Tuesday, September 7, 2010

Thank you, Addgene, for the award!

A big "Thank You!" to Addgene for giving Andy Maloney and our lab a "Resource Sharing Award!"  The award is a $5,000 donation to our lab that we can use to further our kinesin research.  Very generous and very helpful to our lab.  Big props also to Andy for applying for the award with no help from me!  One more piece of evidence that the students in the lab are much better at grant writing than I am :) 

The award was given to Andy and our lab for our commitment to open science.  This includes open notebook science, open data, sharing protocols, designs, etc.  Andy has been a very impressive open scientist.  It's just a guess, but I'd say so far, probably his biggest impact has been with the very detailed "do it yourself" biology projects he's contributed.  He's absolutely amazing with designing solutions from off-the-shelf components, and equally amazing with using Google Sketchup and photographs to describe the designs to the public. A good example is his microscope objective heater, which was somewhere around $500 and is working very well for our gliding motility assays.

There are now many labs around the world deserving of this award, and it feels really good to receive it.  And I think it was a great contest for Addgene to sponsor.  I actually wasn't aware of Addgene before Andy told me about the contest.  So just learning about them made the effort worthwhile.  I had a great conversation with Melanie Herscovitch on the phone a few weeks ago and she explained to me Addgene's mission and services.  Here's a picture from their website to explain what they do: (used without permission! :) )

In a nutshell, addgene is a non-profit organization dedicated to making it easier for researchers to share and obtain published plasmids.  Authors of papers submit their plasmids to Addgene (either purified DNA or transfected cells, as I understand it).  Readers who would like to obtain the plasmid contact Addgene, and Addgene provides the plasmids for just a cost-recovery fee.  This works out well for all parties.  Without Addgene, it's often a very inconvenient process.  The authors are burdened with keeping track of plasmids that may have fallen out of use.  And researchers requesting the plasmids often face a long delay in obtaining them.  I think Addgene is a wonderful service and I look forward to working with them as we create and publish our own plasmids in the coming years.  I also got the feeling from talking with Melanie that Addgene is a really great place to work.  I don't know whether or how often they're hiring, but you can take a look here for current job openings.

Thanks again, Addgene!  If you're reading this, it'd be great to post a little thank you comment (on friendfeed or the blog) or congratulations to Andy!

FriendFeed Thread:

Sunday, February 21, 2010

Science Commons Symposium Pacific Northwest 2010, quick summary #scspn

Today I was lucky to attend the amazing Science Commons Symposium.  There were back-to-back fascinating presentations by Cameron Neylon, Jean-Claude Bradley, Antony Williams, Peter Murray-Rust, Heather Joseph, Stephen Friend, Peter Binfield, and John Wilbanks.  It was wonderful to meet in person a few people that I either did not know before, or whom I'd only know online previously, including Lisa Green (who went out of her way to invite me to attend this conference, thank you!), Heather Piwowar, Anali Perry, and Brian Westra.  It was also a great pleasure to meet again people whom (with the exception of Cameron) I'd only met in person a few weeks ago at the ScienceOnline2010 conference: Jean-Claude, Cameron, Hope Leman (another tireless organizer of the conference who graciously invited me to attend), Bill Hooker, Pete Binfield, and Antony Williams.  (My apologies if I missed out on name-dropping anyone, it hurts me more than you!)

I'm off to the Biophysical Society meeting tomorrow morning, and a bit out of steam, so I'm going to cop-out a bit and just embed a mindmap of my notes from the meeting.  Before doing that, I'll post a few action items from the meeting, and maybe later I'll come back and link to specific friendfeed or other threads for the items:
  • Antony and I made some progress discussing our athletic challenge to raise money for asthma research or other charity.  I think it's promising we can make it "generative," and successful.
  • Pete Binfield used Heather Piwowar's PLoS ONE paper as an example.  I want to read it and then rate it.
  • Improve our lab's Open Notebook Science.  This is ill-defined, but there are many steps we can begin taking immediately to work towards a system that works for us as well as it does for Jean-Claude Bradley and his students / collaborators.
OK, Here's the mindmap.  I started doing it as an example for Heather, Hope, Bill and others from a discussion at dinner.  Too tired to convert it into regular text now...would be interested to know if it's useful at all to you!

FriendFeed comment thread:

Thursday, January 21, 2010

ScienceOnline2010 -- Top N things I learned and was inspired to do at #scio10

I had a blast at ScienceOnline2010 last weekend!  Thank you Anton, Bora and others who spent so much energy organizing it!  Approximately 250 people attended and it was a very diverse crowd of scientists, science writers, publishers, librarians, science outreach specialists, high school teachers, even high school students.  Much has already been blogged about the conference, including many "Top N" lists.  You can find a list of them here.  My favorite so far is Jonathan Eisen's "Enough w/ the good: here are the top10 problems w/ the #scio10 meeting."  Hilarious!  Despite everything having already been done, I hereby present my belated list of things I learned, things I did, and things I've been inspired to do:

1.  I had a ton of fun interacting with a bunch of e-friends, old and new.
I attended as a scientist with an interest in all of the other areas.  It was definitely a new feeling to be in a session and have the speaker ask, "how many of you are scientists?" with the answer being a very small fraction of the participants in the room.  It was also a very new and thrilling experience to finally meet in person many people I've known only virtually for the past year.  I think Cameron Neylon was the only person I'd met in person previously.  Despite that fact, it was incredibly easy to have conversations during lunch, between sessions, and of course at the bar.  I uniformly enjoyed these people even more in person.  An incomplete list of the people I had the pleasure of chatting with include: Bill Hooker, Jean-Claude Bradley, Pawel Szczesny, Walter JessenChristina Pikas, Hope Lehman, Peter Binfield...  Plus I found some completely new friends at the conference, including Antony Williams, Greta Munger, Dorothea Salo, Andy Farke, Natalie Villalobos, Michael Habib, Annie Crawley, ...  Now, those previous two sentences could be perceived as egregious name dropping, which I am guilty of, simply because it's quite an amazing list of people, none of whom I knew before I became active in open science.  Clicking through those names and reading what they're saying, and you'll realize why I feel so lucky to have met them!
(Note, I forgot: Fabiana Kubke, ...)

2.  Antony Williams and I made some kind of running challenge.
I knew of Antony Williams from his ChemSpider fame.  I also had recently read one of his personal blog entries, about running 1000 miles in a year, along with his ugly and unfortunate calf injury.  I'm not sure I knew these were the same person, though.  Nevertheless, he walked passed me in the hotel bar, and I accosted him to inquire about his calf injury.  I'm pretty sure he didn't know me at all, but luckily we had on slick name badges and I was surrounded by credible people.  It'd be a big challenge for me to recount the conversation (I swear I remember it perfectly, I just don't feel like writing it down).  Let's just say that I was happy to learn that he'll be back running again within a week or so and that he has a goal of raising money to fight asthma.  I have had an idea mulling in my head that I could raise money and get motivated to get better at running by setting a race time goal.  I thought this was a perfect match with Antony's goal, so I quickly challenged him to a running competition.  He quickly agreed (fearlessly) and I tweeted/friendfeeded it to lock in the deal.  Over the next week, I'll see if I can clarify the challenge and I'll post updates to that thread.  I'm thinking I'll setup a Google spreadsheet for me and others to place their pledges and monitor the progress.  Antony already knows about Nike+ technology, and I'm looking forward to doing something like that too.  It'd be a good way to try out new things in open data, and open notebook science, actually.  Suffice to say that I'm going to get better at running, lose a lot of weight, and hopefully we'll raise some money too!

3.  I and KochLab are going to get better at doing Open Notebook Science and sharing data & software this year
I learned a lot at the conference about tools that exist for carrying out open notebook science and sharing data, methods, software, etc.  I still have a lot to learn, and indeed many tools still need to be developed.  But I know that our lab can make improvements this year.  Here's some concrete things that we'll do:
  • I've sent an email to Amy Jackson, Digital Initiatives Librarian at UNM, requesting a meeting.  I had briefly spoken to her via email in October and now I'm fully energized to have a meeting with her and see what kinds of first steps we can take towards building a partnership between the library and our lab in terms of sharing data and conducting open science.  I'll try to leave updates on this FriendFeed thread.
  • Get better at sharing software.  Currently we use LabVIEW, which is a wonderful programming environment.  One of the major benefits is that it's a graphical, data flow language.  This makes the code a 2-dimensional diagram...so in my opinion, it's exceptionally easy to read other people's code.  Unfortunately, it's a proprietary and expensive coding environment.  You are allowed to compile .exe and .dll files for others to use freely.  But that's not open source.  So, there are two routes to go: (1) We could compile virtual machines (VM) and send those to people for exploring our code.  For example, referees of papers we submit.  This was an idea from Deepak Singh at the meeting. Licensing is an issue here, and what I'd like to do is find someone at National Instruments (creators of LabVIEW) and discuss what can be done to serve our open source needs.  (2)  Learn a text-based, freely available language.  I think this would be valuable for our students anyway, in terms of building their resumes.  While at the meeting, I thought Ruby was a good idea, but now not so sure.  I've posted a FriendFeed message about this, and have received all kinds of very valuable advice.
  • Adopt techniques to make it easier to capture our workflow in the lab.  OpenWetWare has innovations coming up soon and we'll certainly jump on those.  Cameron also hinted at something revolutionary coming up this year, but said he'd have to kill Bill if he told him what it is.  It wasn't clear that he'd have had to have killed others in the room, so I was disappointed he didn't say what it was.  (Just kidding, Bill!)   But the fact is, I don't think our current tools are nearly sufficient.  I'll put in more effort to make positive steps here, but I'm not sure exactly what yet.
4.  Improve the state of publishing, one article at a time: Try out some ideas via PLoS ONE.
I was delighted to have the opportunity to talk with Peter Binfield at the bar and discuss publishing ideas with him.  I have a lot of ideas that I'd like to try out, and it hasn't yet been proven that all of them are lousy.  I ran many of them past Peter and his general response was, PLoS ONE would love that -- it's just that whatever scientific community you're in may not respect it.  Very true.  However, I do think many in my community would respect anything that showed how publishing could be better by being different.  And I now realize that PLoS ONE is a very good platform for trying out a few things.
  • At lunch with Bill and Pawel, they mentioned an idea that others had been talking about.  Unfortunately, I don't know to whom to attribute the idea. (Note: Bill and Pawel give attribution to Fabiana Kubke, which sounds right to me now.)  The idea is that publishing one very good figure would be a good idea.  I like this idea enough to think about trying it out.  It is related to an idea Larry Herskowitz and I were discussing a few days before the conference:  Can we publish a paper without an introduction?  Or an introduction that just says, "see such-and-such other paper for introduction?"  So much time is wasted rewriting introductions (in my opinion), especially when trying to avoid copying prior written work.  Is this necessary?  Publishing a single figure takes this even further.  I have some interesting data from grad school and postdoc that I have not been able to publish.  It pains me that it's just sitting around, useless.  Do you think it's worth using this data to test out the "publish one figure" method?   If I make progress on this, I'll post updates on this FriendFeed thread(Note added: Cameron Neylon reminded me that BMC Research Notes may be a better venue than PLoS ONE for this.)
  • For maybe ten years now, I've thought that the value of anonymous peer review is overstated.  During that time, I've heard other people, much more eloquent than me also express this opinion.  Just briefly, I think fully-attributed, non-anonymous peer review would solve many problems that exist with today's science, and I discussed this a bit at the meeting.  Two of these problems are: (a) good referee work is difficult, and good referees are not credited for the work and the original ideas, and (b) a whole lot of incomplete and sloppy work is submitted and much of it is published due to ineffective referees / editors.  The solution I like is for every aspect of the peer-review process to be published, including the original manuscript submitted, all subsequent revisions, and all communication between authors, editor, and referees.  Clearly this solves problem (a).  As for problem (b), people often say, "but people aren't going to say negative things if their name is on it!"  First of all, that's not necessarily true.  Secondly, referees have the option to decline without comment.  If the editor cannot find someone willing to slam the paper, then it's just returned to the authors.  Voila!  One less crappy paper published.  The arguments get more complicated, especially when considering that grant review is anonymous, providing a lot of opportunity for underhanded retaliation.  I can't mathematically prove that it's a good or bad idea, so I'd like to try it out and see what happens.  It occurs to me that I could submit a manuscript to PLoS ONE and request that the Academic Editor implement this idea.  Why not?  Should be OK as far as I understand the rules.  I don't expect to submit garbage, so it won't be a complete experiment.  But something may be learned, and at least all the referees will get credit.  I may update progress on this idea on this FriendFeed thread.
OK, That's enough for now.  I can always add more later, especially since I aptly named this post.  For example, I may talk about the rebranding of our blogs that Walter Jessen recommended.  It's a good and valid suggestion, but I'm not adding it yet, because I'm not sure how soon I'll be able to think about that :)

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