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!

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

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!

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

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

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

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

*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

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

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)

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.

The best way to not get a job: don’t apply

As I announced on Twitter about a week ago, I am now making all of my grant proposals open access. To start with I’m doing this for all of my sole-PI proposals, because I don’t have to convince my collaborators to participate in this rather aggressively open style of science.

As I announced on Twitter about a week ago, I am now making all of my grant proposals open access. To start with I’m doing this for all of my sole-PI proposals, because I don’t have to convince my collaborators to participate in this rather aggressively open style of science. At the moment this includes three funded proposals: my NSF Postdoctoral Fellowship proposal, an associated Research Starter Grant proposal, and my NSF CAREER award.

On making my grant proposals open access

Ethan and I have been watching the emergence of crowdfunding in science with great interest. We meant to blog about it, but our rate of blog idea generation is &gt;&gt; our rate of blog writing.

Ethan and I have been watching the emergence of crowdfunding in science with great interest. We meant to blog about it, but our rate of blog idea generation is &gt;&gt; our rate of blog writing.

Crowdfunding for Science 101 [guest post]

Sadly, Ethan and I are missing ESA this year, but our group still has a strong presence this year. In fact you can see a weecologist every day of the conference if you so desire!

Sadly, Ethan and I are missing ESA this year, but our group still has a strong presence this year. In fact you can see a weecologist every day of the conference if you so desire! If you’re at ESA and want to know what the weecologists are up to, go check out our various talks and posters.

Weecology at ESA 2012

I logged into one of my reviewer accounts at a Wiley journal this morning and was greeted by a redirect that took me to a page with the following message: CONSENT We appreciate your involvement with this publication, which is published by a John Wiley &amp; Sons company.

I logged into one of my reviewer accounts at a Wiley journal this morning and was greeted by a redirect that took me to a page with the following message:  Asking someone who is already working for you for free if it’s OK to also try to sell them stuff while they’re doing it seems like a pretty good definition of classless to me.

Stay Classy Wiley

Next week is the annual meeting of the Ecological Society of America.

Next week is the annual meeting of the Ecological Society of America. If you’ve ever been to ESA, then you know it’s….big, often between 3000-5000 ecologists (which I thought was big until I heard about some of the biomedical conferences which have the attendance of a small city). It seems like most of those people are giving talks or posters.

Navigating ESA

Recently, NSF has changed the process for proposal submission for the core panels in the Directorate for Biological Sciences. Wondering if this might be important to you?

Recently, NSF has changed the process for proposal submission for the core panels in the Directorate for Biological Sciences. Wondering if this might be important to you? Please answer the following questions: do you study some aspect of biology (defined as anything from the molecular to ecosystem levels)?, do you intend to submit a proposal to NSF someday?

NSF Proposal Changes – Follow-up

Therapy for interdisciplinary biologists

I’ve been waiting for a while now for Ted Hart’s blog to get up enough steam to send folks over there, and since in the last two weeks he’s had three posts, revamped the mission of the blog, and engaged in the ongoing conversation about Lindenmayer &amp; Likens, it seems like that time has arrived.

Distributed Ecology [Blogrolling]

Here at Weecology we’re really into open science and that’s why we’re excited to announce our first serious attempt to facilitate open science beyond the confines of our own research – The Ecological Data Wiki. The idea behind this project is simple.

The Ecological Data Wiki

UPDATE: As of April 2012 Wiley has now changed their feeds to include the full list of authors. Thanks to Brady Allred for letting us know. An open letter to John Wiley &amp; Sons Inc.

UPDATE: As of April 2012 Wiley has now changed their feeds to include the full list of authors. Thanks to Brady Allred for letting us know.

 
 An open letter to John Wiley &amp; Sons Inc.
 

Dear Wiley, I like a lot of things that you do, but a few months ago you quietly changed your RSS feeds in a way that is both disrespectful and frankly not good for your business.

Putting the first back in first author

There is an excellent post on open science, prestige economies, and the social web over at Marciovm’s posterous*. For those of you who aren’t insanely nerdy** GitHub is… well… let’s just call it a very impressive collaborative tool for developing and sharing software***. But don’t worry, you don’t need to spend your days tied to a computer […]

There is an excellent post on open science, prestige economies, and the social web over at Marciovm’s posterous*. For those of you who aren’t insanely nerdy** GitHub is… well… let’s just call it a very impressive collaborative tool for developing and sharing software***. But don’t worry, you don’t need to spend your days tied to a computer or have any interest in writing your own software to enjoy gems like:  Thanks to Carl Boettiger

A GitHub of Science? [Things you should read]

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.

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.

Postdocs Galore [Jobs]

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.

Postdoc opportunity in macroecology, quantitative ecology, and ecoinformatics

We’ve had a bit of discussion here at JE about potential solutions to the tragedy of the reviewer commons, so I found a recent letter in Nature (warning – it’s behind a pay wall) suggesting that there may not actually be a problem interesting.

We’ve had a bit of discussion here at JE about potential solutions to the tragedy of the reviewer commons, so I found a recent letter in

 Nature

(warning – it’s behind a pay wall) suggesting that there may not actually be a problem interesting.

No peer review crisis after all?

The Ecological Database Toolkit Large amounts of ecological and environmental data are becoming increasingly available due to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets.

The Ecological Database Toolkit

Large amounts of ecological and environmental data are becoming increasingly available due to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets. As a result, ecology is entering an era where progress will be increasingly limited by the speed at which we can organize and analyze data.

Beta Release of Database Toolkit

I really appreciated Jeremy and Owen’s follow up to my original post about PubCred.

I really appreciated Jeremy and Owen’s follow up to my original post about PubCred. They have clearly thought a lot about the feasibility of implementing their system and while I still don’t agree that it’s quite as straightforward as they propose

 1

I am will to concede that they would get the details figured out pretty quickly. So, that leaves three questions: 1) Who should decide the details of the system?

The real problem with PubCred

A group of 5th and 6th graders where asked to define either “science” or “writing” and when the answers were combined this definition of creativity was the result. In scientific education, and as we conduct scientific research, we often lose track of the fact that creativity is critical to the scientific process.

A group of 5th and 6th graders where asked to define either “science” or “writing” and when the answers were combined this definition of creativity was the result. In scientific education, and as we conduct scientific research, we often lose track of the fact that creativity is critical to the scientific process. This is a great reminder of its importance.

Creativity = Science + Writing

All truth passes through three stages [Quote]

I’ve been meaning to get around to posting about Stuart Hurlbert and Cecilia Lombardi’s recent paper (2009; Ann. Zool. Fennici 46: 311–349) on the use of p-values in drawing scientific conclusions… but thankfully Jarrett Byrnes over at i’m a chordata! urochordata!

I’ve been meaning to get around to posting about Stuart Hurlbert and Cecilia Lombardi’s recent paper (2009; Ann. Zool. Fennici 46: 311–349) on the use of p-values in drawing scientific conclusions… but thankfully Jarrett Byrnes over at i’m a chordata! urochordata! wrote such a great post about it that all I need to do is point you over to his place. Just so you know what you’re getting into, Hurlbert &amp;

Rise of the neoFisherian statistical paradigm

I just read the excellently forward thinking year end editorial of the new journal Ideas in Ecology and Evolution. The editorial was written by Lonnie Aarssen and Christopher Lortie and is filled with Aarssen’s trademark,creative, outside the proverbial box, thinking.

Ideas in Ecology and Evolution

I’m going to be participating in a Royal Society Discussion Meeting and they’ve asked us to advertise this to interested parties so I figured I’d just post about it here. The meeting is on Biological Diversity in a Changing World and (other than your humble narrator) has a pretty impressive list of speakers.

I’m going to be participating in a Royal Society Discussion Meeting and they’ve asked us to advertise this to interested parties so I figured I’d just post about it here. The meeting is on

 Biological Diversity in a Changing World

and (other than your humble narrator) has a pretty impressive list of speakers. Here are the key bits of information (straight from the meeting’s web page).

Biological Diversity in a Changing World – Royal Society Discussion Meeting

The current model of writing up collaborative research in science is that a single individual “takes the lead” and writes a complete draft of the manuscript, which is then sent on to coauthors for comments, corrections, etc.

Another opportunity to change the way we collaborate – G o o g l e  W a v e  I n v i t e s for ecologists

We just read this great piece from the Huffington Post by Todd Palmer and Rob Pringle on why including funds for NSF and NIH in the stimulus bill was a good idea (thanks to Ecotone for pointing us to the article). The great thing about the piece is that it doesn’t just make a cogent […]

Morgan &amp; Ethan

We just read this great piece from the Huffington Post by Todd Palmer and Rob Pringle on why including funds for NSF and NIH in the stimulus bill was a good idea (thanks to Ecotone for pointing us to the article). The great thing about the piece is that it doesn’t just make a cogent argument for the stimulus funds, but for why funding basic science is economically beneficial in general.

Amen brothers: why stimulus funding for science was a good idea

Summary Likelihood, likelihood, likelihood (and maybe some other complicated approaches), but definitely not r^2 values from fitting regressions to binned data. A bit more nitty gritty detail In addition to causing issues with parameter estimation, binning based methods are also inappropriate when trying to determine which distribution provides the best fit to empirical data.

Summary

Likelihood, likelihood, likelihood (and maybe some other complicated approaches), but definitely not r^2 values from fitting regressions to binned data.

 A bit more nitty gritty detail

In addition to causing issues with parameter estimation, binning based methods are also inappropriate when trying to determine which distribution provides the best fit to empirical data.

Frequency distributions for ecologists IV: comparing model performance

Ecological Samuri

Unless you’ve been living under a rock (or are a new assistant professor), you are surely aware by now that Darwin’s 200th birthday is this week. However, unless you’re a certified blog-crawler, you may not be aware of Blogging the Origin.

Blogging the Origin

Anyone who has been around the halls of academia for a while has heard some well meaning soul talk about how we produce too many PhD students for the number of faculty positions, that this is unfair, and that therefore we should take fewer students.

Anyone who has been around the halls of academia for a while has heard some well meaning soul talk about how we produce too many PhD students for the number of faculty positions, that this is unfair, and that therefore we should take fewer students. The most recent version of this idea on the web goes so far as calling the academic enterprise a Ponzi scheme. I’ve never personally found this argument very convincing.

Courting controversy &amp; academic ponzi schemes [Things you should read]

The Weecology lab group run by Ethan White and Morgan Ernest at the University of Florida is seeking a Project Manager to conduct and manage a long-term field study of breeding wading bird colonies in the Florida Everglades.

Florida Everglades Wading Bird Project Manager

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

Back when I had optimistic views of my time, I vowed to do more blogging this year. Sadly, life had other plans. But I return with an update to an earlier post on the Portal rodent community. To recap, in April 2023, my student Pat Dumandan and I were afraid.

Back when I had optimistic views of my time, I vowed to do more blogging this year. Sadly, life had other plans. But I return with an update to an earlier post on the Portal rodent community. To recap, in April 2023, my student Pat Dumandan and I were afraid. Afraid that

 Chaetodipus penicillatus

(the Desert pocket mouse) was about to undergo a population explosion.

Regime shift still cometh?

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

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?

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

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

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

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

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

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

Pregnancy in Kangaroo rats

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

The Spectabulous Spectabs of Portal

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

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 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

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.

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 (@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

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 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

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

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

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]

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

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

Over at Dynamic Ecology this morning Jeremy Fox has a post giving advice on how to decide where to submit a paper.

Over at Dynamic Ecology this morning Jeremy Fox has a post giving advice on how to decide where to submit a paper. It’s the same basic advice that I received when I started grad school almost 15 years ago and as a result I don’t think it considers some rather significant changes that have happened in academic publishing over the last decade and a half. So, I thought it would be constructive for folks to see an alternative viewpoint.

Some alternative advice on how to decide where to submit your paper

Slides and script from Morgan Ernest’s Ignite talk on Why constraint based approaches to ecology from Elita Baldridge and Ethan White’s thought provoking ESA 2013 session on Constraints in Ecology. Slides are also archived on figshare. Slide 1-3: As this coral reef food web so aptly demonstrates, nature is complex.

Slides and script from Morgan Ernest’s Ignite talk on Why constraint based approaches to ecology from Elita Baldridge and Ethan White’s thought provoking ESA 2013 session on Constraints in Ecology. Slides are also archived on figshare.


 Slide 1-3:

As this coral reef food web so aptly demonstrates, nature is complex.

Ignite Talk: Why constraint based approaches to ecology?

Before we start, this post refers to posts already written on this topic. To make sure no one gets lost, please follow the sequence of operations below: Step 1: Do you know about the new pre-proposal process at NSF?

Before we start, this post refers to posts already written on this topic. To make sure no one gets lost, please follow the sequence of operations below:

 Step 1:

Do you know about the new pre-proposal process at NSF?

The NSF Pre-Proposal Process: Pt 1. Judging Preproposals

Over the past year, you can’t get two scientists together who submit to the BIO Directorate at NSF without the conversation drifting to the radical changes in the proposal process. If you have no idea what I’m talking about, I’ve added some links at the bottom of the post for you to check out.

The NSF Proposal Revolution: The DEB Data

Joan Strassman has a very nice post about why it is sometimes useful to step back from the intricate details of biological systems in order to understand the general processes that are operating.

Joan Strassman has a very nice post about why it is sometimes useful to step back from the intricate details of biological systems in order to understand the general processes that are operating. Here’s a little taste of the general message  The whole post is definitely worth a read.