Jabberwocky Ecology

A GitHub of Science? [Things you should read]

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:

Evangelists for Open Science should focus on promoting new, post-publication prestige metrics that will properly incentivize scientists to focus on the utility of their work, which will allow them to start worrying less about publishing in the right journals.

Thanks to Carl Boettiger for pointing me to the post. It’s definitely worth reading in its entirety.

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*A blog I’d never heard of before, but I subscribed to it’s RSS feed before I’d even finished the entire post.

**As far as biologists go. And, yes, when I say “insanely nerdy” I do mean it as a complement.

***For those interested in slightly more detail it’s a social application wrapped around the popular distributed version control system named Git. Kind of like Sourceforge on steroids.

Thoughts on developing a digital presence

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

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

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

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

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

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

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

Daily Routines [Things you should read]

I just restumbled over the Daily Routines blog. The blog is about “how writers, artists, and other interesting people organize their days” and is basically just excerpts from interviews with famous creative folks. The blog appears to be “on hold” pending an upcoming book, but I definitely recommend pulling it up some lazy afternoon and working your way through how some of the most creative people around structure their days.

Beta Release of Database Toolkit

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. To help improve ecologists’ ability to quickly access and analyze data we have been developing software that designs database structures for ecological datasets and then downloads the data, processes it, and installs it into several major database management systems (at the moment we support Microsoft Access, MySQL, PostgreSQL, and SQLite). The database toolkit system can substantially reduce hurdles to scientists using new databases, and save time and reduce import errors for more experienced users.

The database toolkit can download and install small datasets in seconds and large datasets in minutes. Imagine being able to download and import the newest version of the Breeding Bird Survey of North America (a database with 4 major tables and over 5 million records in the main table) in less than five minutes. Instead of spending an afternoon setting up the newest version of the dataset and checking your import for errors you could spend that afternoon working on your research. This is possible right now and we are working on making this possible for as many major public/semi-public ecological databases as possible. The automation of this process reduces the time for a user to get most large datasets up and running by hours, and in some cases days. We hope that this will make it much more likely that scientists will use multiple datasets in their analyses; allowing them to gain more rapid insight into the generality of the pattern/process they are studying.

We need your help

We have done quite a bit of testing on this system including building in automated tests based on manual imports of most of the currently available databases, but there are always bugs and imperfections in code that cannot be identified until the software is used in real world situations. That’s why we’re looking for folks to come try out the Database Toolkit and let us know what works and what doesn’t, what they’d like to see added or taken away, and if/when the system fails to work properly. So if you’ve got a few minutes to have half a dozen ecological databases automatically installed on your computer for you stop by the Database Toolkit page at EcologicalData.org, give it a try, and let us know what you think.

Some days…

Some days I really wonder whether the bureaucratic infrastructure at institutions of higher education has any idea whatsoever that their job is to support the research and teaching missions of the university.

The top idea in your mind [Things you should read]

Successfully doing creative science is hard. The further along you get in a research career the more things are competing for your time and energy and the more distracted you are from your primary goals. This distraction becomes increasingly problematic when it distracts your subconscious as well as your conscious mind. A short post by Paul Graham does an excellent job of describing why this is the case and how you can manage access to that creative part of your brain. In particular he recommends minimizing the amount of time spent chasing money and being involved in disputes. These are both things that we end up doing a lot of in academia and in my experience Graham is right about their ability to consume the productive thought processes we rely on. I also love this quote from Newton:

I see I have made myself a slave to Philosophy, but if I get free of Mr Linus’s business I will resolutely bid adew to it eternally, excepting what I do for my private satisfaction or leave to come out after me. For I see a man must either resolve to put out nothing new or become a slave to defend it.

Go check out the full post.

(via James Horey)

If we embrace the fact that no one can or should ever care about the health of our passions… [Quote]

If we embrace the fact that no one can or should ever care about the health of our passions as much as we do, the practical decisions that help ensure Our Good Thing stays alive can become as “simple” as a handful of proven patterns—work hard, stay awake, fail well, hang with smart people, shed bullshit, say “maybe,” focus on action, and always always commit yourself to a bracing daily mixture of all the courage, honesty, and information you need to do something awesome—discover whatever it’ll take to keep your nose on the side of the ocean where the fresh air lives. This is huge.

– Merlin Mann

A great quote from an interesting article about Future-Proofing Your Passion that includes lots of great advice for young and old scientists alike.

Spring Break = Think Week for academic scientists

Transient Theorist is planning on doing something with his Spring Break that most of us don’t do often enough – take a week to think. In the rush to do all of the things that have to be done, we often lose track of doing the things that are really important to our core mission – advancing scientific knowledge as quickly as possible. A large part of accomplishing this mission is taking the time to think, explore ideas, consider the broader contexts in which one’s interests lie and develop linkages beyond the narrow confines of one’s discipline. It also includes taking the time to develop new skills, be they in the lab or on the computer. These activities rarely have short-term benefits and they practically never have meaningful deadlines. As such, it is easy for them to be sacrificed for things that need to be done now. So, I’d suggest that you go read Theo’s post for inspiration (and check out some of the posts in the Study Hacks Primer), start saying no so that you have a chance to assign time to bigger things, and try to find at least a few days over this Spring Break to really think about where your science is going over the next year.

Getting things done in academia

In a couple of days I’m participating in a panel to help young faculty be ready for their 3rd year review (the halfway step to tenure, which is kind of a big deal at my institution). This is the sort of thing that I normally say no to, but I’ve been to a couple of these things and I just couldn’t bear the thought of another group of young faculty being told that what they really needed to do to get tenure is to have a really spiffy tenure binder… so I’m going to talk about what they actually need to do to get tenure – get stuff done – and I thought it would be worth posting my thoughts on this here for broader consumption. This advice is targeted at assistant professors at research universities, but folks in other situations may be able to adapt it to their individual circumstances (e.g., if you’re at a small liberal arts college or other teaching centered school try swapping research and teaching below). Since the goal of the workshop is getting through the first phase of tenure, this is about what you need to do to accomplish that goal, not what you should be doing in any sort of broader philosophical sense. This advice is built on the lessons that Morgan (my wife and co-blogger for those of you new to JE; in fact she was so instrumental in developing these ideas that even though I’m using the first person singular this will be listed as a co-authored post) and I have learned during our time as assistant professors.

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[Quote] Nilsson on credit for scientific work

Some years ago, someone wrote a book called “The Seven Laws of Money.” One of the “laws” went something like this: “Do good work and don’t worry about money; it will come along as a side effect.” Whether or not that’s true of money, I don’t know, but in my experience, it’s true of credit for scientific work. Just make sure you keep working at important problems, enjoying a life of science, and don’t worry so much about credit. You will probably get what you deserve — as a side effect.

Nils Nilsson (via Vladimir Lifschitz)

Why you should use a feed reader to monitor journal table of contents

A couple of weeks ago we made it possible for folks to subscribe to JE using email. We did this because we realized that many scientists, even those who are otherwise computationally savvy, really haven’t embraced feed readers as a method of tracking information. When I wrote that post I promised to return with an argument for why you should start using a feed reader instead – so here it is. If anyone is interested in a more instructional post about how to do this then let us know in the comments.

The main argument

I’m going to base my argument on something that pretty much all practicing scientists do – keeping track of the current scientific literature by reading Tables of Contents (TOCs). Back in the dark ages the only way to get these TOCs was to either have a personal subscription to the journal or to leave the office and walk the two blocks to the library (I wonder if anyone has done a study on scientists getting fatter now that they don’t have to go to the library anymore). About a decade ago (I’m not really sure when, but this seems like it’s in the right ballpark) journals started offering email subscriptions to their TOCs. Every time a new issue was published you’d receive an email that included the titles and authors of each contribution and links to the papers (once the journal actually had the papers online of course). This made it much easier to keep track of the papers being published in a wide variety of journals by speeding up the process of determining if there was anything of interest in a given issue. While the increase in convenience of using a feed reader may not be on quite the same scale as that generated by the email TOCs, it is still fairly substantial.

The nice thing about feed readers is that they operate one item at a time. So, instead of receiving one email with 10-100 articles in it, you receive 10-100 items in your feed reader. This leads to the largest single advantage of feeds over email for tracking TOCs. You only need to process one article at a time. Just think about the last time you had 5 minutes before lunch and you decided to try to clear an email or two out of your inbox. You probably opened up a TOC email and started going through it top to bottom. If you were really lucky then maybe there were only a dozen papers and none of them were of interest and you could finish going through the email and delete it. Most of the time however there are either too many articles or you want to look at at least one so you go to the website, read the abstract, maybe download the paper, and the next thing you know it’s time for lunch and you haven’t finished going through the table so it continues to sit in your inbox. Then, of course, by the time you get back to it you probably don’t even remember where you left off and you basically have to start back at the beginning again. I don’t know about you but this process typically resulted in my having dozens of emailed TOCs lying around my inbox at any one time.

With a feed reader it’s totally different. If you have five minutes you start going through the posts for individual articles one at a time. If you have five minutes you can often clear out 5 or 10 articles (or even 50 if the feed is well tagged like PNAS’s feed), which means that you can use your small chunks of free time much more effectively for keeping up with the literature. In addition, all major feed readers allow you to ‘star’ posts – in other words you can mark them in such a way that you can go back to them later and look at them in more detail. So, instead of the old system where if you were interested in looking at a paper you had to stop going through the table of contents, go to the website, decide from the abstract if you wanted to actually look at the paper, and then either download or print a copy of the paper to look at later, with a feed reader you achieve the same thing with a one second click. This means that you can often go through a fairly large TOCs in less than 10 minutes.

Of course much of this utility depends on the journals actually providing feeds that include all of the relevent information.

Other benefits

Keeping your TOCs and other feeds outside of your email allows for greater separation of different aspects of online communication. If you monitor your email fairly continuously, the last thing you need is to receive multiple TOC emails each day that could distract you from actually getting work done. Having a separate feed reader let’s you actually decide when you want to look at this information (like in those 5 minutes gaps before lunch or at the end of the day when you’re too brain dead to do anything else).

Now that journals post many of their articles online as soon as the proofs stage is complete, it can be advantageous to know about these articles as soon as they are available. Most journal feeds do exactly this, posting a few papers at a time as they are uploaded to the online-early site.

Sharing – want to tell your friends about a cool paper you just read. You could copy the link, open a new email, paste the link and then send it on to them. Or, you could accomplish this with a single click (NB: this technology is still developing and varies among feed readers).

And then of course there are blogs

I’ve attempted to appeal to our non-feedreader-readers by focusing on a topic that they can clearly identify with. That said, the world of academic communication is rapidly expanding beyond the walls of the journal article. Blogs play an increasingly important role in scientific discourse and if you’re going to follow blogs you really need a feed reader. Why? Because while some blogs update daily (e.g., most of the blogs over at ScienceBlogs) many good blogs update at an average rate of once a week, or once a month. You don’t want to have to check the webpage of one of these blogs every day just to see if something new has been posted, so subscribe to its feed, kick back, and let the computer tell you what’s going on in the world.

A message to journal editors/managers about RSS feeds

  1. If you don’t have an easily accessible RSS feed available (and by easily accessible I mean in the browser’s address bar on your journal’s main page) for your journal’s Table of Contents (TOCs), there is a certain class of readers who will not keep track of you TOCs. This is because receiving this information via email is outdated and inefficient and if you are in the business of content delivery it is, at this point, incompetent for you to not have this option (it’s kind of like not having a website 10 years ago).
  2. If, for some technophobic reason, you refuse to have an RSS feed, then please, pretty please with suger on top, don’t hide the ability to subscribe to the TOCs behind a username/password wall. All you need is a box for people to add their email addresses to for subscribing and a prominent unsubscribe link in the emails (if you are really paranoid you can add a confirmation email with a link that needs to be followed to confirm the subscription).
  3. Most importantly. Please, for the love of all that is good and right in the world, DO NOT START AN RSS FEED AND THEN STOP UPDATING IT. Those individuals who track a large number of feeds in their feed readers will not notice that you stopped updating your feed for quite some time. You are losing readers when you do this.
  4. If you have an RSS feed that is easily accessible (congratulations, you’re ahead of many Elsevier journals) please try to maximize the amount of information it provides. There are three critical pieces of information that should be included in every TOCs feed:
    1. The title (you all manage to do this one OK)
    2. All of the authors’ names. Not just the first author. Not just the first and last author. All of the authors. Seriously, part of the decision making process when it comes to choosing whether or not to take a closer look at a paper is who the authors are. So, if you want to maximize the readership of papers, include all of the authors’ names in the RSS feed.
    3. The abstract. I cannot fathom why you would exclude the abstract from your feed, other than to generate click throughs to your website. Since those of you doing this (yes, Ecology, I’m talking about you) aren’t running advertising, this isn’t a good reason, since you can communicate the information just as well in the feed (and if you’re using website visits as some kind of metric, don’t worry, you can easily track how many people are subscribed to your feed as well).

If this seems a bit harsh, whiny, etc., then keep this in mind. In the last month I had over 1000 new publications come through my feed reader and another 100 or so in email tables of contents. This is an incredible amount of material just to process, let alone read. If journals want readers to pay attention to their papers it is incumbent upon them to make it as easy as possible to sort through this deluge of information and allow their readership to quickly and easily identify papers of interest. Journals that don’t do this are hurting themselves as well as their readers.