Wednesday, October 29, 2008

Information management tools

The key to success as an academic scientist lies in successful management of two vital resources: time and information. Poor management of one or both of these will make success (as measured by the usual metrics of tenure, grants and publications) extremely difficult, if not impossible. I've been thinking about information management recently (I'll save time management for another post).

We live in the information age - ready access to the internet can easily lead to information overload, a debilitating condition that can lead directly to a lack of focus and an inability to act efficiently. This isn't the first time people have had to deal with information overload (or at least worried about it). James Burke notes in The Knowledge Web that the powers that be were concerned that the printing press would overload the citizens of the time with worthless knowledge (or more likely, knowledge the overlords would have preferred kept to themselves), so both church and state imposed strict censorship. Efforts to censor the internet have, so far, failed. In fact the internet has become such a ubiquitous part of our lives that I suspect any large-scale censorship efforts are doomed to fail.

So how to manage the vast amounts of information flooding our professional lives? Here I'm referring to external sources (i.e. not the flood of data from your lab). Buggered if I know a really good answer to that. I do know that the first step is to filter. Ruthlessly. The vast majority of the information flooding my academic life is useless, irrelevant and/or unimportant. Delete it. Block it. Just get rid of it. Otherwise you'll spend your days whacking useless moles.

Below I describe the tools and/or approaches I use to handle the bulk of the rest of the information. Your mileage may vary. I'd welcome comments from others describing other ways to handle this stuff. Note that I'm a Mac user, so some of the stuff I describe is Mac-centric.

I find if I don't handle important emails within a day they tend to get ignored for too long. So I reply to the important stuff within a few hours when I can. Everything else is filed away or deleted. In some cases I've set up signatures I can use as a sort of form-letter reply, but I only use those for form-letter-style emails (e.g. the dozens of form-letter emails I get a week from people looking for a position in my lab).

And I make liberal use of Apple Mail's junk mail-learning feature.

I do tend to keep copies of most non-junk emails. I have set up numerous folders in Mail for this purpose. This has proven very useful at times when I've wanted to track down some piece of information I was sent some time ago.

I have a personalized home page I've set up with iGoogle. Right there on the front page I have gadgets for Google Reader, Google Calendar, Gmail Contacts, and gadgets I've created myself (a very easy process) for access to Big State U.'s web interface to email, links to my lab's homepage and various other links I use several times a day. My homepage also has a set of tabs linking to other personalized pages with gadgets for Google Docs and Google Notebook, various search engines (PubMed, Google Scholar etc.), the news, weather etc. etc. This is all very easy to set up and puts a whole bunch of stuff I use a lot all in one easy to access place. Furthermore, I can access it from any computer connected to the internet.

Google Reader
I love Google Reader. I have journal table of content feeds, grantmaking agency feeds, feeds from ISI's Web of Knowledge tracking citations to my published work, etc.* All in one place. Makes dealing with all that stuff really easy.

I just wish I could get my saved PubMed searches fed into Google Reader... Anyone know how to do that?

Alright, so these are really time management tools, but they contain information too. I like iCal on the Mac. I have it synced with Google Calendar (via Busymac shareware - I'm too cheap to invest in MobileMe). This allows me to keep iCal on Macs at home and work all synced. And give me access to my calendars via my iGoogle home page. Any changes made to any of the calendars is automatically transmitted over the internet to the others. Cool.

Address Books
It's good to have the same address book on my Macs at work and home, my cell phone, and in Gmail Contacts. Good, but not as easy as I would like. My cell phone has Bluetooth, so that's not too bad. I did need a plugin to get it to play nice with Apple's iSync, but that was easy enough. Syncing the Mac Address book with Gmail Contacts isn't so easy (unless you have an iPhone or iPod Touch...). I use a little freeware program called A to G to help with this. Unfortunately any changes I make on either Mac or on Gmail Contacts isn't automatically transmitted to the others... Apparently this is being added to Busymac at some point. SpanningSync is another option for Mac users, but is a subscription service.

One day I'm getting me one of those newfangled iPhone gadgets...

Google Notebook
I've just started using this as a sort of glorified To Do device. I have notebooks with short-term plans for my various research projects, one for a new project I'm planning, one for non-research lab-related plans etc. The jury is still out on this one, but I like the idea of having ready access to this kind of stuff from where ever.

You could keep track of bookmarks via Google, but I find that a little cumbersome. I use Firefox as my main browser and have downloaded an Add-In called Foxmarks. This syncs my bookmarks from Firefox on my Mac at work with that at home via the internet.

Back in the Dark Ages when I was a grad student I used to make photocopies of papers relevant to my research. This continued into my postdoc years. With the advent of PDF's I began printing them out. A lot of trees died. A lot. Early on as a postdoc I realized my ever-growing pile of papers was getting out of hand. So I hit on a system of labeling them before filing them away after reading. I started numbering them, starting at one. I'm now up to 2310 (I keep a note of where I am, and no, I haven't actually read all 2310 in detail, just most of them). That way I could file the papers numerically. At about the same time I started using EndNote. EndNote has a field called "Label" for each entry - that's where I put my numbers. So I can look up a paper in EndNote and find it in seconds in my files. In recent years I've tried to wean myself of the environmentally-unfriendly habit of printing out every paper I think I want to read. Instead I try to save and read the PDF on my computer. I rename each PDF with a number and enter it into EndNote with the number in the "Label" field. That way I can look it up and find it on my computer in seconds. And the Mac search feature, Spotlight, can be used to search via keywords etc. to dig up all papers related to a certain subject.

That's it for now. As I said above, I'd welcome comments from others describing other ways to handle this stuff.

Damn I'm getting into the habit of very long posts. Perhaps I should market them as a cure for insomnia...

* I like to know where my work has been cited. In part because it helps me keep track of the field, and in part because of vanity. :-)


Nat Blair said...

getting PubMed searches into Reader is a snap.

Make a search in pubmed, then in the pull down menu that says "Send To" select RSS feed.

Next you'll get a page that let's you select how many items to include on the feed. Usually 15 is fine, if you have targeted searches.

Then click "create feed" button, and you'll get a page with a little orange "XML" button. Click on that, and the "Add to Reader" page should appear.


Great post, as I've been grappling with these time and info issues a lot lately. Too little of the first, and too much of the latter, as most everyone is feeling I'd guess.

Nat Blair said...

Also, why not just add the pdf directly to the EndNote record, in the "Link to pdf" or the "Insert Object" field? I think that's been in EndNote since version 7 (well, certainly the insert object, I think the LinkTopdf came later). A new copy of the pdf is automatically stored, and you don't have to manually change the file name if you don't want to.

And why add your own number in the label? Each entry in the library gets a unique "Record Number" though the idea is the same. That's how I've organized my physical copies for a long time.

Still, I think that a better reference manager software could take the pdfs on your computer, extract the relevant bibliographic data automatically, and then let you search through it, organize it, etc. SOmething like Papers for Mac or Mendeley for Mac or PC. Think something analogous to Picasa for photos, but for pdfs instead.

I tried an earlier Mendeley version, and it didn't quite work well enough, and I'm a PC person so Papers is out.

yolio said...

Papers is a still new but incredibly slick pdf management tool for Macs. If you haven't checked it out, you really should. It is still in development, and so doesn't quite take over the reference management niche of endnote or bibdesk. But is suspect it will wihtin a release or two, and then there will be no competition.

I use and love Omnifocus. It is a glorified to-do list, but it gets all the little details just right. There was a bit of a learning curve, but once I got it up and going then it is very easy to maintain.

I think google recently released feature called "canned mail" that might be better than your current signature system.

Odyssey said...


Thanks for the PubMed hint. Not sure how I missed that...

Also, why not just add the pdf directly to the EndNote record, in the "Link to pdf" or the "Insert Object" field?

'Cos I'm a slow learner? :-)

And why add your own number in the label? Each entry in the library gets a unique "Record Number" though the idea is the same.

I had started with other reference managing software plus my labels. Using the EndNote tags would have meant renumbering a whole bunch of papers.


I'll check out Papers and Omnifocus. The google "canned email" sounds interesting, but I like using Apple's Mail rather than Gmail.

Nat Blair said...

Thanks for the PubMed hint. Not sure how I missed that...

It's not that obvious. I'm not sure how I learned about it honestly.

'Cos I'm a slow learner? :-)

Eh, I have only upgraded EndNote twice in 11 years of using it. Once when the Pubmed output changed, so EndNote 3 didn't work. And then once for EndNote X2, for some other reason. Maybe Office XXXX compatibility? But this recent yearly version increase from Thomson worries me, one reason I'm interested in other solutions.

I had started with other reference managing software plus my labels.

Good point. It brings up another instance of getting "locked" into a certain software package, and worries about whether it's easy to transfer your previous work into new software.

Here's another question though: what software do you use to store the tacit knowledge of the lab? Do you use a lab website to store some of that stuff? A lab wiki? Mostly just curious.

Odyssey said...

Here's another question though: what software do you use to store the tacit knowledge of the lab? Do you use a lab website to store some of that stuff? A lab wiki? Mostly just curious.

Neither. I would like to implement a wiki, but haven't got to it as yet.

Liam said...

nice post....i am working my way up the academic ladder and get busier (it seems) with each passing month.

I have been using iGoogle and gmail for awhile now...but just for personal use...i will rethink that. I especially want to try Google Reader for eTOCs.

Nat Blair said...

Gmail is definitely great. I especially like using suffixed addresses and autolabeling to store science stuff. If your email is yourname@gmail, then anything sent to comes to your account. Add a filter that labels it with whatever, (data, science_diary, etc.) and then it's easy to sort on those labels and find what you need.

As for wikis, I've been using a free wiki from, which is pretty useful (mediaspaces is another one). Mostly to store my own things and then easily access them from any computer. It has user control (passwords, read only, etc) and email notification of changes, and built in tags and comments on things. Setting one up intralab would be great too though, as a way to help capture all the tacit knowledge in the lab. Haven't seen many people using them though.