Last week Zack Brym and I formally announced a semester long Data Carpentry course that we’ve have been building over the last year. One of the things I’m most excited about in this effort is our attempt to support collaborative lesson development for university/college coursework.
I’ve experience first hand the potential for this sort of collaborative lesson development though the development of workshop lessons in Software Carpentry and Data Carpentry. Many of the workshop lessons developed by these two organizations now have 100+ contributors. As far as I’m aware, Software Carpentry was the first demonstration that large-scale open collaboration on lessons could work (but I’d love to hear of earlier examples if folks are aware of them) and it has resulted in what is widely regarded as really high quality lesson material. Having seen this work so effectively for workshops, I’m interested in seeing how well it can work for full length courses.
Most college and university courses that I’m aware of start in one of three ways: 1) someone sites down and develops a course completely from scratch; 2) the course directly follows a text book; or 3) a new professor inherits a course from the person who taught it previously and adapts it.
Developing a course from scratch, even one following a text book fairly closely, is a huge time commitment. In contrast, with collaboratively developed courses new faculty, or faculty teaching new courses, wouldn’t need to start from scratch. They would be able to pick up an existing course to adapt and improve. I can’t even begin to describe how much easier this would have made my first few years as a faculty member. More generally, if we are teaching similar courses across dozens or hundreds of universities, it is much more efficient to share the effort of building and improving those courses than to have each person who teaches them do so independently.
In addition to the time and energy, there are often a lot of things that don’t work well the first time you teach a course and it typically takes a few rounds of teaching it to figure what works best. One of the challenges of developing lessons in isolation is that you only teach a class every 1 or 2 years. This makes it hard and slow to figure out what needs work. In contrast, a collaboratively developed course might be taught dozens or hundreds of times each year, allowing the course to be improved much more rapidly through large scale sampling and discussion of what works and what doesn’t. In addition to having more information, the fact that faculty are spending less time developing courses from scratch should leave them with more time for improving the materials. In combination this results in the potential for higher quality courses across institutions.
By involving large numbers of lesson developers, collaborative development also has the potential to help make courses more accurate, more up-to-date, and more approachable by novices. More lesson developers means a greater chance of having an expert on any particular topic involved, thus making the material more accurate and reducing the amount of bad practice/knowledge that gets taught. New faculty with more recent training on the development team can help keep both the material and the pedagogical practices up-to-date (this is hard when the same person teaches the same course for 20 years). More lesson developers also increases the likelihood that someone who isn’t an expert in any given piece of material is also involved, which should help make sure that the lesson avoids issues with expert blindness, thus making the material more accessible to students.
Collaborative college/university lesson development will not be without challenges. The skills required for collaborative lesson development in the style of Software and Data Carpentry require proficiency with computational approaches not familiar to many academics. The necessary skills include things like version control, developing materials in markdown, and working with static site generators like Jekyll. This means this approach is currently most accessible for those with some computational training and may initially work best for computing focused courses. In addition, organizing open collaborations takes time and energy, as does collectively deciding on how to design and update classes. Universities and colleges are not typically good at valuing time invested in non-traditional efforts and that would need to change to help support those managing development of courses with large numbers of faculty involved. More substantial may be the fact that faculty are not used to collaborating with other people on course development and are therefore not used to compromising and negotiating what should go into a course. This can be compensated for to some degree by making courses easy to modify and customize, as we’ve tried to do with the Data Carpentry Semester course, but ultimately there will still need to be a shift from prioritizing the personal desires of the faculty member to the best interests of the course more broadly. This approach will likely work best where there are a number of places that all want to teach the same general material.
Is it time? When I built my first version of Programming for Biologists back in 2010 I was really excited about the potential for collaborative open course development. I built the course using Drupal, emailed a bunch of my friends who were teaching similar courses and said “Hey, we should work together on this stuff”, and stuck some welcoming language on the homepage. Nothing happened. A few years later I was on sabbatical at the University of North Carolina and got the opportunity to talk a fair bit with Elliot Hauser who was part of a team trying to encourage this through a start-up called Coursefork. I was somewhat skeptical that this approach would work broadly at the time, but I thought it was really awesome that they were trying. They ended up pivoting to focus on helping computing education through a somewhat different route and became trinket. A couple of years I converted my course to Jekyll on GitHub and told a lot of people about it. There was much excited. Still nothing happened. So why might this work now? I think there are three things that increase the possibility of this becoming a bigger deal going forward. First, open source software development is becoming more frequent in academia. It still isn’t rewarded anywhere close to sufficiently, but the ethos of using and contributing to collaboratively developed tools is growing. Second, the technical tools that make this kind of collaboration easier are becoming more widely used and easier to learn through training efforts like Software Carpentry. Third, more and more people are actively developing university courses using these tools and making them available under open source licenses. Two of my favorites are Jenny Bryan’s Stat 545 and Karl Broman’s Tools for Reproducible Research. Our development of the Data Carpentry semester course has already benefited from using openly available materials like these and feedback from members of the computational teaching community. I guess we’ll see what happens next.
This post benefited from a number of comments and suggestions by Zack Brym, who has also played a central and absolutely essential role in the development of the Data Carpentry semester long course. The post also benefited from several conversations with Tracy Teal, the Executive Director of Data Carpentry about the potential value of these approaches for college courses
Over the last year and a half we have been actively developing a semester-long Data Carpentry course designed to be easily customized and integrated into existing graduate and undergraduate curricula.
Data Carpentry for Biologists contains course materials for teaching scientists how to work more effectively with data. The course provides introductions to data management and relational databases, data manipulation and analysis, and data visualization. It covers the same general types of material as a two-day Data Carpentry workshop, but expands the materials and opportunities for practice into a full-length university course. The teaching material uses R and SQLite, with some corresponding materials for Python as well. To help students understand the direct applications to their interests, the examples and exercises focus on biological questions and working with real data. The course emphasizes using best practices to produce reusable and reproducible data analysis.
Active-learning Teaching Materials
Learning computing requires active practice by working through programming problems. Just diving in to computing is challenging for most scientists, so the course instruction is designed to combine short live-coding introductions to concepts followed immediately by the students working on a related exercise. Additional exercises are assigned later for practice. This follows the “I do”, “We do”, “You do” approach to teaching, which leverages the benefits of active-learning and flipped classrooms without leaving students who are less comfortable with the material feeling lost. The bulk of class time is spent working on assigned exercises with the instructor moving around the room helping guide students through things they don’t understand and engaging with students who are thinking about advanced applications of what they’ve learned.
This approach is the result of lots of reading about effective teaching methods and Ethan’s experience teaching this and related courses over the last six years at Utah State University and the University of Florida. It seems to work well for both students that get the material easily and those that find it more challenging. We’ve also tried to make these materials as useful as possible for self-guided students.
Open course development
Software Carpentry and Data Carpentry have shown how powerful collaborative lesson development can be and we’re interested in bringing that to the university classroom. We have designed the course materials to be modular and easy to modify, and the course website easy to clone and set up. All of the teaching materials and associated website files are openly available at the Data Carpentry for Biologists repository on GitHub under CC-BY and MIT licenses. The course materials are all written in Markdown and everything runs on Jekyll through GitHub Pages. Making your own version of the course should take less than an hour. We’ve developed documentation for how to create your own version of the course and how to contribute to development. Exercises and assignments are modular and changing exercises and assignments simply involves reordering items in a list. Adding a new exercise involves creating a new Markdown file and then adding its title to the list of exercises for an assignment.
If you teach, or want to teach, a course like this, we’d love to get you involved. Here are some useful links for getting started.
We want to be sure getting involved is as easy as possible. We’ve worked hard to provide documentation and help resources for students and instructors. Students can find all they need to know at our student start guide. Instructors have access to course content and site design documentation.
Development of this course was generously support by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4563 to Ethan White and the National Science Foundation as part of a CAREER award to Ethan White.
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 fight the air too, and I’m finally making real progress toward finishing my dissertation again.
I ruthlessly culled everything that wasn’t directly working on my dissertation. I was going to attend the Gordon Conference this year, as I had heard fantastic things about it for years, but had not been ready to go yet, but I had to drop that because I wasn’t physically able to travel. I did not go to ESA, because I couldn’t travel. There are working groups and workshops galore, all involving travel, which I cannot do. Right now, the closest thing that we have to bringing absent scientists to an event is live tweeting, which is not nearly as good as hearing a speaker for yourself, and is pretty heartbreaking if you had to cancel your plans to attend an event because you were too infirm to go.The tools that I’m using to do science remotely are not just for increasing accessibility for a single chronically ill macroecologist. They are good tools for science in general. I’m using GitHub to version control my code, and Dropbox to share data and figures. Ethan can see what I’m working on as I’m doing it, and I’ve got a clear record of what I was doing and what decisions that I made. While my cognitive dysfunction may be a bit more extreme of a problem, I know that we’ve all stayed up too late coding and broken something we shouldn’t have and the ability to wave the magic Git wand and make any poor decisions that I made while my brain was out to lunch go away is priceless.
Open access? Having open access to papers is really important when you are going to be faced shortly with probably not having any institutional access anymore. Also, important for everyone else who isn’t at a major university with very expensive subscriptions to all the journals. Having open access to data and code is crucial when you can’t collect your own data and are going to be doing research from your home computer on the cheap because you can’t rely on your body to work reliably at any given point in time.
Video conferencing is working well for me to meet with the lab, but could also be great for attending conferences and workshops. This would not only be good for a certain macroecologist, but would also be good to include people from smaller universities, etc. who would like to participate in these type of things too, but can’t otherwise due to the travel. I did my master’s degree at Fort Hays State University, and I still love it dearly. This type of increased accessibility would have been great for me while I was a perfectly healthy master’s student. Fort Hays is a primarily undergraduate institution in the middle of Kansas, about four hours away from any major city, and it does not have some of the resources that a larger university would have. No seminar series, no workshops, not much travel money to go to workshops or conferences, which doesn’t mean that good science can’t still be happening.
Many of my labmates are looking for post-docs, or are already in postdoc positions at this point. I’m very excited for all of them, and await eagerly all the stories of the exciting new things they are doing. Having a chronic illness limits what I am capable of doing physically. I am not going to be able to move across the country for a post-doc. That does not mean that I do not want to play science too. I’ve got my home base set up, and I can reach pretty far from here. I still want to be a part of living science, I don’t want to have to get to the party after everyone else has gone home.
And I wonder, why can I not do these things? Is it not the future? Do we not have the internet, with video chat? I get to meet with Ethan and talk science at our weekly meetings every week. I go to lab meetings with video chat, and get to see what my labmates are doing, and crack jokes, and laugh at other people’s jokes. It wouldn’t be hard to get me to conferences and working groups either.
With technology, I get to be a part of living, breathing science, and it is a beautiful thing.
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 (email@example.com) 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.
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. She wrote an excellent post on the PhDisabled blog about the initial development of her illness that I encourage you to read first.
During my time as a Ph.D. student, I developed a host of bizarre, productivity eating symptoms, and have been trying to make progress on my dissertation while also spending a lot of time at doctors’ offices trying to figure out what is wrong with me. I wrote an earlier blog post about dealing with the development of a chronic illness as a graduate student at the PhDisabled Blog.
When the rheumatologist handed me a yellow pamphlet labeled “Fibromyalgia”, I felt a great sense of relief. My mystery illness had a diagnosis, so I had a better idea of what to expect. While chronic, at least fibromyalgia isn’t doing any permanent damage to joints or brain. However, there isn’t a lot known about it, the treatment options are limited, and the primary literature is full of appallingly small sample sizes.
There are many symptoms which basically consisting of feeling like you have the flu all the time, with all the associated aches and pains. The worst one for me, because it interferes with my highly prized ability to think, is the cognitive dysfunction, or, in common parlance, “fibro fog”. This is a problem when you are actively trying to get research done, as sometimes you remember what you need to do, but can’t quite figure out how navigating to your files in your computer works, what to do with the mouse, or how to get the computer on. I frequently finish sentences with a wave of my hand and the word “thingy”. Sometimes I cannot do simple math, as I do not know what the numbers mean, or what to do next. Depending on the severity, the cognitive dysfunction can render me unable to work on my dissertation as I simply cannot understand what I am supposed to do. I’m not able to drive anymore, due to the general fogginess, but I never liked driving that much anyway. Sometimes I need a cane, because my balance is off or I cannot walk in a straight line, and I need the extra help. Sometimes I can’t be in a vertical position, because verticality renders me so dizzy that I vomit.
I am actually doing really well for a fibromyalgia patient. I know this, because the rheumatologist who diagnosed me told me that I was doing remarkably well. I am both smug that I am doing better than average, because I’m competitive that way, and also slightly disappointed that this level of functioning is the new good. I would have been more disappointed, only I had a decent amount of time to get used to the idea that whatever was going on was chronic and “good” was going to need to be redefined. My primary care doctor had already found a medication that relieved the aches and pains before I got an official diagnosis. Thus, before receiving an official diagnosis, I was already doing pretty much everything that can be done medication wise, and I had already figured out coping mechanisms for the rest of it. I keep to a strict sleep schedule, which I’ve always done anyway, and I’ve continued exercising, which is really important in reducing the impact of fibromyalgia. I should be able to work up my exercise slowly so that I can start riding my bicycle short distances again, but the long 50+ mile rides I used to do are probably out.
Fortunately, my research interests have always been well suited to a macroecological approach, which leaves me well able to do science when my brain is functioning well enough. I can test my questions without having to collect data from the field or lab, and it’s easy to do all the work I need to from home. My work station is set up right by the couch, so I can lay down and rest when I need to. I have to be careful to take frequent breaks, lest working too long in one position cause a flare up. This is much easier than going up to campus, which involves putting on my healthy person mask to avoid sympathy, pity, and questions, and either a long bus ride or getting a ride from my husband. And sometimes, real people clothes and shoes hurt, which means I’m more comfortable and spending less energy if I can just wear pajamas and socks, instead of jeans and shoes.
Understand that I am not sharing all of this because I want sympathy or pity. I am sharing my experience as a Ph.D. student developing and being diagnosed with a chronic illness because I, unlike many students with any number of other short term or long term disabling conditions, have a lot of support. Because I have a great deal of family support, departmental support, and support from the other Weecologists and our fearless leaders, I should be able to limp through the rest of my Ph.D. If I did not have this support, it is very likely that I would not be able to continue with my dissertation. If I did not have support from ALL of these sources, it is also very likely that I would not be able to continue. While I hope that I will be able contribute to science with my dissertation, I also think that I can contribute to science by facilitating discussion about some of the problems that chronically ill students face, and hopefully finding solutions to some of those problems. To that end, I have started an open GitHub repository to provide a database of resources that can help students continue their training and would welcome additional contributions. Unfortunately, there doesn’t seem to be a lot. Many medical Leave of Absence programs prevent students from accessing university resources- which also frequently includes access to subsidized health insurance and potentially the student’s doctor, as well as removing the student from deferred student loans.
I have fibromyalgia. I also have contributions to make to science. While I am, of course, biased, I think that some contribution is better than no contribution. I’d rather be defined by my contributions, rather than my limitations, and I’m glad that my university and my lab aren’t defining me by my limitations, but are rather helping me to make contributions to science to the best of my ability.
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. While BES’s formal policy is still a little more vague than I would like*, they have confirmed via Twitter that even preprints with open licenses are OK as long as they are not updated following peer review.
Preprints are important because they:
- Speed up the progress of science by allowing research to be discussed and built on as soon as it is finished
- Allow early career scientists to establish themselves more rapidly
- Improve the quality of published research by allowing a potentially large pool reviewers to comment on and improve the manuscript (see our excellent experience with this)
BES getting on board with preprints is particularly great news because the number of ecology journals that do not allow preprints is rapidly shrinking to the point that ecologists will no longer need to consider where they might want to submit their papers when deciding whether or not to post preprints. The only major blocker at this point to my mind is Ecology Letters. So, my thanks to BES for helping move science forward!
*Which is why I waited 3 weeks for clarification before posting.
Doing science in academia involves a lot of rejection and negative feedback. Between grant agencies single digit funding rates, pressure to publish in a few "top" journals all of which have rejection rates of 90% or higher , and the growing gulf between the number of academic jobs and the number of graduate students and postdocs , spending even a small amount of time in academia pretty much guarantees that you’ll see a lot of rejection. In addition, even when things are going well we tend to focus on providing as much negative feedback as possible. Paper reviews, grant reviews, and most university evaluation and committee meetings are focused on the negatives. Even students with awesome projects that are progressing well and junior faculty who are cruising towards tenure have at least one meeting a year where someone in a position of power will try their best to enumerate all of things you could be doing better . This isn’t always a bad thing  and I’m sure it isn’t restricted to academia or science (these are just the worlds I know), but it does make keeping a positive attitude and reasonable sense of self-worth a bit… challenging.
One of the things that I do to help me remember why I keep doing this is my Why File. It’s a file where I copy and paste reminders of the positive things that happen throughout the year . These typically aren’t the sort of things that end up on my CV. I have my CV for tracking that sort of thing and frankly the number of papers I’ve published and grants I’ve received isn’t really what gets me out of bed in the morning. My Why File contains things like:
- Email from students in my courses, or comments on evaluations, telling me how much of an impact the skills they learned have had on their ability to do science
- Notes from my graduate students, postdocs, and undergraduate researchers thanking me for supporting them, inspiring them, or giving them good advice
- Positive feedback from mentors and people I respect that help remind me that I’m not an impostor
- Tweets from folks reaffirming that an issue or approach I’m advocating for is changing what they do or how they do it
- Pictures of thank you cards or creative things that people in my lab have done
- And even things that in a lot of ways are kind of silly, but that still make me smile, like screen shots of being retweeted by Jimmy Wales or of Tim O’Reilly plugging one of my papers.
If you’ve said something nice to me in the past few years be it in person, by email, on twitter, or in a handwritten note, there’s a good chance that it’s in my Why File helping me keep going at the end of a long week or a long day. And that’s the other key message of this post. We often don’t realize how important it is to say thanks to the folks who are having a positive influence on us from time to time. Or, maybe we feel uncomfortable doing so because we think these folks are so talented and awesome that they don’t need it, or won’t care, or might see this positive feedback as silly or disingenuous. Well, as Julio Betancourt once said, "You can’t hug your reprints", so don’t be afraid to tell a mentor, a student, or a colleague when you think they’re doing a great job. You might just end up in their Why File.
What do you do to help you stay sane in academia, science, or any other job that regularly reminds you of how imperfect you really are?
 This idea that where you publish not what you publish is a problem, but not the subject of this post.
 There are lots of great ways to use a PhD, but unfortunately not everyone takes that to heart.
 Of course the people doing this are (at least sometimes) doing so with the best intentions, but I personally think it would be surprisingly productive to just say, "You’re doing an awesome job. Keep it up." every once in a while.
 There is often a goal to the negativity, e.g., helping a paper or person reach their maximum potential, but again I think we tend to undervalue the consequences of this negativity in terms of motivation [4b].
[4b] Hmm, apparently I should write a blog post on this since it now has two footnotes worth of material.
 I use a Markdown file, but a simple text file or a MS Word document would work just fine as well for most things.
As a budding macroecologist, I have thought a lot about what skills I need to acquire during my Ph.D. This is my model of the four basic attributes for a macroecologist, although I think it is more generally applicable to many ecologists as well:
- Knowledge of SQL
- Dealing with proper database format and structure
- Finding data
- Appropriate treatments of data
- Understanding what good data are
- Monte Carlo methods
- Maximum likelihood methods
- Power analysis
- Higher level calculus
- Should be able to derive analytical solutions for problems
- Should be able to write programs for analysis, not just simple statistics and simple graphs.
- Able to use version control
- Once you can program in one language, you should be able to program in other languages without much effort, but should be fluent in at least one language.
Achieve expertise in at least 2 out of the 4 basic areas, but be able to communicate with people who have skills in the other areas. However, if you are good at collaboration and come up with really good questions, you can make up for skill deficiencies by collaborating with others who possess those skills. Start with smaller collaborations with the people in your lab, then expand outside your lab or increase the number of collaborators as your collaboration skills improve.
Achieving proficiency in an area is best done by using it for a project that you are interested in. The more you struggle with something, the better you understand it eventually, so working on a project is a better way to learn than trying to learn by completing exercises.
The attribute should be generalizable to other problems: For example, if you need to learn maximum likelihood for your project, you should understand how to apply it to other questions. If you need to run an SQL query to get data from one database, you should understand how to write an SQL query to get data from a different database.
In graduate school:
Someone who wants to compile their own data or work with existing data sets needs to develop a good intuitive feel for data; even if they cannot write SQL code, they need to understand what good and bad databases look like and develop a good sense for questionable data, and how known issues with data could affect the appropriateness of data for a given question. The data skill is also useful if a student is collecting field data, because a little bit of thought before data collection goes a long way toward preventing problems later on.
A student who is getting a terminal master’s and is planning on using pre-existing data should probably be focusing on the data skill (because data is a highly marketable skill, and understanding data prevents major mistakes). If the data are not coming from a central database, like the BBS, where the quality of the data is known, additional time will have to be added for time to compile data, time to clean the data, and time to figure out if the data can be used responsibly, and time to fill holes in the data.
Master’s students who want to go on for a Ph.D. should decide what questions they are interested in and should try to pick a project that focuses on learning a good skill that will give them a headstart- more empirical (programming or stats), more theoretical (math), more applied (math (e.g., for developing models), stats(e.g., applying pre-existing models and evaluating models, etc.), or programming (e.g. making tools for people to use)).
Ph.D. students need to figure out what types of questions they are interested in, and learn those skills that will allow them to answer those questions. Don’t learn a skill because it is trendy or you think it will help you get a job later if you don’t actually want to use that skill. Conversely, don’t shy away from learning a skill if it is essential for you to pursue the questions you are interested in.
Right now, as a Ph.D. student, I am specializing in data and programming. I speak enough math and stats that I can communicate with other scientists and learn the specific analytical techniques I need for a given project. For my interests (testing questions with large datasets), I think that by the time I am done with my Ph.D., I will have the skills I need to be fairly independent with my research.
We had a great time at ESA this year and enjoyed getting to interact with lots of both old and new friends and colleagues. Since we’re pretty into open science here at Weecology, it’s probably not surprising that we have a lot of slides (and even scripts) from our many and varied talks and posters posted online, and we thought it might be helpful to aggregate them all in one place. Enjoy.
- Morgan Ernest‘s Ignite talk on Why Constraint Based Approaches to Ecology (with script)
- Morgan Ernest‘s talk on Biotic Responses to shifting Ecological Drivers in a Desert Community
- Ethan White‘s Ignite talk on Big Data in Ecology (with script)
- Ethan White‘s talk on Evaluating a General Theory of Macroecology
- Dan McGlinn‘s Ignite talk on Constraint Based Species-Area Relationships
- Dan McGlinn‘s talk on Modeling Geographic Patterns in the Species Abundance Distribution
Ken Locey‘s Ignite talk on The Feasible Set: Putting Pattern Into Perspective
Thanks to Dan McGlinn for help to assembling the links.
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. Since this is really a response to Jeremy’s post, not a description of my process, I’m going to use his categories in the same order as the original post and offer my more… youthful… perspective.
- Aim as high as you reasonably can. The crux of Jeremy’s point is “if you’d prefer for more people to read and think highly of your paper, you should aim to publish it in a selective, internationally-leading journal.” From a practical perspective journal reputation used to be quite important. In the days before easy electronic access, good search algorithms, and social networking, most folks found papers by reading the table of contents of individual journals. In addition, before there was easy access to paper level citation data, and alt-metrics, if you needed to make a quick judgment on the quality of someones science the journal name was a decent starting point. But none of those things are true anymore. I use searches, filtered RSS feeds, Google Scholar’s recommendations, and social media to identify papers I want to read. I do still subscribe to tables of contents via RSS, but I watch PLOS ONE and PeerJ just as closely as Science and Nature. If I’m evaluating a CV as a member of a search committee or a tenure committee I’m interested in the response to your work, not where it is published, so in addition to looking at some of your papers I use citation data and alt-metrics related to your paper. To be sure, there are lots of folks like Jeremy that focus on where you publish to find papers and evaluate CVs, but it’s certainly not all of us.
- Don’t just go by journal prestige; consider “fit”. Again, this used to mater more before there were better ways to find papers of interest.
- How much will it cost? Definitely a valid concern, though my experience has been that waivers are typically easy to obtain. This is certainly true for PLOS ONE.
- How likely is the journal to send your paper out for external review? This is a strong tradeoff against Jeremy’s point about aiming high since “high impact” journals also typically have high pre-review rejection rates. I agree with Jeremy that wasting time in the review process is something to be avoided, but I’ll go into more detail on that below.
- Is the journal open access? I won’t get into the arguments for open access here, but it’s worth noting that increasing numbers of us value open access and think that it is important for science. We value open access publications so if you want us to “think highly of your paper” then putting it where it is OA helps. Open access can also be important if you “prefer for more people to read… your paper” because it makes it easier to actually do so. In contrast to Jeremy, I am more likely to read your paper if it is open access than if it is published in a “top” journal, and here’s why: I can do it easily. Yes, my university has access to all of the top journals in my field, but I often don’t read papers while I’m at work. I typically read papers in little bits of spare time while I’m at home in the morning or evenings, or on my phone or tablet while traveling or waiting for a meeting to start. If I click on a link to your paper and I hit a paywall then I have to decide whether it’s worth the extra effort to go to my library’s website, log in, and then find the paper again through that system. At this point unless the paper is obviously really important to my research the activation energy typically becomes too great (or I simply don’t have that extra couple of minutes) and I stop. This is one reason that my group publishes a lot using Reports in Ecology. It’s a nice compromise between being open access and still being in a well regarded journal.
- Does the journal evaluate papers only on technical soundness? The reason that many of us think this approach has some value is simple, it reduces the amount of time and energy spent trying to get perfectly good research published in the most highly ranked journal possible. This can actually be really important for younger researchers in terms of how many papers they produce at certain critical points in the career process. For example, I would estimate that the average amount of time that my group spends getting a paper into a high profile journal is over a year. This is a combination of submitting to multiple, often equivalent caliber, journals until you get the right roll of the dice on reviewers, and the typically extended rounds of review that are necessary to satisfy the reviewers about not only what you’ve done, but satisfying requests for additional analyses that often aren’t critical, and changing how one has described things so that it sits better with reviewers. If you are finishing your PhD then having two or three papers published in a PLOS ONE style journal vs. in review at a journal that filters on “importance” can make a big difference in the prospect of obtaining a postdoc. Having these same papers out for an extra year accumulating citations can make a big difference when applying for faculty positions or going up for tenure if folks who value paper level metrics over journal name are involved in evaluating your packet.
- Is the journal part of a review cascade? I don’t actually know a lot of journals that do this, but I think it’s a good compromise between aiming high and not wasting a lot of time in review. This is why we think that ESA should have a review cascade to Ecosphere.
- Is it a society journal? I agree that this has value and it’s one of the reasons we continue to support American Naturalist and Ecology even though they aren’t quite as open as I would personally prefer.
- Have you had good experiences with the journal in the past? Sure.
- Is there anyone on the editorial board who’d be a good person to handle your paper? Having a sympathetic editor can certainly increase your chances of acceptance, so if you’re aiming high then having a well matched editor or two to recommend is definitely a benefit.
To be clear, there are still plenty of folks out there who approach the literature in exactly the way Jeremy does and I’m not suggesting that you ignore his advice. In fact, when advising my own students about these things I often actively consider and present Jeremy’s perspective. However, there are also an increasing number of folks who think like I do and who have a very different set of perspectives on these sorts of things. That makes life more difficult when strategizing over where to submit, but the truth is that the most important thing is to do the best science possible and publish it somewhere for the world to see. So, go forth, do interesting things, and don’t worry so much about the details.
We’re looking for a new student to join our interdisciplinary research group. The opening is in Ethan’s lab, but the faculty, students, and postdocs in Weecology interact seamlessly among groups. If you’re interested in macroecology, community ecology, or just about anything with a computational/quantitative component to it, we’d love to hear from you. The formal ad is included below (and yes, we did include links to our blog, twitter, and our GitHub repositories in the ad). Please forward this to any students who you think might be a good fit, and let us know if you have any questions.
GRADUATE STUDENT OPENING
The White Lab at Utah State University has an opening for a graduate student with interests in Macroecology, Community Ecology, or Ecological Theory/Modeling. Active areas of research in the White lab include broad scale patterns related to biodiversity, abundance and body size, ecological dynamics, and the use of sensor networks for studying ecological systems. We use computational, mathematical, and advanced statistical methods in much of our work, so students with an interest in these kinds of methods are encouraged to apply. Background in these quantitative techniques is not necessary, only an interest in learning and applying them. While students interested in one of the general areas listed above are preferred, students are encouraged to develop their own research projects related to their interests. The White Lab is part of an interdisciplinary ecology research group (http://weecology.org) whose goal is to facilitate the broad training of ecologists in areas from field work to quantitative methods. Students with broad interests are jointly trained in an interdisciplinary setting. We are looking for students who want a supportive environment in which to pursue their own ideas. Graduate students are funded through a combination of research assistantships, teaching assistantships, and fellowships. Students interested in pursuing a PhD are preferred. Utah State University has an excellent graduate program in ecology with over 50 faculty and 80+ graduate students across campus affiliated with the USU Ecology Center (http://www.usu.edu/ecology/).
Additional information about the position and Utah State University is available at:
Interested students can find more information about our group by checking out:
Our websites: http://whitelab.weecology.org, http://weecology.org
Our code repositories: http://github.com/weecology
Our blog: http://jabberwocky.weecology.org
And Twitter: http://twitter.com/ethanwhite
Interested students should contact Dr. Ethan White (firstname.lastname@example.org) by December 1st, 2012 with their CV, GPA, GRE scores (if available), and a brief statement of research interests.
UPDATE: If you’re looking for publicly available grants go check out our new Open Grants website at https://www.ogrants.org/. It has way more grants and is searchable so that you can quickly find the grants most useful to you.
Recently a bunch of folks in the biological sciences have started sharing their grant proposals openly. Their reasons for doing so are varied (see the links next to their names below), but part of the common justification is a general interest in opening up science so that all stages of the process can benefit from better interaction and communication, and part of it is to provide examples for younger scientists writing grants. To help accomplish both of these goals I’m going to do what Titus Brown suggested and compile a list of all of the available open proposals in the biological sciences (if you’re looking for math proposals they have a list too). Given the limited number of proposals available at the moment I’m just going to maintain the list here, sorted alphabetically by PI. Another way to find proposals is to look at the ‘grant’ and ‘proposal’ tags on figshare, where several of us have been posting proposals. If you know of more proposals, decide to post some yourself, or have corrections to proposal in the list, just let me know in the comments and I’ll keep the list updated. Enjoy!
- 2014 / Postdoctoral fellowships (several) – Making sense of cancer data: Implications for personalized therapy and cancer biology
- 2008 / Tools and Resources Development Fund Application – pubmed2ensembl: a resource for linking biological literature to genome sequences (BBSRC) *funded
- 2008 / New Investigator Grant Application (NERC) *funded
- 2008 / EMBO Young Investigator Programme Application (EMBO)
- 2007 / Responsive Mode Grant Application (BBSRC)
- 2014 / Children’s Foundation Research Institute – Prediction of Weight Gain in Inbred Mouse Strains *funded
- 2012 / NSF Office of Cyberinfrastructure proposal, Materials and Workshops for Cyberinfrastructure Education in Biology supplement to BEACON. *funded
- 2012 / NSF CAREER proposal, Assembling Extremely Large Metagenomes
- 2012 / NSF BIGDATA proposal, Low-memory Streaming Prefilters for Biological Sequencing Data
- 2012 / Moore Foundation proposal on marine metagenomics
- 2011 / NSF CAREER proposal: “Scaling and Improving de Bruijn graph assembly”
- 2010 / Next-gen course (NIH R25) *funded
- 2009 / Web tools for next-gen sequence analysis (USDA) *funded
- 2007 / Cartwheel
- Kathryn Fuller Doctoral Fellowship application (WWF)
- 2010 / Prairie Biotic Research proposal *funded
- 2009 / Ecological and evolutionary impacts of pollinator sharing between cultivated and wild sunflowers (Norman Hackerman Advanced Research Program)
- 2009 / Lewis and Clark grant proposal (American Philosophical Society)
- Doctoral Dissertation Improvement Grant proposal (NSF)
- Forest Shreeve Award proposal
- Ariel Appleton Research Fellowship Proposal – Ecological Networks
- How do crop-mediated changes in mutualist and antagonist communities affect selection on floral and defense traits?
- 2015 / Marie Skłodowska-Curie Individual Fellowship *funded
- 2011 / “Automated and community synthesis of the tree of life” (NSF AVATOL) *funded
- 2010 / “Towards a comprehensive, community-owned and sustainable repository of reusable phylogenetic knowledge” w/Hilmar Lapp (NSF ABI)
- 2009 / “A network for enabling community-driven standards to link evolution into the global web of data (EvoIO)” w/Hilmar Lapp (NSF INTEROP)
- 2009 / NSF Plant Genome *funded
- 2013 / “Reversing long-term experiments to understand regime shifts” (NSF DEB preproposal) *funded
- 2012 / Understanding range shift model error: The inﬂuence of generation time and rate of adaptation on species distribution model predictions. w/Scott Chamberlain (NCEAS proposal).
- 2008 / Evolution under simulated climate change in response to trophic shifts. (NSF DDIG) *funded
- 2010 / Protein Design Using Quantum Mechanics (Danish Center for Supercomputing) *funded
- 2008 / Computational Design of Stable Enzymes (Danish National Science Foundation, DSF-NABIIT) *funded
- 2006 / Modeling pH-Dependence in Drug Design (EU Marie Curie Program) *funded
- 2006 / Computational Prediction and Validation of Protein Structure and Function in Protein Engineering and Rational Drug Design (Danish National Science Foundation, FNU) *funded
- 2006 / Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation – MCB; rescinded when I moved to Denmark) *funded
- 2002 / The Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation – MCB) *funded
- 2010 / Ontology-enabled reasoning across phenotypes from evolution and model organisms w/Todd Vision (NSF) *funded
- 2013 / NSF Postdoctoral Research Fellowship in Biology
- 2010 / Leakey Foundation General Research Grant
- 2009 / US Student Fulbright
- 2009 / NSF Dissertation Improvement Grant
Heather Piwowar (@researchremix) & Jason Priem (@jasonpriem) (read their thoughts on sharing proposals)
- Uptake proposal (CIHR)
- 2007 / Sxy proposal (CIHR) *funded
- 2001 / CIHR proposal *funded
- 1999 / NIH proposal *funded
- 2009 / USDA/NIFA: “Scanning for yield: high-throughput discovery of candidate agronomic loci for marker-assisted selection in maize” *funded
- 2015 / NSF Plant Genome Research Program: “The genetics of highland adaptation in maize” *funded
- Netherlands organization for scientific research postdoc fellowship
- Netherlands organization for scientific research PhD fellowship
- Netherlands organization for scientific research PhD fellowship
- Netherlands organization for scientific research PhD fellowship *funded
- Netherlands organization for scientific research postdoc fellowship *funded
- 2010 / NSF Graduate Research Fellowship *funded
- 2016 / NSF Postdoctoral Fellowship *funded (associated reviews)
- 2014 / Gene Wiki: Expanding the ecosystem of community intelligence resources (R01 GM089820)
- 2017 / Gene Wiki renewal
- 2014 / Dynamic macroecology: Globally assessing body size diversity response to environmental change (NSF Postdoctoral Fellowship) *funded
- 2012 / Data Management and Computational Skills Training for LTER Scientists w/Ethan White & Greg Wilson (LTER Training Working Groups Proposal)
- 2011 / Fuelwood, Savannas, and Climate Change: Integrating Modeling, Field Experimentation, and Optical and Radar Remote Sensing (NASA Predoctoral Graduate Fellowship) *funded
- 2014 / NSF Postdoctoral Fellowship – Diversity-stability relationships and coexistence: new theory and empirical tests *funded
- 2012 / Genomic tools to study coral reef resilience (University of Melbourne)
- 2012 / Plastid endosymbiosis: a detailed study of genome dynamics (Australian Research Council)
- 2012 / Evolutionary dynamics of the algae: Understanding adaptive potential under environmental change (Australian Research Council) *funded
- Probing key innovations with next generation sequencing
- 2009 / Macroevolutionary dynamics of marine algae
- 2012 / Sustainable and Scalable Infrastructure for the Publication of Data (NSF) *funded
- 2008 / A Digital Repository for Preservation and Sharing of Data Underlying Published Works in Evolutionary Biology (NSF) *funded
- 2013 / ERC AdG IMMUNENESIS *funded
- 2014 / Moore Investigator in Data Driven Discovery proposal *funded
- 2010 / CAREER: Advancing Macroecology Using Informatics and Entropy Maximization (NSF CAREER Award) *funded
- 2005 / Broad-scale patterns of the distribution of body sizes of individuals in ecological communities (NSF Postdoc Fellowship) *funded
- 2008 / Understanding multimodality in animal size distributions (NSF Research Starter Grant) *funded