Proxy Server Bookmarklet

Like so many of us, when I’m off campus, in order to read journal pdfs and the like is a chore. I have to go to my university’s library website, login to their proxy server, go back to the article in question – either by surfing there from the library webpage, or adding the relevant text to the journal article URL.

Pain in the tuchus.

Then, the ever helpful Sean Anderson tweeted a link to a little code he’d written for a bookmarklet using Dalhousie’s ezproxy.

Create a bookmark with this address:
(create some dummy bookmark and then edit the address)


Then go to a journal page and click the bookmark when you want to log in through the library server.

I modified it for UMB:


Or just, if you’re at UMB, drag the following link to your browser bookmarklet bar: umb-ezproxy – go to an article you want but can’t read, and click it. Such naches!

I’m sure the rest of you kinder can modify it to match your own situation!

How I Use Different Social Media Platforms for Science

OK, so, you’re a scientist interested in jumping into the world of online social networking for interacting with colleagues, fun and profit bringing science to the world at large. Fantastic!

So, you log on, and are suddenly confronted by a dizzying array of sites you could use to communicate. Facebook, Instagram, Twitter, Google+, Myspace (yes, it’s back), Blogspot, WordPress, FriendFeed, Tumblr, …. I could go on for a while. And then you may also have concerns about mixing personal and private.

So, which should you use? And why? Before going on, read Bik and Goldstein. Just, trust me. In particular, their Box 1, Box 2, and Fig 2. That paper is gold.

For me, I’ll be honest, I only use three of the above – and each for a distinct purpose. Other social media mavens out there might have different takes, or find that different platforms have better milage for them – and I’d love to hear what you’re using and why! But, this is my take on the platforms I use and how I handle things like privacy and the kind of things I’ll say in each.

0) A Personal Webpage – This one seems obvious, but I find so many instances of people *not* having at least a professional web presence as a slice of hypertext on someone else’s webpage (e.g., advisor, organization you work for, etc.) that it bears repeating. This is the face you present to the world, and often the first hit on a search for you. Make it count!

If you’re not HTML savvy and don’t know where to start, services like Weebly and WordPress not only provide tools to build a site, but reams of wonderful templates. They’ve also got some fancier options for a small fee. Or host your own on a site service like Hostmonster as I do. Such sites often have tools for easily installing content rich professional websites (often using things like WordPress) with just a few clicks.

1) Twitter – To me, this is the ur-site for social media and science. It’s quick, easy, has a ton of tools (HootSuite, TweetDeck, etc.) to make the information firehose that it contains easy to sort (hashtags and lists are fabulous), and provides a great way to dip into the stream of scientific conversation very easily. It’s also fully public. What you say there will tell a lot of people about who you are. It really is your choice who you want to be. So, it is where my professional scientific persona lives, as it were. Which is pretty much just me, but with some guardrails on, as it were. The brevity of posts is also a huge benefit, as it’s a low barrier to entry, and low barrier to interaction. And there are a ton of Ecologists, Evolutionary, and Marine Biologists on it.

2) Blogs – This is where one can go long-form and really lay out some thoughts or a meaty juicy piece of what they’re doing. There’s no set form, structure, or rules, really. Basically, I view my blog as an intellectual sandbox. And it’s excellent practice for writing. Heck, I’ve even knitted together significant pieces of papers from blog posts. Basically, I view blogs as the place for good, well thought out, detailed, interaction and communication to take place. It’s where you can show all of who you are and how you think. It’s where you can try and connect with audiences – public and scientific – using the broadest most informative brush. It’s not a substitute for the peer reviewed literature, but rather a place where the scientific ebb and flow of ideas can find a home when we’re not all at a meeting or somesuch.

3) Google+ – I’m still not sure about this one. I LOVE hangouts, and am going to be trying some experiments with them in the future. They’ve basically replaced Skype for me, and I’ve found that G+’s groups and communities are terribly convenient for organizing and posting to groups of folk working on a project. But as a primary source of social media presence….you can post longer things than you can on Twitter? I think the multi-media capabilities and hangouts are key for what G+ has to offer, and, so, that’s what I use it for!

4) Facebook – you notice that I haven’t mentioned Facebook up to this point? Curious, no? Maybe it’s because of historical reasons (remembering a long line of social media sites – Friendster, Orkut, Myspace, etc.), maybe it’s because of the higher degree of immediate interaction, maybe its because my mom is on it (hi, mom!) – I’m not totally sure why, but I, at least, use Facebook for personal purposes only. I mean, I pipe my Twitter feed into it, and enjoy the conversation that occurs off of it. But I generally only add folk who I have met personally or have a personal connection of somesort. Basically, folk I’m willing to let in to see who I am a little less guardedly – my not-so-professional online persona, if you will (there are a lot of cat photos, I admit). This is not true of all fields. For example, my wife is in theater, and theater is all about being social. Thus, Facebook becomes a professional space.

This is not to say that Facebook cannot evolve into a professional space. Actually, my favorite use of it lately has been the number of fellow scientists with whom I have a professional relationship sharing some of their inside thoughts regarding their own careers, their daily struggles, and a good bit of camaraderie and commiserations.

Oh, last, a word of caution to those of you not yet aquatinted with this fact – everything you say on the internet is forever able to be associated with you. It will come up when you least expect it. What you say online shapes how folk perceive you. Even things that you think are completely 100% private…not always so much (particularly if Facebook randomly changes its privacy settings). This is not to say that people are not forgiving of context – they are or should be delightfully so – but, you know, think before you hit post.

In fact, all of this brings me to a point I make a lot in public, and, I should perhaps post here so that I can have it in digital print: If you are not curating your online identity, someone or something else is doing it for you. By someone I don’t mean some specific person (usually), but, rather, a combination of the crowd and information sifting algorithms. So, want to leave a good impression? Be known as a person interested in topic X? Only you have that power. And with great power…

So, feel free to use the above as a general guide, or discover that, in internet terms, I’m a fuddy-duddy and there are better ways of using social network tools that are at your disposal. Or, heck, I’m sure there are tools waiting out there somewhere on the horizon that can enhance the scientific conversation even more!

Updated 10/2013 with some links to sites to help you build professional websites

Marshall the generalists! Generalize the marshallists!

While working more on the bacterial network stuff, Jen and I realized I was wrong. Yep, I was wrong on the internet. Namely, in my post on bacterial networks, I got the answer wrong on the abundance of OTUs with different degrees of specialization. I had a rowSum after inverting a matrix instead of before, producing wonky vertex sizes. Jen cleverly discovered it when totaling up some of the data by hand, and after alerting me to the issue I produced the following plot which doesn’t agree with the network at all:

Screen Shot 2013-07-02 at 1.29.24 PM

So, I went back in, found the error, and now I give you the corrected network. Still very interesting – and it really shows that in the marsh, generalist bacteria dominate numerically, although they are relatively rare with far more specialists.

Screen Shot 2013-07-02 at 1.23.17 PM

Updating the github soon…

Giving Honest Resources to Prospective Students

A question for the peanut gallery –

I’m starting to get a trickle of the interested-in-grad-school student emails. So far the few I’ve gotten have been great. So, I’m revising my prospective students page after noticing a few things in year one. The first was a lack of some students realizing that I wanted to know their interests beyond ‘marine ecology’. I wanted a research question – any question, no matter how broad – as having a question does not guarantee it’s what you’re going to follow in your graduate career. It was just to see how students think and what I might expect from them. Now I’ve made that a wee bit more explicit, and the division between potential masters and PhD students on the page. This is all ok

OK – honesty aside, as who knows if one of the potential mentors I interviewed with is reading this, but, one of my potentially most embarrassing moments as a prospective PhD student was my first meeting with her. I had just taken a cross country flight or two, and then went to dinner with them. The first thing they asked me was, “What are you interested in?” And, indeed, I answered, after far too long of a pause, “Marine ecology.” Long pause. Then, they were kind enough to gently say, “OK, what about marine ecology?…” After I screwed my head back on a bit straighter, we had a lovely conversation about ideas, work, etc., and I passed out as soon as my head hit my pillow that night. So, you know, everyone flounders a bit. Particularly when extremely jet-lagged and getting an adrenaline rush of peering into the future.

OK, so, my question – One thing I’ve been pondering, though, is putting a piece on the page as a heads-up about the prospects of a PhD or masters student. In particular in reading Jacquelyn’s recent piece and the excellent discussion therein, and thinking about the answers to my question, “Why this degree?” to prospectives last year, I’ve realized that most students just haven’t thought about it, or have unrealistic expectations. My question is, what should we be telling them? This page – the prospective students information – is perhaps the venue they will scan most closely, and hence one of the best places to give students some knowledge about what this degree can do for them and what long-term challenges will be once they enter the employment market. I’m trying to be brief, and provide a few helpful, if sobering, links to start further reading. So – do you think this is a good idea? And if so, does the tone veer too far one way or another? I’ve tried to be gentle, if cautionary.

Or, maybe I won’t put this up at all…

— Here’s the new section

Why a graduate degree?

Why are you interested in a graduate degree? If you have no research experience aside from working as a lab tech, a masters degree might be what you’re looking for. Or it’s excellent as there are a wide variety of career options that are open to you with a masters. Do some homework – ask yourself how this degree will help you achieve your professional goals. For a PhD, I know the default answer is always “So I can be a university professor.” That’s great, and I look forward to working together to help you achieve that goal. Do some reading, though, and make sure you know what you’re jumping into (and be sure to read the comment thread at that link). The job market for academics is never great. This is not to discourage you, but take a breath before diving in and think about long-term goals. Know also that a PhD is amazing training for a wide variety of careers as well. So, think about your long-term goals and why a PhD is the right road for you. You may also be interested in checking out this book.

Beautiful Bacterial Networks in the Marsh

“So,” I’m sure you aren’t wondering, how did that creating ‘ecospecies’ from bacterial sequences based on sequence similarity, co-occurrence, and network theory work out for you?”

Quite well, thanks for asking! Heck, have a git repository, why dontcha!

Jen is furiously writing the manuscript, but, the technique indeed seems to indicate that 12% sequence similarity was the optimal number.

Once we got that down, and started plotting the network with individual Operational Taxonomic Units (OTU) each connected to one or more of the 8 plots they were found in, we started seeing some neat things. More more than that, they were just pretty pictures! I mean, come on, these plots are always cool.

Screen Shot 2013-06-26 at 4.18.40 PM

First, you can see that there is indeed some separation of species by plot and treatment (# is plot, letter is treatment). We got really excited about this, and so dug deeper to produce…

Screen Shot 2013-06-26 at 4.19.49 PM

Yes. Not you can see that most OTUs are specialists. True generalists are exceedingly rare.

We had one other piece of information up our sleeve, though. Abundance. We have abundances of OTUs. Playing around with edge widths (abundance in plot) didn’t produce anything striking. But then we looked at total abundance of an OTU across the whole marsh, and resized OTU nodes accordingly. I think this is exceedingly beautiful. And shows some striking patterns with respect to treatment and who is most abundant.

Screen Shot 2013-06-26 at 4.19.10 PM

Jen knows this experiment backwards and forwards, so is writing a much more nuanced discussion of what this means, and analyzing the data in more detail. But it’s pretty awesome. And pretty beautiful.

Just another way of viewing the wonder of nature.

p.s. I am learning to love RColorBrewer in a serious way

Les Miserables Larides

One of the great things about field stations is the silliness they engender. I mean, there you are, in the middle of nowhere, with no one but other scientists thinking about the wonder of the natural world. Awe and wonder can only take you so far. And then, at some point, you cross over, and start to get a little silly.

It leads to things like dressing up as fouling panels, launching serious plans to make an ‘underwater office,’ elaborate nail-polish-marking designs for crab carapaces, and no small number of pranks.

And then, there’s this. This may be on the order of the silliest things ever to come out of field station. I heard the gull interns (seagull science is notorious for producing silliness alongside great science) talking about this idea to sync some of their videos up with the Les Mis soundtrack and now…now I found they’ve… well..

You must see this to believe it. Astounding. My hats off to the SML 2013 Gull crew. Marine science music video of the year?

(also, who is singing on ‘I dreamed a dream’ – amazing voice!)

PeerJ Turns One!

x-posted from openpub

One year ago, one of the more intereting experiments in open access publishing – PeerJ – launched. It’s model of membership rather than paying by the article is still something people are grappling with – it’s just so different, so delightfully disruptive. Not only that, but PeerJ has stepped in to fill the void in providing a biology preprint server (which we have used), as well as coming up with a more intuitive interface for commentary on preprints and published work – along with supplying reviews alongside published work. A number of other great open access journals have tried one or more of these innovations, but few have tried them all *at once*. Not only that, but I have the feeling they’re not going to stop there.

After all, if they’ve tried this many new things in year one, I, for one, want to know what year two is going to hold…