I am renewing my efforts to blog and tweet after about a 9 month hiatus aka “starting my tenure-track gig.” I thought I’d write up some of the activities that I have been up to. Moving to the awesome Ames, Iowa Despite our trepidation, my husband and I have really enjoyed Ames so far (note that I have been here over a winter, which there are no kind words for). We’ve found good food, sufficient beer, a lot of green space, and super nice people. There is hardly any traffic. We’re about a 20 minute walk to Iowa State campus.... Read more...
I went through an exercise this weekend trying to think of the questions I ask myself when designing sequencing-based experiment to describe microbial communities. I am finding myself in many collaborations where I have to answer these questions with investigators with little to no experience with sequencing and its opportunities and limitations. I thought I’d put it here for some feedback from the universe. Should you even perform/use/initiate sequencing What is your research question? What is your budget? What are your resources? Samples? Computational? Do you have a hypothesis – or what do you expect to see? Do you have... Read more...
Tomorrow will mark the completion of the first two (academic) weeks of my employment at Iowa State University as an assistant professor. One word summary: “WHEW!” I have been so busy that I haven’t taken some much needed time to sit down and reflect on how things are going and send an update out to friends and family…and so here it is! After two weeks in the job I’ve been working towards for 12 years…here I am. So far, I am going through these five emotions every day, to different degrees, and pretty much in this order. Excited Let’s go... Read more...
Background Hi! My name is Adina Howe, and I thank you for considering my qualifications to serve on the Steering Committee of the Software Carpentry Foundation. Software Carpentry has played a major role in my professional development, and I would argue played an integral role in my ability to fulfill my dreams as becoming a tenure-track professor. In 2008, I participated in a Software Carpentry bootcamp at Michigan State University as a postdoc. At the time, my research required some computational prowess, which frankly, I didn’t possess. SWC provided me a foundation, resources, and mentors to help me improve my... Read more...
When I was writing job applications, I wished I had some references of how others did it. So here are mine… I’m sorry I lost the solicitation for this, but it was fairly similar to this year’s solicitation. Cover Letter - I would suggest getting this down to one page if you can. Research Statement - Again, get this down to two pages if you can. I think I was rushed on this particularly application and couldn’t find the time to fuss with it. Teaching Statement CV Job Talk - I was asked to give a 90 minute talk, but... Read more...
The Next Adventure Starting in January, 2015, I will be beginning my adventure at Iowa State University in Agricultural and Biosystems Engineering. There, I’ll be leading up the GERMS lab. I cannot understate how excited I am about this and how grateful I am to have this opportunity and for the help along the way. My Plans You can read my application material on the lab website, but I summarize the gist of it here. My personal goals for this lab are simple: Use what I’ve learned to make measurable impacts on understanding and managing the microbes around us Create... Read more...
Some may have noticed a complete lack of blogging in the recent past, and this is the result of the replacement of my blogging activity with my decision to pursue a tenure track position. To make up for this absence, I spent this weekend trying to put some helpful thoughts together on my perspective of the 2014 job hunt (also see here). Prologue I started actively job-hunting in August, 2013. At the time of my application, I had two postdocs, 2 first author papers from my PhD, a few papers with collaborators, and a competitive funding record. I knew that... Read more...
The Other Story Behind “Tackling soil diversity with the assembly of large, complex metagenomes” This post accompanies our recent publication in collaboration with Janet Jansson, Stephanie Malfatti, Susannah Tringe, Jim Tiede, and Titus Brown. The paper is openly accessible on the PNAS website. There’s also been some well-written press releases that summarise the effort, and my mom told me she read these rather than the paper :) Additionally, Titus has written up a really nice blogpost about our story behind the paper, mainly from a technical perspective. This blogpost is an extension of that story from my (the postdoc’s) personal... Read more...
We’re looking for someone to join our team! If you’re enthusiastic, curious, and believe in “work hard, play hard!” – you’ll enjoy working with Kirsten and me. I’ve spent years training under Titus Brown and Jim Tiedje to become a metagenomics guru and hopefully a fabulous mentor. I want to answer challenging questions with thoughtful experimentation and with multiple approaches. This research will make a difference for our future. Interested? Apply! The official job listing A postdoctoral position is available to investigate microbial communities in agricultural soils and their impacts on ecosystem function and stability. The postdoc position will be... Read more...
I’ve been working on comparing multiple soil metagenomes and am revisiting the topic of how to compare datasets with large variations in the number of reads (e.g., sampling depth). I think its an important and often overlooked topic in metagenomic comparisons. I’ve previously struggled with this topic, and you can see some posts on here and a guest post which I’ve decided I don’t generally agree with here. The Problem - Different sampling depths If you generate 20 different metagenomes from the same soil plot, I can guarantee that they will differ in the number of reads each will yield.... Read more...
Last week, I had an opportunity to instruct a Software Carpentry bootcamp for an outstanding audience of women in science and engineering (WISE). This bootcamp was unique for multiple reasons: All participants were women – including instructors and helpers It was large (~120 students + more than 20 helpers/instructors). Each class had 40 students, 2-3 main instructors, and 6 or more helpers. There was a division of “skill” sections (beginner, intermediate, and advanced) It was specifically sponsored by NumFOCUS and J.P. Morgan both financially and with volunteers to help instruct Our collective goal for this workshop (and all others) was... Read more...
The 2013 ASM general meeting in Denver was one of the best ASM meetings I’ve attended. I thought I’d write about some of lessons learned from it. Clear leaders in analysis workflows continue to deliver One of the most useful sessions for me was the pre-meeting workshop “Metagenomic Approaches: Frontiers of Annotation and Assembly, Networking and Discovery” which should’ve been entitled “QIIME domination and then some”. More than half of the speakers are/were from Rob Knight’s lineage of awesome scientists. It was quite clear that QIIME has really “won” the game in 16S rRNA analysis and they demo-ed many of... Read more...
I’ve just returned from the EPA Air Sensors Workshop in sunny and warm Raleigh, NC (grrr…Michigan winter). I was invited out as a suggestion by my previous boss, a sequencing big-data guru. Some folks at the EPA community had heard his talk at the National Academy of Sciences and invited him out, but they got me instead. Bwahahahahah. My relationship defining talk with Big Data Initially, I was more than a little tenuous about my ability to deliver a big data talk. Reflecting back, per the norm, I was being silly. What defines a big data expert after all? I’ve... Read more...
One of my first tasks as a new postdoc at my new gig was to be the “bridge” for a soil metagenomics project between Kirsten Hofmockel’s “sequencing generation” team at Iowa State University and the “tool development” MG-RAST team at ANL. Given two months to extract, sequence, and analyze the complex diversity of soil aggregates, my role was to integrate KBase tools and to enable Team Hofmockel to deliver results at the DOE Grantee’s meeting held in February. I learned a great deal from this experience and attempt at a summary below. Preliminary non-sequencing data, replicates, and aggregates…solid experimental design... Read more...
Kevin Keegan in our group suggest the following normalization procedure to make samples more comparable (i.e., if one sample had a really good/bad sequencing run to over/under estimate resulting abundances)… (This is a reflection of what a nice guy Kevin is – he took the time to write this out for me…) Through a decade or more of struggling, researches who utilize micro-array data came to a general conclusion that high throughput abundance profiles (e.g. expression profiles from microarrays or annotation abundance profiles from generated from high throughput sequence data) should always undergo a procedure that attempts to reduce global... Read more...
I just came back from a week at Iowa State University with Kirsten Hofmockel and her fantastic group. Team Hofmockel is interested in studying soil microbial communities in bioenergy crop systems (something I know a little bit about from Jim Tiedje and C. Titus Brown). We’re combining a nice experiment that involves lots of useful biogeochemistry measurements with deep metagenomic sequencing (oh yeah…). Throw in the support of the DOE KBase initiative and my colleagues at ANL, we’ve got a lot of experts, tools, and resources in one room. (FYI - these resources are coming soon to a laboratory near... Read more...
This is part II of II discussing “How to become a bioinformatician”. You can see part I here. I spent our long holiday car trip coming up with some advice I’d give my past self when I first started dabbling in computational biology three years ago and here’s what I came up with: 1. Commit (and stop whining) You’d think years of experience of trying new things would prepare me that learning new things is hard, but I still get frustrated at how long it takes for me to become efficient at new adventures. Learning to use my computer in... Read more...
This is Part I of II of a set of blogs centered on “How to become a bioinformatician”: "”My gast was pretty well flabbered.” - Jim Butcher in Ghost Story This week my boss referred to me as one of a few foremost experts on metagenomic assembly. Huh? ::checks around room for the expert:: How did this happen? My boss knows A LOT of experts in the field. On top of this, this week, I’ve received a couple invitations to review bioinformatic papers and registered to lead a workshop on metagenenomic assembly at a major conference in my field. Heh?... Read more...
About a year ago, I was sitting on a 3 billion read soil metagenome trying to figure out how to take it from data to information, or sequencing to function. I needed some annotations! So, the not-so-brilliant bioinformatician I was, I decided to take a subset of my data, break it up into a thousand chunks, and run a BLAST and even a BLAT (because I heard this was faster) on it. Luckily, I figured that this would take another 50 years before it would finish, even for a subset. Jared Wilkening does a nice write up on computational costs... Read more...
Recently, I’ve been spending a lot of time combining overlapping short sequencing reads (100 bp) into longer sequences called contigs. Since I’m doing this without any reference genomes, this is called de novo assembly. (Here’s a really nice introduction into the subject from the University of Maryland, Primer. The datasets I’m working with are challenging in a couple unique ways. Firstly, they’re ginormous, 3 billion reads (300 billion bp or the equivalent of 75,000 E. coli genomes). This has been the subject of many of my pal and previous boss, C. Titus Brown’s blogposts, Living in an Ivory Basement). We... Read more...
Hello world I’ve been working with a lot of smart people doing useful research. There has been an increasing demand for me to discuss some of the lessons I’ve learned. Thus, the birth of this blog. Things I do I have a bit of experience with big data generation and analysis using now generation sequencing technologies. I work with microbial communities in all sorts of environments including soils, wastewater, and the human gut. Recently, I’ve developed interests in viruses that are around us. Things I’m not so good at…yet. Please bear with me on the formatting of this blog. I... Read more...