Wednesday, July 16, 2008

Labmeeting.com - "Make science easier"

Stanford students are nothing if not entrepreneurial. Only a couple months after reporting on Ologeez (out of the Genetics department), I receive an email about Labmeeting.com, the product of a group of students in Vijay Pande's lab, headed by a graduate student in the Physics department created by three folks who knew each other from their undergrad days at Harvard, one of whom is now a biophysics PhD student at Stanford.

The website grew out of their desire to "solve some of the organizational problems we've encountered while doing our Ph.Ds", and includes a PDF organizer, a space for labs to share protocols and files, and mechanisms for discovering and recommending papers.

After registering and doing a brief tour, it appears to be a well thought-out and executed entrant into what is starting to become a crowded market for tools that help you organize, search for, and share papers, or tools that help your lab share data and files. Because of the many offerings, however, some with much earlier and more widespread adoption, I'd be surprised if Labmeeting gathers much of a foothold. Then again, it's not claiming to be another OpenWetWare, so if it does what it does well, perhaps those looking for a smaller feature set (and a bit of relief from social networking) will find it just right.

Tuesday, July 1, 2008

Survey of bioinformatics

Michael Barton over at Bioinformatics Zen is collecting responses from those working in the field of bioinformatics to survey the current climate (and projected future) of bioinformatics, with data to be made public and back analysis encouraged. The (fully functional) survey is replicated below, the original can be found here.


Thursday, June 19, 2008

Is there a one stop shop for (good) science videos?

My advisor has recently become enamored with the idea behind SciVee, which is essentially a place where you can view video blurbs of people's research, but is convinced that nothing short of YouTube will catch on. His plot for world science domination is for all of us graduate students to tape ourselves talking about our papers for a few minutes and upload the videos to YouTube, with dramatic increases in paper readership sure to follow.

While it's undeniable that YouTube is by far the most popular video server and thus wins by breadth and pure viewership, one could argue that SciVee and JoVE provide a service by being specific - one features research blurbs, the other features video explanations of protocols and experiments. You can be assured that the videos will be high-quality and reputable, at the very least. But there are also many videos that may not fall under those two categories but are still interesting to scientists, or those interested in science.

The Inner Life of a Cell, various TED talks, and this demonstration of cornstarch physics come to mind as some science-related videos that I've enjoyed recently. Maybe even science humor. What YouTube has going for it is precedence and near monopoly, but quality control is dismal and it can be impossible to find good, engrossing science videos (their "Science and Technology" category is mostly dominated by technology - software, hardware, gaming, etc - and the science offerings are hardly scientific).

What I'd like to see is a way to aggregate high-quality science-related videos, categorized by type (protocol, experiment, research/paper promotion, cinematic, humor, etc - how would one categorize the TED talks?). Because sometimes a video is worth a hundred readings of a paper or protocol, because we're all just curious about so many things, and because we all need a bit of reinspiration every now and again.

Is there anything like this that exists now?

Probably old news by now, but JoVE's got this going for it - published videos will be indexed on PubMed! Will the day come when we have citation rates for videos, and can list number of hits as a bullet point in our CVs?

Wednesday, June 11, 2008

Would open science profit from a non-profit?

In my first foray organizing a formal meeting (the PSB workshop), I've learned that pretty much everything comes down to money. Having a successful meeting requires getting people to attend, and getting people to attend often involves money. Getting money to allow people to attend can even require money (for example, publishing costs for conference proceedings).

One idea Cameron's mentioned a few times during our fundraising discussions is the Open Science Collective, and though he hasn't fully described what this is to me, I get the impression that it would be some abstract entity comprising individuals, organizations, resources, and activities - some larger body that would provide support for open science-related endeavors. At the very least, I think it would provide a means to fund raise separate from any particular event such that we (in the collective sense) could act independently. By this I mean that the OSC could support individuals to go to meetings, sponsor meetings like the PSB workshop, or even organize its own meetings.

The idea hasn't really been taken further yet, with whimsical t-shirt ideas pretty much our only tangible revenue strategy so far. But to give the OSC a step towards reality, perhaps it's time to start talking about building a non-profit. From a quick glance through of one website's guide to starting a non-profit, it appears that we need to create a mission statement, obtain a board of directors, and eventually file for either incorporation (plus maybe other things, like tax-exempt or tax-deductible status). This is about where I start getting fuzzy on the details, so if anyone has experience with non-profits or foundations (I don't even know what the difference is) please feel free to enlighten me!

At the most basic level, it would be nice to have some external entity with a bank account into which we could funnel funds that we (again, the collective we) could apply towards open science activities. If that t-shirt shop ever sells anything, the proceeds should go into that account. What the best way to accomplish that is, I'm not quite sure. If it is to start a non-profit, then perhaps the first step is to see who else is interested and start drafting a mission statement together?

According to idealist.org, a mission statement should cover the purpose, the business, the values, and the beneficiaries of the organization; i.e. the what, how, why, and who/where. This can be accomplished in one line but can also be expanded into paragraphs. But let's start small - here's a stab at a one liner mission statement:

"The Open Science Collective is an international and interdisciplinary [non-profit] organization that promotes open exchange and collaboration in science, and provides resources and support for the advancement of open science."

So some concluding questions: Does it make sense to have something like the Open Science Collective? If so, what should it be and how do we get there? What would be the mission statement of the OSC? If not the OSC, what do we need?