Ethan White and Morgan Ernest's blog for discussing issues and ideas related to ecology and academia.

It is with great excitement that we release DeepForest 2.0! This is the first major release since the project took shape in its current form. The codebase has been updated to match modern machine learning workflows, including better command line tools, configurations and package management.

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It is with great excitement that we release DeepForest 2.0! This is the first major release since the project took shape in its current form. The codebase has been updated to match modern machine learning workflows, including better command line tools, configurations and package management. These improvements will help users scale research projects quickly, test out new ideas and make their work more reproducible and long-lasting.

DeepForest 2.0!

Last week an exciting new addition to the R ecosystem was announced: webR.

Last week an exciting new addition to the R ecosystem was announced: webR. webR lets you run R from inside your browser, without installing R

 1

. This is a really exciting development for educational materials, because it makes it possible to provide interactive materials where students can modify, create, and run code right inside a web page with zero setup.

A brief introduction to using WebR and Quarto for client-side interactive lesson material

Zoom works great: I’ve seen up to ~50 folks attending the talk remotely and slides with video. Everything connection wise worked well except for a single committee member with some minor freezing during the private defense. Have backup options: Give yourself time and backups in case things go wrong.

Zoom works great:

I’ve seen up to ~50 folks attending the talk remotely and slides with video. Everything connection wise worked well except for a single committee member with some minor freezing during the private defense.

 Have backup options:

Give yourself time and backups in case things go wrong. Set up the connection early (15+ minutes) and ask the committee to show up early to check everything is working.

Tips for an effective remote defense

Engaging in Art and Science Collaborations This is a guest post by Zack Brym (@ZackBrym). He is a graduate student in our group interested in the form and function of orchard trees. He has also developed an interest in scientific communication.

Engaging in Art and Science Collaborations

 This is a guest post by Zack Brym (@ZackBrym). He is a graduate student in our group interested in the form and function of orchard trees. He has also developed an interest in scientific communication.

Getting the Most Out of Science through Art

This is the first of a new category of posts here at Jabberwocky Ecology called Research Summaries. We like the idea of communicating our research more broadly than to the small number of folks who have the time, energy, and interest to read through entire papers.

This is the first of a new category of posts here at Jabberwocky Ecology called Research Summaries. We like the idea of communicating our research more broadly than to the small number of folks who have the time, energy, and interest to read through entire papers. So, for every paper that we publish we will (hopefully) also do a blog post communicating the basic idea in a manner targeted towards a more general audience.

Characterizing the species-abundance distribution with only information on richness and total abundance [Research Summary]

As I’ve mentioned before I’m not a big fan of the configuration of most comprehensive exams, but my post on the matter keeps languishing on my out of control To Do list.

Fighting the snake [Things you should read]

I think we make things that we like and… [Quote]

I went to graduate school with Ford and would strongly recommend that those looking for PhD opportunities on the quantitative side of ecosystem ecology consider the opportunity below.

PhD opportunities in Theoretical Ecosystem Ecology with Ford Ballantyne [PhD Position]

Understanding and managing forests is crucial to understanding and potentially mitigating the effects of climate change, invasive species, and shifting land use on natural systems and human society. However, collecting data on individual trees in the field is expensive and time consuming, which limits the scales at which this crucial data is collected.

Data science competition: Converting remote sensing into trees

Interested in understanding how ecological systems change through time? Morgan Ernest’s Lab at the University of Florida has an opening for a PhD student to start Fall 2025.

Interested in understanding how ecological systems change through time? Morgan Ernest’s Lab at the University of Florida has an opening for a PhD student to start Fall 2025. The new student will work with our long-term field site in Portal, Arizona to study biodiversity dynamics of mammals and plants to understand and predict changes in species abundances and biodiversity in response to changing climate and biotic conditions.

PhD Student Opening: Small Mammal Community Dynamics

Every episode in a tv series starts with a recap. So… Previously, on Portal: the Regime Shift — In fall of 2023, one of the ruling families of Portal — the Desert Pocket Mouse (Chaetodipus penicillatus for my mammalogy friends) — fell from favor with no warning.

Every episode in a tv series starts with a recap. So… Previously, on Portal: the Regime Shift — In fall of 2023, one of the ruling families of Portal — the Desert Pocket Mouse (

 Chaetodipus penicillatus

for my mammalogy friends) — fell from favor with no warning. With each passing month, hopes for a recovery faltered and then dimmed. By fall of 2024, this once thriving population had become a dismal shade of yore.

Regime Shift: A Winter of Grim

When last we left our rodent community at Portal, things were still…weird. Recap: In fall of 2023, one of our most abundant species, Chaetodipus penicillatus (Desert pocket mouse), experienced a population crash right before their seasonal torpor for the winter. Had they hibernated early or had we really lost individuals?

When last we left our rodent community at Portal, things were still…weird. Recap: In fall of 2023, one of our most abundant species,

 Chaetodipus penicillatus

(Desert pocket mouse), experienced a population crash right before their seasonal torpor for the winter. Had they hibernated early or had we really lost individuals? We could only wait and see what happened in the spring. Spring came and still no Desert pocket mouse.

Regime Shift Status: Ongoing?

Every 10 years, the desert rodent community at the Portal Project reorganizes. We know this thanks to a paper led by former graduate student Erica Christensen where we documented the long-term dynamics of change in the Portal rodent community.

Regime Shift Cometh?

We’re looking for a new PhD student to join weecology! The new student will work on our Everglades project, developing actionable forecasting models for this actively managed ecosystem, with a focus on understanding the influence of scale on ecological forecasting.

PhD Student Position In Ecological Forecasting Of Everglades Wading Birds

This year is the 25th anniversary of The Carpentries, a non-profit teaching “foundational coding and data science skills to researchers”. As part of this anniversary community members were invited to describe “How has The Carpentries made an impact on you?”. I wrote about this for The Carpentries Blog and am cross posting it here. In short, in my case, The Carpentries has changed every aspect of my professional life.

How has The Carpentries made an impact (on me)

We are excited to announce the first release of a new Julia package that let’s you run our Data Retriever software with a native Julia interface.

We are excited to announce the first release of a new Julia package that let’s you run our Data Retriever software with a native Julia interface. For those of you not familiar with Julia it is a new programming language that is similar to R and Python, has a central focus on data analysis, and is designed from the ground up to be fast. It is an emerging scientific programming and data analysis language.

A Julia Package for the Data Retriever

The Ernest Lab at the University of Florida has an opening for a PhD student interested in ecological forecasting of desert rodents to start Fall 2024. This position is funded on an NSF grant to study ecological forecasting under novel conditions using data from the Portal Project, our long-term field site located in southeastern Arizona.

PHD STUDENT IN ECOLOGICAL FORECASTING OF SMALL MAMMALS

One of weecology’s newest projects involves monitoring wading birds in the Everglades using drones. We need to quickly turn this imagery into data to drive ecological forecasts &amp; guide management decisions. We do this in near real-time using computer vision models to detect birds in imagery &amp; automated workflows to update this data as soon as new imagery is available.

Monitoring wading birds in near real-time using drones and computer vision

New dataset of canopy tree maps for 100 million trees in the National Ecological Observatory Network with information on location, species identify, and size.

We just published a dataset of canopy tree maps for 100 million trees in the National Ecological Observatory Network (NEON) with information on location, species identify, size, and whether the tree is alive.

New dataset on 100 million canopy trees across the National Ecological Observatory Network

After posting yesterday that we were ramping up the blog again, my RSS feed let me know that arguably the most impactful ecology blog of all time, Dynamic Ecology, was doing the same thing!

After posting yesterday that we were ramping up the blog again, my RSS feed let me know that arguably the most impactful ecology blog of all time, Dynamic Ecology, was doing the same thing! We also heard from Terry McGlynn who has recently moved and renamed his really important blog, now a newsletter named Science For Everyone. And we heard from multiple other folks that they are in the process of spinning up new blogs/newsletters.

It really is the return of the ecology blogosphere!

We’re excited to announce the initial release of crown maps for 100 million trees in the National Ecological Observatory Network (NEON) with information on location, species identify, size, and alive/dead status.

We’re excited to announce the initial release of crown maps for 100 million trees in the National Ecological Observatory Network (NEON) with information on location, species identify, size, and alive/dead status.  Using NEON’s remote sensing data we’ve been developing computer vision models to locate tree crowns for all individuals visible from above and classify those crowns to species (Weinstein et al. 2019, 2020, 2023; Marconi et al. 2022).

Data on 100 million individual trees in the National Ecological Observatory Network

We started Jabberwocky Ecology back in 2008 when blogs were becoming the dominant medium for informal (online) academic discussions.

We started Jabberwocky Ecology back in 2008 when blogs were becoming the dominant medium for informal (online) academic discussions. About the same time a handful of other ecology blogs got going and for a while the academic “blogosphere” was the hub for the sorts of things we now often talk about on other social media platforms.

Return to (and of?) the ecology blogosphere

A funny thing happened on the way to the pandemic… In the summer of 2019 a colleague of mine, Dr. Peter Frederick – an expert in the wading birds of the Everglades – emailed me. Peter and I served on some university committees together, so I assumed we were just getting together to chat about […]

A funny thing happened on the way to the pandemic…  In the summer of 2019 a colleague of mine, Dr. Peter Frederick – an expert in the wading birds of the Everglades – emailed me. Peter and I served on some university committees together, so I assumed we were just getting together to chat about changes in graduate student admissions or something else administrative.

Weecology, the Everglades, and Wading Birds, oh my!

PH.D STUDENT POSITION IN COMMUNITY ECOLOGY The Ernest Lab at the University of Florida has an opening for a Ph.D student interested in research in the area of community ecology, forecasting, and/or temporal dynamics to start fall 2020.

PH.D STUDENT POSITION IN COMMUNITY ECOLOGY

The Ernest Lab at the University of Florida has an opening for a Ph.D student interested in research in the area of community ecology, forecasting, and/or temporal dynamics to start fall 2020.

Ph.D Student Opening in Weecology

Do you have a graduate degree and are looking for a job? The US Government hires thousands of people with your skill set. Here I’ll give a quick overview of the scope of those jobs. If you’re looking for the exhaustive guide for applying on USAjobs its here.

Do you have a graduate degree and are looking for a job? The US Government hires thousands of people with your skill set. Here I’ll give a quick overview of the scope of those jobs. If you’re looking for the exhaustive guide for applying on USAjobs its here. Why should I work for the federal government? A career with a federal agency can be just as rewarding, and sometimes extremely similar, as a career in academia.

Jobs in the US Government for graduate students

How has our collection of weather data at the Portal Project changed through time? Weecology Project Manager Glenda Yenni recounts the saga of the weather stations.

The Portal Weather Station

Adjust expectations, be flexible, support your groups Research will be different from normal for a while and even in the best cases it will also be slower. The shift to working remotely will limit the kinds of work we can do and everyone doing research is experiencing a dramatic disturbance to their lives.

Adjust expectations, be flexible, support your groups

Research will be different from normal for a while and even in the best cases it will also be slower. The shift to working remotely will limit the kinds of work we can do and everyone doing research is experiencing a dramatic disturbance to their lives. This means the people in our labs will need flexibility and support.

Supporting and managing academic labs during a pandemic, some thoughts

A guest post from last week on the Portal Blog about studying Kangaroo rat placentas!

Pregnancy in Kangaroo rats

It’s not uncommon to hear stories of mistakes resulting in graduates students missing paychecks. This is a major problem because most students live month-to-month and can’t wait for a missed check to be fixed in the next pay cycle.

It’s not uncommon to hear stories of mistakes resulting in graduates students missing paychecks. This is a major problem because most students live month-to-month and can’t wait for a missed check to be fixed in the next pay cycle. Despite the commonness and dramatic impact of missed pay in graduate school*, it’s common to see these issues written off as isolated incidents and not part of a more systematic problem.

Way too many examples of graduate students not getting their paychecks

The weecology group is coming in force to the annual meeting of the Ecological Society of America which is being held in New Orleans next week. We’ve been up to a quite diversified list of things over the past year ranging from temporal dynamics of communities to forecasting and remote sensing.

The weecology group is coming in force to the annual meeting of the Ecological Society of America which is being held in New Orleans next week. We’ve been up to a quite diversified list of things over the past year ranging from temporal dynamics of communities to forecasting and remote sensing. We also have people involved in a number of outreach or training events this year.

Weecology at #ESA2018 [updated]

Scaling-up ecological patterns and processes is crucial to understanding the effects of environmental change on natural systems and human society. We are piloting a Data Science Challenge where multiple groups attempt to use the same remote sensing data from low flying airplanes to infer the location and type of trees in forests.

Scaling-up ecological patterns and processes is crucial to understanding the effects of environmental change on natural systems and human society. We are piloting a Data Science Challenge where multiple groups attempt to use the same remote sensing data from low flying airplanes to infer the location and type of trees in forests. This will allow forests to be studied in detail at much larger scales than is currently possible.

Data science competition for converting remote sensing to ecological data

Love to see paired photos of places in the past and now? My PhD student Erica Christensen has a treat for you. Here’s a post about her attempts to reshoot old photos from the site.

Portal: Then and Now

Someone (**cough** **cough** Morgan) fell down on their job rebloging the Portal Project 40th anniversary posts to Jabberwocky. But that means this week is the week o’ Portal as we reblog the various posts from the past few weeks. First up, what happens when we go out in the summer to count plants?

2017 Summer Plant Census

The latest installment from the Portal Project Blog on the watch for Banner-tailed Kangaroo Rats

The Spectabulous Spectabs of Portal

How did we get those daily pics of the desert turning green in a week? Meet Portal’s new toy: the Phenocam.

Portal Phenocam

We are exited to announce a new release of the Data Retriever, our software for making it quick and easy to get clean, ready to analyze, data. The Data Retriever, automates the downloading, cleaning, and installing of data into your choice of databases and flat file formats.

Data Retriever 2.1: Python Interface, Autocomplete &amp; More

While the Portal Project focuses primarily on rodents and plants, there is more to our ecosystem than just those taxa. This week’s Portal Project post focuses on some insect work at the site.

Ode to six-legged wonder

The Portal Project turns 40 this year! In celebration, we will be regularly posting about the history of the site, new things going on, natural history of the desert, and other fun things over at the Portal Blog.

The Portal Project 40th Anniversary

We have a modest sized group of current folks at ESA this week presenting on all the cool things they’ve been doing. We’re also around and always happy to try to find time to grab a coffee or just a few minutes to chat science.

We have a modest sized group of current folks at ESA this week presenting on all the cool things they’ve been doing. We’re also around and always happy to try to find time to grab a coffee or just a few minutes to chat science. Our schedule for the week is:

 Monday

Get a double dose of rapid change in ecological communities from the Portal Project with Morgan Ernest and Erica Christensen. 02:50 PM – 03:10 PM in C120-121.

Weecology at ESA

Counting plants and rats in the desert is fun to collect but also hard won data. Another Portal Project blog post is up!

Walking the beat

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.

Postdoctoral research position in the Temporal Dynamics of Communities

Should you cite preprints in your papers and should journals allow this? This is a topic that gets debated periodically. The most recent round of Twitter debate started last week when Martin Hunt pointed out that the journal Nucleic Acids Research wouldn’t allow him to cite them.

Should you cite preprints in your papers and should journals allow this? This is a topic that gets debated periodically. The most recent round of Twitter debate started last week when Martin Hunt pointed out that the journal Nucleic Acids Research wouldn’t allow him to cite them. A couple of days later I suggested that journals that don’t allow citing preprints are putting their authors’ at risk by forcing them not to cite relevant work.

Is it OK to cite preprints? Yes, yes it is.

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.

Data Analyst position in ecology research group

[Update: A little bird pointed out I didn’t have a link to the actual Portal blog.

[Update: A little bird pointed out I didn’t have a link to the actual Portal blog. That has been remedied along with a link to the Portal Project website for those who’d like more info on the project]  A couple weeks ago, I posted about the new data paper from my long-term field site, the Portal Project.

The story behind the paper: Xiao et al. 2016

In a big step forward for allowing proper credit to be provided to all of the awesome folks collecting and publishing data, the journal Global Ecology &amp; Biogeography has just announced that they will start supporting an unlimited set of references to datasets used in a paper.

In a big step forward for allowing proper credit to be provided to all of the awesome folks collecting and publishing data, the journal

 Global Ecology &amp; Biogeography

has just announced that they will start supporting an unlimited set of references to datasets used in a paper. These references will be included immediately following the traditional references section in both the html and pdf versions of the paper.

GEB adds unlimited data references section to papers

For the past few years I’ve been involved in a collaboration to put together a broad-coverage life history database for mammals, reptiles, and birds.

For the past few years I’ve been involved in a collaboration to put together a broad-coverage life history database for mammals, reptiles, and birds. The project started because my collaborator, Nathan Myhrvold, and I both had projects we were interested in that involved comparing life history traits of reptiles, mammals, and birds, and only mammals had easily accessible life history databases with broad taxonomic coverage.

Trait Databases: What is the End Goal?

*This is a guest post by Elita Baldridge.** This is the third in a series of posts about my experiences completing a PhD with a chronic illness (Part 1, Part 2, and background information). Not only is this about the tools that I used to complete my PhD, but I am optimistic that these tools/coping […]

*This is a guest post by Elita Baldridge.** This is the third in a series of posts about my experiences completing a PhD with a chronic illness (Part 1, Part 2, and background information). Not only is this about the tools that I used to complete my PhD, but I am optimistic that these tools/coping mechanisms will allow me to be a scientist that gets paid for doing science.

 The tips &amp;

Sciencing with a chronic illness: Tips, tricks, &amp; technology

This is a guest post by Elita Baldridge (@elitabaldridge). She is a recently finished PhD in our group who has been navigating the development of a chronic illness during graduate school and beyond.

This is a guest post by Elita Baldridge (@elitabaldridge). She is a recently finished PhD in our group who has been navigating the development of a chronic illness during graduate school and beyond.

This is the second in a series of posts about my experiences completing a PhD with a chronic illness (Part 1, see also these two earlier, posts). As I mentioned in the first post, having a chronic illness means that there can a lot of

External challenges of chronic illness (in graduate school)

This is a guest post by Elita Baldridge. I am working on organizing an Inclusive Ecology Section within the Ecological Society of America.

This is a guest post by Elita Baldridge.

I am working on organizing an Inclusive Ecology Section within the Ecological Society of America. This section will provide resources and support for all ecologists, regardless of race, sex, physical or mental ability or difference, gender identity or expression, sexual orientation, ethnicity, socio-economic status, culture or subculture, national origin,  parental status, politics,

Starting an Inclusive Ecology section in the Ecological Society of America

Recently, over at the blog Ecological Rants the eminent ecologist Charles Krebs wrote a post about the ills of simplification in ecology. The post focuses specifically on how ecology has been ‘led astray’ by simplified models and lab studies.

Recently, over at the blog Ecological Rants the eminent ecologist Charles Krebs wrote a post about the ills of simplification in ecology. The post focuses specifically on how ecology has been ‘led astray’ by simplified models and lab studies. This has recently been picked up on Dynamic Ecology by Jeremy Fox who responded generally to the post but specifically to the affront to microcosms.

On Ecological Rants and Microcosms

This is a guest post by Elita Baldridge Most people aren’t familiar with the challenges of working on a PhD with a disability or chronic illness, and yet there’s a good chance that someone you know is in this situation and isn’t talking about it. This is the first in a series of posts about […]

This is a guest post by Elita Baldridge

Most people aren’t familiar with the challenges of working on a PhD with a disability or chronic illness, and yet there’s a good chance that someone you know is in this situation and isn’t talking about it. This is the first in a series of posts about my experiences completing a PhD with a chronic illness, and about the things that we can do to support our colleagues and students so that they can

Successfully completing a dissertation with a chronic illness

A couple of months ago Micah J. Marty and I had a twitter conversation and subsequent email exchange about how citations worked with preprints. I asked Micah if I could share our email discussion since I thought it would be useful to others and he kindly said yes.

A couple of months ago Micah J. Marty and I had a twitter conversation and subsequent email exchange about how citations worked with preprints. I asked Micah if I could share our email discussion since I thought it would be useful to others and he kindly said yes. What follows are Michah’s questions followed by my responses. At the level of the journal nothing happens.

Thoughts on preprints and citations

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.

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.

White Lab PhD openings at the University of Florida

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.

EcoData Retriever now supports R and environmental data, and has more datasets

A few months ago Mick Watson wrote an awesome post about How to recruit a good bioinformatician.

A few months ago Mick Watson wrote an awesome post about How to recruit a good bioinformatician. We’re in the process of hiring a scientific software engineer so I thought I’d use Mick’s post to illustrate why you should come work with us doing scientific software development and data-intensive research, and hopefully provide a concrete demonstration of the sort of things Mick suggests for appealing to talented computational folks.

We’re recruiting a good Scientific Software Engineer

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.

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.

Ecology Letters now allows preprints; and why this is a big deal for ecology

As I’ve argued here, and in PLOS Biology, preprints are important. They accelerate the scientific dialog, improve the quality of published research, and provide both a fair mechanism for establishing precedence and an opportunity for early-career researchers to quickly demonstrate the importance of their research.

Why the Ecology Letters editorial board should reconsider its No vote on preprints

The newly created Early Career Ecologist Section of the Ecological Society of America is to organizing a mentoring program for the upcoming ESA meeting in Baltimore. ESA can be a big and intimidating meeting for students and postdocs.

The newly created Early Career Ecologist Section of the Ecological Society of America is to organizing a mentoring program for the upcoming ESA meeting in Baltimore. ESA can be a big and intimidating meeting for students and postdocs. Let’s face it, many of us are socially awkward and meeting new people can be hard – especially if the people you want to meet are more senior.

[Announcement] ESA Centennial Mentoring Program Organized by Early Career Ecologist Section

This is a guest post by Elita Baldridge (@elitabaldridge) I am currently the remotely working member of Weecology, finishing up my PhD in the lower elevation and better air of Kansas, while the rest of my colleagues are still in Utah, due to developing a chronic illness and finally getting diagnosed with fibromyalgia.  The relocation is […]

This is a guest post by Elita Baldridge (@elitabaldridge)

I am currently the remotely working member of Weecology, finishing up my PhD in the lower elevation and better air of Kansas, while the rest of my colleagues are still in Utah, due to developing a chronic illness and finally getting diagnosed with fibromyalgia.  The relocation is actually working out really well.  I’m in better shape because I’m not having to

How technology can help scientists with chronic illnesses (or Technology FTW!)

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.

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,

Ernest Lab Ph.D opening at University of Florida

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.

Weecology is moving to the University of Florida

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.

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.

Which preprint server should I use?

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.

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.

Organizing a Gender Balanced Conference

This is a guest post by Elita Baldridge (@elitabaldridge). She is a graduate student in our group who has been navigating the development of a chronic illness during graduate school. She is sharing her story to help spread awareness of the challenges faced by graduate students with chronic illnesses.

This is a guest post by Elita Baldridge (@elitabaldridge). She is a graduate student in our group who has been navigating the development of a chronic illness during graduate school. She is sharing her story to help spread awareness of the challenges faced by graduate students with chronic illnesses.

I am a graduate student. I have fibromyalgia.

A couple of weeks ago Eli Kintisch (@elikint) interviewed me for what turned out to be a great article on “Sharing in Science” for Science Careers. He also interviewed Titus Brown (@ctitusbrown) who has since posted the full text of his reply, so I thought I’d do the same thing.

A couple of weeks ago Eli Kintisch (@elikint) interviewed me for what turned out to be a great article on “Sharing in Science” for Science Careers. He also interviewed Titus Brown (@ctitusbrown) who has since posted the full text of his reply, so I thought I’d do the same thing.  Definitely. Sharing code and data helps the scientific community make more rapid progress by avoiding duplicated effort and by facilitating more reproducible research.

Sharing in Science: my full reply to Eli Kintisch

Martorell, C. &amp; R.P. Freckleton. 2014. Testing the roles of competition, facilitation and stochasticity on community structure in a species-rich assemblage. Journal of Ecology doi:10.1111/1365-2745.12173 At a given location in nature, why are some species present and others absent?

Martorell, C. &amp; R.P. Freckleton. 2014. Testing the roles of competition, facilitation and stochasticity on community structure in a species-rich assemblage. Journal of Ecology doi:10.1111/1365-2745.12173  At a given location in nature, why are some species present and others absent? Why do some species thrive and have lots of individuals and others are barely eeking out an existence? What determines how many species can live together there?

Why I like this: Martorell and Freckleton (2014)

The British Ecological Society has announced that will now allow the submission of papers with preprints (formal language here). This means that you can now submit preprinted papers to Journal of Ecology, Journal of Animal Ecology, Methods in Ecology and Evolution, Journal of Applied Ecology, and Functional Ecology.

The British Ecological Society has announced that will now allow the submission of papers with preprints (formal language here). This means that you can now submit preprinted papers to Journal of Ecology, Journal of Animal Ecology, Methods in Ecology and Evolution, Journal of Applied Ecology, and Functional Ecology. By allowing preprints BES joins the Ecological Society of America which instituted a pro-preprint policy last year.

British Ecological Society journals now allow preprints

Graduate Student and Postdoctoral Mentoring Program
 


 
 Gordon Research Conference:  Unifying Ecology across Scales
 


 ADDED BELOW:

Who can apply is added under financial support (why it’s where will make more sense when you read it)


Time and Place: July 19-25, 2014 at the University of New England in Biddeford, Maine Conference Description: Ecological patterns and processes

UPDATED: Unifying Ecology across Scales: Mentoring Program [announcement]

As some of you may know, I’ve been working with Michael Angilletta for the past year on organizing a Gordon Research Conference. I announced the mentoring program that is affiliated with the conference last week, but here is the official info on the conference itself. Please forgive a little repetition from the mentoring program post.

Unifying Ecology Across Scales: The role of nutrients, metabolism, and physiology [Announcement]

This is a guest post by Dan McGlinn, a weecology postdoc (@DanMcGlinn on Twitter). It is a Research Summary of: McGlinn, D.J., X. Xiao, and E.P. White. 2013. An empirical evaluation of four variants of a universal species–area relationship. PeerJ 1:e212 http://dx.doi.org/10.7717/peerj.212.

This is a guest post by Dan McGlinn, a weecology postdoc (@DanMcGlinn on Twitter). It is a Research Summary of: McGlinn, D.J., X. Xiao, and E.P. White. 2013. An empirical evaluation of four variants of a universal species–area relationship. PeerJ 1:e212 http://dx.doi.org/10.7717/peerj.212.

Exploring MaxEnt based species-area relationship predictions [Research Summary]

Sam Scheiner published a piece recently on ecology’s lack of engagement with theory. Frankly, the title pretty much tells you his conclusion “The ecological literature: an idea free distribution”, but if you want to know more, either read the original piece (it’s short) or EEB &amp;

Sam Scheiner published a piece recently on ecology’s lack of engagement with theory. Frankly, the title pretty much tells you his conclusion “The ecological literature: an idea free distribution”, but if you want to know more, either read the original piece (it’s short) or EEB &amp; Flow’s nice write up on it.  The empirical-theoretical divide is a topic I’ve been pondering for a while.

The empirical-theoretical divide in ecology

UPDATE: Both Ecology Letters and the British Ecological Society journals now allow preprints. Thanks to both groups for listening to the community and supporting the rapid and open exchange of scientific ideas.

UPDATE: Both Ecology Letters and the British Ecological Society journals now allow preprints. Thanks to both groups for listening to the community and supporting the rapid and open exchange of scientific ideas. Dear Ecology Letters and the British Ecological Society ,  I am writing to ask that you support the scientific good by allowing the submission of papers that have been posted as preprints.

An open letter to Ecology Letters and the British Ecological Society about preprints

Academic publishing is in a dynamic state these days with large numbers of new journals popping up on a regular basis. Some of these new journals are actively experimenting with changing traditional approaches to publication and peer review in potentially important ways.

Academic publishing is in a dynamic state these days with large numbers of new journals popping up on a regular basis. Some of these new journals are actively experimenting with changing traditional approaches to publication and peer review in potentially important ways. So, I thought I’d provide a quick introduction to some of the new kids on the block that I think have the potential to change our approach to academic publishing.

New journals that are changing the way we publish

A friend of mine once joked that doing ecological informatics meant working with data that was big enough that you couldn’t open it in an Excel spreadsheet.

Going big with data in ecology

It’s job season. It’s that time of year again when our young scientists pour over a wide variety of job ads and ask themselves that critically important question: do I apply? In some ways, this is the most critical step in the entire job application process. Yes, your job packet is important.

It’s job season. It’s that time of year again when our young scientists pour over a wide variety of job ads and ask themselves that critically important question: do I apply? In some ways, this is the most critical step in the entire job application process. Yes, your job packet is important. There’s the goldilocks problem of conveying your awesome in the cover letter but worrying about sounding conceited.