Andy Maloney - FriendFeed

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

November 24, 2011 - Comment - Like - Share

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

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

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

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

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

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

The persistence of ONS http://andymaloney.wordpress.com/2011...

November 4, 2011 - Comment - Like - Share

Graham Steel, Cameron Neylon, Steve Koch and 2 other people liked this

If you do search for deuterium-depleted water on your google, how many pages until Anthony's notebook shows up? Assuming your google is more neutral than mine... I agree misinformation is an issue, but I think ONS overall helps much more than hurts. I think it's tempting, but wrong to worry about concealing results for benefit of public. Those who would misuse will misuse and mislead regardless of whether they find good data, bad data, or no data. - Steve Koch from Android

Just got the day job to start using Mendeley for papers.

September 15, 2011 - Comment - Like - Share

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

September 14, 2011 - Comment - Like - Share

Clark Kent, Jonathan Eisen and Steve Koch liked this

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

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

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

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

May 18, 2011 - Comment - Like - Share

Bill Hooker and Steve Koch liked this

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

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

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

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

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

April 27, 2011 - Comment - Like - Share

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Steve Koch liked this

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

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

April 1, 2011 - Comment - Like - Share

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

March 29, 2011 - Comment - Like - Share

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

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

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

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

Steve Koch liked this

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

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

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

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

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

Ha! - Andy Maloney from Bookmarklet

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.

February 23, 2011 - Comment - Like - Share

Claudia Koltzenburg, Patricia F. Anderson, Yaroslav Nikolaev and 15 other people liked this

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

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

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

Björn Brembs, Bill Hooker and Steve Koch liked this

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

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

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

February 8, 2011 - Comment - Like - Share

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

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

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

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

Mike Chelen, Bill Hooker and Steve Koch liked this

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

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

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

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

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

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

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

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

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

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

Mike Chelen, Bill Hooker and Steve Koch liked this

Cheap and easy. - Andy Maloney from Bookmarklet

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

January 18, 2011 - Comment - Like - Share

Mickey Schafer and Steve Koch liked this

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

January 6, 2011 - Comment - Like - Share

Claudia Koltzenburg, Mike Chelen, Andrew Perry and 17 other people liked this

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

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

December 16, 2010 - Comment - Like - Share

Steve Koch, Heather Piwowar, science3point0 and 9 other people liked this

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

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

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

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

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!

July 30, 2010 - Comment - Like - Share

Jamie McQuay, Mike Chelen and Steve Koch liked this

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

Question to the community: Where do you draw the line with what you post in your open notebook? For instance, do you keep your notebook focused and only post results/failures with your experiments, or do you make a point to post things that are tedious lab necessities such as "mixing solutions, analyzing data, or cleaning..."?

July 26, 2010 - Comment - Like - Share

Piotr Byzia, Davide Bennato, Heather Piwowar and 13 other people liked this

It makes sense to catalog everything you do in the lab so that you can see how your time is appropriated. That way when you return to your notebook, you can see how much time it takes to do things. But, is it necessary? I'm on the fence about this one since there are pluses and minuses to both sides of the argument. - Andy Maloney

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I try and just keep notes as I go. It's always the minor detail you don't think work recording that is the critical piece of information you want six months down the track. The mixing solutions one has bitten us a few times when one lot of buffer was good and one was bad. I've certainly never regretted putting too much in the notebook. On the other hand those details probably aren't... more... - Cameron Neylon

Cameron: I know exactly what you mean about mixing buffers as I'm making one right now that doesn't seem to be working. Perhaps I should make a category in my notebook that I tag things that I think are "lab drudgery". - Andy Maloney

Taking Cameron's idea a little further: top layer = homepages for each project, featuring an intro and any published work; second layer = lab notes focused on experiments; third layer = everything that happened in the lab and was recorded, by a human or by a machine. That way readers could choose their own level of detail. In my daydreams every lab links to this kind of layered notebook directly from their own homepage... - Bill Hooker

Steve Koch pointed out that I have been lax lately with posting to my notebook. I agree with him completely. However, what I have been doing lately seems to me more along the lines of engineering necessities and not science. Thus, no postings as of late from me. But it seems that even posting the engineering nightmares I have to go through to make science is important as well. - Andy Maloney

Bill: I've tried to implement your idea in my notebook. This is not trivial and is proving to be quite time consuming to try and tag my entries properly so that there is some sort of layering affect. Both for my own sanity and those that may come across my page. http://www.openwetware.org/wiki... - Andy Maloney

One negative idea I have about posting everything to my notebook probably has to do with how I feel about Twitter. No one cares (or at least they shouldn't care in my opinion) about how I had to order more vials. Of course, I may be taking that sentiment too far when it comes to my notebook. - Andy Maloney

Not to say Twitter is bad. It's great for those that want to use it. - Andy Maloney

"it seems that even posting the engineering nightmares I have to go through to make science is important as well" -- absolutely. This is exactly the kind of tacit knowledge that gets lost, and rediscovered, and lost, and rediscovered, and so on. If you solved a problem, engineering or scientific, then you did something that someone else might be able to use. Perhaps running out of vials... more... - Bill Hooker

+1 Bill and the challenge remains how to make it both easy to record all of that detail effectively and to make the right thing easily discoverable when someone somewhere wants it. - Cameron Neylon

I would not log 'making solutions', never logged that on books. But what I do is put the date on which a solution was made (date and maker's initials) and that gets logged in the experiment. Same with chemicals like antibodies: when I aliquot I tape the bottle label to the notebook and the 'internal' tag/batch that identifies the tubes in the freezer. The internal reference is what I... more... - Kubke

In my imagination we have a little web widget which is part recipe and buffer calculation engine and part logging in of buffer making. This serves two purposes, it makes it appealing to log the creation of the buffer because you get that as a side effect of bringing up/calculating the recipe and it also allows you connect other automatic logging of e.g. a balance that could let you go... more... - Cameron Neylon

I ask my students to keep a time log of what they do and observe. Invariably new students don't record enough detail. But that comes out naturally when I step through their logs and can't recreate exactly what they did - and I will comment on this directly in their notebook. Maybe they will remember a critical missing detail or maybe all that was learned from the experiment was what... more... - Jean-Claude Bradley

This is a terrific discussion -- one that I plan to use with students when discussing the practice/ethics of recording science. From a social science perspective, the mere existence of thoroughly noted lab notebooks is quite interesting... - Mickey Schafer

Sure D :) - BTW there is a recent paper in J Chem Ed about using wikis for chem lab - unfortunately none of them are public - via Brent Friesen http://ff.im/olji7 - Jean-Claude Bradley

Great discussion! My work is all theory and I don't get all my blackboard scraps into the notebook, though often I wish i had (learning that a camera is faster than LaTeX), while git records all the micro-level changes in the code so I just comment on the larger ones. I try and use tags to avoid the most useful stuff getting buried in the details but haven't found OWW Categories or search to be quite good enough for me. Open to suggestions for that one. - Carl Boettiger

Carl: Using OWW categories is a pain but, it is nice to have a page that links dynamically to all my notebook entries with specific category tags. I include a template in my notebook that allows me to write a short description about the entry and that description is visible in my DPL page. It's just a shame that I learned how to do this a year after I started my notebook, so I have a... more... - Andy Maloney

This is a reason why you should write everything down in your notebook no matter how silly you may think at the time it is. http://www.openwetware.org/wiki...

July 26, 2010 - Comment - Like - Share

Science 2.0, Pierre Lindenbaum, Björn Brembs and 2 other people liked this

Thanks Bill and Cameron! I'm a convert now to write down everything in my notebook. - Andy Maloney

4th google hit for "casein PEM buffer" is your notebook, Andy. This is what I mean when I say the primary value of an Open Notebook is in searchability. (Also, could it be a pH issue? The spec sheet says to dissolve in 1M NaOH, which has a theoretical ph of 13... you may be able to save yourself some time and heating by predissolving the casein at a high pH, if enough protein goes in you could effectively use the casein solution to pH your buffer.) - Bill Hooker

Bill: You bring up a very interesting idea. I have read about the pH dependent solubility before but I never thought to use it to my benefit. I'll have to think about this one and do some calculations to see if it will work with my preps. - Andy Maloney

Haven't posted in a while but I think some people will be able to use a cheap microscope objective heater that is super easy to build and works fantastically. http://www.openwetware.org/wiki... Just ignore my extraneous notebook stuff included in the page.

June 17, 2010 - Comment - Like - Share

Daniel Mietchen, Mr. Gunn, Joshua Shaevitz and 2 other people liked this

You rock - Steve Koch

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Not really. The write up is not very in depth and I'm sure it will confuse people. Of which, I apologize in advance for. I just hope someone can use it to build something similar and to use the guys at TeTech. But thanks for the vote of confidence. - Andy Maloney

Feel free to ask questions about the build if anyone wants to build one. - Andy Maloney

Well, I didn't read it all, but with all the great photos, I'm sure people Will be able to replicate it.plus you rock for getting it done so quickly anyway! - Steve Koch from Android

OK, Now I've read the whole page, and I think it is great--all necessary information seems to be there, plus humor throughout. I have a couple comments / questions. - Steve Koch

1) why would a lightpipe help any further? with the objective heated above ambient with your new system, doesn't that buffer the sample from the heating of the microscope body? I'd say your newly flat kinesin speed data demonstrate that is true. So, I wouldn't think lightpipe would help any further. - Steve Koch

(Thank you once again to Erik Schäffer and Diez for explaining this effect to us, BTW!) - Steve Koch

2) I'm skeptical about the remaining initial heating effect being due to photons. But could be wrong. (I guess once you analyze the dim diode data you'll know). But if it is photons, then I don't see how you can solve the problem--whatever your light source, if it's as bright as you like it, then it will heat the sample. - Steve Koch

If it is photons, easiest solution is to just use data >10 minutes for now. - Steve Koch

Maybe it's an effect of the slide changing the thermal gradient on the heated objective? Maybe if you have a blank slide on it ahead of time it would help? In any case, to reiterate, I think you've solved the major problem of long-long time temperature increase! - Steve Koch

Haven't looked at it, but let me guess: It doesn't involve a large trash bag and temperature controlled switch with a hair dryer plugged into it. That was possibly the most ghetto microscope heating setup I've ever seen, but it did seem to work ok for my colleague. - Mr. Gunn

Steve: #1) I see what you are saying and maybe it is #2. I'll just have to look at the data to find out. Not using the Hg lamp is for some reason alluring to me. Maybe because I got a "sunburn" from one and I just don't like them. - Andy Maloney

Mr. Gunn: That sounds like the most awesome thing ever! Although I'm not entirely sure what the garbage bag is used for. - Andy Maloney

Well, the LEDs should last a lot longer and be easier to align, right? - Steve Koch

Oh, the bag was to try to slow down the drying out of the slides. There were live cells in there. - Mr. Gunn

I came across the words "lifestream" and "aggregator" recently. I know, I'm behind the times. And, I came across Cameron Neylon's blog entry on science lifestreaming. http://blog.openwetware.org/science... Very cool and informative.

March 12, 2010 - Comment - Like - Share

Walter Jessen, suze, Graham Steel and 5 other people liked this

I have been in contact with a web designer that I went to school with and he seems to be interested in making a science lifestreamer. The big questions about doing this project would be; would anyone use it and how important would it be to open scientists? - Andy Maloney

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I have been literally jonesing for something that would logically contain the projects I work on that use the services like friendfeed, YouTube, and OWW. It seems that I'm not alone but, with no web design knowledge, this task seems pretty daunting. - Andy Maloney

Heh, there's been quite a bit of discussion about this recently, and from my perspective many of those who initially made "social networks for scientists" are now trying to jump on the "lifestreaming for scientists" bandwagon, but it worth considering how open and how successful their initial efforts were when considering how useful their new lifestreaming services will be. In terms of standard formats for sharing data, they all fall pretty short right now IMO - Mr. Gunn

Mr. Gunn: So far lifestreaming and aggregators are all very new to me. I had no idea people tried to create lifestreams geared towards scientists. If you have examples, I'd love to see them. - Andy Maloney

This is where things get a bit tricky with the idea of a lifestream for scientists. I think a lifestream would be pretty useless if you want to show multiple data from multiple projects in the stream. Lifestreams aren't setup with the ability to organize posts in a logical manner. If I tweet about project A and then about project B, a lifestream would show both tweets in the stream as... more... - Andy Maloney

What you describe in the previous comment, Andy, is just the "groups"/"lists" concept in Friendfeed: You would have Group A and Group B and could bundle them under a list "Projects" (others might be "Literature", "Tools" etc.). I find this pretty handy, and we are discussing to set up an Open Friendfeed at http://ff.im/gLtCJ and http://ff.im/gXoNX . - Daniel Mietchen

OWW test.

January 30, 2010 from iPhone - Comment - Like - Share

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

December 16, 2009 - Comment - Like - Share

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

I have added a very quick description for motivation behind my experiments. http://www.openwetware.org/wiki...

December 16, 2009 - Comment - Like - Share

Mickey Schafer and Graham Steel liked this

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, 2009 - 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

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, 2009 - 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