Andy Maloney - Comments

Andy Maloney to Andy's feed, Science 2.0

How would you track the addition of an ONS logo to a notebook? It's a great idea but, how do you do it? I'm referring to a comment by Bill Hooker on Andrés G. Saravia's new notebook, http://friendfeed.com/science....

November 24 - Comment - Like - Share

Cameron Neylon, Jean-Claude Bradley and Steve Koch liked this

I can think of two ways. 1. Use Google image search and it will find all the instances of that image that it has indexed. Unfortunately there are a lot of ONS logos to check. 2. We could wrap the logo in code that links back to the set of logos page. Then we could track incoming links. Not everyone would like this though and some would remove the link wrapper. - Andrew Lang

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I think that having both a link wrapper and allowing the user to link to the ONSclaims wiki is a good idea. I'll be including the link with the logo from now on. - Andy Maloney

I was thinking of the link wrapper method. Image searching hadn't occurred to me. I hadn't thought about someone doing ONS objecting to the wrapper (they are free to make themselves less searchable but why would they?). - Bill Hooker

I created a friendfeed group "open notebooks" with RSS feeds from ONS I could find. Sort of the reverse of automatically finding them. If we could find the feeds from some kind of ONS logo search, then we could use Yahoo Pipes to create an RSS feed of all ONS feeds. http://friendfeed.com/open-no... (Not sure if this group is useful, but I'll use it for a while) - Steve Koch

I've found the google-image search to do a poor job even bringing up all sites that use the image. I was also surprised that google search for all websites linking to onsclaims.org page was also far short. The wrapper code sounds like the way to go (something like the way researchblogging.org works) - Carl Boettiger

Andy Maloney to Andy's feed, Science 2.0, Kochlab

Stumbled across Morgan Langille & Jonathan Eisen's BioTorrents site http://www.biotorrents.net/. Looks like it could be extremely useful but, how do you make sure your system is safe while hosting a torrent? I'm sad to admit it but, I know basically zilch about torrents. Any suggestions on what to do?

September 14 - Comment - Like - Share

Clark Kent, Jonathan Eisen and Steve Koch liked this

I've been asked for the data I've posted on YouTube multiple times and it seems like a torrent would be a good idea since the data is ~100MB. - Andy Maloney

There's no safety issue - treat a torrent the same as you would any other file you download from the internet - know your source. As far as hosting data, a torrent is no better than any other method if you're the only one seeding. The hard part is getting other people to save the data and leave the torrent app open. It's also a challenge at many institutions where torrent still == piracy in their mind. - Chris Miller

Thanks Chris. I should edit my above comment to note that the file is more like 100GB. This means popular services like Dropbox are out of the question. Maybe PLoS ONE would host it for me? Any one tried to get them to host gigantic files? - Andy Maloney

Cameron Neylon

I give up - http://nsaunders.wordpress.com/2011...

July 15 from Google Reader - Comment - Like - Share

Chris M, Steve Koch, Joe and 6 other people liked this

Tuesday, I was in a training meeting with some undergrad tutors, and two of them made a huge deal over NOT using Twitter -- as though reactionary obstinance was something to be proud of. But then during a workshop with physics students last week, the coordinator of the REU program told a story about refusing to share a former student's code with her current supervisor...b/c it... more... - Mickey Schafer

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"I countered with Andy Maloney's work" -- I cannot say how happy this makes me. - Bill Hooker

:) - Graham Steel

A colleague and I helped a prof get his undergrad research methods class on Twitter a few weeks ago. He wants the class to use twitter to discuss what they're researching. It was fun. - John Dupuis

Ha! It's nice to know one was useful for something. - Andy Maloney from iPhone

Giorgio Gilestro to Giorgio's feed, Science Online, The Life Scientists

What does a postdoc want? http://gilest.ro/2011...

May 26, 2011 - Comment - Like - Share

Jo Young, Andy Maloney, Daniel Mietchen and Björn Brembs liked this

I don't know!!! - Jan Wessnitzer

I'm guessing a post doc wants to retain being able to work in the lab since that's what graduate school trains you to do. However, they don't want to deal with the 29 daily meetings, asinine mountains of paperwork, dealing with whiny students in class and the lab, and giving up doing actual physical hands on research at the bench which, is what professors have to deal with. - Andy Maloney

The over confidence of the survey respondents are, I feel, quite disgusting and a shame. Especially since I know the type of over confident physicists that think they are "holier than thou". - Andy Maloney

Andy Maloney to Andy's feed, Kochlab

Another confirmation of BRB80 being attributed to Dr. Bill Brinkley.

May 18, 2011 - Comment - Like - Share

Bill Hooker and Steve Koch liked this

I got an email today from Virginie Stoppin-Mellet who is an Assistant Professor in L. Blanchoin's lab in France that I think is called the CEA Fontenay-aux-Roses. Dr. Stoppin-Mellet found my Flavors page (which is an electronic version of my CV) and actually read some of my silly dissertation. She stated that BRB80 "means Bill Brinkley Buffer, 80 stands for 80mM PIPES". - Andy Maloney

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Another gem from Dr. Stoppin-Mellet. "I've always been told that tubulin, which is a difficult protein to work with, has a tendancy to aggregate in the presence of Na, thus KOH was used to buffer solutions." - Andy Maloney

I thought the two most likely choices were "Borisy Reassembly Buffer" or "Brinkley Reassembly Buffer?" (Not BBB80) I still think it's a "backronym." http://friendfeed.com/the-lif... Too bad all of Neil's comments were deleted from the thread. - Steve Koch

Drop Bill Brinkley a line - he's a really nice guy and would probably be amused whether it's named for him or not. brinkley@bcm.edu - Chris Miller

Andy Maloney to Andy's feed, The Life Scientists, Science 2.0, Kochlab

I finally have videos of tobacco seed growth in varying amounts of heavy water.

April 27, 2011 - Comment - Like - Share

ovigia, Mike Chelen, Graham Steel and 2 other people liked this

100% 18.2 MΩ-cm H2O. http://youtu.be/SqDbllaJtQg - Andy Maloney

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100% Tap water. http://youtu.be/L8Vj1KuIZfA - Andy Maloney

25% D2O and 75% 18.2 MΩ-cm water. http://youtu.be/5Y3on5S1jPs - Andy Maloney

50% D2O and 50% 18.2 MΩ-cm water. http://youtu.be/Bs_CK38HLAk - Andy Maloney

There was supposed to be more but something happened with either the cameras I was using, or the software. The videos of 3 of the assays just didn't work. The 3 other experiments were 75% D2O and 25% 18.2 MΩ-cm water, 100% D2O, and deuterium depleted water. - Andy Maloney

Would love some narration, Andy - if possible. Also, here's a wee possible background MP3 track as well CC-BY:- http://www.macjams.com/song... Never got round to remixing this one in full. At least for me, it works here in it's orig. form. here. - Graham Steel

Takes me back to 2010 this does:- http://steelgraham.posterous.com/koch-la... - Graham Steel

Graham: Yep, that was hilarious. As for the narration on the new movies, I'll have to figure out a time to do it if you think it is better than the comments I attached to it. - Andy Maloney

Sorry, I had not seen the comments, Andy. - Graham Steel

Well, it makes sense to add narration as I suspect that no one will read the comments. - Andy Maloney

It would be useful to see a few photos of the setup from different angles -- I initially had trouble working out what I was seeing. - Bill Hooker

Andy Maloney

The making of Kiney. - http://childsownstudio.blogspot.com/

April 7, 2011 from Bookmarklet - Comment - Like - Share

Steve Koch liked this

Every lab should have a mascot and they should get Wendy to make it for them! - Andy Maloney from Bookmarklet

Andy Maloney

My response to my committee's desire for me to make my dissertation less colloquial.

April 1, 2011 - Comment - Like - Share

Cesar Sanchez, Matthew Todd, Claudia Koltzenburg and 5 other people liked this

I feel strongly about this. Yes, I'm a scientist. Yes, I use jargon and have the capability to describe everything I've done, and can do, in the most obtuse manner possible. As physicists, we place a lot of weight on being able to have conversations about science. We even hold weekly meetings called ''colloquiums'' in order to spark up conversations about science. Why then do we insist on writing in an archaic manner in which we actively attempt to confuse people and fellow scientists? This is illogical and as a logical person, I find it unnecessary. I will not compromise my principles about writing in a manner that is clear and easy to understand. - Andy Maloney

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I agree with you for the most part. Since you weren't there "behind closed doors," I can say that the predominant concern was basically for whether _other_ scientists (i.e. future bosses / colleagues) would understand your goals with your dissertation. I.e., like the one member said to you, he literally wasn't sure whether you were talking tongue-in-cheek or not, and you know we really... more... - Steve Koch

Ha! I'm not bitter. Just passionate about not being a "high brow" linguist. I've thought of this already and I am going to add a prologue that describes this very issue and why I have decided to not write so formally. - Andy Maloney

Hey, I remember having this discussion with my PI too! I won the fight about "active voice is the voice that is preferred by us" by showing them Nature's guidelines which specifically call for it, but I gave in on some of the more innovative document structure concepts I used initially. I think new PhD's have a duty to keep pushing the envelope, because they're the only ones who will and someone has to, but I also see the arguments about too much too soon being a distraction from the paper itself. - Mr. Gunn

Some jargon and field-specific conventions are there for a real purpose, not just to confuse the plebs and make us look smarter. One of the easiest examples is methods: I don't want to read a thousand different descriptions of how a plasmid library was constructed, no matter how good and clean the prose. If you used a standard method, I want you to describe it in standard terms --... more... - Bill Hooker

Andy or Steve, can you repost the link to Andy's diss? I'd like to read through it -- I'm very interested in this idea of clarity in scientific writing, and to what extent formalisms help and hinder that goal. - Bill Hooker

Bill, for now the wiki chapters are linked on Andy's OWW home page here: http://www.openwetware.org/wiki... - Steve Koch

Chapter 1 is probably a good place to start--it's methods http://www.openwetware.org/wiki... - Steve Koch

Thanks, Steve. Andy, for what it's worth, I think I'm seeing two kinds of "colloquial" writing here. First, there's the kind in your introduction section, which is chatty and fun and completely fucking pointless in a scientific document. I'm not there to swap movie quotes with you. Blog that stuff if you gotta get it out. Then, there's the actual methods section, where the colloquial... more... - Bill Hooker

What I'm saying -- and again, fwiw, meaning you shouldn't listen too much to random weirdos on the internets -- is that your stated goal is to make the writing clearer, the transmission of information to the reader more efficient. Where it works, where you stick to the point, your writing does this extremely well, and I would defend it for clarity against any of the usual formalisms. I... more... - Bill Hooker

Bill: Ha! Love it! I completely agree with you about the "Chatty Cathy" segments. Very true. But, sometimes it's good to have your attention shaken a little bit with some randomness because I bet you $10,000 that you remember the section where I spoke about DMSO and I can guarantee you won't remember what section has glucose in it. - Andy Maloney from iPhone

Bill: You are also correct that I would not want to have verbal diarrhea in a paper. I'd never want to read such dribble in a journal article myself if all I'm after is the methods. In fact, I'd just read the methods section and be done with it. This is why I structured the chapter to have links to the important methods sections and can be navigated to if so desired. But, this wasn't a... more... - Andy Maloney from iPhone

Oh, and for some awesome dribble from actual journal articles where you can read about scientists bitching about each other, you should read some articles from the early 1900's. - Andy Maloney from iPhone

Bill: Here's a good question, when was the last time you read a dissertation? Better question, when was the last time you read a dissertation that you didn't want to stop reading and have a stiff drink? I was under the impression that dissertations sat in the library with the $20 you planted in there and that was it. So, from you reading it Bill, I suppose I owe you $20. :) - Andy Maloney from iPhone

Nah, you only get the $20 if you find it in the physical copy! Last time I read a dissertation was a couple of months ago; it was a bit of a slog because it wasn't my field (behavioural risk factors for HIV -- lots of stats). I still think it wouldn't have been improved by asides about how milk tastes! But when I read dissertations, even more than when I read papers, I'm usually looking for something specific -- so your point about structure and navigation is well taken. - Bill Hooker

Andy Maloney

Response to an important question posted on the talk pages to my dissertation.

March 29, 2011 - Comment - Like - Share

Carl Boettiger: I haven't figured out the best solution to this. I had a horrible time finding a program that converted wiki to LaTeX but I did find one. It wasn't perfect, but it got the job done for the most part. Once I get all the corrections from my committee, I will use another program to convert LaTeX to wiki and update these pages. This will be the "final" snapshot of the dissertation. I'm hopeful that these pages will never die in the sense that any new information that I obtain about this line of research, will get updated here. Thanks for looking! - Andy Maloney

Jean-Claude Bradley: That is a good point about the reference to SMIRP being misleading. I will fix it immediately. I should also point out that it was the SMIRP paper that led me to posting about the fluorescent Schlieren microscope (which was a dead project) since the paper basically inspired me to try and "post everything". - Andy Maloney

Andy Maloney to Andy's feed, Kochlab

Vote for Your Favorite Scientist Homepage | BenchFly Blog - http://www.benchfly.com/blog...

March 17, 2011 from Bookmarklet - Comment - Like - Share

Steve Koch liked this

Personally, I like Jim Caryl's and Jaime Freitas's sites. - Andy Maloney from Bookmarklet

I voted! I'll send out the link on FF and FB tomorrow morning because as it stands now it's crazy that you're not winning :) - Steve Koch

Also, after you're done with your presentation, remind me to send the link to peeps @ UT-Austin who I know. Let's see if we can get you a general seminar talk where you can meet some peeps. - Steve Koch

Andy Maloney

McSweeney's Internet Tendency: FAQ: The "Snake Fight" Portion Of Your Thesis Defense. - http://www.mcsweeneys.net/2010...

March 16, 2011 from Bookmarklet - Comment - Like - Share

Ha! - Andy Maloney from Bookmarklet

Steve Koch to Steve's feed, Kochlab, Andy Maloney

2011 March Microtubule gliding speeds, kinesin-1 heavy-hydrogen and heavy-oxygen water - FigShare - http://figshare.com/figures...

March 6, 2011 from Bookmarklet - Comment - Like - Share

science3point0, Cameron Neylon, Björn Brembs and 3 other people liked this

This is the first figure our lab has added to FigShare that is new and very likely to be (formally) published soon. It's Andy Maloney's data for microtubule gliding speed on a kinesin-1 surface as he varies the concentration of deuterium or heavy-oxygen in the water. I think his data are exceptionally high-quality and I'm really proud of his work. These two plots are the culmination of a ton of work by him and Larry Herskowitz (image tracking) over the past two years (since we began working on kinesin). I'm not sure but I think there are between 100GB to 1 TB of raw image data associated with these graphs. Not a lot, but not a little data either. It's all open data and we're working on methods for sharing the data. Probably a good page to jump to is Andy's methods in his open dissertation: http://www.openwetware.org/wiki... - Steve Koch from Bookmarklet

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So, now an interesting part about open data: we don't know how to interpret the results yet! And I bet someone out there has some good ideas. We were steered towards these experiments by a collaboration with the Susan Atlas group, who is working on a Charge-Transfer Embedded Atom Model (CT-EAM) force field for molecular dynamics (MD) simulations. We have been thinking about water as a... more... - Steve Koch

How was the viscosity measured? I'm a bit surprised to see the isotopes make such a difference but that is probably just my ignorance in action. Cytoplasm is very viscous compared to water -- are there any in vivo data available for comparison? Jennifer Lippincott-Schwartz does amazing work on organelle dynamics in living cells, using video and molecular labelling... - Bill Hooker

Hey Bill -- one quick answer: we did NOT measure the viscosity. I just looked it up in primary literature and / or Wikipedia. - Steve Koch

Also, Bill, I am behind on the latest in intracellular studies, though I agree they are fascinating. Without all of the latest information, I'd be shocked if an intracellular measurement could detect the subtle (<25%) effects that we're seeing above. Andy's method is more suited for biophysical study of the isolated motor system, as a way of probing the solvent effect on the system. No... more... - Steve Koch

http://www.articlesofbusiness.com - Carri Shabi

http://starsjobs.blogspot.com - Carri Shabi

I'll be sure to fix those error bars. - Andy Maloney from iPhone

Yeah I know you will. And I know they won't be much different, so didn't want to wait to publish to FigShare. - Steve Koch

Very nice work, Andy! - Steve Koch

Yeah, I forgot to say so, but nice work deserves recognition and this is nice work. Good data are hard to come by and it warms an old experimentalist's heart to see such attention to detail. - Bill Hooker

Something else you've probably already thought of -- the Pi exchange/ADP release is a good idea, so I wonder if there are other well characterised systems which include a similar step that would be amenable to study in your setup. I got there from here: what do seeds (Lewis) and tumors (PubMed search for DDW) have in common? Rapid growth and proliferation, which requires rapid DNA... more... - Bill Hooker

Steve Koch to Steve's feed, Andy Maloney

Andy, one thing that occurred to me last night: if you restart the tobacco seed experiment again, you should probably try pre-soaking some of the seeds at 4C in the dark, in case there's a substantial time delay for hydrogen/deuterium exchange.

March 6, 2011 - Comment - Like - Share

Andy Maloney and Bill Hooker liked this

I've been jonesing for more data on this question! - Bill Hooker

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Me too! Andy has overhauled the data acquisition system with like 8 web cams now. It's a very cool system, but because it kept crashing, we had to abandon the idea of real-time data to the web. I think he started a new experiment yesterday and it will be fun to see what happens. For what it's worth, though, my bet is still that we will not have enough precision to discern a difference... more... - Steve Koch

Well, I didn't soak anything so we shall see what happens. - Andy Maloney from iPhone

It may be fine, just depends on how much H is stored in seeds and how quickly it exchanges. - Steve Koch

Andy Maloney to Andy's feed, Kochlab, DIYBio, Science 2.0

DIY Laser Shutter - http://www.instructables.com/id...

February 22, 2011 from Bookmarklet - Comment - Like - Share

Björn Brembs, Bill Hooker and Steve Koch liked this

There is an RSI article about using an old hard drive as a laser shutter. Unfortunately/fortunately I didn't know about it when I built this one. Well, at least the design is now in the public domain. - Andy Maloney from Bookmarklet

We're using several of these in our lab, too, using the instructions in the same paper you're citing. These things are really great! - Björn Brembs

Andy Maloney to Andy's feed, Kochlab, Science 2.0

I've updated my dissertation with easier navigation. http://www.openwetware.org/wiki...

February 8, 2011 - Comment - Like - Share

Heather Piwowar, Steve Koch, Bill Hooker and Mickey Schafer liked this

I even have a few comments on it. Granted, the comments come from a great friend and my father in law but, at least I can now say that this open dissertation is reaching beyond the lab. - Andy Maloney

Björn Brembs to Björn's feed, The Life Scientists, Steve Koch

I'm looking for someone to brainstorm and perhaps collaborate on a piconewton torque sensor - for measuring fly turning maneuvers.

February 2, 2011 - Comment - Like - Share

Greg Tyrelle, Jan Wessnitzer, Mickey Kosloff and 3 other people liked this

Was thinking that perhaps Steve Koch might know someone: http://www.aip.org/pnu... - Björn Brembs

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These guys use MEMS but for some reason torque is not on the horizon: http://fly.ini.unizh.ch/joomlas... - Björn Brembs

And yes, of course I mean piconewtonmeter... - Björn Brembs

Just curious (it's not my field, so call me ignorant if that's a silly question)... Can you calculate torque from tracking data (assuming you can track precisely in time position of both ends of a fly)? - Pawel Szczesny

You want to measure the torque that a fly exerts on a tether, or on its own body? The former seems do-able, the latter so difficult as to approximate impossible... - Bill Hooker

All good - Being the non scientist around these here parts, the best I can offer (on this one) is from AC/DC :- http://www.youtube.com/watch... - Graham Steel

As per Bill's tether example, if you can assume that the fly changes its shape much less than the tether, you could get the torque from measuring the fly's angular velocity (in principle obtainable from tracking data, as per Pawel) and multiplying that with its moment of inertia (hard to calculate but possible to measure). - Daniel Mietchen

We would like to measure the torque the fly exerts on a tether, see here: http://www.youtube.com/watch... - Björn Brembs

That's way cooler than I thought. I didn't imagine one can hold a fly and let it fly at the same time :). So you want to build a torque meter (similar to the one you have) but more sensitive, or I'm still missing the idea? - Pawel Szczesny

I just want more of them. Nobody builds these things and the few which are around are mostly own developments by the different people, so they're not for sale. Mine was built in 1963 and I inherited it from the person who inherited it... - Björn Brembs

Now I get it. I've just sent an email to a friend who might know somebody who might know somebody... BTW, where's Steve Koch? - Pawel Szczesny

He must be offline, I guess... - Björn Brembs

Queried a "DIY science' colleague of mine. - Kubke

Have you ever taken it apart? Not even clear to me how you could make something sufficiently sensitive. - Cameron Neylon

Currently, there are three main principles of measuring torque of this magnitude: 1964: http://dx.doi.org/10... 1988: http://dx.doi.org/10... and very recently also http://www.plosone.org/article... Yes, I have repeatedly opened my own device. The mechanics is only one of the difficult problems (nobody is around any more who built these things), the analog electronics are also beyond my abilities (but I do have all the plans). - Björn Brembs

The lowest measuring range is probably in the hundreds of piconewtonmeters, the highest for sure in the tens of nanonewtonmeters. - Björn Brembs

"Have you ever taken it apart?" -- this made me laugh! I'd have bet a lot of money on the answer being "yes". :-) - Bill Hooker

hi bjoern, it was suggested that Michael Dickinson in caltech would be a good person to contact- he should have both the know how and the means. if you have the wiring diagram, I could take a look at it. bioengineering institute here might be able to help - Kubke from BuddyFeed

I know Michael very well and he has in all these years never built a torque meter (but a lot of other very cool stuff!). - Björn Brembs

Hey all, sorry I have been completely out of it! This is a really fascinating experiment! I was completely unaware of it, and looking now at the PLoS ONE article (can't get the other two) and the excellent youtube video. Here are some of my initial thoughts (1) the level of force we were measuring was 10's of piconewtons, and the spring arm length was 100's of microns. This would put... more... - Steve Koch

If looking at option (3) above, you could also put the lasers on the device or neighboring devices so the punishment could be applied from on-chip laser. - Steve Koch

This looks promising: http://iopscience.iop.org/0960-13... "A capacitive MEMS force–torque sensor has been presented that is able to measure forces at sub-µN resolution and torques at sub-nNm resolution. This is the ﬁrst time that both forces and torques are measured simultaneously using a capacitive MEMS sensor... The magnitude of the measured forces and torques range up to 1419 µN and 2257 nNm, respectively" - Steve Koch

I can access the above PDF via my library. It looks very fly-ready. The remaining component would be adapting software for digital feedback control. - Steve Koch

I think these are the same group, and are definitely thinking about tethered fruit fly studies http://www.springerlink.com/content... - Steve Koch

Yes, the MEMS guys in the last two papers are the ETH guys in Switzerland. Steve Fry is a former student of Michael Dickinson's (see above) and he told me about 2-3 years ago that a usable torque meter for flies would still be some ways away. It seems they are getting closer, I need to read these papers in detail, to see how far they've gotten. - Björn Brembs

@Steve in reverse order: (6) Then the fly would get feedback: it would be rotating and flies have gyroscopes to notice that (i.e., halteres) (5) I'd so love to make this an open science project! (4) The less analog electronics, the better. I want as much software to do the controlling as possible. (3) I don't have access to the PDFs you linked, so I'm not sure what the MEMS breakthrough... more... - Björn Brembs

This sounds very interesting. I'd love to look at the schematics of your device Bjorn. I have zero knowledge of what is doable with flies but if you were to post some parameters that aren't possible with them, it would help out to determine what is possible. Tell me if I'm wrong but it seems that the devices are holding the fly somewhere on its body and then some electrodes are... more... - Andy Maloney

The papers I referenced above show the schematics of the three principle ways to do it and the papers from Steve show the fourth, MEMS sensors. The one you mean is depicted in Fig. 1 of the paper and the electrodes are only there in addition to the torque measurements, they have nothing to do with these measurements themselves (see my YouTube video) - they record brain activity while the flies are flying. - Björn Brembs

Andy Maloney to Andy's feed, DIYBio, Kochlab

My Instructables showing how to make a DIY objective heater/temperature controller. - http://www.instructables.com/id...

January 19, 2011 from Bookmarklet - Comment - Like - Share

Mike Chelen, Bill Hooker and Steve Koch liked this

Apparently this post is quite popular. I never would have dreamed it but I've gotten over 700 views in one day. I'm flabbergasted since I thought I did a horrible job with it due to what I feel was a lack of pictures in the Instructable. - Andy Maloney from iPhone

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That's amazing for one day! And the guy you're commenting with seems very cool as well. - Steve Koch

Can't wait to see how your stir/heat plate write-up takes off too :) - Steve Koch

It would appear that I've some how stirred up open science exposure with this post. It's also apparent that the Instructables community is not afraid to post comments, which is refreshing. - Andy Maloney

It's also apparent that this site may be a great place for people to post materials and methods sections to a community that will be receptive to it. - Andy Maloney

Andy Maloney

YouTube - So You Want a PhD in Clinical Psychology? - http://www.youtube.com/watch...

January 27, 2011 from Bookmarklet - Comment - Like - Share

Oh man, this is hilarious. And nope, I don't call my friends with PhDs doctor either. - Andy Maloney from Bookmarklet

Andy Maloney to Andy's feed, DIYBio, Kochlab

My Instructable on how to make a DIY Stirrer/Hot Plate. - http://www.instructables.com/id...

January 21, 2011 from Bookmarklet - Comment - Like - Share

Mike Chelen, Bill Hooker and Steve Koch liked this

Cheap and easy. - Andy Maloney from Bookmarklet

Andy Maloney to Andy's feed, Kochlab

Splash page! http://flavors.me/andy_maloney

January 18, 2011 - Comment - Like - Share

Mickey Schafer and Steve Koch liked this

Steve requested I make this so I found the easiest way to do it, use the GUI at flavors.me. - Andy Maloney

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Looks awesome. I'd hire you! - Steve Koch from Android

That really is classy. Nitpick: I would change "I am an experimentalist THAT..." to "I am an experimentalist WHO..." Non-nitpick, that is, nontrivial question: why a SA license? (See here: http://www.sennoma.net/main... for my take. This: http://opencontent.org/game... is also fun.) - Bill Hooker

Bill: I'm not sure about the SA license. I read your take and agree with it but, at the bottom of every page in my notebook, it has the SA license on it or the GNU free documentation license. I'm not sure about the differences and all I did was restate what is already on the notebook I use. - Andy Maloney

Huh, I never noticed that OWW uses CC-BY-SA. I don't use OWW myself so I don't know whether there is an option to change the licensing. GNU FDL is a copyleft license, so probably does much the same as CC-SA (though IANAL!). Clicking the link at the bottom of each notebook page goes to a page that says all content is CC-BY-SA with an option for the user to add GNU FDL, so at a guess I'd say the FDL is more restrictive. - Bill Hooker

I knew about the CC-BY-SA 4 years ago when we started at OWW, but it didn't mean much to me at the time. I haven't thought about it or noticed it recently. If there were still some tech peeps there, I bet we could relicense all our KochLab stuff. But not sure if there's anyone there. I think after teaching on S30 wiki this semester, I may be ready to migrate us all over and then, of... more... - Steve Koch

That all makes sense -- it's not as though it's a Big Hairy Deal in practical terms right now anyway, since any form of Open is a step forward. Plus, you can always change to a less restrictive license with no back-compatibility problems. I was just curious, having never noticed the licensing on OWW. - Bill Hooker

I think we're OK in the near-term, but for the long-term, I'm glad you noticed this, since eventually it will cause problems and we need to license better. - Steve Koch

By the way Andy was struggling today in choosing a license for his latest "Instructable" (http://friendfeed.com/diybio...) I wasn't sure what to recommend. I know you're PD / CC0 for all, but I don't think he is there yet. What's next best option? Creative Commons Attribution? - Steve Koch

If I could have everything CC0 I would. But when that's not an option, I end up not knowing what to do since I have no desire to read copyright laws. Especially since there are so many with subtle differences. It becomes a pain and bore to read about them. What would be nice is if someone made a reference cheat sheet that gave a quick explanation for the laws and why an open scientist... more... - Andy Maloney from iPhone

Why did Steve make the request? I'm showing the page to my thesis students in an hour or so -- I see the immediate "introduce me" value since my dept. has begun doing general web searches on all our hires. I am also teaching students how to carve out their presence more authoritatively, so this is an interesting example. - Mickey Schafer

Mickey: I'm not sure why Steve requested I make this page. It has brought up an interesting debate about sharing though. I'm pretty sure that most everyone in this forum will state that sharing is the right thing to do with data and intellectual findings. Unfortunately there is a myriad of ways to share that apparently are not equivalent. It's unfortunately not as easy as just sharing a... more... - Andy Maloney

From the Instructables TOS: "...Instructables claims no ownership or control over any Content posted by users of Instructables. The author retains all patent, trademark, and copyright to all Content posted within available fields... With respect to Content you submit or make available for inclusion on publicly accessible areas of Instructables, you grant Instructables the world-wide,... more... - Bill Hooker

The problem with the cheat sheet idea is that this: "a quick explanation for the laws" contains an irresolvable contradiction in terms. The damn law is such a mess that there are no quick explanations for most situations where you'd want one. This is one of the main reasons why I use CC0 for everything I do, and think that CC0 should be the automatic default for all things scientific or... more... - Bill Hooker

@Andy: I didn't request you make the page, but I did suggest you do so and this was because I thought it could only help you find a good job after you desert our lab :) Now that I've seen what a great job you did on the site, I _know_ what an awesome suggestion I made. - Steve Koch

Great arguments, Bill. I'm heavily leaning towards CC0 now & at least we're already there for our data from the lab. - Steve Koch

Mr. Gunn

For those still looking for work, try http://www.rim.com/careers/ (via @gnat) SFW, I promise ;-)

January 13, 2011 from Twitter - Comment - Like - Share

<sarcasm>Looking forward to starting job hunting in 2 months.</sarcasm> Thanks for the link, I'll definitely use/need it! - Andy Maloney

Bora Zivkovic

What is a "least publishable unit"? http://amontenegro.blogspot.com/2011... by @aemonten

January 9, 2011 from Twitter - Comment - Like - Share

Bill Hooker, Mickey Schafer, Kubke and 2 other people liked this

This is an interesting question in the context of PLoS ONE (and Nature ONE) plus Nature Precedings and Open Notebook Science. What belongs on your lab wiki, and what do you publish in a journal? I think that if a single, well controlled experiment is sufficient to establish something new, it could be published on its own. It would presumably have to falsify something, since it usually... more... - Bill Hooker

Ha! The most spectacular comment I have ever heard/read is in the comments section of the blog: "KISS - Keep It Simple and Stupid". Words of wisdom. Especially for experiments. - Andy Maloney

very nice discussion in the comments. - Mickey Schafer

Andy Maloney to Andy's feed, Science 2.0

A wonderful thing happened to me; someone asked me for the data I've taken.

December 16, 2010 - Comment - Like - Share

Steve Koch, Heather Piwowar, science3point0 and 10 other people liked this

Some of it can be found here: http://www.kochlab.org/files.... - Andy Maloney

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Unfortunately, talk has turned to author lists and publications so the exchange isn't moving smoothly. This is why I wrote an email stating the following. - Andy Maloney

<rant> Of course, it would be nice to be acknowledged but, we all know that people who are in an unfortunate race for publications are in a precarious position. And, I do not envy that position. Let me be the first in your professorial career to state that I seriously, with out a doubt in my mind, unequivocally, and consummately don't care about having my name on publications. The... more... - Andy Maloney

Like button once again insufficient. Need "this is awesome" button instead. - Bill Hooker

Cameron Neylon

Why you may not like your job, even though everyone envies you - http://lemire.me/blog...

November 22, 2010 from Google Reader - Comment - Like - Share

Andrew Perry, Anders Norgaard, Bill Hooker and 5 other people liked this

Amen! Although, being a former artist, the blog really only applies to scientists. My art and my music is...(strike that) WAS a pure abstraction from life even though I was making things. As a scientist, I have to say I agree with this post. In the lab I get to tinker and make. But, I see what professors do. 70% or more of their time is spent grant writing. 30% is classes and the last... more... - Andy Maloney from iPhone

Candidates for this? http://jayjay.posterous.com/reminde... - AJCann

Steve Koch

Effects of surface passivation on gliding motility assays : Nature Precedings - http://precedings.nature.com/documen...

November 18, 2010 from delicious - Comment - Like - Share

In this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of αs1, αs2, β, and κ casein, supported motility and averaged speeds of 966 ± 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and supported gliding motility and average speeds of 949 ± 4 nm/s. Beta casein did not support motility very well and averaged speeds of 870 ± 30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa casein with the proportions found in bovine whole casein supported motility and averaged speeds of 966 ± 7 nm/s. - Steve Koch

Ah poppycock and fiddle sticks. There's a bad typo with the SEM on either the mixed casein or whole casein. I know they are different but I can't remember which one is not 7. - Andy Maloney from iPhone

I screwed up the second alphas1 alphas2 also. You can email precedings@nature.com and ask them to fix it. We can fix the PLoS ONE submission at some point, not a big deal. - Steve Koch

Steve Koch

Hey Jean-Claude & others -- for our submission to PLoS ONE, what do you think about citing a single page such as this on in the paper? - http://www.openwetware.org/wiki...

November 17, 2010 from Bookmarklet - Comment - Like - Share

Kubke and Bill Anderson liked this

Or is it much better to do the hard work of contextually citing individual pages throughout the text? - Steve Koch from Bookmarklet

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Kinda think we should walk the walk... - Mr. Gunn

Well Andy's definitely walking the walk as far as ONS goes! It's all Google discoverable, and the preprint (which I'll post soon) has AWESOME methods write-up. This is now more onto the formal writing, and what the tradeoff is between driving Andy crazy and serving the needs of the reader. - Steve Koch

I have an argument against citing my notebook: It's unstructured and incomplete in places. On the other hand, an argument for it would be: It's raw and may be beneficial to a historian or someone interested in open science. Has anyone cited an open notebook before? - Andy Maloney from iPhone

I think if you're not connecting up the raw record that underlies what's in the paper that you're really limiting that value of what you've recorded. I would guess that through a paper would be the most common entry point for most notebooks for the immediate future at least. At least where the research is quite specific. - Cameron Neylon

Let me clarify some: first it's not an argument of whether to cite it or not. It's just how much context should be in the published paper. The above link is to a nice page Andy made that links to the notebook entries relevant to the paper. We could cite that page once in the manuscript. Or we could go through and try to link up the individual pages throughout. I'm not sure whether... more... - Steve Koch

And yes, Andy, Jean-Claude has many nice examples. But he sorta kicks ass already :) - Steve Koch

sorta? - Kubke from BuddyFeed

yes, that is some kind of grammatical construction that is even more of a compliment. you have to read it like it sounds in my head :) - Steve Koch

:) It was meant as removing the sorta might make the statement more accurate :) - Kubke from BuddyFeed

I actually think it would be rather relevant to cite if nothing else in the materials and methods (perhaps on figures that are specific examples of what is 'representative'). Anyone with any specific procedural questions beyond that can then easily trail back to the details. It could go a long way for the ability to replicate. - Kubke

I agree Cameron. It's quite interesting to see what I did in my notebook and what I wrote in the paper. It's the same thing just, prettier? More better speaked in the paper than the notebook. Or is it wroteded? - Andy Maloney from iPhone

Here's the Nature Precedings link (same document as what I linked above) http://precedings.nature.com/documen... Not sure how they spelled my name wrong, hmmm - Steve Koch

Steve Koch

Bad Ass: Larry and Andy have built a system for monitoring the seed growth with four web cams. Should be easy to make the latest images display on a web page. For sure it will be easy to share all the images in real time. Cool!

October 14, 2010 from Android - Comment - Like - Share

Daniel Mietchen, Andy Maloney, Dan Hagon and Graham Steel liked this

So I can get the chemicals necessary to make a phosphate buffered saline that has deuterium instead of hydrogen. This will allow us to add the deuterium back into a depleted water supply. The only problem is that phosphate will sequester calcium and magnesium in the solution but, I can add those back with anhydrous forms of CaCl2 and MgCl2. What we should figure out, if we are going to... more... - Andy Maloney

18 more comments

The dipotassium deuterium phosphate is pricey unfortunately. 10g for $300. The potassium dideuterium phosphate is worse at $40 for 1g but I can at least get 1g of it and not the 10g for the other chemical. - Andy Maloney

See this link for background on Andy's suggestion: http://friendfeed.com/steveko... - Steve Koch

I sort of like the idea of using DCl and NaOD to make "regular water," and then adding NaCl to the D-depleted water to make it just as salty. I think if we worry too much about buffering, we'll go crazy, especially having to worry about the pH difference when we go to D-rich water. Shouldn't the seeds be OK at fixing their own pH? - Steve Koch

Yeah, I don't know that I'd worry too much about buffering -- I'm still baffled why the DI water isn't germinating 'em, and I'd say just a touch of Na, Mg, Ca chlorides would do the trick. - Bill Hooker

I may have failed to update: both the DI and D-depleted ended up germinating, just much more slowly than tap water. - Steve Koch

Yeah, I missed that part. That makes more sense to me, and leaves me even more confident that a tiny amount of the usual salts will probably do what you want. Do you have a botany dept at UNM? This (what do seeds need to germinate, what's a good buffer to use) seems like something that should have been thoroughly characterized already. A quick Google got me nothing much, but then my search-fu is middlin' at best. - Bill Hooker

So there is a "best" growing formula for seeds. It's called a rooting medium and is named Murashige and Skoog medium. So Sigma sells a basal salt version and sever other types that have additives to them. I think we should get the basal salt version and add it to the ultra pure water and observe the growth. Thanks to Dr. Gerhard Leubner for this information. - Andy Maloney

Also, Dr. Leubner stated that sodium is not used by plants and a better alternative to add deuterium to the solution would be to use KOD. With DCl, I should be able to replenish the deuterium in a deuterium depleted water source and see how things grow. With the media in the sample. - Andy Maloney

Cool. I'm really looking forward to these results. (Plants don't use sodium... who knew? Not me, that's for sure. /feels dumb) - Bill Hooker

Sorry. The statement was, plants don't need sodium. I have no idea if they use it or not as this is not my field. Just thought I should be clear. - Andy Maloney from iPhone

I'm not worried about the purity of the M-S solution. I looked at the specs and it seems to be okay. There are some excess water molecules on some of the chemicals used but, I don't think that matters to us at all. Plus, it only cost $9 so I went ahead and bought some. If anything, using it in the ultra pure water will give us a measure for how quickly the seeds will sprout, given the most ideal environment. - Andy Maloney from iPhone

So the tobacco seed has 2 major "layers" to it. The outer layer is the testa and the inner layer is the endosperm. Once the seed sprouts out of the layers, which always happens at the micropylar end (pointy end), the seed has germinated. Manz et. al. http://www.seedbiology.de/pdf... describes this nicely. The paper talks about how important water is for a seed to bust through the testa and endosperm to germinate. - Andy Maloney

From my initial skim of the above article, it would seem that the D2O could be interacting with the testa in a way to prevent rupture. Also, the tobacco seed may not be able to replace its oils with water, which seems to be important to the seed growth as well. So, for the seed to grow, it has to uptake water to break the testa, it then has to uptake more water to break the endosperm,... more... - Andy Maloney

I can see why it is important to have the M-S sauce in the mix. The seed has to use nutrients in order to grow. This is most likely why the seeds in the ultra pure water didn't sprout quickly. There wasn't anything in the water to use in order to grow. But, over time perhaps some of the seeds started to deteriorate and give up nutrients to the one seed that had a tough enough testa to... more... - Andy Maloney

Andy, quick comment. If you want to make deuterated salts cheaper then dissolve in D2O and then freeze dry a couple of times. Exchangeable protons (i.e. the only ones you really care about) will exchange and be replaced with deuterons, and the excess water gets lost to vapour. - Cameron Neylon

Cameron: That does sound cool to do but since I'm not a chemist, I would have no way of knowing if what I made, was really what I made. Although, it may be cool to see if one could make deuterated ATP for my gliding motility assays. - Andy Maloney

No need to be a chemist for this. The salt can't change you've got sodium and you've got phosphate. Oh...actually to be fair not precisely sure how you ensure you have the correct protontation of dueteration state of the phosphate. Will have to think on't and come up with a solution. Bottom line you can always test by checking pH (pD) of solution. - Cameron Neylon

p.s. ATP is a lot harder...anything with C-H bonds doesn't qualify for this method.... - Cameron Neylon

I just thought I should update and say I've finally ironed out the observation cells to use in this experiment. I'm happy to say that I finally got a sprout and that I have started a page that aggregates my notebook entries about the tobacco seed experiment. http://www.openwetware.org/wiki... - Andy Maloney

Steve Koch

Another excellent primary lab notebook from Sebastian Rosales and Matthew Cordova. Love it! - http://openwetware.org/wiki...

October 28, 2010 from Bookmarklet - Comment - Like - Share

Daniel Mietchen and Bill Hooker liked this

His summary: http://openwetware.org/wiki... - Steve Koch

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Love the "warts and all" approach to teaching science. There's really no other way to *do* science, so it's always frustrated me that it's taught in this sanitized, predigested format which does nothing to prepare you for the way real experiments are going to kick your ass. - Bill Hooker

Agree, Bill! I love it when the students realize i'm not gonna just give them magic answers. Especially when I don't know the answer. The look in their eyes when I say, "how would I fucking know that? Let's look at Klimov's notebook from 2008, I remember he kicked ass on this lab..." - Steve Koch from Android

Bill & Steve: Ha! and twice Ha! - Andy Maloney

Carl Boettiger

Not that anyone would follow it, but new notebook has rss feed, http://www.carlboettiger.info/feed, so prob won't twitter it to keep a record. thoughts?

October 21, 2010 from Twitter - Comment - Like - Share

Heather Piwowar and Jean-Claude Bradley liked this

So is your notebook still on OWW? If it is, how did you get a RSS fees from it? - Andy Maloney from iPhone

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Im still embedding the iframes into my oww notebook, but actually that was one reason I'm experimenting with moving to my wordpress site. RSS, plus the tag, search and categories seem to work better. Downside is mostly not having the oww community connection; hoping the rss/ social stuff can balance that. - Carl Boettiger from Android

I've tried using feed rinse with some success. However, trying to get an RSS feed from a wiki entry is not human readable, since the RSS displays the wiki markup and not the processed version. - Andy Maloney from iPhone

I found that RSS didn't work that well for our notebooks on Wikispaces but email alerts integrate well into our workflows. Partially it is a formatting issue but it is also the way Gmail automatically organizes alerts into conversations it doesn't cause much clutter. And I check email much more frequently than my RSS reader. - Jean-Claude Bradley

JCB: How exactly did you integrate email to wiki updates? What I still don't understand is why there doesn't exist a script that will RSS wiki entries in OWW. - Andy Maloney from iPhone

Wikispaces has a feature where you can get email alerts (with the changes) either for a page or the whole wiki - also available as RSS feed but like I said email alerts work better for me - Jean-Claude Bradley

Steve Koch

Submitted to PLoS ONE: A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension : Nature Precedings - http://precedings.nature.com/documen...

October 20, 2010 from Bookmarklet - Comment - Like - Share

Khader Shameer, Kubke, Jean-Claude Bradley and 4 other people liked this

Larry submitted first paper for peer review from our lab. PLoS ONE, of course. Congrats, Larry! - Steve Koch from Bookmarklet

13 more comments

From the abstract: "Our modeling applications are available as LabVIEW open-source code and compiled executables for PCs, which will allow other research groups to adapt the model and rate constants...". Sweet. - Bill Hooker

Congrats! I didn't see any references to lab notebook pages - is this a project that wasn't done ONS or was that a problem that you ran into? - Jean-Claude Bradley

Jean-Claude -- Embarrassingly, it didn't even occur to me to cite his notebook, believe it or not. The short answer is that Larry is ONS, but his notebook is very very thin. The past few months he has spent writing / editing LabVIEW code and writing / editing the paper. I would have like his notebook to have more information, but well, you know...I will take a look to see if there are notebook entries we should cite and maybe take care of that with our revision. - Steve Koch

@Bill if you have bandwidth and time, you should take a look at Larry's screencasts for the software available on the sourceforge site. Maybe I'm unrealistic, but I feel like with the software available and the instructions, some people may actually even use it. - Steve Koch

Here is a link to Larry's notebook entries...you can see there aren't many...a deficiency on my part http://openwetware.org/wiki... - Steve Koch

Hmm. Citing an open notebook intrigues me. Perhaps I should do this. But, what's the measure to have the notebook in the same state when published? A permalink? What happens when things are updated and never cited properly? Or should I not care since knowledge is dynamic and thus, so should publications be dynamic. - Andy Maloney from iPhone

Steve - I always thought that one of the best ways to legitimize ONS is to use the notebook pages as references when publishing in peer-reviewed journals. By definition every detail mentioned in a paper would have already been disclosed in the ONS notebook so referencing these would flow naturally and provide the link to the actual claim to priority. For example see this paper where we reference m.p., NMRs, etc. http://www.jove.com/index... - Jean-Claude Bradley

Steve - this is also why we write (or I push my students) to write in such a format that one can identify the context on the lab notebook page itself (i.e. - objective, results, discussion, conclusion, log). That way we can use each notebook page as mainly self-contained references for any purpose. (Again - this is what we strive to do and experiments in progress will necessarily be... more... - Jean-Claude Bradley

Andy - the dynamic nature of the wiki is a very good point. Strictly speaking, because the wiki has a versioning system, one could look a the actual state of a page at the time the paper was submitted. But this isn't very intuitive and doesn't help much with linked raw data. That's why Andy Lang and I put together a system to take a snapshot archive of the entire wiki and all associated... more... - Jean-Claude Bradley

In contrast with Larry's, Andy's notebook is much better. So definitely, Andy, we should cite your notebook pages. Rob (the data curation librarian we met with) has been working on archiving your notebook and ways for archiving the data. I don't think he will have the data done in time for your submission. However, I will send him an email to see if he's already worked out how to archive your wiki pages. - Steve Koch

Rob says he's not there yet as far as notebook archiving. So, I think we'll link to OWW URLs. I think linking to permalinks makes the most sense for now. - Steve Koch

I do have a tagging system in place so that I can dynamically link my notebook pages to a single URL. Rob says this is a great idea and will help him a lot. I'm super psyched about referencing my notebook. - Andy Maloney from iPhone

Just finished second round of revisions w/ Andy's paper. We will definitely put in a bunch of citations to his ONS. - Steve Koch

Steve/Andy - that's awesome! I don't think it is a problem to link to the lab notebook pages directly but in the future it would add value to link to a snapshot archive of the entire notebook as well. If you guys need help with that Andy and I can take a look. We can probably adapt the code to handle OWW. - Jean-Claude Bradley

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