Abstract clouds

Hey--

So I'm sure you've all seen word clouds ala wordle, where it takes all the text from a word document or webpage and then uses word frequencies to generate a kind of infographic where you can see the most used words, the big ideas if you will. 

Check it--someone made an app that you can input an author, it pulls all their pubmed abstracts, and then you can input that into wordle. It's called pubmed2wordle.

I decided to look up some of the PIs on my floor, in case I'm ever in the elevator with one of them, I can have some talking points. 

For example, 

I will know to talk about microRNAs with this dude, or

microRNAs but specifically let-7 with this woman, and also, oh look she works on C. elegans and development.

I think can be a great resource if there's a visiting faculty giving a seminar, or you're trying to pick a lab to rotate in, or you just want to know a little bit more about someone's research without spending hours poring over papers, this might be the first place I go from now on for all those things.

And just to mix it up a little big, because contrary to popular belief I'm not only interested in microRNAs...

That's my dad. He works on yeast and kinetochores and chromatin and microtubules!

It also makes for an interesting discussion of how much information do we actually need to understand something. And is relying on a tool like this, is that being lazy or being efficient? Obviously, it will never become a substitute for reading papers, but it's a pretty neat tool regardless. 

Do you think you could find yourself using something like this? Could you see yourself directing a student to it?  

How To Read a Really Complicated Paper

Because I am a glutton for punishment/really know how to party, I chose a really complicated/awesome paper to present for journal club this coming week.

Some of my criteria for choosing a Really Complicated Paper are:

• An unpronounceable protein in the title (Serine Palmitoyltransferase, anyone?)
• Lots of equations
• Lots of figures
• Microsoft Word only recognizes half of words in the title as actual words.

Without further ado, I give you:

MicroRNA-137/181c Regulates Serine Palmitoyltransferase and In Turn Amyloid B, Novel Targets in Sporadic Alzheimer’s Disease

PMID: 21994399

So here we go. My tips and tricks for reading a paper.

• Get comfortable. We’re going to be here for a while. I include coffee in this step.
• Be an active reader. I used to silently make fun of my freshman year roommate when she would line up all of her differently colored highlighters before doing a reading for class. Little did I know, that nothing makes you unretain information more than just mindlessly skimming through a paper. Who would have thought! When I’m reading reading a paper, I’m armed with a highlighter for important words/phrases/concepts, and a pen for notes to myself. 
• It’s all about you. Remember that pen you had from step two? While some of your notes might be, “look this up” or “wtf.” Reserve some space for applying what you’re reading to your research/interests. See a method that you might use four years from now if all your experiments go perfectly to plan? Star that one. Applying things from the paper you’re reading to what you’re doing is a great way to retain knowledge. There has got to be a study about that. It must reinforce some short-term/long-term memory pathway loop something that just helps you remember it. Plus, then you just learned something applicable to what you do. Bam. 
• Prioritize. I tend to read Abstract-->Introduction--> Discussion-->Results-->Methods. Papers aren't novels, there's no right or wrong way to read them.
• Do a presentation. Volunteer to present a paper that you're reading for a journal club. Making and practicing a presentation will help you understand the paper. As you pull out figures and rethink your own captions and what you're going to say, you'll "connect" with your paper all the more. You'll also get some feedback and insight from other members of your lab/journal club.
• PDF vs. Full Text. I like printing papers out and taking them with me to get coffee, sometimes taking them to lunch (I'm such a great date!), and reading and re-reading and highlighting and writing. I print out the .pdfs to do this. It's important to remember that .pdfs are destined for the print version of a journal, so figures and tables aren't always (or, almost never) in a comprehensible order. If this is messing you up, try going to the full text version online. It's not as pretty as a .pdf, but the figures are right there in text, so when the results refer to a table or a figure, that table or figure is usually directly below it, in a handy window that you can pop out.

And finally,

• Try not to procrastinate. It's hard getting through a paper that's really dense. You just have to sit down and do it. I'm really bad at this. For instance, instead of reading my paper and working on my journal club presentation, I wrote this entry.

Back to the paper!

Any other tips that you have that I missed? What are your secrets to reading a paper?