assured I have not fell off the planet; the purpose of this blog was to be a communication, teaching, disseminating tool for when I attend workshops, conferences, develop courses or read literature. Indeed apparently I don't travel as much as some in terms of conferences and workshops so I've had little write about...

That and I got swept away in the bid for grant funds available at my institution...was successful--HUZZAH, 4th year of trying was the charm apparently and now am in the thick of my own research as well as what I do on a daily basis as the Viral Diseases Branch bioinformatician.

However following the Workshop on Genomics this last January (and coming up again this January) I have been teaching a basic class on bioinformatic sequence analysis and recently attended a meeting on the NIAID - Dengue Vaccine Initiative.

Blog Series: WoG, Cesky Krumlov; Day 1: Introduction

Greetings!

Day 1: Introductions, Reasons, Rationales and Methods to the Madness amounting to the creation of this workshop.

So last night we had the opening reception where everyone was able to meet; it is quite the diverse crowd but I simply had to corner Scott Handley and ask the question I'm sure he gets several times over--so much so that he's got slides worked into his introduction presentation talking about how the workshop came about and how it ended up in an isolated idyllic town 3 hours south of Prague.

Scott and his colleagues have been hosting workshops for several years now. Originally he'd attended, then TA'd for the workshop out of Woods Hole, MA which focused on molecular evolution. A workshop I tried for many years to go to as a graduate student, but alas was unable. But from others I have heard over and over how amazing of a workshop it is and therefore I highly recommend you look into it if that's the direction you'd like to go in your research. From a Woods Hole start they commenced doing workshops in other areas such as doing one for the CDC in Atlanta at the Smithsonian as well as Fort Collins, CO. Then they decided to do one in Europe and in the course of their research and contacts, found Cesky Krumlov. Cesky Krumlov was ideal--it had infrastructure for computer analysis (internet, ability to charge laptops easily), it was beautiful and different, but not so exciting that you'll miss classes to 'see the sights', and inexpensive. The workshops pay for themselves via the registration fees, there is no  outside grant that covers workshop costs here. If they get enough registrants the workshop is on, if not it's cancelled. So far attendance has been good and the workshops have all been rewarding experiences for all involved-so they've continued to host them.

Through the course of our conversation it came up, the rationale for this kind of workshop. When they first hosted the genomics workshop most of their attendees were PIs that had just gotten next generation sequencing capabilities and now had all this data they had no idea what to do with. Now in it's third year the attendance has moved more toward graduate students and postdocs who now are wrestling with mass quantities of data produced in their labs. He used the analogy of a tidal wave of data, easily overwhelming anyone in its path. There are simply not enough folks with the training and skills to manage and analyze this deluge; hence the workshop on genomics was borne.

Another topic of consideration is the value of continuing education in our field. Many times family members are asking me 'what? you're taking classes?...didn't you get your Ph.D.? Aren't you done with school already!?' Quite frankly in our line of work, the 'schooling' never stops, when it does, your career will be dead. If you are not moving as fast or at least attempting to catch up with your field through continual reading, workshops, collaborations, short courses, conferences...then you will become a relic before your career even starts. In the past it took 30 years to become a relic in biological research--then they invented high throughput sequencing--curses! Now if you don't keep up you can be easily outdated within a year--a year! Not only that, but it takes a skill set in order to conduct bioinformatic analysis, a skill set that has be learned flexibly so that it can easily and quickly change and adapt as the technology does. And it takes time to learn that skill set and perfect it's flexibility, so you have to invest that time (and money) to seek out those opportunities that allow you to grow and learn with the field.

Often times I think researchers have the impression that once the laboratory experiment (as in, wet lab) is run that the hard part is truly over. Not so much. Bioinformatics is not a 'magic black box' you push data into and out comes the next Science paper. Utilizing software, writing code, implementing bioinformatics is an experiment in and of itself. It can malfunction, you can put the wrong 'reagents' (Parameters) into it causing you to have to re-do it, it can break altogether, you can set up the experiment incorrectly and the computer gives you garbage back--after running for 48 hrs--doh!!! In silico computer based 'experiments' can take just as long or even longer to obtain results from as any laboratory experiment and more and more there should be a growing respect for this in the field. Quite frankly, though things are moving faster--they are still going to take as long as they take. And believe me I scream and yell at the computer runs as much as any gel or culturing experiment--both can take days and days to run, only to find our you missed one small crucial point and now have to start all over. SO, have the same patience and respect for bioinformatics as you would any wet lab experiment, believe me--it'll save you frustration, anxiety and exhaustion in the long run.

And that's just getting to the point of getting output from your computer experiment...

Now you have to figure out if the result makes sense or if you goofed and have to troubleshoot. See, no different than the wet lab. Honestly, sometimes I wish I could fix the problem with duct tape, new wiring, cleaning the system and tubing as opposed to having to glean through hundreds of lines of code or parameters to find the misplaced semi-colon! In the lab you visualize everything on your bench, in bioinformatics, it's all in your head, in the computer software (be it code or software parameters) and of course 500 little sheets of paper littering your desk with the schematics and flow of what you are doing or trying to do at each computational step.

Continuing education? Best thing ever.

Ready, set, sequence! Read on for todays highlights...

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

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--GMOD/Gbrowser

Section 6: GMOD/Gbrowse

GMOD was set up to be a kind of community for biologists to allow them to focus on research and 'the science' if you will instead of fretting over the nitty gritty application acrobatics they need to implement to obtain useful information from their data. It is a series of interconnected applications and databases for scientific use.

GBrowse is a component of GMOD that is for, as you might have guessed, Genome Browsing. I did see a magic word in the description that is dreaded by many who work at institutions with enhanced security protocols...'install'. Here's where the disclaimer from the first blog entry comes in...make sure of how it installs and that you've submitted all the proper paperwork and links so that information assurance can approve and install the program. Yep, it's doubtful you'll get to install in, your IT or IA department will usually take care of that either remotely or by coming to your computer. This of course applies to all of the programs mentioned in previous blogs as well.

Other components include: Community Annotation, Comparative Genome Visualization, Database tools, Gene expression visualization, Genome annotation, Molecular pathway visualization and Blast sequence alignment...I lifted all this from the GMOD wiki, so check it out, it is also one of the suggested 'readings'.

It will be interesting to explore Galaxy and GMOD and see how and if they overlap...they seem to target the same audience but potentially with different available functionality...

The other suggested reading focuses on GBrowse: Stein et al., 2002. The generic genome browser: a building block for a model organism system database. Genome Research. 12:1599-1610.

Looks like we'll be learning about some really interesting platforms and packages of tools available. Myself, I tend to gravitate toward the web-based platforms (I'm already clicking through Galaxy) as most of the time it doesn't require a software install which reduces my work headache by leaps and bounds and spares the bottle of wine at home that would've been in danger of being drank in one swallow the minute I walked in the door!

Next Up: Preparation--Metagenomics

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

Section 5: Galaxy

This will be a short one (and the people rejoiced!).

Galaxy is an open source, web-based platform designed to assist in computational analysis for researchers. It helps in data management and contains analysis tools in the framework ranging from converting from one data format to another, manipulating fasta files, fetching sequence data, calculating statistics as well as conducting some evolutionary analyses and metagenomic analyses. It also has a link to the ENCODE projects tools.

Nuff said...to dive in see the suggested readings:

1. Goecks, J; A Nekrutenko and J Taylor. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible and transparent computational research in the life sciences. Genome Biology. 11:R86.
2. Blankenberg, D et al., Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database (Oxford) 2011:bar011.
3. J Goecks also has a slideshare up on Galaxy that shows some of the nifty graphics that can be generated from some of the tools.
4. 2 years ago David Coil put up a series of tutorials using Galaxy to visualize various datasets. Not sure how up to date the push to click operation is (Galaxy in 2010 versus 2013), but worth a view. Below is the first video in the set. David Coil actually has a nice set of videos on his profile all less than 10 min long so the commitment is minimal, see if any are of interest--most deal with sequencing and programs for analysis.

Or just hop to the website directly: Galaxy and perhaps take a tutorial on how to get started.

Next Up: Preparation--GMOD/Gbrowse

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

Section 4: Assembly

This next section deals with an introduction to assembly and assemblers. All the suggested readings are freely available which is awesome:

1. Birol, I et al., 2009. De novo transcriptome assembly with ABySS. Bioinformatics. 25:2872-2877.
2. Zerbino, DR and E Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.
3. Langmead, B. 2010. Aligning short sequencing reads with Bowtie. Current Protocols in Bioinformatics, Chapter 11, Unit 11.7.

There two general ways in which you can compile short reads to make your genome; reference mapping assembly and de novo assembly. There are benefits and caveats to both.

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

Section 3: Transcriptomics

Four readings were suggested for this section which sadly are not open access, I'll link them below and then we'll dive into some crash-course transcriptomics and explore other resources available to round out your knowledge base on the subject.

• Garber, M et al., 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods. 8:469-477.
• Pepke, S; B Wold and A Mortazavi. 2009. Computation for ChIP-seq and RNA-seq studies. Nature Methods. 6(11 Suppl):S22-S32.
• Mortazavi, A et al., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628.
• Johnson, DS et al., 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science. 316:1497-1502.

Richard Twyman writes a nice short sum up of Transcriptomics and it's applications on the Wellcome Trust site. He defines transcriptomics as the global study of gene expression at the RNA level. So now we are not only talking about genes and their nucleotides, we are now talking about what those genes are doing, when those genes are active and to what degree those genes are active and regulated. All of this is measured through various forms of RNA (mRNA, tRNA, rRNA, ncRNA, siRNA or total RNA). The type of RNA you are interested in depends on what question are you asking. Richard Twyman has assisted in many research publications involving bioinformatic analysis and his recent publications can be found on the writescience site.

In terms of more articles to sift through that explore transcriptomics you can try the OmicsGateway with subject: Transcriptomics through Nature Publishing, though I cannot guarantee they'll be open access. Alternatively you can go to BMC Genomics which has a whole section on Transcriptomics where many of the articles are open access.

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

Section 2: Genomic Structure

The prep section for genomic structure was small with two articles suggested, one of which you'll need a subscription to read; the other is freely available! Huzzah!

• Alkan, C; BP Coe and EE Eichler. 2011. Genome structural variation discovery and genotyping. Nature Reviews Genetics. 12:363-376. (subscription needed)
• Mills, RE et al., 2011. Mapping copy number variation by population-scale genome sequencing. Nature. 470:59-65. (FREE!)

So lets jump into Mills et al. and learn something...the one caveat to this article is they automatically assume you know what a 'structural variant' is and they are specifically talking about this with respect to the human genome. So lets back-track a little--skim if you're already a structural 'pro'...or better yet, add your two cents in the comments along with other links to clarify this topic.

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Modern Genome Sequencing Technology

Given the workshop will be moving quite quickly the organizer(s) suggested for those of us with less background to do some reading up in certain topics which they outline and include links to on the website in a section called Preparation.

This page, with respect to the workshop on genomics, is broken down into sections. Total there are a suggested 23 readings or websites, unfortunately many (11 of 23) of the links, you have to have a subscription to view the articles beyond the abstract; which unfortunately I do not have and my institution has limited subscriptions; besides most of my preparation is being done at home where I would't have access to the institutional subscriptions anyway. I'll be going section by section with the papers linked and offer some additional suggestions for those unable to access articles due to lack of subscription.

Time for a Tutorial...or how about 10

Greetings, Salutations and Happy New Years Eve!

So I have decided to run a 'live-blog' starting January 7, 2013 with the expressed intent of conveying whatever I learn to you--the blog reader.

For those unfamiliar with who I am, you can read my byline: aspiring infectious disease ecologist. I am currently a bioinformatician at Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. My educational background is quite varied and if that interests you click over to my LinkedIn Profile which also has a list of my recent scientific publications.

Crib Sheet Bio: Grew up everywhere...ended up in Hawaii and graduated from Maui High School in 1997. I did my undergraduate degree at Pacific Lutheran University in Tacoma, WA--Major PreMed/Biology and Spanish Language and Literature, graduated in 2001. Worked for a plastic surgeon 2 years back in Hawaii then promptly opted out of medical school and in 2003 entered into a Ph.D. program in Ecology and Environmental Sciences at Montana State University in Bozeman, MT (microbiology focus; Advisor Dr. David M. Ward, Land Resources and Environmental Science Dept). I graduated in 2010 and immediately started a post-doctoral fellowship courtesy of the National Research Council in Bangkok, Thailand at the Armed Forces Research Institute of Medical Sciences (AFRIMS; Advisor: Dr/MAJ Richard Jarman, Virology Dept). In May 2012, I was offered a position at WRAIR helming the massive amounts of sequence data being generated through the introduction of their 454 Roche FLX and Ion Torrent sequencing platforms. We may also be obtaining a MiSeq at some point as well. So I am currently running the gauntlet of various sequencing technologies and implementing bioinformatic pipelines developed in-house as well as utilizing the best of what academia has been able to offer in terms of open source software. I am also coincidentally (or not so coincidentally perhaps) a 2013-2014 ASM/BWF Science Teaching Fellow, so as you might surmise--I enjoy research and teaching and aspire to an academic posting in the future.

My current research muse is dengue virus. Specifically, dengue virus quasispecies characterization and dynamics over time and space. I have also worked on sequence data from thermophilic Synechococcus spp. bacteria, influenza A (pH1N1, sH1N1, H3N2), influenza B (Yamagata and Victoria lineages) and Hepatitis E virus. 

WRAIR as well as other military institutions have certain restrictions on what software can be installed and there is a lengthy approval process to ensure information assurance policies are followed. For that reason, those of you following this blog may not be able to immediately use the software, pipelines or even access certain internet links. Fear not, I feel you pain. I will make every attempt to make sure links I provide will allow you to access the information no matter where you are at. This means I will provide links to the sites where you can find downloads for academic open source software, I will not be providing actual downloads through this blog (see disclaimer).

DISCLAIMER: Please do not attempt to install any software discussed on this blog without prior authorization and approvals if you work for an institution with enhanced security policies in place. 

This disclaimer will appear at the top of any blog post that contains links leading you to software download sites to remind you to be aware; annoying but necessary. If you work at WRAIR and need assistance with the approval process, please contact me directly. If you work elsewhere, please check the regulations of your institution for guidance on policies regarding software downloads, installation and implementation.

I am not a professional science blogger so apologies if the the prose is less than polished. As you also probably noticed, I opted for the fantastically bland and ever-so boring 'simple' display for this blog, but that was by design. I plan on conveying as much material (text, links, diagrams etc.) as possible and want that to be the highlight of this blog as opposed to fancy displays which can get distracting for me. I have always been the girl who gravitates to shiny objects--great for picking up pennies, not so great when I am attempting to focus.

The field of bioinformatics can be quite daunting for those with little or no background in computational biology. Bioinformatics is also a catch-all for all the specialized fields within the discipline. For instance, there are researchers who only focus on whole genome sequencing and comparision studies, others deal primarily in transcriptomics/proteomics, still others are metagenomic analysts. Additionally, those in the field of epidemiology have their own bioinformatic analysis packages; not to mention all the bioinformatic programmers who create the packages and pipelines used today. Personally, I have experience with whole genomes, single and multiple gene analyses, microbial/viral evolution analysis and some metagenomics. I have dealt with sequence data derived from sanger and next generation sequencing platforms. I don't program beyond shell and bash scripts, though I have some working knowledge of python and R (stats package) but I only program when I have to and my knowledge of transcriptomics is minimal; hence the attractiveness of the workshop I will be blogging about. The field itself moves at lightening pace and it is not unusual to feel as though you are in a constant state of 'catch up'. Just when you acquire useful knowledge, it suddenly becomes 'outdated'. This can prove to be an immense frustration.

The goal of this blog is to provide, hopefully, practical tutorials and resources on things I learn in real-time and to serve as an archive...it helps to have decipherable e-notes readily available. I also desire to make what I do more 'accessible' to other investigators who would like to manhandle their own data (or have a grad student or technician learn how to do it) instead of waiting several months for a potentially incredibly busy bioinformatic collaborator to get back to them. I am going to sheepishly raise my own hand on this as I have reports and data to get back to collaborators myself in addition to my own research and routine obligations at WRAIR. Granted I only started 7 mos ago, so I'll catch up--BUT it is easy to get bogged down, so let's dispense some knowledge and hopefully lighten everyone's load! The only way I personally learn things is to keep copious notes and re-write/view them in different ways--we'll see how this works out.

Blog Series #1: Workshop on Genomics, Cesky Krumlov, Czech Republic, 7-18 Jan 2013.
First Blog: 7 January 2013
Last Blog: 18 January 2013
Assumed Audience: Investigators, students, technicians who know what sequencing is, what a nucleotide is, what an amino acid is and if I showed them 'ATGC' and 'AUGC' they know what both are. Background in software packages, evolutionary or genomic analysis and programming would be helpful but will not be assumed. So for some this may be a little more of a hand-hold than you might like--feel free to skim. 

I have obtained approval to 'live blog' this workshop from Dr. Scott Handley, many thanks!

I will post a preparation blog prior to officially starting on 7 Jan 2013. Blog posts will arrive in the evening as I cannot blog what I have not learned!

Comments and questions are welcome, what I cannot answer I will ask someone at the workshop--please identify yourself in your comment if you don't use a profile, I'm not a fan of anonymous posting and will not bother to answer/reply to anonymous posts.

Following the workshop, I cannot guarantee how often posts will appear as I stated earlier; I'm not a science blogger really, but feel free to subscribe and then you'll get a notice when postings do happen. You will probably only see postings on this blog site when I feel I have something functionally useful to convey or I am attending a workshop where I have organizer permission to live-blog or a conference.

Ok! For those of you without 2 weeks to spare to flit off to the Czech Republic to learn the latest and greatest in genomic analysis, care to join the journey and have a somewhat 'virtual-workshop' experience?

Excellent, I wish us both luck then.

Kind Regards,
Mel
---
Melanie Melendrez, Ph.D.
Contractor-CNTS
Chief, Bioinformatics, Lead Scientist
2013-2014 ASM/BWF Science Teaching Fellow

Walter Reed Army Institute of Research

Viral Diseases Branch

Silver Spring, MD 20910

melanie.c.melendrez.ctr@us.army.mil

mmelendrez@gmail.com