Jabberwocky Ecology

Data Analyst position in ecology research group

The Weecology lab group run by Ethan White and Morgan Ernest at the University of Florida is seeking a Data Analyst to work collaboratively with faculty, graduate students, and postdocs to understand and model ecological systems. We’re looking for someone who enjoys tidying, managing, manipulating, visualizing, and analyzing data to help support scientific discovery.

The position will include:

  • Organizing, analyzing, and visualizing large amounts of ecological data, including spatial and remotely sensed data. Modifying existing analytical approaches and data protocols as needed.
  • Planning and executing the analysis of data related to newly forming questions from the group. Assisting in the statistical analysis of ecological data, as determined by the needs of the research group.
  • Providing assistance and guidance to members of the research group on existing research projects. Working collaboratively with undergraduates, graduate students and postdocs in the group and from related projects.
  • Learning new analytical tools and software as needed.

This is a staff position in the group and will be focused on data management and analysis. All members of this collaborative group are considered equal partners in the scientific process and this position will be actively involved in collaborations. Weecology believes in the importance of open science, so most work done as part of this position will involve writing open source code, use of open source software, and production and use of open data.

Weecology is a partnership between the White Lab, which studies ecology using quantitative and computational approaches and the Ernest Lab, which tends to be more field and community ecology oriented. The Weecology group supports and encourages members interested in a variety of career paths. Former weecologists are currently employed in the tech industry, with the National Ecological Observatory Network, as faculty at teaching-focused colleges, and as postdocs and faculty at research universities. We are also committed to supporting and training a diverse scientific workforce. Current and former group members encompass a variety of racial and ethnic backgrounds from the U.S. and other countries, members of the LGBTQ community, military veterans, people with chronic illnesses, and first-generation college students. More information about the Weecology group and respective labs is available on our website. You can also check us out on Twitter (@skmorgane, @ethanwhite, @weecology, GitHub, and our blog Jabberwocky Ecology.

The ideal candidate will have:

  • Experience working with data in R or Python, some exposure to version control (preferably Git and GitHub), and potentially some background with database management systems (e.g., PostgreSQL, SQLite, MySQL) and spatial data.
  • Research experience in ecology
  • Interest in open approaches to science
  • Experience collecting or working with ecological data

That said, don’t let the absence of any of these stop you from applying. If this sounds like a job you’d like to have please go ahead and put in an application.

We currently have funding for this position for 2.5 years. Minimum salary is $40,000/year (which goes a pretty long way in Gainesville), but there is significant flexibility in this number for highly qualified candidates. We are open to the possibility of someone working remotely. The position will remain open until filled, with initial review of applications beginning on May 5th. If you’re interested in applying you can do so through the official UF position page. If you have any questions or just want to let us know that you’re applying you can email Weecology’s project manager Glenda Yenni at glenda@weecology.org.

Postdoctoral research position in the Temporal Dynamics of Communities

The Weecology lab group run by Morgan Ernest and Ethan White at the University of Florida is seeking a post-doctoral researcher to study changes in ecological communities through time. This position will primarily involve broad-scale comparative analyses across communities using large time-series datasets and/or in-depth analyses of our own long-term dataset (the Portal Project). Experience with any of the following is useful, but not required: long-term data, macroecology, paleoecology, quantitative/theoretical ecology, and programming/data analysis in R or Python. The successful applicant will be expected to collaborate on lab projects on community dynamics and develop their own research projects in this area according to their interests.

Weecology is a partnership between the Ernest Lab, which tends to be more field and community ecology oriented and the White Lab, which tends to be more quantitative and computationally oriented. The Weecology group supports and encourages students interested in a variety of career paths. Former weecologists are currently employed in the tech industry, with the National Ecological Observatory Network, as faculty at teaching-focused colleges, and as postdocs and faculty at research universities. We are also committed to supporting and training a diverse scientific workforce. Current and former group members encompass a variety of racial and ethnic backgrounds from the U.S. and other countries, members of the LGBTQ community, military veterans, people with chronic illnesses, and first-generation college students. More information about the Weecology group and respective labs is available on our website. You can also check us out on Twitter (@skmorgane, @ethanwhite, @weecology), GitHub, and our blog Jabberwocky Ecology.

This 2-year postdoc has a flexible start date, but can start as early as June 1st 2017. Interested students should contact Dr. Morgan Ernest (skmorgane@ufl.edu) with their CV including a list of three references, a cover letter detailing their research interests/experiences, and one or more research samples (a PDF or link to a scientific product such as a published paper, preprint, software, data analysis code, etc). The position will remain open until filled, with initial review of applications beginning on April 24th.

White Lab PhD openings at the University of Florida

I’m looking for one or more graduate students to join my group next fall. In addition to the official add (below) I’d like to add a few extra thoughts. As Morgan Ernest noted in her recent ad, we have a relatively unique setup at Weecology in that we interact actively with members of the Ernest Lab. We share space, have joint lab meetings, and generally maintain a very close intellectual relationship. We do this with the goal of breaking down the barriers between the quantitative side of ecology and the field/lab side of ecology. Our goal is to train scientists who span these barriers in a way that allows them to tackle interesting and important questions.

I also believe it’s important to train students for multiple potential career paths. Members of my lab have gone on to faculty positions, postdocs, and jobs in both science non-profits and the software industry.

Scientists in my group regularly both write papers (e.g., these recent papers from dissertation chapters: Locey & White 2013, Xiao et al. 2014) and develop or contribute to software (e.g., EcoData Retriever, ecoretriever, rpartitions & pypartitions) even if they’ve never coded before they joined my lab.

My group generally works on problems at the population, community, and ecosystem levels of ecology. You can find out more about what we’ve been up to by checking out our website. If you’re interested in learning more about where the lab is headed I recommend reading my recently funded Moore Investigator in Data-Driven Discovery proposal.

PH.D STUDENT OPENINGS IN QUANTITATIVE, COMPUTATIONAL, AND MACRO- ECOLOGY

The White Lab at the University of Florida has openings for one or more PhD students in quantitative, computational, and/or macro- ecology to start fall 2015. The student(s) will be supported as graduate research assistants from a combination of NSF, Moore Foundation, and University of Florida sources depending on their research interests.

The White Lab uses computational, mathematical, and advanced statistical/machine learning methods to understand and make predictions/forecasts for ecological systems using large amounts of data. Background in quantitative and computational techniques is not necessary, only an interest in learning and applying them. Students are encouraged to develop their own research projects related to their interests.

The White Lab is currently at Utah State University, but is moving to the Department of Wildlife Ecology and Conservation at the University of Florida starting summer 2015.

Interested students should contact Dr. Ethan White (ethan@weecology.org) by Nov 15th, 2014 with their CV, GRE scores, and a brief statement of research interests.

UPDATE: Added a note that we work at population, community, and ecosystem levels.

How I stay sane in science and academia: My Why File

Doing science in academia involves a lot of rejection and negative feedback. Between grant agencies single digit funding rates, pressure to publish in a few "top" journals all of which have rejection rates of 90% or higher [1], and the growing gulf between the number of academic jobs and the number of graduate students and postdocs [2], spending even a small amount of time in academia pretty much guarantees that you’ll see a lot of rejection. In addition, even when things are going well we tend to focus on providing as much negative feedback as possible. Paper reviews, grant reviews, and most university evaluation and committee meetings are focused on the negatives. Even students with awesome projects that are progressing well and junior faculty who are cruising towards tenure have at least one meeting a year where someone in a position of power will try their best to enumerate all of things you could be doing better [3]. This isn’t always a bad thing [4] and I’m sure it isn’t restricted to academia or science (these are just the worlds I know), but it does make keeping a positive attitude and reasonable sense of self-worth a bit… challenging.

One of the things that I do to help me remember why I keep doing this is my Why File. It’s a file where I copy and paste reminders of the positive things that happen throughout the year [5]. These typically aren’t the sort of things that end up on my CV. I have my CV for tracking that sort of thing and frankly the number of papers I’ve published and grants I’ve received isn’t really what gets me out of bed in the morning. My Why File contains things like:

  • Email from students in my courses, or comments on evaluations, telling me how much of an impact the skills they learned have had on their ability to do science
  • Notes from my graduate students, postdocs, and undergraduate researchers thanking me for supporting them, inspiring them, or giving them good advice
  • Positive feedback from mentors and people I respect that help remind me that I’m not an impostor
  • Tweets from folks reaffirming that an issue or approach I’m advocating for is changing what they do or how they do it
  • Pictures of thank you cards or creative things that people in my lab have done
  • And even things that in a lot of ways are kind of silly, but that still make me smile, like screen shots of being retweeted by Jimmy Wales or of Tim O’Reilly plugging one of my papers.

If you’ve said something nice to me in the past few years be it in person, by email, on twitter, or in a handwritten note, there’s a good chance that it’s in my Why File helping me keep going at the end of a long week or a long day. And that’s the other key message of this post. We often don’t realize how important it is to say thanks to the folks who are having a positive influence on us from time to time. Or, maybe we feel uncomfortable doing so because we think these folks are so talented and awesome that they don’t need it, or won’t care, or might see this positive feedback as silly or disingenuous. Well, as Julio Betancourt once said, "You can’t hug your reprints", so don’t be afraid to tell a mentor, a student, or a colleague when you think they’re doing a great job. You might just end up in their Why File.

What do you do to help you stay sane in academia, science, or any other job that regularly reminds you of how imperfect you really are?


[1] This idea that where you publish not what you publish is a problem, but not the subject of this post.

[2] There are lots of great ways to use a PhD, but unfortunately not everyone takes that to heart.

[3] Of course the people doing this are (at least sometimes) doing so with the best intentions, but I personally think it would be surprisingly productive to just say, "You’re doing an awesome job. Keep it up." every once in a while.

[4] There is often a goal to the negativity, e.g., helping a paper or person reach their maximum potential, but again I think we tend to undervalue the consequences of this negativity in terms of motivation [4b].

[4b] Hmm, apparently I should write a blog post on this since it now has two footnotes worth of material.

[5] I use a Markdown file, but a simple text file or a MS Word document would work just fine as well for most things.

Postdoc in Evolutionary Bioinformatics [Jobs]

There is an exciting postdoc opportunity for folks interested in quantitative approaches to studying evolution in Michael Gilchrist’s lab at the University of Tennessee. I knew Mike when we were both in New Mexico. He’s really sharp, a nice guy, and a very patient teacher. He taught me all about likelihood and numerical maximization and opened my mind to a whole new way of modeling biological systems. This will definitely be a great postdoc for the right person, especially since NIMBioS is at UTK as well. Here’s the ad:

Outstanding, motivated candidates are being sought for a post-doctoral position in the Gilchrist lab in the Department of Ecology & Evolutionary Biology at the University of Tennessee, Knoxville. The successful candidate will be supported by a three year NSF grant whose goal is to develop, integrate and test mathematical models of protein translation and sequence evolution using available genomic sequence and expression level datasets. Publications directly related to this work include Gilchrist. M.A. 2007, Molec. Bio. & Evol. (http://www.tinyurl/shahgilchrist11) and Shah, P. and M.A. Gilchrist 2011, PNAS (http://www.tinyurl/gilchrist07a).

The emphasis of the laboratory is focused on using biologically motivated models to analyze complex, heterogeneous datasets to answer biologically motivated questions. The research associated with this position draws upon a wide range of scientific disciplines including: cellular biology, evolutionary theory, statistical physics, protein folding, differential equations, and probability. Consequently, the ideal candidate would have a Ph.D. in either biology, mathematics, physics, computer science, engineering, or statistics with a background and interest in at least one of the other areas.

The researcher will collaborate closely with the PIs (Drs. Michael Gilchrist and Russell Zaretzki) on this project but potentiall have time to collaborate on other research projects with the PIs. In addition, the researcher will have opportunties to interact with other faculty members in the Division of Biology as well as researchers at the National Institute for Mathematical and Biological Synthesis (http://www.nimbios.org).

Review of applications begins immediately and will continue until the position is filled. To apply, please submit curriculum vitae including three references, a brief statement of research background and interests, and 1-3 relevant manuscripts to mikeg[at]utk[dot]edu.

Postdoc position in Jim Brown’s group studying the major patterns of biodiversity

There is a new postdoctoral research position available in Jim Brown’s lab at the University of New Mexico to study some of the major patterns of biodiversity. We know a bit about the research and it’s going to be an awesome project with a bunch of incredibly bright people involved. Jim’s lab is also one of the most intellectually stimulating and supportive environments that you could possibly work in. Seriously, if you are even remotely qualified then you should apply for this position. We’re both thinking about applying and we already have faculty positions :). Here’s the full ad:

The Department of Biology at the University of New Mexico is seeking applications for a post-doc position in ecology/biodiversity. The post doc will be expected to play a major role in a multi-investigator, multi- institutional project supported by a four-year NSF Macrosystems Ecology grant. The research will focus on metabolic processes underlying the major patterns of biodiversity, especially in pervasive temperature dependence and requires a demonstrated working knowledge of theory, mathematical and computer
modeling skills.

Applicants must have a Ph.D. in ecology or a related discipline.

Review begins with the first applications and continues until the position is filled. Applicants must submit a cover letter and a curriculum vitae along with at least three phone numbers of references, three letters of recommendation and PDF’s of relevant preprints and publications to be sent directly to ecohire@unm.edu attn: James Brown. Application materials must be received by July 25, 2011, for best consideration.

Questions related to this posting may be directed to Dr. James Brown at ecohire@unm.edu or to Katherine Thannisch at kthannis@unm.edu.

The University of New Mexico is an Equal Opportunity/Affirmative Action Employer and Educator. Women and underrepresented minorities are encouraged to apply.

Postdocs Galore [Jobs]

Advertisements for three exciting postdoctoral positions came out in the last week.

Interface between ecology, evolution and mathematics

The first is with Hélène Morlon’s group in Paris. Hélène and I were postdocs in Jessica Green’s lab at the same time. She is both very smart and extremely nice, oh, and did I mention, her lab is in PARIS. Here’s the ad. If it’s a good fit then you couldn’t go wrong with this postdoc.

A postdoctoral position is available in my new lab at the Ecole Polytechnique and/or at the Museum of Natural History in Paris to work at the interface between ecology-evolution and mathematics. Candidates with a background in biology and a strong interest in modeling, or with a theoretical background and a strong interest in biology, are encouraged to apply. More information is available here. Potential candidates should feel free to contact me. The deadline for application is May 8th.

The other two postdocs are associated with Tim Keitt’s lab (which I consider to be one of the top quantitative ecology groups out there).

Mechanistic niche modeling and climate change impacts

A postdoctoral position is anticipated as part of a collaborative project to develop and evaluate mechanistic niche models that incorporate geographic variation in physiological traits. The post doc will be based in Michael Angilletta’s laboratory at Arizona State University, but will interact with members of Lauren Buckley’s lab at the University of North Carolina in Chapel Hill and Tim Keitt’s lab at the University of Texas in Austin. The post doc will be expected to engage in modeling activities and coordinate lab studies of thermal physiology. Experience with mathematical modeling in C++, MATLAB, Python or R is beneficial and familiarity with environmental data and biophysical ecology is beneficial. More here.

Ecological forecasting or statistical landscape genetics

The Keitt Lab at the University of Texas at Austin seeks a postdoctoral investigator to join an interdisciplinary NSF-funded project linking ecophysiology, genomics and climate change. The position requires excellent modeling skills and the ability to engage in multidisciplinary research. Research areas of interest include either ecological forecasting or statistical landscape genomics. More here.

So, if you’re looking for a job go check out these great opportunities.

Postdoc opportunity in macroecology, quantitative ecology, and ecoinformatics

Our truly excellent postdoc, Kate Thibault, is moving on to bigger and better things heading up the mammal work at NEON. So, we’re looking for someone to join our group to do research in the areas of macroecology, quantitative ecology, and ecoinformatics.

The short job ad:

Ethan White’s lab at Utah State University is looking for a postdoc to collaborate on research studying approaches for unifying macroecological patterns (e.g., species abundance distributions and species-area relationships) and predicting variation in these patterns using ecological and environmental variables. The project aims to 1) evaluate the performance of models that link ecological patterns by using broad scale data on at least three major taxonomic groups (birds, plants, and mammals); and 2) combine models with ecological and environmental factors to explain continental scale variation in community structure. Models to be explored include maximum entropy models, neutral models, fractal based models, and statistical models. The postdoc will also be involved in an ecoinformatics initiative developing tools to facilitate the use of existing ecological data. There will be ample opportunity for independent and collaborative research in related areas of macroecology, community ecology, theoretical ecology, and ecoinformatics. The postdoc will benefit from interactions with researchers in Dr. White’s lab, the Weecology Interdisciplinary Research Group, and with Dr. John Harte’s lab at the University of California Berkeley. Applicants from a variety of backgrounds including ecology, mathematics, statistics, physics and computer science are encouraged to apply. The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Applications will be considered starting on March 7th, 2011. Go to the USU job page to see the full advertisement and to apply.

UPDATE: This position has now been filled.

Thoughts on developing a digital presence

A while ago there was a bit of discussion around the academic blogosphere recently regarding the importance of developing a digital presence and what the best form of that presence might be. Recently as I’ve been looking around at academics’ websites as part of faculty, postdoc and graduate student searchers going on in my department/lab I’ve been reminded of the importance of having a digital presence.

It seems pretty clear to me that the web is the primary source of information acquisition for most academics, at least up through the young associate professors. There are no doubt some senior folk who would still rather have a paper copy of a journal sent to them via snail mail and who rarely open their currently installed copy of Internet Explorer 6, but I would be very surprised if most folks who are evaluating graduate student, postdoctoral and faculty job candidates aren’t dropping the name of the applicant into their favorite search engines and seeing what comes up. They aren’t looking around for dirt like all those scary news stories that were meant to stop college students from posting drunken photos of themselves on social networking sites. They’re just procrastinating looking for more information to get a clearer picture of you as a scientist/academic. I also do a quick web search when I meet someone interesting at a conference, get a paper/grant to review with authors I haven’t heard of before, read an interesting study by someone I don’t know, etc. Many folks who apply to join my lab for graduate school find me through the web.

When folks go looking around for you on the web you want them to find something (not finding anything is the digital equivalent of “being a nobody”), and better yet you want them to find something that puts your best foot forward. But what should this be? Should you Tweet, Buzz, be LinkedIn, start a Blog, have a Wiki*, or maybe just get freaked out by all of this technology and move to the wilderness somewhere and never speak to anyone ever again.

I think the answer here is simple: start with a website. This is the simplest way to present yourself to the outside world and you can (and should) start one as soon as you begin graduate school. The website can be very simple. All you need is a homepage of some kind, a page providing more detailed descriptions of your research interests, a CV, a page listing your publications†, and a page with your contact information. Keep this updated and looking decent and you’ll have as good an online presence as most academics.

While putting together your own website might seem a little intimidating it’s actually very easy these days. The simplest approach is to use one of the really easy hosted solutions out there. These include things like Google Sites, which are specifically designed to let you make websites; or you can easily turn a hosted blogging system into a website (WordPress.com is often used for this). There are lots of other good options out there (let us know about your favorites in the comments). In addition many universities have some sort of system set up for letting you easily make websites, just ask around. Alternatively, you can get a static .html based template and then add your own content to it. Open Source Web Design is the best place I’ve found for templates. You can either open up the actual html files or you can use a WYSIWYG editor to replace the sample text with your own content. SeaMonkey is a good option for a WYSIWYG editor. Just ask your IT folks how to get these files up on the web when you’re done.

So, setting up a website is easy, but should you be doing other things as well and if so what. At the moment I would say that if you’re interested in trying out a new mode of academic communication then you should pick one that sounds like fun to you and give it a try; but this is by no means a necessity as an academic at the moment. If you do try to do some of these other things, then do them in moderation. It’s easy to get caught up in the rapid rewards of finishing a blog post or posting a tweet on Twitter, not to mention keeping up with others blogs and tweets, but this stuff can rapidly eat up your day and for the foreseeable future you won’t be getting a job based on your awesome stream of 140 character or less insights.

*Yep, that’s right, it’s a link to the Wikipedia page on Wiki’s.
†And links to copies of them if you are comfortable flaunting the absurd copyright/licensing policies of many of the academic publishers (or if you only published in open access journals).

Postdoctoral position in macroecology, quantitative ecology, and ecoinformatics

We have a postdoc position available for someone interested in the general areas of macroecology, quantitative ecology, and ecoinformatics. Here’s the short ad with links to the full job description:

Ethan White’s lab at Utah State University is looking for a postdoc to collaborate on research studying approaches for unifying macroecological patterns (e.g., species abundance distributions and species-area relationships) and predicting variation in these patterns using ecological and environmental variables. The project aims to 1) evaluate the performance of models that link ecological patterns by using broad scale data on at least three major taxonomic groups (birds, plants, and mammals); and 2) combine models with ecological and environmental factors to explain continental scale variation in community structure. Models to be explored include maximum entropy models, neutral models, fractal based models, and statistical models. The postdoc will also be involved in an ecoinformatics initiative developing tools to facilitate the use of existing ecological data. There will be ample opportunity for independent and collaborative research in related areas of macroecology, community ecology, theoretical ecology, and ecoinformatics. The postdoc will benefit from interactions with researchers in Dr. White’s lab, the Weecology Interdisciplinary Research Group, and with Dr. John Harte’s lab at the University of California Berkeley. Applicants from a variety of backgrounds including ecology, mathematics, statistics, physics and computer science are encouraged to apply. The position is available for 1 year with the possibility for renewal depending on performance, and could begin as early as September 2010 and no later than May 2011. Applications will begin to be considered starting on September 1, 2010. Go to the USU job page to see the full advertisement and to apply.

If you’re interested in the position and are planning to be at ESA please leave a comment or drop me an email (ethan.white@usu.edu) and we can try to set up a time to talk while we’re in Pittsburgh. Questions about the position and expressions of interest are also welcome.

UPDATE: This position has been filled.

Post-doctoral fellowship in ecology and/or natural resource management

It’s probably not really to our benefit to be advertising competing positions when we’re currently looking for a post-doc ourselves, but this is a great opportunity so I thought I’d pass it along. The Department of Wildland Resources at Utah State has a post-doctoral fellowship available to work with one (or more) of it’s faculty. It is available to work with anyone in the department, but I would recommend checking out the labs of Peter Adler (plant community ecology) and David Koons (population ecology). I’ve worked with Peter and interact regularly with both Peter and Dave. They are both smart, young, enthusiastic faculty and you couldn’t go wrong working with either of them. Here’s the full ad:

The Department of Wildland Resources at Utah State University is offering a post-doctoral fellowship in ecology and/or natural resource management. Applicants must contact a sponsoring scientist from within the department’s faculty (http://www.cnr.usu.edu/wild/htm/faculty-staff) and then jointly develop a one-page research proposal. Applications are due April 1, 2010. Duration of funding is one year, renewable to two years subject to satisfactory performance and continued availability of funds. The salary is $40,000 in addition to the standard benefits package for USU employees. Contact Johan duToit (johan.dutoit@usu.edu) for more details on the application process.

Faculty position in experimental conservation ecology

The Community and Conservation Ecology group at the University of Groningen in the Netherlands, has a job opening for a tenure track assistant professor in Experimental Conservation Ecology (details below). This is a very impressive group that is headed by Han Olff and includes Rampal Etienne and David Alonso. I’ve worked with all three of these folks and I have no doubts that working in this group would make for a very intellectually stimulating environment. So, if you’re interested in moving to the Netherlands, check out the ad below and put in an application.

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