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 (firstname.lastname@example.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.
We are very excited to announce the newest release of our EcoData Retriever software and the first release of a supporting R package, ecoretriever. If you’re not familiar with the EcoData Retriever you can read more here.
The biggest improvement to the Retriever in this set of releases is the ability to run it directly from R. Dan McGlinn did a great job leading the development of this package and we got ton of fantastic help from the folks at rOpenSci (most notably Scott Chamberlain, Gavin Simpson, and Karthik Ram). Now, once you install the main EcoData Retriever, you can run it from inside R by doing things like:
install.packages('ecoretriever') library(ecoretriever) # List the datasets available via the Retriever ecoretriever::datasets() # Install the Gentry dataset into csv files in your working directory ecoretriever::install('Gentry', 'csv') # Download the raw Gentry dataset files, without any processing, # to the subdirectory named data ecoretriever::download('Gentry', './data/') # Install and load a dataset as a list Gentry = ecoretriever::fetch('Gentry') names(Gentry) head(Gentry$counts)
The other big advance in this release is the ability to have the Retriever directly download files instead of processing them. This allows us to support data that doesn’t come in standard tabular forms. So, we can now include things like environmental data in GIS formats and phylogenetic data such as supertrees. We’ve used this new capability to allow the automatic downloading of the Bioclim data, one of the most widely used climate datasets in ecology, and the supertree for mammals from Fritz et al. 2009.
I am incredibly excited to announce that I am the recipient of one of the Moore Foundation’s Investigators in Data-Driven Discovery awards.
To quote Chris Mentzel, the Program Director of the Data-Driven Discovery Initiative:
Science is generating data at unprecedented volume, variety and velocity, but many areas of science don’t reward the kind of expertise needed to capitalize on this explosion of information. We are proud to recognize these outstanding scientists, and we hope these awards will help cultivate a new type of researcher and accelerate the use of interdisciplinary, data-driven science in academia.
I feel truly honored to have been selected. All the finalists that I met at the Moore Foundation in July were amazing as were all of the semi-finalists that I knew. I did not envy the folks making the final decisions.
So what will we be doing with this generous support from the Moore Foundation?
- Doing data-intensive prediction and forecasting in ecological systems: We’ll be focusing on population and community level forecasting as well as ecosystem level work where it interfaces with community level approaches. We’ll be using both process based ecological approaches with machine learning, with an emphasis on developing testable predictions and evaluating them with independent (out-of-sample) data. As part of this effort we’ll be making publicly available forecasts for large ecological datasets prior to the collection of the next round of data, following Brian McGill’s 6th P of Good Prediction (in fact we’ll be trying to follow all of his P’s as much as possible). There’s a lot of good work in this area and we’ll be building on it rather than reinventing any wheels.
- Increasing the emphasis on testable prediction and forecasting in ecology more broadly: Industry and other areas of science have improved their prediction/forecasting through competitions that provide data with held out values and challenge folks to see who can do the best job of predicting those values (most notable in Kaggle competitions). We’ll be helping put together something like this for ecology and hopefully integrating that with our advanced predictions to allow other folks to easily make predictions from their models public and have them evaluated automatically as new data is released.
- Tools for making data-intensive approaches to ecology easier: We’ll be continuing our efforts to make acquiring and working with ecological data easier. Our next big step is to make combining numerous ecological and environmental datasets easy so that researchers can focus on doing science rather than assembling data.
- Training: We’ll be helping build and grow Data Carpentry, a new training effort that is a sister project to Software Carpentry with a focus on data management, manipulation and analysis.
I’m very excited to be joined in this honor by my open science/computational training/data-intensive partner in crime C. Titus Brown(@ctitusbrown). I was also particularly thrilled to find out that I wasn’t the only investigator studying ecological systems. Laurel Larsen is in the Geography department at Berkeley and I can’t wait to interact with her more as we both leverage large amounts of ecological data to improve our understanding of ecological systems and our ability to forecast their states in the future. We are joined by astronomers, statisticians, computer scientists, and more. Check out the entire amazing group at the official Moore Foundation Investigators site and see the full press release for additional details about the program.
The award is being run through the University of Florida since we are in the process of relocating there, but I owe a huge dept of gratitude to the Biology Department and the Ecology Center at Utah State University for always supporting me while I spent time developing software, working on computational training initiatives, and generally building a data-intensive ecology program. Without their support I have no doubt that I wouldn’t be writing this blog post today.
So here it is, the first of the positions we’ll be advertizing as part of our move to the University of Florida. The official ad is below, but a few comments first. The position is for a student to work with me, but for those who aren’t really familiar with our groups, it’s important to note that my group works closely with Ethan White’s lab (we provide desk space that mixes the labs together, we have a single group lab meeting, etc). My group tends to attract people who like to do field work. Ethan’s tends to attract people who are more quantitatively or computationally inclined. We mix our groups because we believe that the divide that exists between quantitative and field-based approaches to ecology is bad for our science and that we need more people trained to serve as bridges between the quantitative and field-oriented worlds of ecology.
Here are some links to the papers my students have published from their dissertations to get a feel for what my students have intellectually gotten out of this environment:
PH.D STUDENT OPENING IN COMMUNITY ECOLOGY
The Ernest Lab at the University of Florida has an opening for a Ph.D student in the area of Community Ecology to start fall 2015. The student will be supported as a graduate research assistant as part of an NSF-funded project at a long-term research site (portalproject.weecology.org) in southeastern Arizona to study regime shifts (rapid shifts in ecosystem structure and function). This position will participate in data collection efforts in Arizona on rodents and plants.
The Ernest lab is interested in general questions about the processes that structure communities, with a particular focus on understanding how ecological communities change through time. Students are free to develop their own research projects depending on their interests.
The Ernest 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.
More information about the lab is available at: http://ernestlab.weecology.org
Interested students should contact Dr. Morgan Ernest (email@example.com) by Nov 15th, 2014 with their CV, GRE scores, and a brief statement of research interests.
We are excited to announce that Weecology will be moving to the University of Florida next summer. We were recruited as part of the UF Rising Preeminence Plan, a major hiring campaign to bring together researchers in a number of focal areas including Big Data and Biodiversity. We will both be joining the Wildlife Ecology and Conservation department, Ethan will be part of UF’s new Informatics Institute, and Morgan will be part of UF’s new Biodiversity Initiative.
As excited as we are about the opportunities at Florida, we are also incredibly sad to be saying goodbye to Utah State University. Leaving was not an easy decision. We have amazing colleagues and friends here in Utah that we will greatly miss. We have also felt extremely well treated by Utah State. They were very supportive while we were getting our programs up and running, including helping us solve the two-body problem. They allowed us to take risks in both research and the classroom. They have been incredibly supportive of our desires for work-life balance, and were very accommodating following the birth of our daughter. It was a fantastic place to spend nearly a decade and we will miss it and the amazing people who made it home.
So why are we leaving? It was a many faceted decisions, but at its core was the realization that the scale of the investment and recruiting of talented folks in both of our areas of interest was something we were unlikely to see again in our careers. The University of Florida has always had a strong ecology group, but between the new folks who have already accepted positions and those we know who are being considered, it is going to be such a talented and exciting group that we just had to be part of it!
As part of the move we’ll be hiring for a number of different positions, so stay tuned!
As announced by Noam Ross on Twitter (and confirmed by the Editor in Chief of Ecology Letters), Ecology Letters will now allow the submission of manuscripts that have been posted as preprints. Details will be published in an editorial in Ecology Letters. I want to say a heartfelt thanks to Marcel Holyoak and the entire Ecology Letters editorial board for listening to the ecological community and modifying their policies. Science is working a little better today than it was yesterday thanks to their efforts.
For those of you who are new to the concept of preprints, they are manuscripts, that have not yet been published in peer reviewed journals, which are posted to websites like arXiv, PeerJ, and bioRxiv. This process allows for more rapid communication of scientific results and improved quality of published papers though more expansive pre-publication peer-review. If you’d like to read more check out our paper on The Case for Open Preprints in Biology.
The fact that Ecology Letters now allows preprints is a big deal for ecology because they were the last of the major ecology journals to make the transition. The ESA journals began allowing preprints just over two years ago and the BES journals made the switch about 9 months ago. In addition, Science, Nature, PNAS, PLOS Biology, and a number of other ecology journals (e.g., Biotropica) all support preprints. This means that all of the top ecology journals, and all of the top general science journals that most ecologists publish in, allow the posting of preprints. As such, there is not longer a reason to not post preprints based on the possibility of not being able to publish in a preferred journal. This can potentially shave months to years off of the time between discovery and initial communication of results in ecology.
It also means that other ecology journals that still do not allow the posting of preprints are under significant pressure to change their policies. With all of the big journals allowing preprints they have no reasonable excuse for not modernizing their policies, and they risk loosing out on papers that are initially submitted to higher profile journals and are posted as preprints.
It’s a good day for science. Celebrate by posting your next manuscript as a preprint.
If you want more info, you should email one of the people who signed the below email (I’ve linked to their websites). I’m not an organizer, just a messenger!
We are delighted to announce an upcoming joint meeting of the BES Macroecology Group, the GfO Macroecology Group, and the Center for Macroecology, Evolution & Climate (CMEC). The meeting will be hosted by CMEC in Copenhagen, Denmark during June 2015. We are sure it will provide an exciting opportunity for the members of these groups to share their latest research and ideas, and to initiate new collaborations in the relatively informal atmosphere consistent with the society group meetings.
To help us find the best dates, length of meeting and a good estimate of participant numbers, we would appreciate it if you could spare a couple of minutes to fill out this very short survey: https://www.surveymonkey.com/s/KKFBMHY
Thanks very much
The organising committee
BES Macroecology: http://macroecologyuk.weebly.com/
GfO Macroecology: http://www.gfoe.org/en/gfoe-specialist-groups/macroecology.html
UPDATE: Fixed lots of broken links and a couple of typos
There is a lot of discussion on the internet about highly skewed speaker lists at symposia and conferences. For the past year, I’ve been co-organizing a small conference (~110 people) with Michael Angilletta where we’ve been practicing some of the approaches I developed and blogged about earlier for organizing a seminar series. However, in ecology we know that what works at small scales may not apply to larger scales. So, do I still think organizing a conference that is both strong on research and gender diversity is very doable? Read and find out.
But before I give you my thoughts, first, some stats and background. For this conference, we had a lot of moving pieces: Discussion Leaders who helped organize their sessions, Invited Speakers – both for long and short talks, a Mentoring Program for Young Scientists which involved selecting both mentors and mentees. In the end (I hope, I’m writing this about a week before the conference, so hopefully things don’t change drastically), we ended up with the following numbers for each of these parts.
Discussion Leaders: 5 men, 4 women
Invited Long-Talk Speakers (40 min talks): 9 men, 9 women
Invited Short Talk Speakers (12 min talks):9 men, 7 women
Students/Postdocs in Mentoring Program: 10 men, 10 women
Professors (all ranks) in Mentoring Program: 11 men, 9 women
So over all the slots that we invited people to fill, we have 53% men.
What did we do? Just like I talked about in my post about the seminar series, we generated a large pool of names. We started by making a big list of people to lead the various sessions at the conference and developed an invite list that was balanced. We then used our balanced group of Discussion Leaders to brainstorm potential speakers. Each Discussion Leader provided a list of people they thought would be excellent for their session. They were given detailed instructions about how to generate their list – diverse perspectives on their topic, diversity of taxa/ecosystems, including domestic and international scientists, and a reminder to be aware of the gender ratios of their list.
From those lists, Mike and I sat down and constructed our dream team speaker list – balancing research areas, topics and taxa/ecosystems, career stages, making sure we had some international representation, and keeping an eye on gender balance in the process. Then we set out to convince these people to come speak at the conference.
For the Mentoring Program, we ran an application process. We advertised on every social media outlet and listserv we could think of. Our pool of applicants was very gender balanced (23 women, 21 men). We selected 20 young scientists, equally split among male and female, again balancing across various dimensions of research & people diversity.
The Mentors and Short Talk Speakers were harder. Most of our Short Talk Speakers are students from the mentoring program but we had some slots leftover to fill. Both the mentor and short talk speakers needed to fill specific topic requirements either for the program or to overlap with already chosen mentees.
So what lessons did I learn?
Gender balancing a conference is hard, but not in the ways I generally heard about before I started. It is not harder to find female speakers – as long as you don’t restrict yourself to only senior female professors. There are lots of kickass women out there, but you need to embrace the fact that they are scattered across career stages. Women were not more likely to say no. I don’t know why we didn’t experience this commonly reported problem. Maybe it was because I was sending the invites. Are women more likely to say yes to another women asking? I also spent a lot of time sending personalized emails communicating why we thought they in particular would be a good fit for the conference and why we wanted them there (I did this for the men too). What was hard about it was spending the extra time sending personalized emails to communicate clearly why I was inviting them. Did those efforts make a difference? I really don’t know. You’ll have to ask the amazing scientists who said yes to our invites.
Developing at the get-go a diverse pool of people you would like involved is critical. This is another time intensive step. Crowd-sourcing this to our Discussion Leaders helped a lot. Many of them knew speakers (men and women) we hadn’t thought of. When we pooled all those suggestions, we had 123 suggestions for 16 speaking slots. That gave us a ton of flexibility when thinking about the program we wanted to create. It was also really handy when someone said no because all the brainstorming work had already been done. We could sit down with our list and come to consensus quickly on the next invite to send. We often saved up rejections to fill as a group, thus allowing us to manage the diversity better.
The more restricted the slot you’re trying to fill, the harder it is to get gender balance. If your need is 2 kickass people who work in general area X, then gender balance is easy. The more criteria you place or the fewer the number of slots (or both) the harder it gets. Need a senior researcher studying organism X on specific subtopic Y and need another senior researcher studying organisms Z on specific subtopic A in ecosystem Q? Yeah, both those slots are probably going to end up being men, just because of the numbers game. View your program creatively. Be willing to think about different ways people can fit into the program given the diversity of research you’re trying to cover and the multiple facets that everyone has in their research programs.
So my final thoughts on the matter? Making a gender balanced conference is not easy and because of the strong gender skew at the senior levels, it doesn’t just magically happen. It takes work, planning, creativity, and a great team of people helping you brainstorm names. But a 80:20 split in invited speakers is far from the grim ‘reality’ that some might think.
Create a calendar and block out time for you.
Sounds simple, and honestly a little stupid, but it’s the best advice I can give. Why?
When you start your job, or a semester, your calendar is empty. You have oodles and oodles of time for you to work on your science. However, you will quickly find that there are a lot of demands on your time. Students want meetings. Faculty want meetings. Collaborators want meetings. Administrators want meetings. You name a type of person (and some you suspect might not be people at all) and they will want you to do something for them. Many of these things will seem quick. The most dangerous words are “This will only take 5 minutes” (It won’t. I promise you, it never does). Next thing you know you have a week chopped up into meetings with only 15 minutes here or there of ‘free time’. That’s now the free time you have to do all that science you were planning on. Trust me, in the 15 minutes you’ll have between meetings and things you have to do to prepare for meetings, you won’t feel like working on your science.
This is where the calendar comes in. Schedule blocks of time during each week for research. Once on your calendar, these blocks are sacrosanct. You wouldn’t cancel that meeting with the Department Chair to meet with Fred down the hall to talk about the seminar committee. Your research is in many ways more important for your future than the Department Chair, so don’t cancel on it.
Why do you need the calendar? Why can’t you just tell yourself that every Monday morning you will focus on research? Because it doesn’t work. When someone comes and asks for a meeting and you think about your week, Monday morning will be ‘free’ in your head. The easiest thing in the world is to fill that ’empty’ slot and now you’ve just broken up your research time into useless chunks. (Trust me, I’ve been there). On the other hand, if that time is already blocked out on your calendar as ‘busy’ then it’s a reminder that you have something you need to be doing during that time.
As an ancillary note, blocking out time for you and your mental health is also important. Exercise important for keeping you sane? Need time for activities with friends or you go ballistic? Whatever you need to keep you sane and happy, make sure you schedule time for it. Because when you’re insane, your work is never as good as you think it is. Trust me on this.
Preprints are rapidly becoming popular in biology as a way to speed up the process of science, get feedback on manuscripts prior to publication, and establish precedence (Desjardins-Proulx et al. 2013). Since biologists are still learning about preprints I regularly get asked which of the available preprint servers to use. Here’s the long-form version of my response.
The good news is that you can’t go wrong right now. The posting of a preprint and telling people about it is far more important than the particular preprint server you choose. All of the major preprint servers are good choices.Of course you still need to pick one and the best way to do that is to think about the differences between available options. Here’s my take on four of the major preprint servers: arXiv, bioRxiv, PeerJ, and figshare.
arXiv is the oldest of the science preprint servers. As a result it is the most well established, it is well respected, more people have heard of it than any of the other preprint servers, and there is no risk of it disappearing any time soon. The downside to having been around for a long time is that arXiv is currently missing some features that are increasingly valued on the modern web. In particular there is currently no ability to comment on preprints (though they are working on this) and there are no altmetrics (things like download counts that can indicate how popular a preprint is). The other thing to consider is that arXiv’s focus is on the quantitative sciences, which can be both a pro and a con. If you do math, physics, computer science, etc., this is the preprint server for you. If you do biology it depends on the kind of research you do. If your work is quantitative then your research may be seen by folks outside of your discipline working on related quantitative problems. If your work isn’t particularly quantitative it won’t fit in as well. arXiv allows an array of licenses that can either allow or restrict reuse. In my experience it can take about a week for a preprint to go up on arXiv and the submission process is probably the most difficult of the available options (but it’s still far easier than submitting a paper to a journal).
bioRxiv is the new kid on the block having launched less than a year ago. It has both commenting and altmetrics, but whether it will become as established as arXiv and stick around for a long time remains to be seen. It is explicitly biology focused and accepts research of any kind in the biological sciences. If you’re a biologist, this means that you’re less likely to reach people outside of biology, but it may be more likely that biology folks come across your work. bioRxiv allows an array of licenses that can either allow or restrict reuse. However, they explicitly override the less open licenses for text mining purposes, so all preprints there can be text-mined. In my experience it can take about a week for a preprint to go up on bioRxiv.
PeerJ Preprints is another new preprint server that is focused on biology and accepts research from across the biological sciences. Like bioRxiv it has commenting and altmetrics. It is the fastest of the preprint servers, with less than 24 hours from submission to posting in my experience. PeerJ has a strong commitment to open access, so all of it’s preprints are licensed with the Creative Commons Attribution License. PeerJ also publishes an open access journal, but you can post preprints to PeerJ Preprints with out submitting them to the journal (and this is very common). If you do decide to submit your manuscript to the PeerJ journal after posting it as a preprint you can do this with a single click and, should it be published, the preprint will be linked to the paper. PeerJ has the most modern infrastructure of any of the preprint servers, which makes for really pleasant submission, reading, and commenting experiences. You can also earn PeerJ reputation points for posting preprints and engaging in discussions about them. PeerJ is the only major preprint server run by a for-profit company. This is only an issue if you plan to submit your paper to a journal that only allows the posting of non-commercial preprints. I only know of only one journal with this restriction, but it is American Naturalist which can be an important journal in some areas of biology.
figshare is a place to put any kind of research output including data, figures, slides, and preprints. The benefit of this general approach to archiving research outputs is that you can use figshare to store all kinds of research outputs in the same place. The downside is that because it doesn’t focus on preprints people may be less likely to find your manuscript among all of the other research objects. One of the things I like about this broad approach to archiving anything is that I feel comfortable posting that isn’t really manuscripts. For example, I post grant proposals there. figshare accepts research from any branch of science and has commenting and altmetrics. There is no delay from submission to posting. Like PeerJ, figshare is a for-profit company and any document posted there will be licensed with the Creative Commons Attribution License.
Those are my thoughts. I have preprints on all three preprint servers + figshare and I’ve been happy with all three experiences. As I said at the beginning, the most important thing is to help speed up the scientific process by posting your work as preprints. Everything else is just details.
UPDATE: It looks like due to a hiccup with scheduling this post than an early version went out to some folks without the figshare section.
UPDATE: In the comments Richard Sever notes that bioRxiv’s preprints are typically posted within 48 hours of submission and that their interpretation of the text mining clause is that this is covered by fair use. See our discussion in the comments for more details.