Andy Maloney - Comments

This is an old project of mine. http://www.openwetware.org/wiki...

Ricardo Vidal, Jean-Claude Bradley and Steve Koch liked this

It's all about ultrasound. I even have a nifty movie where you can see the sound waves coming from the transducer. - Andy Maloney

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After reading Jean-Claude Bradley's paper, SMIRP-A Systems Approach to Laboratory Automation, I got inspired to post it in my notebook since it definitely does not fit into the standard article format. So, I "offer access to data which may not be publishable because it does not fit into a sufficiently integrated format". - Andy Maloney

Andy - of course you know I think it is a good idea for you to do that :) You just never know what new contacts you'll find by making your work discoverable on Google. That was a key reason for moving away from the password protected closed SMIRP system to public wikis. As an example of how small a world it is I was exposed to the Schlieren microscopy technique when I collaborated with... more... - Jean-Claude Bradley

I find your study of the effect of ultrasound on lipid membranes particularly interesting as well since I spent a good deal of time as a postdoc trying to manipulate giant vesicles with electric fields http://dx.doi.org/10... - Jean-Claude Bradley

Took a look at your giant vesicles paper, Jean-Claude. Found it really interesting. I don't know much about lipids/liposomes, so I found it surprising how many authors I recognized cited in your introduction: Needham, Gaub, Sackmann, Astumian, ... So, a lot of overlap with single-molecule manipulation and force spectrosopy field (probably through biomembrane force probes, magnetic... more... - Steve Koch

small world Steve - some things are easier to do with vesicles than monolayers - another tool to keep in mind - Jean-Claude Bradley

Andy Maloney

This is a notebook entry of mine that is trying to use an "atomistic" approach that links recipes I use to run the experiment. http://www.openwetware.org/wiki...

December 9 - Comment - Like - Share

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

I understand that the context will be lost without more introduction but I'm still constructing the how and why I do experiments for each notebook entry. Hopefully this will generate a template for my notebook entries that will allow anyone to be able to reproduce what I do if they want. - Andy Maloney

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(My comment on your notebook page): Oh man, I'm dying to know the answer!!! Larry and I discussed possibilities of making his tracking software output a velocity, so that you could manually find out these kinds of answers in a matter of minutes. Not sure how long it will take him to do that. The long-term answer of how to fully automate everything is still a puzzle. Also, in terms of... more... - Steve Koch

Steve's point about instances is a good one here. Let's say the anomaly turns out to (perhaps) be connected to a specific bottle of D2O which is (say) contaminated with magnesium or something. I think the key point about "atomistic" approaches is that whatever the implementation, as far as possible the user shouldn't have to worry about creating the atoms - it should be done for them.... more... - Cameron Neylon

That certainly makes it a lot clearer Andy. So what you are saying is that your protocols are so standard that you never vary anything? In our work that just doesn't happen - but it would be nice if it did :) Maybe I missed it but what is the type of microscope you are using and what is the magnification? - Jean-Claude Bradley

To follow up on Cameron's point we did try to modularize at one point but from a practical standpoint we were never able to do so without removing too much information necessary to understand exactly what happened in each experiment http://usefulchem.blogspot.com/2008... - Jean-Claude Bradley

Andy I don't know how deep you want to get into the concept of an experiment as an instance of a protocol but you might find some useful info and refs here (from the dark ages of closed notebook science) http://www.jalajournal.com/article... - Jean-Claude Bradley

Yep, and the message to me is that with an atomistic approach it either all has to happen automatically while you're writing a higher level description or you have to accept that you end up doing both (the high level and the low level description). The atomistic/modular approach fails faster in JC's lab I believe because experiments are more clearly defined than in our work. Because our... more... - Cameron Neylon

JCB: I've tried very hard to make the setup for experiments mind numbingly simple and repetitive. So yes, my standards are all the same. I find this makes my life easier because I don't have to think about the setup, I just do it. This leaves me time to think creatively about what I am doing and what I want to look at in an experiment. It also works when something goes wrong. I can easily back track to find mistakes if I make everything the same. - Andy Maloney

JCB: I have not made a page for the microscope setup yet. I actually completely forgot to do that so thank you for reminding me. Just for right now, I'm using an Olympus IX71 microscope with a 60x objective and a rhodamine filter cube that has filters from Chroma. - Andy Maloney

CN: I'm not 100% sure but I think I have done this "low level" description with a very crude "high level" description in my most recent notebook. Or, at least I'm starting to implement it. There is still a lot of low level stuff that I need to make, such as the suggestion from Jean-Claude about making a page describing my microscope setup, so it's still a work in progress. It would be... more... - Andy Maloney

There's an interesting point around these cases where you "always do the same thing" its a classic case of tacit knowledge. Even if you were forced to write it down you'd probably miss the one thing that three weeks/months down the line you wish you knew. I suspect its a good case for just videoing proceedings, or having a tape of the user just narrating what is happening along with a timestamp - Cameron Neylon

Hi, Andy. So first, let me clarify that I could in no way intelligently comment on the science itself. I'm looking at the page simply as a reader, and with the intent being to use such pages as examples to undergrads of what is meant by "open science". What I am curious about from a reader's point of view is whether the notebook has the "significance" or "research question" stuff... more... - Mickey Schafer

BTW, one of the things I really like about the OWW, and other wiki-like objects, is that I can use Diigo to take notes. Diigo cannot see inside .pdfs and some kinds of html, so it's neat to be able to use it here. - Mickey Schafer

Andy, I suspect that's exactly what you're doing - and don't take any of this as a criticism or even an expectation that you shoudl dall all of this stuff. No-one does this perfectly and its interesting just to have a good example to talk about that is different to what's gone before. The problem as I see it is that this record is serving all sorts of different purposes to different... more... - Cameron Neylon

To get funded, aren't there narrative portions of grant applications? Those would funnel nicely into a lab's OWW page, with the projects doing the work branching off without the need for further explanation. Or, since OWW hosts blogs, that would be another option, though one that might require more upkeep than is ideal. - Mickey Schafer

Also, Andy, just in case, I want to chime in with Cameron that I meant no criticism at all. Rather, I was visualizing a future class, where I bring this up, and one of my generally brilliant neurosci students asks "And what is the project all about?" especially b/c I've been harping at them to be able to explain their own work. And I, of course, would have no intelligent -- or even unintelligent -- answer to give! - Mickey Schafer

Mickey: Writing down the broad context of this experiment is a big thing that I need to do. It would be nice to have a purpose spelled out for each new experiment, and relate that purpose to an old experiment. That way, there is a sort of logical evolution behind what is being done, not to mention the broad picture as well. Ultimately, I'm hoping that what I write in OWW will be the... more... - Andy Maloney

Mickey & Cameron: No worries about criticism since it is all constructive. Actually, I encourage it because it has made me think more deeply into what I want my notebook to look like and how other people can read/will it. - Andy Maloney

Open objects take on a life of their own -- or something like that. I need to figure out a way to say it, but I think it's rooted in Cameron's observation that readers will bring so many different needs. The creator is not responsible for answering all those needs, but it is helpful, IMO, to have a stage like what you're going through where we all get to see what happens when open... more... - Mickey Schafer

Mickey the grant is a good start when one exists and it bears some resemblance to reality. But these are the case much less often than you might think - Cameron Neylon from Android

Andy thanks for the info on the microscope - how does that translate into a scale bar in the image? You'll probably need that when it comes time to publish. It wasn't clear to me what you were saying about how you handle changes in the protocols - if you find an error or make a small improvement will you just create a new protocol page on the wiki and link to that? You can't edit your current protocol page because it would misrepresent what you did in older experiments that link to it. - Jean-Claude Bradley

Jean-Claude, it's an imperfect system now, because it takes a lot of clicks to create instances of things (as discussed above). However, in terms of preserving information, the "history" feature of wikis is nice. Andy and I discussed whether we can create a system that makes it very easy to link to the "permalink" for a protocol. That way, if the page evolves, the lab notebook will... more... - Steve Koch

Steve - I guess you would have to make it clear to a naive user that they must check the wiki history when they click the link for the protocol. But doing it that way how could you add more detail to an old protocol - whenever I read a lab notebook I'm thinking - is there enough information to publish without needing to contact the student? - so more details get added to our experiment pages over time. The other issue is wiki pages in the history don't get archived on Google. - Jean-Claude Bradley

Steve - what you are talking about reminds me of the "snapshot" approach we are trying to use. Where an archive contains a copy of every document as it existed on that day. Andy Lang has already written some code for this - if you want it could be modified slightly to work on any similar systems: http://onsarchive.wikispaces.com/ - Jean-Claude Bradley

Andy Maloney

I think I have finally gotten my notebook organized such that anyone can read and hopefully understand how I run a kinesin and microtubule experiment. It's still a work in progress and any and all comments will help. http://www.openwetware.org/wiki...

November 21 - Comment - Like - Share

Pierre Lindenbaum, Graham Steel, Jean-Claude Bradley and 2 other people liked this

I'm going to try and use this page as the spot for referencing all my notebook entries that use kinesin and microtubules. - Andy Maloney

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Will try to have a look later today...I'm probably a good test case. - Cameron Neylon

Great start Andy - it is hard for me to give you feedback without seeing an example of a particular experiment from set up to the analysis of the results. Only then can I assess if there is any critical missing information required to repeat it. I'd be happy to evaluate any experiment you want to bounce off of me. - Jean-Claude Bradley

Great! Thanks Dr. Neylon for the help. I'm very interested in making this page "atomistic" but, I'm a little fuzzy on how fine grained one has to be with it. - Andy Maloney

JCB: I plan on running an experiment tomorrow. I'll post my notebook entry here and it would be great for feedback. My hope is that the page I just made is going to be a good reference for people that want to know the details behind my experiments. - Andy Maloney

Sounds good Andy! - Jean-Claude Bradley

Steve Koch

Naturally occurring deuterium is essential for the normal growth rate of cells... [FEBS Lett. 1993] - PubMed result - http://www.ncbi.nlm.nih.gov.li...

November 1 from delicious - Comment - Like - Share

Ian Holmes, Dan Hagon and Jean-Claude Bradley liked this

The role of naturally occurring D in living organisms has been examined by using deuterium-depleted water (30-40 ppm D) instead of water containing the natural abundance of D (150 ppm). The deuterium-depleted water significantly decreased the growth rate of the L929 fibroblast cell line, and also inhibited the tumor growth in xenotransplanted mice. Eighty days after transplantation in 10 (59%) out of 17 tumorous mice the tumor, after having grown, regressed and then disappeared. We suggest that the naturally occurring D has a central role in signal transduction involved in cell cycle regulation. - Steve Koch

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This is one of those papers you have to read (and while you're reading it, I'm patenting my deuterium-depletion filter for home use and sending the press release to the daily mail, national enquirer, and Oprah). - Mr. Gunn

I haven't read it yet. Are you hinting that it's good or bad? - Steve Koch

Haven't read it yet either - Mr. Gunn

Not having read it, it could be that whatever they're doing to deplete the deuterium is leaving some harmful stuff in the water, and that certainly sounds more likely, but one would think the editorial process would weed out such obvious mistakes, but mistakes do happen and I've seen some crazy stuff come out of eastern european labs and the related articles are also all kinda obscure, but prions and transposons were once thought to be crazy fringe ideas too... - Mr. Gunn

Well, you may be onto something. In methods, they say, "Deuterium-depleted water (30-40 ppm D) was obtained from tap water (150 ppm) by electrolysis," ... Seems a bit sketchy to use tap water, even in 1993. ... All that aside, I've been a quite surprised this weekend at how drastically D versus H can change the chemistry of things. I'd been inappropriately biased towards thinking the... more... - Steve Koch

Steve, could you give an example of a case where D versus H is known to change the chemistry? I, too, had (have) the bias you mention. - mkz

@mkz, there're some general examples at wikipedia "kinetic isotope effect" http://en.wikipedia.org/wiki... ... There are also reports that heavy water tastes differently than H2O (can't find link now), which would most likely be chemistry (right?). The strong toxicity of heavy water to eukaryotic cells also argues for chemical effects. I guess I don't know the best example. - Steve Koch

A grad student in our lab, Andy Maloney, did a kinesin motility assay in heavy water on Friday and saw an amazing array of cool effects (http://openwetware.org/wiki...) ... At this point, is tough to figure out the science, but it's nevertheless very exciting. One thing we want to try is to compare D2O to... more... - Steve Koch

Wow, I didn't know heavy water was toxic. I figured the vibrational spectra would change when you change the isotope, and guessed minor changes in molecular structure could similarly occur, but it seems the effects are much more pronounced than that. - mkz

Those experiments look interesting! (Not that I know much about the field.) D2O versus H2(O18) sounds like an interesting experiment, too, hopefully we'll be able to follow the results here. - mkz

I know, amazing, huh? (heavy water toxicity) The funny thing is I was thinking D2O would be a simpler way of probing water activity, compared with osmotic stress. Ha! - Steve Koch

As for the experiments, Andy is an Open Notebook Science (ONS) practitioner, so all his results (as of now) will be available. It's actually been a conundrum for me this weekend as to whether or not to advertise his results. A good case study in ONS--on the one hand, I'm super-excited. On the other hand, we don't know what's going on, and I feel like he may prefer some time to figure some things out. Who knows? Glad you liked his experiments! - Steve Koch

@mkz, I put some thoughts on Andy's notebook's "talk" page here: http://openwetware.org/wiki... I was amazed to find out they actually use D2O to stabilize proteins in vaccines. - Steve Koch

It is indeed a good case study in ONS, I'm happy to hear the results will be available, but I'd understand if you guys changed your minds. I'm not sure how open I could bring myself to be when I make a discovery, waiting to be explained/utilized. Good luck with the project. - mkz

Just looked at your comments, reading that page was fun (and heavy water ice sinks in water?--nice). - mkz

Going to bed now, thanks for your comments. - mkz

Good night, and thanks for your thoughts! - Steve Koch

Steve the videos on Andy's page you link to look awesome but I'm not sure I understand exactly what was done - is there a section with the experimental details or is that what you guys are debating whether or not to release? - Jean-Claude Bradley

@Jean-Claude: What specifics would you like to know? I'm still in the process of making my experimental procedure available on OWW of which I will link to in my notebook. So, I apologize if things are still in disarray when it comes to the specifics of how I do things. - Andy Maloney

There's no debate on releasing anything--all info is desired to be public. In fact, there's no debate at all except in my own mind--as to whether to specifically invite people to look at the results (which I did above) via a blog post or other. @Andy, I think what Jean-Claude is saying is that it's very much not evident what your experimental methods are, mostly because of the... more... - Steve Koch

Andy - I was looking for which materials and in what amounts were added at what times to understand the videos and the effect of the deuterium. I'm intrigued by the effect of isotopes in chemical processes and I think your experiments could yield valuable insight. We've also very briefly looked at the effect of deuteration on smell http://usefulchem.wikispaces.com/Exp218 because of the putative detection of molecular vibration in receptors - Jean-Claude Bradley

It's worth noting that most commercial D2O is pretty filthy from a colloid chemistry perspective. Strictly speaking ultrafiltration or reverse osmosis is required to get to the kind of water quality one routinely expects these days for the normal stuff. But it's way too expensive to blow 10 L of D2O on getting a water purifier fully exchanged... - Cameron Neylon

Jean-Claude: Yep, this is going to take a while to clean up and do what you ask. I'm really motivated right now to start an experiment so, I will have to come back to this later tonight. I'll let you know when I have a draft for a materials and procedure page. - Andy Maloney

from a completely different perspective, then it wouldn't be a good idea to use a D20 moisture mist? The latest thing in cosmetics: http://snipurl.com/t0vih - Mickey Schafer

@Jean-Claude, cool smell experiment! (Is row 2A mislabeled, or am I misreading?) I've been wanting to try some kind of isotopic smell thing ever since reading the Turin book. - Steve Koch

@Cameron thanks for that tip. We're keeping it in mind now that the results could be attributable to contaminants. Question: It's definitely too expensive for us to think of doing that. But wouldn't Sigma be able to afford doing so? - Steve Koch

@Mickey: good find! - Steve Koch

Steve - thanks yest that was a mislabeling and it is fixed now - although note that (as indicated in the conclusion) the results in the table are not meaningful. Designing a statistically valid test like this is harder than it might seem and would require many more samples. The best I would hope from this experiment is to motivate a few more researchers to take a few minutes and sniff -... more... - Jean-Claude Bradley

Thanks Andy - I'm not asking to write a full report. It is probably enough to just post the experimental notes. In our lab that would correspond to the "log" section, whereas the full well formatted report is the "procedure" section to be written later. (e.g. http://onschallenge.wikispaces.com/Exp130 ). If that isn't how you keep track of experiments could you let me know what... more... - Jean-Claude Bradley

Hey Jean-Claude, Interesting smell reference in a review I'm reading: "2.5.1. Olfaction in fish. Hara [40] investigated the ability of the whitefish, Coregonus clupeaformis, to distinguish between the odor of glycine (Gly) and fully deuterated glycine (Gly-ds). Over the concentration range of 10^-8 to 10^-4 M, these fish avoided solutions of Gly-ds and preferred solutions of Gly." From:... more... - Steve Koch

Interesting thoughts from Lewis in his 1934 Science paper on biological effects of heavy water (relevant to the FEBS paper originally linked in this thread): "It is not inconceivable that heavy hydrogen, which exists in small amounts in all natural water, may actually be essential to some plants or animals. A supply of water almost completely freed from the heavy isotope is now being prepared for the purpose of conducting such studies." - Steve Koch

Steve Koch to Steve's feed, Kochlab

Cameron visited our lab today! Here's a photo of Cameron discussing the tweezers with Anthony. I'm doing my best to suck my gut in.

October 27 - Comment - Like - Share

Kubke, Victor / Mendeley Team, Claudia Koltzenburg and 23 other people liked this

Was an awesome day. Thank you so much for traveling and spending time with us today, Cameron! I learned a lot about science and means for carrying out open science. I'm energized about what seems like a very nice future protein-DNA collaboration. And I'm also energized about trying to implement some of the LaBlog and Google wave things you demoed for us. - Steve Koch

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I agree it was a great visit. I enjoyed showing you the version of the $100 spectrometer I'm working on and all the great conversation. I hope KochLab can start a collaboration with our friends across the pond. - Andy Maloney from iPhone

I think I'm going to put some nuggets of information from today onto this thread. Here is a link to the Neylon, Ward, Towrie, and Parker Tus-Ter single-molecule proposal (linked in Cameron's open notebook; see PDF at the bottom): http://blogs.chem.soton.ac.uk/sortase... I think that the system they are studying fits... more... - Steve Koch

I started learning more acronyms having to do with open and linked data. RDF = Resource Description Framework http://en.wikipedia.org/wiki... There was some other acronym that I can't remember or find that Cameron was suggesting as a way of bundling an entire open data set of arbitrary format...lots of vowels, something like OAI... "open access...? NOTE... more... - Steve Koch

Cameron showed us some of the robots he and others have programmed for Google Wave. I learned that it's not crazily complicated to write a robot, and that you can use Google App Engine (http://code.google.com/appengi...) to host your code and run the robot. It currently runs Python and now Java. I still don't understand how it connects with Wave, but it solves a mystery to me of... more... - Steve Koch

(Coincidentally (or maybe not), right after waving with Cameron, Google Wave gave me my 20 invites to send out. Let me know if you need one!) - Steve Koch

I'm sure Cameron and others have already said this in their many fantastic presentations and blog posts about wave. But I was happy to hear Cameron agree with my thinking that google wave + robots would be a very good way of handling data analysis workflows. When we process unzipping data, there are a few layers of software involved. I imagine each software application being run in the... more... - Steve Koch

Cameron's current LaBLog at Rutherford can be found here: http://biolab.isis.rl.ac.uk/cameron... Hopefully I'll be able to get access to this to see the edit features (I "requested" an account by logging in with my yahoo openid). I had previously been impressed by the notebook, but today was really wowed when I saw him edit a new entry. The particular things was the ability to... more... - Steve Koch

+1 for a Wave invite, please (pmiller@liv.ac.uk). - Peter Miller

That's wonderful that Cameron visited your lab Steve! For all the usefulness of communication technologies nothing can replace a productive meatspace interaction. - Jean-Claude Bradley

I had a great time - meeting and talking with Koch and the team. Lots of very cool stuff going on and lots of ideas that just seemed to bubble out of it. The meatspace interaction is really important but having that bit of background about what was going on and the context and trust built up here on Friendfeed amongst other places makes the whole discussion a lot quicker and more interesting. - Cameron Neylon

Agree -- pre-meeting definitely made the in-person meeting very quick to start off. & @Peter Miller, sent the invite - Steve Koch

Sounds like a fun (and productive!) day - thanks for sharing it with us, Steve. Also, I would appreciate a Wave invite (if you have any left!) - thanks! tom.tullius@gmail.com - Tom Tullius

I hope to see some cool pics from this meet-up on Flickr :) Science builds upon Science especially in terms of ONS !! http://farm4.static.flickr.com/3358... - Graham Steel

@Tom sent invite (fyi it takes several days to arrive) @Graham I think this is the only picture they got, unfortunately! - Steve Koch

@Steve, Auch well. Best I can do with this 20.kB image is to B&W it, with a bit of res. conf.:- http://farm3.static.flickr.com/2620... - Graham Steel

@Graham, I think I'm missing something. Is there a whole slew of cool open science photos on Flickr somewhere? - Steve Koch

@Steve - I don't think there is..... yet. I take that back. Starter for 10 with http://farm4.static.flickr.com/3089... - Graham Steel

Small number of people use the tags openscience - http://www.flickr.com/photos... and science2.0 - http://www.flickr.com/photos.... - Neil Saunders

Thanks for wave, Steve - Peter Miller

Thanks, Steve - Tom Tullius from iPod

A few comments back, I was simply looking through this filter http://search.creativecommons.org/... with open science - At worst, some really cool Flickr/CC images for future usage for anyone. - Graham Steel

It occurs to me that in virtually every photo of me online I'm wearing the same jacket and same shirt. Typical academic... - Cameron Neylon

@Graham, loved that one: http://farm4.static.flickr.com/3089... - Steve Koch

Cameron let me in on the mystery acronym: OAI-ORE "Open Archives Initiative" "Object Reuse and Exchange." http://www.openarchives.org/ore... - Steve Koch

For images there are the ONS logos created by Andy Lang and Shirley Wu http://onsclaims.wikispaces.com/ - Jean-Claude Bradley

Andy Maloney

How do people usually prepare to write an article? I'm grasping at straws here and have been just reading a bunch of articles from the journal I want to publish in to get an overall outline of how an article should be written. Am I going overboard?

October 20 - Comment - Like - Share

I like to start with an outline of what I want to talk about. - Anthony Salvagno

Outlines are great and I plan on doing that. I'm just wondering if there exists some structural formula that journals like to use for published articles. Such as, "put this in the introduction or put this in the body". - Andy Maloney

I think you're on the right track. Definitely different journals have different formats -- particularly when length is an issue. I don't know if this will help at all, but you may find some good nuggets of information here: http://ocw.mit.edu/NR... - Steve Koch

Steve Koch to Steve's feed, Andy Maloney

From Pierre: Fwd: Introducing Google Building Maker - http://googleblog.blogspot.com/2009... (via http://friendfeed.com/yokofak...)

October 13 - Comment - Like - Share

That does seem cool. It's of course a great idea for Google to get the masses to make the buildings for them. - Andy Maloney

I am proud of myself for resisting the urge to try it out. I probably would have stayed up all night building buildings for Google. I didn't even download Google Earth, that is how strong my willpower is. - Steve Koch

Steve Koch to Biohysical Society 2011, Science 2.0, Kochlab, Biophysical Society

The organizers of the 2011 Biophysical Society Annual Meeting have sent out a request for suggestions for symposia. All in my lab agree that an "open science" or "e-science" symposium would be a great suggestion. I personally think it'd be one of my favorite sessions at the meeting. What do you all think?

September 23 - Comment - Like - Share

Daniel Mietchen, Lisa Green, Björn Brembs and 5 other people liked this

The meeting is in Baltimore, MD, USA, March 5-9, 2011. - Steve Koch

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There're usually over 6,000 attendees, I believe. So, I think it'd be a great way to spread the word about whatever the cutting edge happens to be 18 months from now. - Steve Koch

To make a suggestion, I'd need to know: (a) symposium title, (b) 100 word description of symposium, and (c) 2-4 speakers who'd I'd recommend. - Steve Koch

I think (a) is important because it defines the topic w/ keywords. "open science?" "e-science?" "science 2.0?" "practical examples of open science?" - Steve Koch

I think (b) is important but can be drafted later. - Steve Koch

I think (c) is important, because it'd probably be best for speakers who'd want to attend the meeting anyway. Or who'd like to meet each other in Baltimore. Or perhaps people who'd incite a riot. Right? I don't know really, I've never organized a symposia. Tough to limit to only 4 I'd like to hear speak! - Steve Koch

The deadline for suggestions is October 13, 2009. Looking forward to hearing any opinions on this. I know that there are already fantastic meetings to discuss open science. I think the difference here is that the audience would be people who may not know anything about the future of science. And thus a big impact could be made within a couple hour symposium. With this in mind, I think a... more... - Steve Koch

Some people I would like to hear from at a symposium include, Jean-Claude Bradley, Cameron Neylon, and Michael Nielsen. Of course this is just the beginning of a very long list that I will think more about. - Andy Maloney

Thanks, Andy & that's a great list. I also just realized that it would be great to have a whole slew of posters that discussed implementations of open science. Grouped into one session would be great, but I'm not yet familiar with how they organize them. Seems possible, though. For those of you who don't know, the Biophysical Society poster sessions are great (except for one deficiency of not having beer). They go over four days and have 500+ posters at each session. - Steve Koch

The schedule for symposia at the upcoming 2010 meeting can be found here: http://www.biophysics.org/2010mee... Note most are focused on specific science topics. And the prior 2009 meeting is here: http://www.biophysics.org/2009mee... - Steve Koch

Steve - great idea! I would very much like to attend and present. I think Science 2.0 would capture more than Open Science. - Jean-Claude Bradley

brilliant idea! John Wilbanks ought to be on the list, if you can get him. Possibly also Sayeed Choudhury, Michael Witt, D. Scott Brandt. - D0r0th34

hey, if it's in b-more i might even be able to wander in. Sayeed probably could too - but he does a lot more with the Astro stuff right? (embarrassing that I know less about what JHU does than people across the country do :( ) - Christina Pikas

Thanks everyone! I'm definitely going to send in a suggestion. I've drafted a Google Doc here: http://docs.google.com/Doc... I'd love any input or suggestions! - Steve Koch

Have finished version / going to submit later tonight. Thank you again everyone! - Steve Koch

Submitted! Survey Monkey form was a bit primitive, so I couldn't submit all the suggestions from everyone, but I think I'll be able to do that later. I suggested me as non-speaking chair, and then had 3 slots left. I decided to list Jean-Claude; Michael-Nielsen; and Christina Pikas. - Steve Koch

I look forward to it Steve! - Jean-Claude Bradley

Sounds great! - Christina Pikas from iPhone

Cameron Neylon

Considering design of an open-source spectrophotometer for under $100. Any ideas on how to tell whether led light output is enough for a given photodiode? And anyone know of any efforts in this general direction?

September 12 - Comment - Like - Share

Anders Norgaard, Björn Brembs, Claudia Koltzenburg and 4 other people liked this

I have found this article, seems to be interesting, although a very simple setup: http://www.rsc.org/Educati... [edit: typo] - Marcos de Carvalho

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Another one: http://openwetware.org/wiki... - Marcos de Carvalho

good line of thinking, we already have open source 3D printers why don't we have really basic & ultracheap open source (hardware/software) lab tools? - Attila Csordas

Seems much in line with DIY Bio. Here's one example of a DIY sterile hood from Mackenzie Cowell's friendfeed: http://friendfeed.com/macowel... - Steve Koch

@Attila, we also have DIY microarrayers: http://cmgm.stanford.edu/pbrown... - Marcos de Carvalho

Also, my advisor has built an micro-injection device to produce transgenic Drosophilas, has worked pretty well. Here is the paper: http://www.scielo.br/scielo... - Marcos de Carvalho

I don't think you will be able to make one for under $100 since the grating alone will break your budget. You may be able to find them on eBay but, you are risking getting a scratched grating. If you go the route of a prism, then you still have to deal with mounting it and getting a reasonable rotation mount (you still have to get this for the grating and it should be motorized so your... more... - Andy Maloney

I was thinkin of avoiding gratings altogether. I don't see why in principle you can't build something with a bunch of leds which have reasonable optical purity and a single photodiode. You would need to calibrate for each individual source diode but that's no great hardship - indeed it might actually help to provide an understanding of what an absorbance actually is. So manual calibration via 100% a 0% transmittance for each individual lights source like I used to do as an undergraduate :-) - Cameron Neylon

Marcos - that RSC paper is very close to what I had in mind - thanks for the link - the OWW doesn't seem to have gone too far though...will have to track down Vincent and see how far it got...what i'm thinking of wouldn't be much use for actual spectral measurements but good for doing time courses or relative sample measurements - thinking around 10% accuracy and 1-5% precision over 0.05 - 1 AU - Cameron Neylon

LEDs typically have pretty broad spectrums and can get fussy, such as peak wavelength shifts, if your power source isn't stable. There may be fewer problems with a broad band source and then using filters to pick off the wavelength you want. Of course, you could correct for wavelength shifts in the LEDs but that requires more optics. Hmm. Okay, I'm sufficiently challenged now to want to try and build something. - Andy Maloney

How much of a shift? I've been looking at specs and most seem to be around 15 nm at FWHM which is no worse than what we use as the bandwidth on our plate reader when doing timecourses. Power stability is an issue though - although we'd probably be powering this off the USB from a computer - how stable are those in practice? My concern with filters is that they get pretty costly for... more... - Cameron Neylon

You're more than welcome to run off with any spectrophotometer data display / management stuff of mine... http://beaconw.cs.manchester.a... - Neil Swainston

I think that I have come up with a design that might work. I'm not sure if it will, but it sure will be fun trying. I will make a special spot in my notebook for the design and build, and I will link to it once I get the parts in. - Andy Maloney from iPhone

Andy Maloney to Andy's feed, Science 2.0

KochLab's 1064 nm optical tweezers http://www.youtube.com/watch...

July 18 - Comment - Like - Share

Jean-Claude Bradley, Björn Brembs, Steve Koch and Mike Chelen liked this

I've posted a movie depicting KochLab's 1064 nm optical tweezers to our YouTube channel. I made it in SketchUp with every part drawn by KochLab except for the microscope, which can be found in Google's 3D Warehouse. It's annotated so if someone wants to reproduce this, they can. - Andy Maloney

Your SketchUp prowess continues to amaze me. I love that video. Plus with annotation, I'd be surprised if it doesn't help out some other researchers somewhere around the globe. Thanks for doing such a great job! I should also add: an excellent example of use of new online tools for science. - Steve Koch

Andy Maloney

Tomorrow will start my 60 papers in 30 days challenge with Koch. The challenge is to continue all my work as usual in the lab, but to also read, review, and understand 60 papers on kinesin and microtubules.

May 31 - Comment - Like - Share

Michael Habib, Deepak Singh, Mike Chelen and 12 other people liked this

Will you tag/annotate all the papers as you go? - Mr. Gunn

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How will you choose the 60 papers ? - Nir London

@Mr. Gunn: I will "annotate" the papers in the same fashion I have been in my notebook. Here's an example http://www.openwetware.org/wiki... - Andy Maloney

@Nir London: The papers are mostly going to be drawn from my professor's (Steve Koch's) collection. He has over 100 papers on the subject that I will start with. Of course, I will have the freedom to start with his papers and then move others I find either more relevant or more interesting. - Andy Maloney

I think 60 papers in 30 days is ludicrous! Maybe 30 in 30? :) - Steve Koch

Also, a lot of those kinesin / microtubules papers in my PDF library will be sort of specialized (e.g. when I was obsessed with tubulin catalysis of ATP). Here are a couple links you can use to find things I'm recently interested in: - Steve Koch

http://delicious.com/skoch3... My "toread" tag on del.icio.us ... The reason I don't use citeulike for papers "toread" is that I like to file my papers in citeulike after I've read them and can put a few notes in. - Steve Koch

http://www.citeulike.org/user... My citeulike library. I think it's sorted by my most recently added articles. You can click on the tags to the right to narrow down for kinesin. These should mostly be papers that I've read (or skimmed) as much as I'm going to in the near-term. - Steve Koch

Dang -- I couldn't figure out how to share my Mendeley library. I was thinking it'd be a good way of finding my most recently added PDFs. But you can do this similarly by sorting by date on the server? - Steve Koch

The reviews you've written so far have been outstanding! E.g. the one you linked above. What further steps should you take to maximize the value of your contribution? Any ideas from people on this thread? One idea is you could join citeulike and link your OpenWetWare review page in the "review" or "notes" section of citeulike. Another idea / question, can "Research Blogging" be used with a wiki (as opposed to a Blog)? - Steve Koch

The way to share your Mendeley library is to set up a shared group in the desktop client, then add people to that shared group. I can show you a screenshot if necessary. - Mr. Gunn

@Koch: So I'll start after work with the most recent paper on the server. Hopefully I can get through 2 but we will see. - Andy Maloney

Andy's first review: http://openwetware.org/wiki... very nice! - Steve Koch

Just wondering how this went. Haven't heard any follow-up. I peaked through Andy's notebook, but didn't find any further references to this. - Chris Lasher

Yep. So I failed miserably. Mostly because I built a functioning optical tweezers in 4 weeks which overlapped with the challenge. I guess I should own this failure and learn from it. - Andy Maloney

I can take 90 - 100% of the blame, since I instituted the insane push for OT data by next week! Not to mention your injury. I still contend that 60 papers in 30 days is crazy, but I am looking forward to you one day doing the 30 in 30 challenge. Your paper reviews are so great, which is what makes 60 in 30 sort of impossible. - Steve Koch

Also: The OT design is truly spectacular. Can't wait for people to see the photos and Google sketchup. Even then, I don't think people will appreciate your gift for optical design and construction. Great work, Andy, and also thanks for so many late nights and weekends putting it together. - Steve Koch

Congrats, Andy! - Mr. Gunn

Jean-Claude Bradley

openchemistry's videos on Vimeo - http://vimeo.com/openche...

June 28 from delicious - Comment - Like - Share

novoseek, A Roy, Berci Mesko, MD and 5 other people liked this

some of my organic chemistry lectures on there - Jean-Claude Bradley

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Very cool. I'm beginning to like Vimeo more and more. - Andy Maloney

What's Vimeo? Is it like youtube, but less sucky? Is Vimeo:YouTube as Facebook:MySpace? - Steve Koch

Haven't used Vimeo as much as I like, but it is a great video service. Key features: allows high-quality upload and in their words "a respectful community". Cue xkcd reference: http://xckd.com/202/. - Neil Saunders

vimeo allows larger file size and greater video length than youtube - Mike Chelen

does vimeo take FLV files? - Jean-Claude Bradley

Jean-Claude: unfortunately vimeo does not support .flv upload, here is a list of their accepted formats: http://vimeo.com/help... - Mike Chelen

Mike - that's too bad - that's the only format I've found that maintains very high resolution with small file sizes. Guess I'll stick with SciVee for a while - Jean-Claude Bradley

Jean-Claude: how about blip.tv? they allow up to 1gb videos and seem to accept any format http://blip.tv/faq#format - Mike Chelen

Mike - thanks I will check it out, especially for screencasts that don't fit as well with the SciVee mission - Jean-Claude Bradley

Mr. Gunn to Mr.'s feed, The Life Scientists

I want you to all hold me to this: When I get done with what I'm doing now, I'm never making another graph or chart in Excel. Way too much of my life spent messing around with stupid shit like font sizes & scales.

June 12 - Comment - Like - Share

Benno Hansen, Jason Winget, Bill Hooker and 7 other people liked this

Amen! - Andy Maloney

R sounds like a good place to start. - Mr. Gunn

grep | sort | uniq | gnuplot ! :-) - Pierre Lindenbaum

Andy Maloney to Andy's feed, Science 2.0

Vimeo and a video absract. http://vimeo.com/4749035

June 10 - Comment - Like - Share

Jean-Claude Bradley, Daniel Mietchen, Steve Koch and 2 other people liked this

My friend is beginning to start open science. He posted a video that describes a paper he did about quantum stocastic walks. - Andy Maloney

Steve Koch

Kinesin follows the microtubule's protofilament ax...[J Cell Biol. 1993] - PubMed Result - http://www.ncbi.nlm.nih.gov/sites...

June 5 from delicious - Comment - Like - Share

Andy Maloney liked this

Ha! I was going to read this paper this weekend. - Andy Maloney

Steve Koch

ScienceDirect - Drug Discovery Today : Drug discovery chemistry: a primer for the non-specialist - http://www.sciencedirect.com/science...

June 5 from delicious - Comment - Like - Share

joergkurtwegner, Maureen and Abhishek Tiwari liked this

Summarized by Richard Grant on his blog: http://network.nature.com/people... (friendfeed: http://friendfeed.com/rpg...) - Steve Koch

I love the line "rife with terminology". - Andy Maloney

Andy Maloney

Paper reading challenge update

June 4 - Comment - Like - Share

Claus Metzner and Steve Koch liked this

So far I am not up to my quota but I have a feeling that the weekends will be catch up days. I find myself not reading papers that have complicated English in them because I don't want to waste my time with them. Even when I know the papers are crazy important. Koch makes a valid point that some readers will be able to understand complex sentences easier than me however, when was the last time someone told you that your sentences and English was too simple for publication? - Andy Maloney

I just thought of a situation where complicated explanations may benefit the writer: grants. Ha! That sentence is so ironic! I've never written a grant but it would make sense to me that a writer would want to be complicated if it puts them at an advantage. Personally, I would try not to be complicated. But, if you are in competition for money, then you do what is necessary. - Andy Maloney

The Life Scientists: Andy Maloney

Can someone tell me what the measure of good/bad agarose is? How about a preferred supplier?

June 2 - Comment - Like - Share

Steve Koch liked this

The only measure I can think of is empirical -- what do your markers look like on a gel? I've always just bought the cheapest I could find. - Bill Hooker

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@Bill: Thanks for the reply! I have no clue about the gel stuff. I'm just supposed to order it and I was supposed to get "good" and "bad" stuff but I have no clue about what this good/bad measure means. - Andy Maloney

One parameter reported by agarose suppliers is electroendoosmosis. This improves resolution as it has a very low binding capacity for DNA. http://www.applichem.com/en... - Mr. Gunn

Hey Andy -- for me "good" and "bad" have to do with purity of samples after gel extraction. This probably correlates well with purity of the agarose. The agarose from Sigma that is something like $100 for a kilogram is "bad." A colleague of mine in grad school labeled this produce, "Guaranteed to produce gel extracted DNA that effs up any transcription reaction." - Steve Koch

That link Mr. Gunn gave seems promising, but I can't find the price. - Steve Koch

I seem to remember the phrase "molecular biology grade" as being "good." Something like this: http://www.polysciences.com/Core... (Remember to select your continent for pricing, because there's no way a supplier could possibly guess what continent you're in based on your IP address.) - Steve Koch

So it seems that a low EEO (electroendoosmosis) and low sulfate is what you want when purchasing agarose. http://www.sigmaaldrich.com/life-sc... - Andy Maloney

Oh, I wasn't suggesting them as a supplier. It was just the best link I could find that explained what EEO was for. I've always had good results with Sigma's Molecular Biology grade agarose. - Mr. Gunn

Ah, I was forgetting about gel extraction. I've never had any trouble with it, so I guess I wasn't using the really cheap stuff. - Bill Hooker

I think after talking with Andy: my worry about 'bad' agarose was overblown...just unlucky in the past to have had that crappy stuff...everything Sigma sells looks pretty decent. Thanks, All - Steve Koch

Steve Koch to Steve's feed, Kochlab

Susan Atlas (our collaborator) Appointed to Serve as Director for New Center for Advanced Research Computing - http://www.unm.edu/~market... (via http://friendfeed.com/univers...)

June 1 - Comment - Like - Share

Awesome! She is definitely the right person for the job. - Andy Maloney

Kavan Modi

Bibliography in pdf files as meta data - http://scientificconfessions.w...

May 21 from an attempt at research - Comment - Like - Share

Steve Koch, Mr. Gunn and Neil Saunders liked this

And there are so many other 21st century things the publishers could be doing too. E.g., how about making it easy to get the supplementary information? (Instead of having to spend another 10 minutes searching for it.) - Steve Koch

6 more comments

Do you know about Mendeley yet? They rely on trying to get this data from PDFs automatically...it works well sometimes and other times not. But clearly publishers could help out a lot by including standard meta data. - Steve Koch

http://www.mendeley.com/ - Steve Koch

Team Mendeley will tell you that metadata can be extracted from PDFs. YMMV. - Neil Saunders

LOL, thanks Steve, your check's in the mail. ;-) I think it works a lot better for some journals than others, and the lookup gets most of the rest, but it will continue to improve. Kavan, if you do try it and have any comments, they'd love to hear what you have to say. - Mr. Gunn

I recently purchased a program called Papers, http://mekentosj.com/papers/ My opinion on it is still to be determined but, it catalogs all your papers and downloads the meta data from websites. You can then export to a BibTeX file all the bibliographic info. Sorry, but it only works on Macs and it doesn't help you for papers you want to reference not in the program, just the papers you... more... - Andy Maloney

Yeah, the blog post was looking for a PC version, which is why I mentioned Mendeley. - Mr. Gunn

I was not aware of Mendeley till Mr. Gunn pointed it out. I am using it now but having some stability issues. I've also been using Papers by MekEnTosj till now. Both of these programs are real nice and take us into the 21st century. But I want a universal standard that the all publisher would follow (I dream). This way we wouldn't need programs to go fishing for meta data. This is what... more... - Kavan Modi

Michael Nielsen

Doing science in the open: Physics World - http://physicsworld.com/cws...

May 8 from delicious - Comment - Like - Share

Richard Akerman, Shirley Wu, Bill Romanos and 22 other people liked this

Nice article, Michael. Didn't know Spires was so used. I think you're quite right to make the point about trust. Being deliberately naive, I'd like to think that incentives for scientists are different from those conducting a trade. One would hope that all parties in a science collaboration are wanting the same thing: deeper understanding, and therefore the collaboration benefits all... more... - Matthew Todd

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I also like the point about the original scientific literature being the open sharing medium of its day. Once could imagine complaints by gentlemen scientists that publishing journals would vulgarise science since any Tom/Dick/Harry could read about things that previously might have been presented to learned societies (with port). Not sure if that ever happened, clearly. Now here we are a couple of centuries later confronting the essential weaknesses of the (formerly great) system. - Matthew Todd

Thanks, Matthew. I think the example of 17th century science shows pretty conclusively that scientists don't simply want a deeper understanding. If they did, they would all have shared their knowledge freely, not locked it up in anagrams and other such capers. - Michael Nielsen

Matthew - About the gentleman scientists: Newton seems to have had something of that attitude. In his case, at least, lack of publication seems to have been in part due to a desire to avoid contact with the mundane masses, as he saw them. He seems to have been a remarkably reclusive and inwards man. - Michael Nielsen

Love it. Thinking of emailing to my colleagues in the physics department...just need to compose a quick email to inspire them to read it. Maybe will send to my chair first. - Steve Koch

Thanks, Steve :-) That tickles me pink - I was, as you know, a grad student at UNM... - Michael Nielsen

Duh! I knew that but wasn't even thinking about it. OK, that makes it more awesome. I recently approached the faculty with an idea of creating a public mission statement about supporting open access activities when evaluating people for new hires and promotion and tenure. (See: http://stevekochscience.blogspot.com/2009... and related friendfeed: http://friendfeed.com/steveko... ) - Steve Koch

It was clear that probably all of the faculty supported this kind of thing, but I was just awful in terms of explaining what I was talking about. It ended with me having a mission of drafting a statement for everyone to look at, but I have not attempted that yet. Basically I am stymied by lack of confidence in being able to draft a statement that others will be inspired by, and don't want to burn up any kind of "open science" momentum I have. Here's what I'm thinking I should do now: - Steve Koch

(1) email your article link to the chair. he'll definitely send it out with a nice message about you being a former grad student. alternatively, I could ask Caves or Deutsch to do this? (2) ask for help from this community in drafting a short statement about supporting open science during T&P and new hiring (probably via google docs?) (3) send the draft statement to department. What do... more... - Steve Koch

An interesting thought I've been toying with quite a bit lately -- as a lecturer, I am not required to publish or even do research for my job; in fact, any sort of publication and any sort of research potentially garners merit pay. It is arguable, then, that there is a lower barrier to my use of ONS because I don't have anything to lose:-) -- it is an odd position for a lecturer to be... more... - Mickey Schafer

Steve - definitely expand beyond open access journals. I worry that people have already entrenched positions/prejudices about open access that might get in your way (Johnathan E is the expert on that). It'll obviously happen the way we want it (imo), but there are a lot of die-hards out there that you don't need to confront. Shifting to open science allows you to pitch a fresh idea that is directly related to *research effectiveness*. - Matthew Todd

Mickey - definitely, why not? I guess this means you're a US-based faculty member. "Lecturer" in the UK and Aus means research+teaching. This is a continual source of confusion. - Matthew Todd

Great article. There is a chorus in my head singing your praises right now. I'm all for being open about science. Science 2.0 is a logical step in the evolution of science and if a 1.0 scientist cannot stand to hear why, then what kind of a scientist are they? That statement is not meant to be rude but it does state the obvious. Usually obvious comments are rude so I apologize if it is... more... - Andy Maloney

Steve - Regarding a statement about support for open science, it might be helpful to contact the people at places like Harvard, Duke and Stanford, where OA mandates are in place. I believe, for example, that Stuart Shieber (http://www.eecs.harvard.edu/shieber... ) was instrumental in getting the Arts and Sciences OA mandate at Harvard, and he might be willing to share draft documents that... more... - Michael Nielsen

My chair sent out your article to the faculty last night (U. New Mexico Physics). Already sparked some interest in getting a colloquium speaker out here to talk about open science--hopefully I can help that happen. Plus, Carl Caves emailed me some very strong praise about you, Michael! - Steve Koch

Steve: Awesome! That's great to hear. Re: your comments above, Peter Suber has an excellent post where he links to a whole bunch of documents used at Stanford to help convince faculty to adopt an OA mandate. This might be useful in constructing something for UNM: http://www.earlham.edu/~peters... - Michael Nielsen

The Life Scientists: Andy Maloney

Does anyone here know what the initials "BRB80" stand for? It's a popular buffer and I've been able to glean that the "80" mean "80 mM PIPES". But, I do not know what BRB means.

May 11 - Comment - Like - Share

Steve Koch liked this

I think it's the same as "Brinkley Buffer 1980" - see for example http://mitchison.med.harvard.edu/protoco.... Presumably after its inventor and the year? - Neil Saunders

15 more comments

Also called Brinkley Reassembly Buffer, e.g. http://www.ciwemb.edu/labs.... - Neil Saunders

I believe the reference is: Brinkley B. R. Microtubule organizing centers. Annu. Rev. Cell Biol. 1985;1:145–172 - Neil Saunders

I know nothing about the buffer, but can confirm that Bill R. Brinkley is a well-known scientist in the fields of mitosis, microtubule organization, etc. (He's also the dean of my graduate school and a great guy). - Chris Miller

I know nothing about any of this, but do know how to search the web ;-) - Neil Saunders

That's a great review, Neil! (3 links above...I now have the PDF if anyone wants it). It doesn't mention BRB80 in the review, but does talk about "reassembly buffer" and cites earlier work (including his own) going back to the early 70's. I'm going to check out a couple. - Steve Koch

Andy, you'll like this quote from a Borisy and Olmsted 1972 Science paper (PMID: 5057625 http://www.ncbi.nlm.nih.gov.li...). I think it's the origin of the EGTA in the buffer (Also I notice the MgSO4): "Because of the apparent stimulatory ef-fects of GTP and Mg2+ ions, and the inhibitory effects of Ca2+ ions on microtubule assembly (4), the homogenizing... more... - Steve Koch

So far I haven't seen any named buffers, except for Borisy using PME (which Cytoskeleton calls PEM--PIPES, EGTA, Mg) and PMEG (GTP). - Steve Koch

The earliest google scholar hit for (BRB80 OR "BRB 80") is in 1987: http://scholar.google.com/scholar... The paper is by Gard and Kirschner (PMID: 3680377 http://www.ncbi.nlm.nih.gov.li...) and at the bottom of the first page, they give definitions. Ironically, they say, "BRB, reassembly buffer; ..." THEY DON'T define the first B! - Steve Koch

In 1988, Kellogg, Mitchison, and Alberts use the term BRB80 in their paper (PMID: 3248521 ), but they do not define it. Interestingly, they also appear not to cite a single paper by Borisy or Brinkley. - Steve Koch

The quoted phrase, "Brinkley Reassembly Buffer" only gets two Google scholar hits and none on Pub Med. In a 1997 Science paper, Dogterom and Yurke define it but do not cite the origin (PMID: 9346483). In a book in 1997, Avila, Brandt, and Kosik define the term on page 261 but do not give a citation. - Steve Koch

From what I can tell, "Brinkley Reassembly Buffer" is a backronym that is not cited. The term "reassembly buffer" is used well back into the early 1970's or maybe even earlier. Both Brinkley and Borisy and many others use that term. At some point, the term "BRB" and "BRB80" appear without explanation, and I think it is reasonable that people assumed the B stood for Brinkley. However, it... more... - Steve Koch

OK, well, does anyone care besides me and Andy? :) I actually learned a lot with this hour or two of reading old literature. A great way to learn a lot very quickly and gain a bunch of insight into this very cool tubulin polymerization assay that we're doing. And BTW: we succeeding in making our first batch of fluoresecent microtubules today! http://openwetware.org/wiki... - Steve Koch

I'm glad you took over Steve :-) I have learned that (1) the etymology of acronyms is often hard to trace; (2) provided you know the composition of a reagent and understand the reason for each component, the name doesn't really matter... - Neil Saunders

I'm glad you posted that link, Neil! I agree with you on both (1) and (2). The funny thing is that (2) was very difficult for us to know as "newbies" to the field. I do believe in this case that you need to go back to the 1970's to understand things, and the acronym etymology inspired us to do so. One clear take home message for me is that BRB80 has a lot of legacy issues with it. It... more... - Steve Koch

Neil: Sometimes Google doesn't give you want you want. But if you try sometimes, you might get what you need...Sorry. Couldn't help myself. As Koch says, nowhere in the literature is BRB80 defined as a term. This is why I asked the question originally. It's funny that we can't trace its origins but, beer discussions about BRB80 is a great idea. - Andy Maloney

Chris: I was very tempted to contact Dr. Brinkley today. I was just afraid my email would not get any response. Thanks again Neil for pointing out the name. It helped start a really fun historical search! - Andy Maloney

Kochlab: Andy Maloney

Koch Lab site page.

May 9 - Comment - Like - Share

Steve Koch liked this

Koch, can you make a list of all the awesome websites you use on the wiki? I had no idea about F1000 and it looks like a great site. Plus, having links to all of the stuff we use is a good thing to have for new students. That way they can look at the stuff in their own time frame but can know about everything we use, like CiteULike etc... - Andy Maloney

3 more comments

Working on it here: http://openwetware.org/wiki... - Steve Koch

Thanks. I really appreciated it. I also filled it out a bit with links to vendors, blogs, etc. - Andy Maloney

Wow! Love it. I put some comments on the talk page--a risk of you misinterpreting them as overly-negative. That's not the case--you did a great job of creating that page, I'm just nitpicking and nothing is needing to be changed. I really like that this was created by a student, because that's our most likely audience. - Steve Koch

Oh, and Thanks! - Steve Koch

Steve Koch to Steve's feed, Kochlab, Science 2.0, The Life Scientists

Introducing Andy Maloney's Open Notebook Science - http://openwetware.org/wiki...

May 9 from Bookmarklet - Comment - Like - Share

I added Andy to the list of ONS on the wikipedia article: http://en.wikipedia.org/wiki... . A chronological list of entries is here:http://openwetware.org/wiki.... He's had an open notebook for a few months. One of the most impressive things to me are the detailed notes he's been taking as he starts learning about kinesin / microtubules from reading the literature. - Steve Koch from Bookmarklet

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Here's a link to his latest article review: http://openwetware.org/wiki... Maybe a bit of an issue with fair use? But aside from that, it's easy to imagine Andy being a leader in the some of the things Michael Nielsen described in his recent... more... - Steve Koch

I see what you mean about fair use. Should I remove the graphs? I don't want to impinge on anyone's rights. - Andy Maloney

I don't think so. The ones you put in are low resolution, and you're not providing the entire paper. You can't even read the captions, really. Other people on here know more about fair use than I do, but in my opinion your use of the images falls under "fair use", though I can see other people arguing otherwise. - Steve Koch

Andy Maloney to Andy's feed, Science 2.0

A great paper describing why people use BRB80 buffers for microtubule experiments, http://pubs.acs.org/doi....

May 8 - Comment - Like - Share

Steve Koch liked this

Great find! Read the abstract and learned a lot. Looks like a fantastic resource to answer many / most of the questions you've been asking about the MT buffers! - Steve Koch

As for rooms, the Science 2.0 room people may not care about this paper so much. "The Life Scientists" would be a better venue...http://friendfeed.com/the-lif... ...maybe we should create a "biophysics" room? Or molecular biology? Or kinesin? Also, the http://friendfeed.com/kochlab room is good for our lab to communicate in (though nobody but me checks it yet, probably :) ) - Steve Koch

Good call. What's nice is that the paper is freely available so it is somewhat for open science, but not really. I forgot we had a Koch Lab room. I'll post things that are more geared towards us there. As for a biophysics room, I love it! I did post a review in my notebook. - Andy Maloney

Science 2.0: Andy Maloney

Koch lab "kinesin and microtubule experiment" logo/mascot. - http://www.openwetware.org/wiki...

April 28 - Comment - Like - Share

Jean-Claude Bradley, Mr. Gunn, Jason Stajich and Steve Koch liked this

Here is a mascot for the upcoming Koch Lab kinesin and microtubule experiments. Anthony Salvagno and I did this today. Although we started out to make a logo, I think this is more of a mascot. I want to call him Kiney. - Andy Maloney

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Looks like he's holding a boombox. What's he listening to? - Mr. Gunn

That's a good question. I want to hear the answer (argument). - Steve Koch

Tubular Bells (sorry) - Andrew Clegg

Ha! Tubular Bells! I do like the idea of notes somehow being ATP. Judging from what Kiney is wearing means he's either listening to the theme song from the A-Team or Young M.C.'s "Bust a Move". - Andy Maloney

I get the Bee Gee's stayin alive in my head when I look at Kiney and the boom box: http://www.youtube.com/watch... - Steve Koch

http://openwetware.org/wiki... I turned kiney into a OWW userbox and added him to my user page: http://openwetware.org/wiki... - Steve Koch

That's what I hear too, Steve! - Mr. Gunn

Science 2.0: Steve Koch

Thinking of my NSF CAREER Award application, due in mid-July. What should I budget / plan for regarding Science 2.0?

April 28 - Comment - Like - Share

Mickey Schafer, Kevin D. White, Jean-Claude Bradley and 4 other people liked this

You can find my proposal from last year here: http://www.scribd.com/doc... On page 16 (section 4.1) I describe some Open Science goals. The open science part of the application was very highly rated by the reviewers. This year I am mulling over how I should make the plans more concrete. One idea I have is to budget to hire an undergraduate to make a virtual classroom in Second Life to allow Physics 102 students (Conceptual Physics) to play with the classroom demos in VR. Is that reasonable? - Steve Koch

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You should probably change this to say that everyone in the lab has open notebooks now. - Andy Maloney

Are you wanting to develop Science 2.0 tools/methods as part of the academic work, or are you wanting to use tools to get to your scientific goals? Are you wanting to answer a question about Science 2.0, or just use it? - Matthew Todd

In regards to your second question, I think definitely we want to use it, rather than study it. I wouldn't mind being a bit innovative, but that's not even necessary. - Steve Koch

As for the first question, I am thinking the focus should be on "broader impacts" and education. So, using Science 2.0 to increase the impact of our research and education. I actually believe that the tools also substantially help us achieve our research mission...but I don't know whether I want to make that argument. I think it's wise to make the research seem achievable w/o the Science 2.0, and then the Science 2.0 to be a really good way to magnify the research impact. - Steve Koch

@Andy: you're right. The progress you and others have made in Open Science since the previous submission are really going to strengthen the proposal. Thank you! - Steve Koch

I think there's a lot of value in "just using" and being engaged with development community rather than re-inventing the wheel again. Plenty of people who would appreciate input on how to build things better and a community need to think about what the rules of should be - Cameron Neylon

It can be tricky to anticipate what the reviewers will value - I would say write what you believe in and hope you get like minded reviewers. Our last proposal got bashed for having Web2.0 components while the one before that it was seen as a positive. - Jean-Claude Bradley

And don't forget Letters of Support R Us ;-) - Cameron Neylon

Cameron and Jean-Claude, I'm on the same pages with you. Last year I wrote what I believed and got lucky that the reviewers really liked it. Hope the same will happen this year! - Steve Koch

Don*t forget to consider http://www.sci-mate.org/wiki.... Unfortunately(!) all the Web 2.0 apps are free, but you can make a voluntary service donation, and we'll customize some aspect of the site or build you a web page or something. - Christopher Dyer

Christopher I tried to register for Sci-mate but it does not give me the option to do so - Jean-Claude Bradley

Andy Maloney

Casein paper review - http://www.openwetware.org/wiki...

April 23 - Comment - Like - Share

Steve Koch liked this

I don't know why I am so excited about this paper. Maybe it's because it is the first paper I've read on the kinesin and microtubule subject that directly answered a question I had. - Andy Maloney

5 more comments

Really awesome review, Andy! I agree that the paper is very good and that kappa-casein looks very promising. I'm going to experiment with putting my comments here as opposed to the wiki talk page. - Steve Koch

My major question is: how did you answer your EGTA question? You find that the casein is to support kinesin activity. But did you find definitively that casein does not contribute calcium to the solution, and thus necessitate EGTA? You say, "Also, I was wrong about why we want to use EGTA," and I don't see how that's supported. I know from work of Andy Boal and Amanda Trent (and others) at Sandia that Ca++ is destructive to taxol-stabilized MTs as well. It's likely there is work prior to them as well - Steve Koch

As for pegylated lipids (or any other surface chemistry), I agree it's highly unlikely that casein is the best method. I agree with you too that you need to get good at the current state of the art before attempting to improve it. We need a place to list ideas of what to try. Some of these may be appropriate for summer undergraduate work, too. Related to the surface chemistry issue is... more... - Steve Koch

I just got a paper that says calcium affects Taxol stabilized microtubules so if you know first hand that calcium still depolymerizes them, then I'm game to say we need the EGTA. But, do we know how much calcium is in casein? From what I understand, calcium is stored in casein in the form of calcium phosphate which is not soluble in water. So, do we really need EGTA when the nonpolar calcium phosphate will stay in the nonpolar regions of casein? - Andy Maloney

Has anyone checked to see how much calcium is in solution after filtering casein through a 220 nm filter? If it's not there, then we don't need EGTA. Plus, if all we want to do is get rid of calcium in solution, then we should use Bapta since it has a crazy high affinity for calcium and not so much for magnesium. - Andy Maloney

It's quite possible that the EGTA / calcium / casein thing is entirely just from my musings. I don't recall anyone else saying that. And I didn't know about the insoluble calcium phosphate form... - Steve Koch

Kavan Modi

The next post - http://scientificconfessions.w...

April 22 from an attempt at research - Comment - Like - Share

Welcome to open science! - Andy Maloney

Andy Maloney

Casein paper - http://www.pubmedcentral.nih.gov/article...

April 22 - Comment - Like - Share

Steve Koch liked this

These guys kick ass! Not only is it an open source article, but the paper itself rocks! - Andy Maloney

Great find. I posted to citeulike, and put my brief summary in my citeulike comments: http://friendfeed.com/e... - Steve Koch

Andy Maloney › Comments