Sunday, May 25, 2008

Science protocols - Recipe for success?

I enjoy cooking and baking, and while I own my share of well-thumbed cookbooks, on a day to day basis I am likely to find my recipes on my favorite cooking websites. There are a number of good ones out there, including Epicurious and Food Network, but the one I go to 99% of the time is AllRecipes.

Why do I prefer this website? For one, the look and feel is inviting, intuitive, and informative. There is no barrier to entry and novice and expert cooks alike will find what they need easily without intimidation or pandering. A nice perk is the ability to search by ingredients, helping you find recipes that will use what you have on hand. But the most important feature is content - the community at Allrecipes is substantial and helpful, not only providing the recipes themselves, but also feedback on the recipes that is often corroborated multiple times. Tips like decreasing the number of eggs or doubling the sauce, roasting at a lower temperature for longer, cutting out the salt, or adding more lime juice can truly be the difference between a successful dish and not.

There has been a lot of discussion on science social networking sites and on whether the promise of "web 2.0" is being delivered in science yet (see David Crotty's post at CSH, Bora's question, and musings at The Scientist over on NN). Some reasons why so-called Science 2.0 hasn't been catching on include the fact that scientists are extremely busy and don't have time to invest in familiarizing themselves with new online networking sites or web tools that have no immediately obvious benefit to them (though some disagree with the claim that scientists are busier than those in other fields). As David points out, much of it boils down to inertia: if we already have a way of doing things, the only way we'll change is if the new way is obviously advantageous and it doesn't take too much effort to adopt it.

It was while reading these related discussions that I started thinking about scientific protocols and how much added benefit could be derived from community content. There are protocol websites out there (OpenWetWare, CSH Protocols, etc) which are a great start, but for the most part these are put up by the original user or published by a journal and rarely generate feedback that could be useful to those looking for a particular protocol - such as slight temperature changes, buffer modifications, or other tweaks that either led to better results or fixed problems. Although it's been a while since I've worked in a wet lab, it seems that a lot of fine optimization goes into a protocol before it produces what is eventually published, and this can often take months to refine.

Given how similar protocols are to recipes, is it that far of a stretch to imagine a protocol version of AllRecipes giving similar benefits? Just as you save time, money, and ingredients by learning from other cooks, you would save time, money, and resources in the lab from other researchers. Granted, this assumes that scientists aren't the type who would say, "What - give other labs a head start by learning from my mistakes? Are you crazy!?" but instead would say, "Think of how much this could help science in general if we all helped each other do experiments more efficiently!" Imagine going to a protocol website, searching by your requirements (protein name, species, type of assay, perhaps), going to the highest rated protocol, and reading a number of reviews that unanimously suggest tweaking one particular step. Or imagine finding the quickest (30-min meals)/most efficient (10 dinners for under $10!)/most popular (95% of people choose this recipe)/best (rated 5 stars by 500 users) protocols for doing X Y or Z as reviewed by scientists like you.

Some might find this kind of crowdsourcing offputting for the scientific domain, others might say it's about time. I know the picture is not so simple, but it just seems silly that we're not benefiting from what other fields (like cooking) have already embraced. Funding is scarce and time is a precious enough resource as it is - why waste both by banging our heads against the same wall others have banged on when we can move forward by finding the door?

I'd be interested to learn if there are actually any protocol websites out there that more fully resemble the types of recipe websites I mention. The solution isn't to create an AllRecipes for protocols (as David mentions in his post) but to provide a service that is useful to scientists and that encourages them to participate. Since the application area is more focused than general science collaboration/networking sites, are the benefits more obvious and will it gain traction more easily?

And for something that is neither here nor there, what is it about science that keeps it from exploiting and embracing the web the way practically everything else has done? (I have inklings but would enjoy hearing others' opinions.)

Thursday, May 22, 2008

Mac hacks for research

As much as I sometimes want to think that Apple is the new Microsoft, I can't deny that they've got something that the evil empire never had - fanatical users who are loyal not because they have to be, but because they truly love Macs. In fact, they love Macs so much that they often devote their free time to developing stunning software applications that range from the quirky and fun (think Delicious Library) to the "how did I ever live without it?" (think Papers). The enormous array of applications available for Macs, unrivaled in their aesthetics, ease of use, and depth of features, serves to reinforce the Mac's reputation as the platform of choice for trendsetting computer users.

It turns out that this is true in the scientific domain as well. Joel Dudley, founder of MacResearch, gave a guest talk for my lab today on a dizzying array of Mac tips, tricks, and software meant to optimize the Mac experience, especially in a scientific research environment. Some of the applications he mentioned looked truly extraordinary, and I thought I'd describe some of the more notable ones here for those interested in getting more out of their Macs.

For the cell and molecular biologists out there, here's a solution for your image processing needs. Macnification is like an extended iPhoto for microscopy. The full feature set looks impressive - you can track experiments, manage metadata, make measurements, create movies, and generate virtual z-slices through multiple images, all in one sleek application. I don't work with microscopy images, but now I wish I did!

For Python programmers wanting to flex their artistic side, NodeBox allows you to create amazingly complex graphics and animations with just a few lines of Python code. NodeBox is free and open source, with plenty of example scripts to get you started. Just looking through their online gallery is enough to get the "what-if" juices flowing.

Graph Sketcher and DataGraph
If you hate pretty much everything about Excel graphs, you might like everything about these two graph programs. Graph Sketcher is for quick, brainstorming type graph drawing - use their simple tools to draw pretty much any abstract relationship in 2D, with or without data. DataGraph is more powerful and meant to plot large volumes of data. The defaults start out fairly aesthetically pleasing, but there are many many ways to tweak the look of graphs, add or switch data, add additional axes, and plot multiple dimensions simultaneously. Both applications export to PDF for high-resolution figures, with DataGraph allowing export to vector-based formats as well for use in publications.

In addition to these, the Omni group has a suite of applications for boosting productivity, managing information, and drawing high-quality graphics (much more easily than the impossibly hard to use Adobe Illustrator); Journler is a great Mail-like program for organizing notes such as your lab notebook; and, of course, Papers is a must for anyone who reads scientific papers on a regular basis.

Be sure to check out MacResearch for more innovative applications geared especially towards science and research.

Wednesday, May 21, 2008

Open Science at PSB - deadline approaching!

The initial deadline for proposals for the first Open Science workshop at PSB is coming up on June 1. We welcome submissions on almost anything related to Open Science - tools, platforms, and resources; applications, first-hand experiences, or case studies; cultural, social, and historical perspectives or studies; Open Access and open source; pretty much anything that will help us get a better picture of how Open Science has developed, where it is now, what's brewing on the horizon, and what's needed going forward. The call for participation has more detailed information on the workshop and submission instructions.

Note that the proposal need not be a fully mature or completely fleshed out abstract - a rough outline of the content of the proposed talk is sufficient. The early deadline is simply for us to get a better idea of what the workshop will look like, and there is ample time to continue refining abstracts thereafter.

There is no selection process for posters; anyone interested in presenting a poster may present. The deadline for submitting a poster abstract is Sept 12; however, early submissions are encouraged so that we may better organize the workshop!

Fellow bloggers and readers - please take a moment to post a short note about our workshop on your own blogs, or send notice of our call for participation to potentially interested friends and colleagues! Thanks in advance. :)

Sunday, May 11, 2008

Echidnas have genomes, too

More t-shirt ideas for fundraising for the "Open Science Collective"...

T-shirt idea #2: If the platypus now has its genome sequenced, shouldn't the echidna, too?

"Fair go, mate" is Aussie slang that apparently translates to "a plea for fair or equitable treatment," according to A twist on "animal rights"?

See it on a shirt on Spreadshirt! It's on sale there, too, but we haven't really launched the official shop yet - it's mostly just to get started and see how things look.

Friday, May 9, 2008

"Worst Result Ever" t-shirts coming soon

You've been there, done that. Spent hours, days, weeks... months?... just to discover that your hypothesis (or "hope-othesis") is completely wrong. Finished a data analysis only to see that what you've just produced can only be described as the Worst. Result. Ever.

But graduate students have better things to do than mope over spilt data - like blog about their bad results, or go on to the next thing and hope history doesn't repeat itself. Inspired by Magda's great idea, I've decided to start a line of t-shirts that will hopefully allow those of us who have ever felt the pain of bad results to laugh a little at our plight - and raise a little money in the process. Yes, that's right. Proudly wear your results on your sleeve - er, chest - and support Open Science at the same time!

We're still in the early stages of brainstorming designs and have yet to put up a shop yet (most likely on CafePress, though other suggestions welcome), but Cameron and I are actively fundraising for the PSB workshop on Open Science and thought t-shirts would be a fun angle.

So here are some initial designs to get the series started. Each one is named after the hapless student who had the pleasure of seeing something very much like it in their own research.

"The Magda" - No correlation

"The Shirley" - No separation

"The Bernie" - No improvement

The back of the t-shirt would be something simple, possibly one of the following:

If you have your own worst result that you'd like to contribute to our cause, feel free to send them to me: shwu19 at stanford dot edu. We are also planning to launch a series of designs reflecting the frustration that is thesis writing. Suggestions and comments of course welcome!

Obviously, we don't expect to raise a significant amount of funding through t-shirts, so if you're interested in contributing more directly to the Open Science workshop, please do contact Cameron or myself. We also encourage everyone interested in Open Science to make it out to Hawaii to participate. :)