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Kochlab

Kochlab

A room for public Kochlab discussions. As of creation in April 2009, I'm not really sure how we will use it. I have in mind posting links to journal articles and commenting on them. Current lab members, alumni, and really anyone welcome!
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Steve Koch
Anthony Salvagno guest blog: Soapbox Science: Tool Tales: figshare & Open Science – Making Your Impact Remain : Soapbox Science - http://blogs.nature.com/soapbox...
Anthony Salvagno guest blog: Soapbox Science: Tool Tales: figshare & Open Science – Making Your Impact Remain : Soapbox Science
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Steve Koch
Dear Friends, Tenure is a no. Sincere and huge thanks to all of you who supported me! https://accounts.google.com/Service...
I'm sorry to hear that Steve. - Andrew Lang
Thanks, Andy. No need for sorries, though! Everything I say in the letter is true, I have been very lucky and am feeling very optimistic about the future. - Steve Koch
That sucks, but it seems you sort of expected it. Extraordinarily positive letter - I wouldn't have been able to write that, had I been in your shoes. - Björn Brembs
Realy sorry to hear that - and impressed with your letter. Takes a lot of integrity to not take those kinds of decisions personally. - Kubke
I am in awe of the maturity, integrity, and clarity of thinking you've shown here. I couldn't have done it. Really sorry this didn't work out better. - Cameron Neylon
Great letter! - Egon Willighagen
Nice letter. Still depressing to see that papers ("... deprioritize EVERYTHING except for writing peer-reviewed publications and grants...") is still the only way. But clearly, it will be UNM's loss. - Rajarshi Guha
There's a good deal of irony in the fact that just before I read this, I was over at Anthony's open notebook discussing his research with him. UNM has missed an opportunity to be ahead of the curve. - Bill Hooker
Not sure what to say, Steve, so I'll just mention a typo: Arst. Just this week, I gave a talk on career perspectives for physicists http://slidesha.re/DPG2012... , and I had checked whether you already had reported back about your tenure decision, in the hope of being able to point to that one example of someone who consciously chose to go for what makes sense rather than what... more... - Daniel Mietchen
I'm sorry, Steve. - RepoRat
I'm very sorry to hear this news. - Dan Gezelter
Bummer. Really sorry to hear about the sad news. - Joe - Systems Analyst
Steve Koch
Started a github project for R code and graphs for Anthony and Alex's deuterium-depletion studies. Learned a bit about binomial confidence intervals, made new graph https://github.com/steveko...
RC Bayes Conf 0.8.png
Steve Koch
Steve Koch Science: Open Access Week event at U. Arizona: Reproducibility, Open Data - http://stevekochscience.blogspot.com/2011...
Steve Koch
Quick advice sought on summarizing online contributions for CV for tenure dossier - https://docs.google.com/documen...
Thank you for any quick ideas! - Steve Koch from Bookmarklet
Looks good, I can't think of anything to add/change. - Bill Hooker
Agreed, looks good. - Heather Piwowar
Sorry - just saw this. Added in the google doc - Kubke
Thank you! - Steve Koch
Andy Maloney
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?
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
Kochlab
Steve Koch
Congratulations to Pranav passing his candidacy exam today!
Steve Koch
Video: ScienceOnline2011 | Data Discoverability: Institutional Support Strategies - http://scienceonline2011.com/watch-2...
Excellent work making this video (Kudos to whoever did it!). This was a fun session. - Steve Koch from Bookmarklet
Love the PLoS advertising. Need to get some anti-shine for my head. - Steve Koch
Andy Maloney
Another confirmation of BRB80 being attributed to Dr. Bill Brinkley.
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
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
I finally have videos of tobacco seed growth in varying amounts of heavy water.
100% 18.2 MΩ-cm H2O. http://youtu.be/SqDbllaJtQg - 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
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
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
Steve Koch
17 minute talk by Michael Nielsen at TEDx Waterloo. Fantastic. -- Open science | Michael Nielsen - http://michaelnielsen.org/blog...
Steve Koch
The making of "Kiney": Child's Own blog - http://childsownstudio.blogspot.com/2011...
The making of "Kiney": Child's Own blog
Wendy Tsao talks about making Kiney doll for our lab members. They gave me the doll for Christmas 2010, and Andy used it as a demo in his recent dissertation defense. - Steve Koch from Bookmarklet
Steve Koch
Woo hoo! Andy Maloney just passed his Ph.D. defense! #opendata #openscience Congratulations!
Congratubloodylations! - science3point0
I like those hashtags, Heather! I quickly wrote up a summary of the committee thoughts here: http://www.openwetware.org/wiki... I'm sure I omitted a ton of stuff, but I figured it was worth recording as many thoughts as I could remember. - Steve Koch
Congratulations to Andy, and also to you Steve. Good stuff. - Bill Hooker
Congratulations! - Björn Brembs
Congratulations! - Kubke
congrats! - Björn Brembs
Steve Koch
Andy Maloney defends his Ph.D. on Wednesday! Here is his chapter on Open Science experiences: User:Andy Maloney/Open Science - OpenWetWare - http://www.openwetware.org/wiki...
Andy Maloney defends his Ph.D. on Wednesday!  Here is his chapter on Open Science experiences: User:Andy Maloney/Open Science - OpenWetWare
It's a huge file (with embedded movies), but you can download his complete dissertation as a PDF from our server: http://kochlab.org/files... All of this information is on the wiki pages as well. - Steve Koch
Congratatulations, Andy! He passed his exam today, just minor revisions to dissertation required. http://www.openwetware.org/wiki... - Steve Koch
I searched the document for "movie" and checked all figures that came up that way. The first two (1.3 and 1.6) did not display for me, all the rest (1.7, 1.9, 2.7, 2.10, 2.11, 2.13, 2.14, 4.2) went fine. - Daniel Mietchen
I also read the "open science" chapter and wish every dissertation would contain such a chapter with reflections about the way in which the research was performed _and communicated_. - Daniel Mietchen
Andy Maloney
Vote for Your Favorite Scientist Homepage | BenchFly Blog - http://www.benchfly.com/blog...
Vote for Your Favorite Scientist Homepage | BenchFly Blog
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
Steve Koch
2011 March Microtubule gliding speeds, kinesin-1 heavy-hydrogen and heavy-oxygen water - FigShare - http://figshare.com/figures...
2011 March Microtubule gliding speeds, kinesin-1 heavy-hydrogen and heavy-oxygen water - FigShare
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
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
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
Kochlab
Andy's microtubule gliding speed data for heavy-hydrogen and heavy-oxygen water - http://kochlab.blogspot.com/2011...
Andy Maloney
Yep, open science works! My open dissertation outlines how to make a gliding motility assay using kinesin and microtubules. It took me nearly a year to perfect the procedure. It took a fellow graduate student at UCSC only two weeks to reproduce my procedures from my open dissertation and get the assay to work. Which, is not trivial and not easy.
Awesome! - Bill Hooker
Cool, found the dissertation page if anyone else wants to see http://www.openwetware.org/wiki... - Mike Chelen
This is so cool! - Cesar Rodriguez-Rosario
Andy Maloney
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
I've updated my dissertation with easier navigation. http://www.openwetware.org/wiki...
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
Andy Maloney
My Instructables showing how to make a DIY objective heater/temperature controller. - http://www.instructables.com/id...
My Instructables showing how to make a DIY objective heater/temperature controller.
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
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
My Instructable on how to make a DIY Stirrer/Hot Plate. - http://www.instructables.com/id...
My Instructable on how to make a DIY Stirrer/Hot Plate.
Cheap and easy. - Andy Maloney from Bookmarklet
Andy Maloney
Steve requested I make this so I found the easiest way to do it, use the GUI at flavors.me. - Andy Maloney
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
Andy Maloney
I am making my dissertation writing completely open and based on my open notebook. Here's the first chapter. http://www.openwetware.org/wiki... This is in the rough draft stage but there is more to come.
Another preview of the future of (mainstream) science, imo. Historians and sociologists and philosophers of science, please note and give due credit to such concrete-action early adopters. - Bill Hooker
You kick a ton of ass, Andy! - Steve Koch
Cool, Dude -- will be referring my thesis students to this, especially since I am using a class wiki for some of their work in a pseudo-ONS fashion. In fact, just sent them the link:-). Will also be a good case study for the relationship b/w science and writing which they are discovering is not such a one-to-one kind of thing. - Mickey Schafer
Steve Koch
Steve Koch
Tobacco seeds arrived! They are incredibly tiny seeds, which must be why Lewis chose them back in 1934.
IMAG0151.jpg
IMAG0152.jpg
Small size = limited effects of diffusion? Or just because (de-)deuterated water was expensive back then? - Bill Hooker
I don't know explicitly why Lewis chose tobacco seeds. I was hoping they'd be small for a combination of the reasons you mentioned. The seeds now have something close to the regular fraction of deuterium (probably). Upon soaking them in water, I want the deuterium in the seeds to be negligible. I also want deuterium exchange to happen as quickly as possible, so the smaller the better. - Steve Koch
Lewis prepared his heavy water himself, so it was extraordinarily precious. I can't remember which paper (probably the Science 1934 or 1935 paper) he laments the fact that he wasted so much on experiments with mice before properly planning the experiments. I remember him saying in one paper that he started with 20 L of regular water and ended up with like 1 milliliter of very pure heavy water to play with. - Steve Koch
Tobacco was the standard experimental plant model, the Arabidopsis of it's day back in the 1930s (and before - Tobacco mosaic virus, Dimitri Ivanovski, 1892), so it was the natural choice. - AJCann
Thanks, AJ -- Are Arabidopsis seeds tiny too? - Steve Koch
Maybe slightly larger than Nicotiana, but yes, pretty small - http://www.flickr.com/photos... - AJCann
Steve Koch
Andy's cool cartoon of casein passivation in the kinesin gliding motility assay - http://openwetware.org/wiki...
I'm having trouble viewin in chrome, but looks good in IE - Steve Koch from Bookmarklet
Steve Koch
Woohoo! Resource Sharing Award from Addgene. Thanks Andy for applying and thank you @Addgene for the award! - http://www.addgene.org/pgvec1...
"Dr. Koch's graduate student, Andy Maloney, enjoys being a member of a laboratory that has taken part in the grass roots campaign to create an open access forum for doing science. Andy says, "Communication is key in science. With open notebooks, I'm completely up to speed with everything everyone is doing in the lab. This really helps science progress." To see what Andy's up to in the lab, feel free to check out his open wetware page at: http://openwetware.org/wiki.... Lab Website: http://openwetware.org/wiki... Lab Blog: http://stevekochresearch.blogspot.com" - Steve Koch from Bookmarklet
Most excellent. What will you spend the money on? - Bill Hooker
Andy wrote up the whole application and budget. I believe he asked to put the money towards a better PCR machine, which would help us in making our DNA constructs. I don't know, though, whether he's able to spend at his own discretion within the rules... - Steve Koch
congrats! - Jean-Claude Bradley
Andy Maloney
Did you know that Google allows you to upload .avi files? I didn't till now. This means that I can upload all my movies from experiments to Google Docs and I can tag them with Adobe CS. The metadata is searchable!
I just have to start tagging my movies. For some non tagged ones, check out here. http://www.openwetware.org/wiki... - Andy Maloney
One issue to watch out for with Google Video is that approval can take many days - and when rejected Google never replied to my emails. That's one reason I mainly use YouTube and SciVee - Jean-Claude Bradley
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