Love-hate relationship with PowerPoint

PowerPoint is a ubiquitous, tedious, and oft-maligned piece of software that everybody loves to hate. Some say PowerPoint is bad because it’s a crutch that has given us a generation of people who don’t know how to give a presentation. I’ve given it my fair share of hating, but sometimes I have to admit that PowerPoint doesn’t really deserve all the flak it gets.

But this post isn’t about how I secretly love PowerPoint (I don’t think I can quite go that far) or how to give a good presentation, or why PowerPoint slides with blue backgrounds should die — DIE — a slow and painful death. This post is about my new favorite use for PowerPoint:

(full res: pharmacy-sign)

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Poster redux

Here’s the final version of the poster. Not drastically different but having other people look at it definitely helped. Thanks to Lars, Iddo, and akb for the feedback!


(First version here)

Poster: Discovering protein functional sites with unsupervised techniques


I’m presenting a poster during the Biosciences graduate admissions dinner in a couple days. Even though it only covers a fraction of my thesis work, I of course still had trouble cramming it all into 40×30 inches. The audience is a bit tricky since it’s a general event covering all of biosciences for pre-graduate students, so I wasn’t sure how much detail to include (but it might not have fit anyway). I like the overall style of the poster but it seems a tad wordy…

If you have any suggestions or comments for organization, content, or aesthetics, I’d appreciate it! For example, is it high-level enough that someone with a basic science background could get the gist? Is it interesting enough to get someone excited about bioinformatics? Does it communicate the research clearly?

(Update: Final version here)

What type of open notebook science are you? (Plus, more logos)

Photo by sararah on Flickr

Photo by sararah on Flickr

A scientist’s notebook is like an artist’s sketchbook mixed with captain’s logs. It can be extremely personal and yet it is the definitive record for both day to day scientific research and for higher-level brainstorming. It can be haphazardly disorganized or meticulously organized. But until electronic media came around, we were stuck with pasting pieces of paper alongside handwritten notes in stacks of bound notebooks or 3-ring binders – a pain not only to store but also to search through when you’re looking for how exactly you ran that particular experiment on that particular sample on that particular equipment.

While it’s not quite the norm yet, these days it’s not uncommon for people to use software such as wikis or journaling programs to record their everyday research activities. This has obvious advantages beyond legibility and saving trees; you can search your notes, link them to data files or figures, and back up multiple copies. You can tag and categorize entries, and the electronic files are automatically timestamped. Wikis, in particular, include versioning, so that any modifications you make to an entry are also recorded and timestamped.

These features should be a boon to any researcher, but there are some important “meta” benefits that can be yours (and ours) if you choose. Making things electronic lowers barriers to access and sharing. If you use a wiki or a blog to record your notes, you can choose to keep them online (useful for accessing from anywhere there’s an internet connection), and further, to make them public. At it’s logical extreme, this translates to “making the entire primary record of a research project publicly available online as it is recorded” along with all raw and processed data, the current definition of open notebook science (ONS) on Wikipedia. A number of scientists and labs practice and advocate ONS, including Jean-Claude Bradley at Drexel, Cameron Neylon at the ISIS Neutron Facility, and Gus Rosania at University of Michigan. They argue that the benefits – both to themselves and to the scientific community at large – far outweigh the risks.

Complete ONS obviously isn’t for everyone, but regardless of whether the practice becomes widely adopted, we should now be able to designate certain labs or notebooks of satisfying the definition of ONS. We can even designate partial ONS – whether all or only part of the content is available, and whether the content is made available immediately or after some time delay (usually for IP or publication purposes). Jean-Claude Bradley has broken down these types of ONS into a set of claims inspired by Creative Commons licenses along with initial logos created by Andy Lang.

The Creative Commons model is great for getting across the terms of your content quickly and unambiguously, so I am a big fan of this initiative. I would love to see more research notebooks online, and to see them displaying badges or banners identifying them as a type of ONS. I got so excited that I started making my own logos, which, happily, Jean-Claude and Andy Lang seem to like:

ons-patch1 ons-patch2

Two potential problems with these logos  that I can think of are:

  • whether it reads as “ons” rather than o-n-s (in which case perhaps uppercase would help),
  • the use of a beaker which could feel exclusive to those not in the experimental or life-sciences,

Incidentally, I made these images in Keynote (Apple’s version of Powerpoint), of all places. I simply couldn’t be bothered to fire up Adobe Illustrator with its bajillions of tools and palettes, and while I had to fudge a bit to get certain things to look right (my way of coloring in the beaker, for example, is hilariously crude), it was still pretty painless. Who knew?

I’ll be making more official mockups for Andy in the next day or two, so if anyone has additional feedback on these designs (or a different design entirely) I’d love to hear it!

Baby’s first Bayesian network

My favorite activity at baby showers these days is decorating onesies – essentially cotton leotards for the infant set. Not only is it a practical gift, but it gives the friends of the expectant mother a chance to flex their creative muscles. For the geekier among us, it’s also an opportunity to ensure that the baby starts off life with an appreciation for science.

So, in addition to the flowers and the butterflies and the general baby themes, we had DNA, Bayesian networks, and chemical structures:

doublehelix21 xx bayesnet21
venndiagram meiosis2 estrogen2

It’s truly a thing of beauty, especially that lovely double helix. I contributed “meiosis” and “Yael ∩ Eli = me”, but I also couldn’t resist trying my hand at humor, nor could I leave without paying homage to a fan favorite:


Best wishes to the expecting couple! If only every baby could be so lucky to wear these fashionable, and educational, garments.

Trick or treat for equality

I won’t be here for Halloween because of the aforementioned tournament, but decided to carve a pumpkin anyway. Since it’s an election year, I went a bit political. Normally I’m not one for posters or bumper stickers but a pumpkin? That I can do.

Off to ISMB 2008


Tomorrow I’ll be heading off to ISMB in Toronto. I haven’t attended the big show before, other than a 1 day SIG 3 years ago in Detroit, so I’m sure it will be enlightening, perhaps for the science, but also for the sheer surreality of packing thousands of normally bunkered down and repressed scientists into a small and contrived space.

I hope I can smuggle my poster tube onto the airplane without them noticing that I also have a carry-on and personal item already. But kind of hard to hide something that’s almost 4 feet long… speaking of transporting posters, how cool would it be to have electronic poster boards at conferences? No more poster tubes, little sheets of paper, curled edges, or push pins – just upload your file before you get on the plane, bring a thumb drive just in case, and you’re good to go. Sure, they’d be expensive, delicate, heavy, and perhaps prone to glitches, but nothing a few years of tech investment can’t fix.