Online Tools

If you’ve visited Cold Spring Harbor Protocols in the last 12 hours or so, you may have noticed that things look a little different. Welcome to Phase 1 of our re-design.

CSH Protocols was originally designed as a database, but over time, our readers and authors made it clear to us that their needs would be better served if it became more journal-like. For an author, publishing a peer-reviewed, PubMed indexed paper offers better rewards than contributing to a database. For readers who are used to digging information out of the published literature, a journal offers better findability. And so, we’ve redesigned the site to bring it into line with Cold Spring Harbor Laboratory Press’ other journal offerings.

The site still offers the same functionality, but now the navigation is greatly improved. The new design also allows us to start experimenting with widgets, adding further functionality. The next step will be migrating to our host, Highwire Press’ new H2O platform, which will allow for even further functionality to be built in (coming in the near future).

So take a look around, maybe you’ll find some things you haven’t found before. And stay tuned for future developments.

The other blog where I write, The Scholarly Kitchen, has been nominated for a Webby, a fairly prestigious award in the online world. Since the winner is determined by the voting public, and since we’re up against some seriously stiff competition (including the NY Times and Wall Street Journal), your help would be greatly appreciated. You can vote for us here. Voting does require you to complete a short registration process. You can only vote once per email address. Voting ends April 29th, and results will be announced May 4th (a visual tutorial on how to vote can be found here).
From the Society for Scholarly Publishing:

On behalf of the SSP leadership, we are very proud that our community has generated a vehicle as widely recognized and effective as the Scholarly Kitchen. Now, we have an opportunity to increase the awareness of the SSP, the Scholarly Kitchen, and scholarly publishing in general.

Thanks in advance for your help!

I’ve recently written two pieces on scientists and social networks over at my other blogging gig, and thought they might be of interest to readers here:

Scientists Still Not Joining Social Networks


NIH Funds a Social Network for Scientists–Is It Likely to Succeed?

Some recent articles discussing computer software designed for use by biologists (I can’t personally vouch for any of these programs, but thought they might be of interest to readers of CSH Protocols):

Even Better Free Molecular Biology Software: Serial Cloner–the always valuable Bitesize Bio website has a review of Serial Cloner, a cross platform program for molecular biologists:

“It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.”

One of the commenters on the article also suggests PlasmaDNA.

iPhone apps every biologist needs: article from The Scientist, detailing 10 apps of interest. While many look useful, I’m not sure how many of them have added appeal on a mobile device (as opposed to use on a laptop or desktop computer). How often do you need to consult the periodic table while you’re on-the-go?

Also, I may be a luddite, but in my lab days, you wouldn’t even take a lab manual to the bench, you’d photocopy the protocol you were going to use because you didn’t want the expensive manual exposed to harsh chemicals and other contaminants. Are people really using expensive and fragile items like the iPhone at the lab bench? Do you set your iPhone down next to the phenol, just behind the HCl? Can you use it while wearing gloves? Wouldn’t you worry about all the E. coli contaminating your gloves from the plasmid preps you’re doing? Do you really want to smear that all over the device you’ll be holding next to your face?

9/12/09–Edited to addHere’s another list, of 50 Useful iPhone Apps for Science Students & Teachers.

Although many feel that RSS is dead, I still find it to be a highly useful tool for finding new interesting reading material. As such, we’re happy to announce some new functionality in Cold Spring Harbor Protocols involving our RSS feeds that send out alerts when new articles are published. Previously you could only sign up for RSS feeds for article types–protocols, emerging model organisms, etc. Now you can sign up for notice of new material by subject area. This will let you see when new protocols are available in your specific subject area, whether it’s Genome Analysis, Imaging Development or Plant Cell Culture. For those more reliant on e-mail than RSS feeds, remember you can sign up for a wide variety of alerts by table of contents, subject, citation, keyword or author.

Time to catch up on some interesting links:

The End Of Free
Last week’s posting at the Scholarly Kitchen, discussing the idea of using free content as a marketing tool, and how some uses are reaching the end of their usefulness. I have a new blog entry there that will be out on Monday discussing Microsoft’s Bing and Google’s Wave.

Teen Practices

Very interesting set of observations of how teenagers use technology. Twitter and e-mail are boring things that old people use. Once again proving the idea that different tools are appropriate at different stages of one’s life and social development. This study backs it up with more numbers.

Landmark study: DRM truly does make pirates out of us all

A few weeks back, I wrote about the Kindle’s DRM:

By providing a product that suffers the limitations of lock-in and prevents users from doing the things they’re used to doing with books, Amazon is encouraging potentially honest customers to become copyright infringers.

This study offers further evidence for such behavior, and argues against DRM.

If Research Papers Had A Comments Section
A cautionary tale, in cartoon form.

Another Blogger Leaves the Seed Blogs
Some dissension in the ranks over at ScienceBlogs. Like we’re seeing at the Nature Networks, these clubhouses are hitting some rough waters.

For Wired, a Revival Lacks Ads
Interesting article on Wired Magazine’s struggles. It notes that Chris Anderson of “Long Tail” fame seems to make around $35-50,000 per lecture he gives to businesses. Ironic in that the concepts he champions seem to be failing at the actual business he runs.

And it wouldn’t be right to end one of these without some Web 2.0 cynicism/snark. So I’ll offer up Conan O’Brien’s painfully accurate Twitter Tracker, and this lovely Social Media Venn Diagram t-shirt.

More interesting articles from the last week or so……

The Comment Is King

A look at comments left on articles in The Washington Post and Slate, which does not bode well for those of us interested in creating commenting systems for science articles.

Will Wolfram make bioinformatics obsolete?
Interesting piece on the potential for Wolfram Alpha to be used as a much easier interface for bioinformatics questions.

Clay Shirky Debunks the WSJ’s “Bloggers For Hire” Feature
The increasingly ubiquitous Clay Shirky does a detailed analysis of Mark Penn’s Wall Street Journal article claiming that there are hordes of people who make their living blogging. Shirky’s pretty much shreds the poorly researched nonsense to pieces.

Too much free
Seth Godin notes that giving away your book or e-book (or whatever) for free is losing its novelty value as a marketing technique.

Wikipedia hoax points to limits of journalists’ research

Two good points made here. 1) Wikipedia is completely untrustworthy, and 2) newspapers continue to hasten their own doom by lowering the quality of journalism they perform.

Kindle wrap-up
New Kindle was announced this week, bigger, even more absurdly expensive, still black and white (which makes it a non-starter for textbooks). Hard to understand why students who are pretty much required to have laptops these days would want an extra big bulky device to lug around as well.
The Kindle Lets Amazon Make a Lot From the Few
Speculation on the Kindle’s business model. Steve Jobs was right, not enough people read to make lots of money selling a device, but Amazon thinks that small group of people will buy lots and lots of e-books, which is where the profit lies.
Publishers Nurture Rivals to Kindle
Meanwhile, publishers are unhappy with Amazon, looking to avoid turning control of their industry over to one company and repeating the mistake the music industry made in ceding control to Apple.

Google book settlement has librarians worried
Librarians weigh in on the increasingly problematic Google Book Settlement.

The Extreme Google Brain
Google’s lead designer left the company recently, and caused a stir with his revelations of how anti-design the company seems to be. This analysis looks at the extreme personality types that thrive in places like Google, and I couldn’t resist this vicious and hilarious description:

My impression of “Googlers,” which I concede is based on little direct knowledge and is prejudicial on its face, is one of undersocialized, uncultured, pampered, arrogant faux-savants who have cultivated an arrested adolescence that the Google working environment further nurtures. Their computer-programming skills, the sole skills valued by the company, camouflage the flaws of their neuroanatomy. Their brains are beautifully suited to the genteel eugenics program that is the Google hiring process but are broken for real-world use.

A bit of a follow-up to last week’s posting on Twitter, which seemed to come out as part of a society-wide post-Oprah/Ashton Twitter backlash.

When assessing something like Twitter, I think it’s important to remember that it’s just a tool, and as David Pogue has written, it is whatever you make of it. My objection is not so much with the tool itself, but to the way it’s being used, or at least the way so many are advising that I use it. I do understand that there is a power in Twitter, in both its immediacy and its accessibility. And that it can be a very valuable tool when used in a correct context. Cameron Neylon gives a great example of a specific situation where Twitter was very handy. He describes an ad hoc group put together to discuss a webcast meeting that led to the organization of a new meeting on the subject. Twitter worked well because people could contact one another in real-time, and more importantly, a widespread group was able to find one another to connect. It’s interesting to note that Neylon and his group needed to move beyond Twitter to other tools better suited for their efforts. While the 140 character limit is often pitched as a “feature” of Twitter, in reality, it’s a drawback to serious conversation and the communication of information. It either leads to shallow discussions or to kludgy workarounds like sending shortened URLs of webpages where you’ve written out what you actually want to say.

The issue isn’t with using something like Twitter in that sort of situation, where it’s appropriate and useful. The issue is with the idea that we’re all supposed to subscribe to one another’s tweets and spend chunks of our day reading through the gibberish that makes up so much of Twitter’s traffic. The telephone is also a useful tool, but no one is suggesting you leave the speakerphone on in your office all day to listen to the idle conversations of strangers. The stereotype so often used to deride Twitter is someone sending out messages about what they are having for breakfast. Jason Kottke attempts to defend the banality in so much of Twitter by noting that people are inherently banal, so trivial and meaningless conversations are to be expected. The problem I have with this is understanding why I would deliberately subject myself to even more banality than I face in my real life. Yes, we all generate and tolerate a good deal of smalltalk in our lives. But do we want to commit extra time to collecting more of it? Is it somehow more meaningful if it comes from a famous or respected person? Am I supposed to get off on the frisson of knowing what Ashton Kutcher is watching on tv?

Like most working professionals, I am limited in my time and attention, and need to spend both judiciously. While serendipity can lead to interesting new directions, it’s a highly inefficient process and directed methods are always going to be preferred where possible. So Twitter strikes me as a tool that can prove useful in a directed manner in specific situations. It’s the idea of using it for sorting haystacks for needles that strikes me as uninteresting.

Haven’t done one of these for a while, so here’s a few recent bookmarks of interest:

Kindle Failings Serve as Early Warning
I’ve got a new gig, well, sort of. I’ve been invited to join the crew at the Scholarly Kitchen, so I’ll be posting there occasionally when I have something relevant to say. My first post was a summary of who I am and what I’ve written about over here. This is my first original post over there, on worries about DRM and how we’re conditioning e-book buyers to act like illegal music downloaders.

America’s Newest Profession: Bloggers for Hire
The Wall Street Journal’s Mark Penn writes a laughably implausible article on how all us bloggers are getting rich. Makes me want to load up the truck and move to Beverly. The comments on his article set him straight, as have other bloggers.

Ford Bets the Fiesta on Social Networking
Ford gives 100 “millenials” a car and makes them Twitter, Facebook, YouTube and Flickr about their experiences. Do companies really expect efforts like this to work? If only they’d read this article first, This is how Social Media really works:

So maybe instead of getting your company on twitter, paying marketers to mention you are on twitter, and paying people to blog about your company, forget all that and just make awesome stuff that gets people excited about your products, hire people that represent the company well, and when your stuff is so awesome that friends share it with other friends, you may not even need “social media marketing” after all.

And finishing up with some follow-up to my recent Twitter rant, we have Maureen Dowd calling Twitter, “a toy for bored celebrities and high-school girls” (found via The Intersection), web-strategist Jeremiah Owyang predicting that alpha-geek early adopters will move on to the next thing as Twitter enters the mainstream, and best of all, the genius of Keith Starky Explains Twitter an in-depth analysis of what Twitterers are really saying with the medium.

This week saw some interesting criticisms of Twitter, which helped reinforce some of my own biases against bothering with it. Science blogger Sheril Kirshenbaum weighed in on her oath to never use Twitter:

Welcome to generation ADD….Privacy is so last millenium.
Well call me old fashioned, but I draw the line at Twitter. Yes folks, the rumors are true. Physioprof and I have made a pact. We will never ever Twitter. It’s time to slow things down a notch. We want to enjoy a few moments disconnected. No electricity required, batteries not included.

Elsewhere, Clay Shirky has an introspective piece about the fallout from Amazon’s recent glitch where “adult”material was removed from their ranking systems, which led to widespread furor in the Twittersphere that discrimination was afoot:

Though the #amazonfail event is important for several reasons, I can’t write about it dispassionately, because I was an enthusiastic participant in its use on Sunday. I was wrong, because I believed things that weren’t true…Those are good conversations to have, we need to have them, but they are not conversations that would enrage thousands of people in the space of a few hours and kick off calls for boycotts and worse.”

Twitter is essentially a public Instant Messaging (IM) system, one where your messages can be read by anyone interested, and you can join in the conversation anyone else is having. For me, that’s the main reason I find the concept unappealing–I’ve never been a big fan of IM. I tried to give it a go back in the days of AOL/IM and found it incredibly annoying. Even with a limited group of contacts, the constant chiming from my desktop was so distracting and interruptive that I found it difficult to get anything done. Twitter strikes me as the same thing multiplied by several powers of ten. I screen my calls as well, by the way.

I know, I know, I’m missing out and I’m an old fogey stuck in the past. So be it. We each have our own time constraints and workflows. I do understand the appeal of chatting online with strangers. I used to be a huge user of usenet back in the day, and enjoyed being a part of the community discussing my favorite basketball team or whatever tv show/music I was listening to at the time. But that was back when I was very early in my graduate career, was still working my way into a research project, and had time to kill. As we get older and gain responsibilities, both career and family, time for such things gets smaller and smaller. As I progressed through graduate school and got closer and closer to my degree, my time spent in newsgroups grew smaller and smaller until I abandoned them altogether. And that’s something that worries me about most of these Web 2.0 mediums (media?) for science–that they’re going to be dominated and used mostly by those with the most time on their hands, and subsequently the least interesting things to say. Here’s a good example of someone reaching the tipping point, realizing where blogging stands in his list of priorities and considering letting it go.

Kirshenbaum makes good points about both the banality of much of what’s posted, and the exhibitionism and odd willingness to give up all sense of privacy by many users. I’ve written about boundaries before, they’re important, and you won’t find me going on about my private life or family in this blog. I don’t have a Facebook or Myspace page. It’s really none of your business. The linked Wired article in that previous blog posting should give you a sense of how easy it is to connect geo-tagged information to the real world, and I expect we’ll see some unpleasant incidents in the near future that begin to change attitudes towards being so open.

There’s also a certain laziness that Twitter seems to breed. While one constantly reads about the incredible discipline needed to edit posts to 140 characters, no one seems to mention the massive quantity of those disciplined 140 character messages that are generated. Merlin Mann describes it as “raging id”. I don’t really have the time nor the desire to read an unchecked stream of consciousness from most people. Several of the bloggers whose writing I enjoy are spending more time on Twitter than on their blogs as of late (John Hodgman for one, Neil Gaiman for another). While both are superb writers, neither generates anything I’m interested in reading via Twitter. I do understand why we’re seeing this shift, it’s easier to just spew out a thought off the top of your head than to sit and spend an hour (or hours) fully fleshing out an idea. Which is why I think it’s a lazy medium (I’m not alone in this). Even famous and talented folks just aren’t all that exciting and clever if you’re being hit with a splatter of every single thought they have. If you want my valuable attention, then you need to do a little work Edit it down, keep the good bits, and develop those ideas further. The raw material is just blather, and frankly, I don’t have a lot of time to listen to other people blathering. You’re just not that interesting.

The other noted advantage of Twitter is the “timeliness”. You can find rave after rave about how we learned about the plane landing in the Hudson or the Mumbai crisis from Twitter before the news networks had full reports on what was happening. So what. Unless you had a relative on that plane or staying in that hotel, would it have affected your life if you had to wait a few hours before knowing the story there? Kirshenbaum calls this “Generation ADD” (I prefer “Generation Now”). I guess this rampant voyeurism is the counterbalance to the rampant exhibitionism mentioned above. Shirky’s article points out how this immediacy can lead to sweeping mob movements based on incorrect and incomplete information. Amazon has apparently suffered from a threatened boycott and massive amounts of negative publicity based on false assumptions.

Even those heavily invested in Twitter advise that you shouldn’t try to read everything, that you should take time off. I’ve been told repeatedly that the key to managing information flow in this day and age is the use of powerful filters, perhaps the most powerful being that you don’t have to join in and use every technology simply because it exists. Usenet, in its time, was highly influential and great fun. But no, you’re not suffering now because you didn’t use it. Something else came along and replaced it, and something then replaced that. If you have the time and interest to join in, well, good for you. It’s an investment I can’t make and it’s good to know I’m not alone in this.

I’ll leave you with this funny, but impressively accurate list of Why Twitter is Evil.

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