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Anthony Salvagno
sonicated .51 um beads - Anthony Salvagno
flowed 10ul BGB - Anthony Salvagno
flowed 10ul 1:2000 beads - Anthony Salvagno
sealed with nail polish - Anthony Salvagno
Anthony Salvagno
I'll be at the P&A ceremony in my gown :) - Steve Koch
OMG, that would be spectacular! - Anthony Salvagno
Hmmmm...with tenure on he line and all those voters there? Maybe I'll find a way :) - Steve Koch
Chelsea Wald
Hi, everyone! Today I'm here discussing my ScienceCareers story, "Scientists Embrace Openness," about the career implications of Open Notebook Science, Open Data, and general science openness: Let me know what you want to talk about...
Hi Chelsea, great article, what led you to write it? - Andrew Lang
Thanks, Andrew! Jim Austin, the editor of ScienceCareers, assigned me this article. (There are two main ways to get work as a freelance writer: pitch or get assignments.) I'm not sure what exactly led him to the topic, but I know that a conversation with Brian Krueger played a role. I knew very little about the topic, but Jim intuited that it would be a good fit for me as a writer. It turned out to be a really fun story to report and write. - Chelsea Wald
Anthony Salvagno asked me in an email: "How long did it take from first concept to publishing?" I sent my first email interview request on Feb 11, so the story took me about two months to write. (This, of course, doesn't count the time Jim spent coming up with the idea.) I wasn't working on the story full-time, though. Depending on my other projects, some weeks I worked intensively;... more... - Chelsea Wald
P.S. I'm not the most sophisticated FF user, so please let me know if I could be using FF more effectively. - Chelsea Wald
HI, Chelsea. I very much enjoyed the article and will be adding it to my ONS delicious tag arsenal! What I appreciated about the read was its focus on practitioners -- in the class where I discuss ONS as a practice (I am not a scientist, but train young scientists to write), there is always at least one student who writes an elegantly argued, pro-ONS piece, and having an essay that is about people rather than focusing on the ideal itself works nicely to help that student feel less isolated. - Mickey Schafer
Hi, Mickey. Yes, I was tasked with writing an article on the practical challenges associated with openness, especially for early-career scientists. I quickly came to appreciate that ONS practitioners have to go to fairly heroic lengths in order to make their notebooks open, and I wanted to emphasize that. I also came to appreciate that those same ONS practitioners realize that it's... more... - Chelsea Wald
Mickey - what you are doing with your class sounds very interesting - are your students willing to share some of their essays? - Jean-Claude Bradley
Hi folks. Thought I would join in here and say that I started developing an interest in Open Science perhaps 6 months ago. I've been monitoring it, but not too closely, since then. A couple of Twitter posts, perhaps channeled from FriendFeed, got me off my butt and made me decide it was time. Though I don't remember what it said, one of those posts was from Brian Krueger. I contacted him and he got me started. I handed this off to Chelsea and she took it from there, very skillfully. - Jim Austin
One of the great things about being an editor is that once you take an interest in something, you can get someone else to study it for you and distill it down to a manageable chunk of information -- for you and your readers. - Jim Austin
Jim - thanks for the feedback on how it came about - I hope your interest in Open Science continues! - Jean-Claude Bradley
I'll definitely continue to keep an eye on it. I think it connects to a couple of other big issues right now -- importantly, data sharing and trying to achieve a more integrative science, especially medical science. There's a lot riding on that, it seems to me, and a lot of people these days are talking about, and working on, integrating research resources. - Jim Austin
Hi Chelsea, thanks for referring me to this discussion! I think the Koch and Bradley labs are great examples of the younger generation of scientists embracing available technologies and trying to improve the research process by taking a new approach, which should be applauded. I really like Jean-Claude's idea of trying an open project out on the side to get started- it's a nice way for... more... - Alan Marnett
Mickey - do you see any trends in your students' opinion of ONS? Is it generally for or against? Any year-to-year trends? - Alan Marnett
Hey Chelsea and Jim and everyone, sorry I'm getting to the party late. Yesterday you mentioned a conversation between you and Koch about parallels between Journalism and ONS. Could you go into more detail? I would like to hear your take on it and figure out if there are any ways the we (the ONS community) could help you attain more openness. Of course, like JCB says, starting small is a great way to get involved. - Anthony Salvagno
Hi, Anthony. The party's going on all day. It's more like an open house, I guess. The back story is this: When I was reporting this story, Steve suggested that I ask his students (including you) questions about working in an open lab. We tossed around the idea of doing it on FriendFeed, so that others could listen in and participate. I liked this idea but became concerned that it could... more... - Chelsea Wald
Do you think you might experiment with live reporting? By this I mean you "publish" information as you receive it in an informal method. Scientists can preprint articles in something like Nature Precedings and get early feedback. Then you could publish your formal written report when it is all done using the information you had previously compiled. - Anthony Salvagno
Also, how likely would it be for journalists to collaborate on a project? Maybe have more names attached to one article like we do for journal articles. - Anthony Salvagno
Because I was reporting the ONS story at the same time, I a) became more sympathetic to the concerns of scientists with respect to being open, and b) began to wonder whether there was a place in journalism for an "open notebook" approach. What would it look like? Would sources agree to participate in it? Would editors agree to it? Would it help establish a priority so that scooping... more... - Chelsea Wald
Anthony, here's an example of a rough-draft article that has left some journalists mystified recently: (Note that the writer is a Science Careers contributor.) I have not discussed this project with anyone in the know. - Chelsea Wald
As for collaboration, it happens sometimes within news organizations, but it would be hard to see how that would work across organizations. In science, if you find out that someone at another institution is working on the same thing, one response is to turn your competitor into a collaborator and publish together. But could that work in journalism? Doubtful. The usual response is to try to get to print as fast as you can. - Chelsea Wald
Chelsea, Thanks for pointing out Beryl's article. Beryl is, as Chelsea notes, a long-time contributor to Science Careers. She has written a monthly column for -- not sure -- maybe 5 years? And she writes on many of those same topics for us. As you may know, Scientific American is now owned by Brits -- the publishers of Nature -- so I suppose that represents a kind of sharing. ;-) - Jim Austin
Hi, Chelsea. I also really enjoyed the human element your article brought to the process, across all levels from tenured to faculty down to graduate students. I'm also intrigued by your parallels in the journalism world. While ONS has led me to new collaborations, it's often been something I've had to approach very cautiously with most collaborators. How do others address this? - Carl Boettiger
There are some really important differences between journalism and science -- but there are also some parallels. As may of you are probably aware, there's a parallel discussion going on about journalism, openness, and business models. - Jim Austin
Usually though this breaks down as bloggers (on the open side) versus traditional journalists (especially those generating content you have to pay for). So in a journalistic context, business models are huge. How do you make money -- even to break even? - Jim Austin
Basically, bloggers want respect. They want to be thought of as journalists even if they don't have an ID from a major publication. - Jim Austin
Hi, Carl! Glad you found this. Many people told me that they had to close off projects due to collaborators. That, or drop the project altogether. Maybe others will weigh in on specific examples. - Chelsea Wald
Yes, Jim's right that we shouldn't forget about major differences between journalism and science. In the article, Jonathan says: "Given that taxpayers are paying for our work, I think that the default should be to be open unless you can prove that it's a bad idea." Taxpayers are NOT paying for my work. Journalism is a public service, but it also has to make money. - Chelsea Wald
I will just add to Chelsea's comment: Non-profit models of journalism exist, but even they need revenue -- which means inventing new ways to ensure objectivity. What happens to National Public Radio when there's a Republican Congress? (A: They lose funding.) So you can see that there are interesting parallels and differences. It's all research, even if the methods, and the nature of the knowledge, are different. - Jim Austin
But in journalism, value typically equates to exclusivity, especially today. If you want to generate revenue, you have to be able to offer something that people can't get for free. I think that's a major difference. - Jim Austin
Now, I'd like to ask a question of the scientists here. One of my preoccupations these days is with translational research -- trying to accelerate the rate at which basic-science breakthroughs become real-world therapies. If you're not biomedical, then consider the obvious parallels, like materials for electronics. Does running an open lab take you completely out of that game? Is an open laboratory only for the non-applied? - Jim Austin
Thanks, Graham. You bring up some interesting questions about tools in your post. I use google docs all the time, and my understanding is that many ONS researchers do, too. Does anyone care to discuss collaboration/ONS tools? - Chelsea Wald
Chelsea, ask Bora Zivkovic about "Open Notebook" journalism: - Martin Fenner
@ Chelsea, Jean-Claude, -- sorry for the late reply -- I am on a grading frenzy and wasn't supposed to be checking in at FF at all until next week! The essays in questions are blog posts replying to Michael Neilson's "Future of Science" essay and an HHMI article titled something like "So you wanted a revolution" (both can be found linked here:... more... - Mickey Schafer
@ Alan -- same apology as above! I have only held this discussion 2 times, so there are no trends to report. Last year, there was more open skepticism, but there were also more argumentative personalities who knew each other well. It will be interesting to watch over time. This year, a couple of students remarked it might have been better to have this conversation before they had finished their research. No student has yet ever heard of it, so also did not know any practitioners. - Mickey Schafer
Thanks for checking back in, Mickey! - Chelsea Wald
@Jim -- "What happens to National Public Radio when there's a Republican Congress? (A: They lose funding.)" -- this is about the scariest thing I've heard in a while. I live and breathe NPR. They had an interesting discussion last week, I think it was, about the fate of CNN. Given the importance of "branding" to attract a particular audience, CNN is losing ground to Fox and MSNBC alike. They quipped the same could be true of NPR -- at least NPR has public supporters paying out of their pockets. - Mickey Schafer
@Mickey, I didn't mean they would be totally unfunded, NPR is notable for having a relatively stable revenue base, and an independent news apparatus. I was thinking of 2005 when, accused of having a liberal bias, their funding -- about $400 million at the time from the CPB (including both NPR and PBS) -- came under threat from Congress. NPR works hard and successfully (as far as I can... more... - Jim Austin
Hi, Martin. Thanks for pointing me to that post (I'm familiar with Bora and his work, but I hadn't seen this). I'm noticing, however, that "traditional media" don't get mentioned until step 4 of his model. I suppose that means it wouldn't work if someone gets assigned a story, as I did in this case; unless, of course, the publication agreed to it. - Chelsea Wald
@Chelsea: "...unless of course the publication agreed to it." I would welcome an intelligent proposal, as long as it was on topic (that is, about Science Careers). I'm always eager to try new things. - Jim Austin
Wow, cool! You all heard it here first! - Chelsea Wald
Very interesting. I let Bora respond to that. - Martin Fenner
Talk about coming to the party late... This is a really good discussion. I thought the article gave a good perspective on the topic. In your research, did you get a feel for how mainstream researchers feel about the topic, Chelsea? I know my quote came off as quite skeptical, but in my work with LabSpaces, I've found most researchers to be unwilling to talk openly and publically about... more... - Brian Krueger - LabSpaces
Its a common sentiment Brian expresses, but I think it is becoming less common. When everyone holds their cards to their chest, they don't learn as fast that their great idea was tried and rejected by 4 people before they happened upon it. Most of the secrets are really neither that secret nor patentable. This is one of the areas I'm most hopeful open science will illuminate. - Mr. Gunn
Hi, Brian. You were here in spirit. ;) My sense is that most researchers would say that Open Notebook Science is fine...for other scientists. You know, everyone I talked to was pretty realistic and probably wouldn't disagree with you: The entire scientific enterprise is not suddenly going to go open. By the way, I'm fascinated by your interaction with the legal department. Any of the scientists here have similar experiences? - Chelsea Wald
Jim, I recently wrote about some of the obstacles of doing medical research online here: Some issues are patient privacy, recruitment and reporting bias when clinical trial results would be openly available in an ongoing study, and commercial interests of pharma companies that sponsor trials. - Martin Fenner
Drug companies are starting to be more open as well: Is open innovation the way forward for big pharma? - Martin Fenner
For this story, I emailed with Sriram Kosuri of OpenWetWare. His comments didn't make it into the story, so I thought I'd add them here (a luxury I don't normally have!): Q: How many users does OWW have? Of those, how many are actually posting bona fide Open Notebooks, as opposed to, say, just hosting lab websites? If you don't have exact numbers, can you estimate? What kind of growth... more... - Chelsea Wald
Sorry for the lousy formatting there. Any help on how to make it better? - Chelsea Wald
Haha! I didn't know it wasn't supposed to be possible. Cut and paste, baby! - Chelsea Wald
@Martin, Thanks for the links to your posts. I will read them with interest. - Jim Austin
@Chelsea, I don't know if you've spoken to Koch about this, but we have a patent for our optical tweezer technique. I don't know all the specifics of it because I'm just a slave in the lab (just kidding) but I know we are open and we have this (as an example of people other than medical sciences). - Anthony Salvagno
As for tools I'm really big into Google Docs. My notebook is on OWW and I hate making tables in html and css and starting using google docs as soon as I discovered they existed. I also use Evernote to quickly get pictures from my pc on the web. Because of friendfeed's ability to add rss feeds (among other things) I can create groups here that contain possible related posts from all my... more... - Anthony Salvagno
I'm providing a bunch of links of pages in my notebook that have integration from different sources. I also have protocol pages not in my notebook and upload video protocols to youtube and embed them in right on the page with the protocol (see here: I've been meaning to switch to BenchFly but I ran into a snafu. Alan has been working on the issues very diligently trying to fix the problem and we've found a workaround for now (thanks Alan!). - Anthony Salvagno
Also if you'll note posting lots of comments could be another way for you to format one really long comment. Sorry if I pissed anyone off. - Anthony Salvagno
One more note... this thread kicks ass! It's so awesome I want to curse more, but I'll hold back. - Anthony Salvagno
@Mickey would it be possible to send me the student essay that hasn't been posted? I could post it on my blog and give you and said student full credit. Another alternative would be to post the essay here on ff as a series of comments with the thread being the title of the essay. What do you think? - Anthony Salvagno
Thanks for these contributions, Anthony. I'm sure people will find it useful to see the tools of ONS in practice. I also have to say that I use google spreadsheets for my personal and business finances, and it's reassuring to know that scientists trust them enough to keep their precious data safe! - Chelsea Wald
Anthony, I enjoy seeing how you embed google spreadsheets into your notebook; I've been frustrated by formatting tables in html and this looks very promising! I've been using OWW's rss reader ( to display articles I've recently added to my library in my notebook, would be interested to see more about how you're using both rss and other apps. - Carl Boettiger
@Carl I really have no good way for handling RSS as I don't use them that much. I don't like how OWW handles RSS. I've actually been trying to figure out a good way to port my notebook as an RSS feed so it goes to friendfeed or yahoo's program that I haven't been able to use yet. The few feeds I do link to get funneled into friendfeed. As for other apps... I've been using Picasa... more... - Anthony Salvagno
One more note about RSS feed from wiki (OWW): I learned recently that there is a mediawiki extension that enables you to export your work as an RSS (see I've emailed Bill asking to implement it but I think he's disappeared. Sorry for digressing off topic. - Anthony Salvagno
Excellent article! And great thread here. Don't know if you saw the video from this panel on Open Science at Columbia about a year ago: As for open journalism - that is tough, but definitely worth a thought. Some newspapeprs (famously Greensboro News & Record as a very early adopter of the practice) now put their... more... - Bora Zivkovic
I know I'm very late to the party here (inconvenient time zones) but the question Chelsea raises about translational research is a very interesting one. For me its all about asking the question "how do we most efficiently maximise return on investment, in _this_ research, for the investor?". Where the investor is the public and its not directly patentable stuff the answer is clear.... more... - Cameron Neylon
Jim and Chelsea, it would be great if discussions like this were linked from the article. Either by allowing comments (as in the PLoS journals and now Nature), or by showing links to blogs, Friendfeed, etc. that talk about the article. - Martin Fenner
@Bora Thanks for the ideas on open journalism. I guess I might try an experiment in the near future here. - Chelsea Wald
@Cameron Thanks for joining! You bring up some great points. Does anyone paying attention to this thread know of some case studies that could help shed light on those "edges"? - Chelsea Wald
Martin and Graham: I agree. I don't know whether something like that is in the works, but I'll make sure that the suggestion gets passed on. - Chelsea Wald
There is a Research Information Network funded study going on in the UK at the moment that is looking at researcher perceptions in this space but I don't know of any solid social science studies of outcomes (as opposed to opinions and perceptions) at the moment. The example I give isn't hypothetical tho - I am involved in a research consortium seeking funding to do such development. If... more... - Cameron Neylon
Great discussion! Concerning embedded Google spreadsheets, my students do use them in our notebooks but I try to discourage their use in general - or at least make sure that there is a link to the spreadsheet nearby in the page. The problem is that when we create an archive of the notebook and all associated data files, embedded content still appears live in the archived version while... more... - Jean-Claude Bradley
On Open journalism, two quotes from : (1) "The Nieman Lab's Josh Benton noted that this "cult of rewriting" is grossly inefficient: what added value do journalists bring to the table when all they're doing is rewriting one another's work? Such journalists are at best aggregators and curators, much like... more... - Daniel Mietchen
The previous comment (and this one too) was submitted from - will try embedding FF threads into OWW as another way of archiving. Jean-Claude's comments above on Google Docs may apply, though. - Daniel Mietchen
@Anthony -- yes, I think either sending to you or posting here would be possible. The teacher-y side of me wants her to be protected, as an undergrad with all that status or lack thereof implies -- I have students getting butts kicked by PIs who've just decided after 2 years to take an interest in their work, 3 weeks before graduating -- turns out there is a strong prejudice against the premeds in many labs that I didn't know about -- very disturbing to me. - Mickey Schafer
Hi, again, everyone: Working on blogging this thread for Science Careers. Anyone object to being in the Science Careers blog? - Chelsea Wald
Nice Chelsea! Keep the discussion going - Jean-Claude Bradley
Here's the post on the Careers blog: It's mainly a copy of this thread for the benefit of people not on FriendFeed (and with the hopes of bringing more people into the conversation). Thanks for making this discussion so amazing! - Chelsea Wald
FF thread for that 2nd discussion: . Less lively but still related thread: . - Daniel Mietchen
Thanks for pointing that out, Graham. It's a really nice discussion! - Chelsea Wald
Yes nice coverage on the podcast - Jean-Claude Bradley
Anthony Salvagno
We are finding a book format really convenient for browsing solubility results and we are in the process of generating a book for reactions as well, where one edition will likely include the UsefulChem blog. But the price charged by these people is insane ($140)! Lulu is less than $10 - Jean-Claude Bradley
Yea that price is insane. Are you making the books yourself (digitally) and then having an ecompany create and distribute? I've been thinking for sometime (seriously) that I can easily make this stuff digitally and maybe even physically. My main goal would be to design products for labs at no charge and let them handle the cost of creation that way it is a bare-bones cost with... more... - Anthony Salvagno
Anthony we are using LuLu to print and ship with a 0% royalty. We are also distributing data disks (CD or DVD) for an export of the entire lab notebook with associated raw data. See here for details: So far I am very happy with LuLu - the books are excellent quality for the price. Contact me or Andy Lang if... more... - Jean-Claude Bradley
Anthony Salvagno
I like this quote: "Once I made the commitment to be open I could never go back. It is like being free." - Jean-Claude Bradley
Thanks! I was going to say naked instead of free, but facial expressions and humor don't translate well in an email. LOL! - Anthony Salvagno
Anthony Salvagno
I am considering that I should start lifting again if I get down to 135. It'd be cool to be ripped one more time before I die. - Steve Koch
U should start lifting now. You could be ripped even without heavy weights. pushups and lunges, and if you have a tree, you have pullups. - Anthony Salvagno
I have a swingset! Maybe I will start pushups and pullups now. - Steve Koch
Anthony Salvagno
Anyone think Chrome is better than Firefox? I've been having problems with Firefox lately and think I'm at wit's end...
I am at 50% chrome/50% firefox these days. There are still a few things I prefer about Firefox, mostly extensions and the awesome bar, but for rapid, quick browsing it's Chrome all the way, and definitely for my google apps and services - Deepak Singh
With Chrom(e | ium), everything just feels snappier, due to quicker rendering. All the important extensions that I use (mostly adblock) have been ported, and my handful of must-have greasemonkey scripts work fine too. I've slowly migrated to the point where 95% of my browsing time is spent in Chromium. - Chris Miller
Definitely, especially now that it has extensions. I've made the jump, and never looked back. Chrome is sleek, fast, and doesn't bother me all the time like ff. - Madelaine
Thanks for all the feedback! - Anthony Salvagno
Anthony Salvagno
Andy asked me about HTML Video Gallery and we did some searching. Embedding video should definitely be a part of and I will need to learn more about it. Here are a couple of places to get started: and There was also JW Player...
HTML5 seems like what we need partly because smart phones and ultimately tablets/slate "computers" don't allow for Flash. Of course we are in a conundrum since none of the browsers support HTML5 yet. - Andy Maloney
Jean-Claude Bradley
That's cool. - Andrew Lang
Awesome! - Khalid Mirza
I already washed it in warm water and seems ok - Jean-Claude Bradley
I gotta get me one of those. I think I might put this [] on a shirt as well. - Bill Hooker
I agree on the zero royalties issue. I have a tshirt store setup there and also don't want royalties, but there really is no other option for me. Spreadshirt uploads my images in a weird way and I've had trouble with cafe press as well. I would like to spring for a direct-to-garment printer, but would need financial backing. Donations? Shirts for Science is what I'll call it. - Anthony Salvagno
That would be great Bill - we'll coordinate our outfits like all the previous conferences :) - Jean-Claude Bradley
Anthony - I think there is probably a service out there that won't have the royalty issue - it sounds expensive to buy a machine - Jean-Claude Bradley
JC - I've checked various sites and haven't found anything yet. Maybe I'm not looking properly? As for expense, it is. Preliminary results put cheap machines in the $1000 range and good ones in the $8000 range. Maybe the zazzle store could fund this acquisition? - Anthony Salvagno
Anthony - I'll keep looking and let you know. In the meantime it really isn't very difficult to drop the image on the t-shirt (or coffee cup, etc.) from Zazzle. Even if you get your own machine, are you going to do all the packaging, shipping, billing, complaints, etc.? - Jean-Claude Bradley
Jonathan Eisen
Scientists Embrace Openness - Science Careers; quotes by me, @cboettig @jcbradley @skoch3 @LabSpaces et al. -
thanks Jonathan - I didn't know it was out yet - Jean-Claude Bradley
the power of google alert searches for "Jonathan Eisen" --- although I keep getting info about another jonathan eisen - Jonathan Eisen
i have a bunch of automated google alerts; i have them set to email me at different frequencies; all of them are filtered to a folder I only look at once in a while so they are not intrusive; they are useful for picking some new posts about various things in addition to ego surfing - Jonathan Eisen
I have one too - it just hasn't kicked in yet for this article - Jean-Claude Bradley
Yeah, it is quite well laid out - Jonathan Eisen
You know, SC first contacted me about this and I pointed them to JCB and Steve :P - Brian Krueger - LabSpaces
Nice one, Brian. - Mr. Gunn
I can confirm that Brian was the guy that got us going on this one. Thanks to all. - Jim Austin - Jim Austin
thanks Brian! - Jean-Claude Bradley
Thanks, Brian! Looks like a very good article. So cool to be in the same article as you all! - Steve Koch
Thanks Brian! - Anthony Salvagno
Thanks for the positive comments, folks, and thanks to all of you who helped. I'm going to be hanging out on FriendFeed tomorrow to discuss the story, science openness, and anything else you want to talk about. In particular, Steve suggested that we discuss some parallels between science and journalism -- scooping in particular. (A teaser: A recent experience with getting scooped made me wonder whether journalism could be done more openly!) I look forward to a fascinating conversation! - Chelsea Wald
Nice article Chelsea. - Andrew Lang
Richard Akerman
Thanks everybody for the kind words / congrats for my new position. It's keeping me busy :)
I'm late! Congratulations, Richard! - Konrad Förstner
Thanks Konrad. - Richard Akerman
I missed this somehow -- belated congratulations from me also. - Bill Hooker
I don't know you and so I don't know what to congratulate on, but I will congratulate you on the genius use of QR codes. And congrats to getting your new position! - Anthony Salvagno
Anthony Salvagno
My Research Explained: The Basics of DNA -
My Research Explained: The Basics of DNA
very interesting. - Mickey Schafer
That's a great exercise - and I'll bet it will come in handy in the future in ways you can't anticipate. - Jean-Claude Bradley
Do u mean the practice of simply explaining what I do? If so I agree. Plus I have fun doing it and I'm sure my family likes to hear it without getting overloaded in conversation. - Anthony Salvagno from Android
Yes explaining what you do in simple terms can put you in a frame of mind for uncovering new insights about your projects. I have found that sometimes when explaining my research to non chemistry audiences. But also Google indexes all of this so you might find your summaries used in somebody's teaching materials or you might be contacted by someone unexpected for a collaboration, etc. - Jean-Claude Bradley
I know exactly what you mean. I enjoy rethinking in simple terms because of exactly what you just mentioned. Plus in areas that I know less about there is an opportunity for SO much learning. It's fun. - Anthony Salvagno
Anthony Salvagno
Final morning session thoughts:
Wasn't able to get anything done. I will need to borrow the camera from Andy's microscope and I hope to be able to do that in the afternoon session. If not I will have to occupy my time with odds and ends. - Anthony Salvagno
Tethering worked decently. There was a bunch of nastiness in the sample and I didn't sonicate properly, but I still got tethers. I will have to increase the concentration of the TpBR. - Anthony Salvagno
Now that I think about it, there wasn't as much gunk in the dsDNA chamber as there was in the unzipping chamber. I can hypothesize that the gunk in both is due to cross contamination. Can it be that the gunk is undissolved agarose? I wouldn't know what microscopic agarose looks like, and if I had a camera I would take a picture of it. We saw the same thing yesterday too. Hmmmm... - Anthony Salvagno
I think if you ran the qiagen that the agarose would be gone, especially any big chunks. Don't have good ideas as to what the gunk would be. Did you get to use the camera in afternoon? Glad you found a fan so quickly to fix the other! - Steve Koch
Anthony Salvagno
Tethering Notes for the morning session here:
One of the channels got a little messed up and I'm hoping there was no cross flow. - Anthony Salvagno
I'm doing a sample with 1.1kb stretching DNA and a sample with the TpBR from yesterday. I want to see if it tethers and I was unlucky yesterday or I need to try something new. - Anthony Salvagno
There is a lot of contamination in the sample. It is very bad in fact, I will just deal with it because I need to work around various problems. Of course I will make a new sample this afternoon. - Anthony Salvagno
Audio notes in Evernote save to a weird audio file that can't actually be used unless you have the proper player. How retarded is that? Why didn't it just save to .mp3 or .wav or something universal? - Anthony Salvagno
The sample with TpBR doesn't have many stuck beads or tethers. The sample with 1.1kb stretching DNA has results typical with previous experiments. I'll try increasing the concentration of TpBR for later on. - Anthony Salvagno
I need to sonicate for longer. This batch of beads is very poorly sonicated. Way too many clumps. - Anthony Salvagno
Anthony Salvagno
Tweezer Notes for the morning session here:
The fan is broken in more ways than one. It is really noisy because one of the blades broke off yesterday. I will try and turn the camera off whenever I am tweezing to reduce noise and to give the camera a break. Despite the noisy issue, the camera isn't overly hot like it was yesterday. It isn't super cold, but it shouldn't over heat. - Anthony Salvagno
The fan as it is now adds a ton of vibration to the sample plane. In other words it HAS to be off when tweezing. It adds so much vibration that when I am looking through the microscope, everything becomes very blurry and almost unseeable (I wanted to say invisible, but that doesn't mean what I want it to mean). - Anthony Salvagno
It is utterly impossible to find the trap in the microscope with the camera and I also have no easy way of moving it around. I managed to trap some gunk at some point and I tried to use that to determine where the trap was in relation to my tethered particle. I then tried to block the trap so the gunk would diffuse away but it didn't and the resulting process ended in my giving up. - Anthony Salvagno
I also tried to use my phone camera to find the trap through the eyepiece but keeping that thing steady is impossible without some kind of mount. I'll ask Andy if he needs the other camera today and I will try using that one. - Anthony Salvagno
Anthony Salvagno
Notes for working with the tweezers go here
We are working on position ramp module. We start piezo at 35 and go to 39 in increments of 0.001. - Anthony Salvagno
Pranav's idea for focusing: Use the sum signal to determine the proper trap alignment. Determine sum with nothing in trap and then place trap over specimen (bead/tether) and adjust trap accordingly. - Anthony Salvagno
Anthony Salvagno
Any additional comments here:
Steve says: We need to get the shutter and two foot switches AKA foot pedals. Maybe uniblitz shutter company also sells the foot switches? - Anthony Salvagno
Steve says: Call Andor about purchasing a replacement fan - Anthony Salvagno
Anthony Salvagno
Ok I've flowed 0.5um beads in a perfusion chamber (not made from tape). I will begin the process.
First I clean the microscope of oil from the previous experiment. - Anthony Salvagno
Next I prep the microscope for this experiment. Run video software, align condenser, adjust lighting, etc. - Anthony Salvagno
I had to adjust the condenser a lot because it was really out of alignment and focus. I was getting all sorts of weird lighting effects. Kinda cool - Anthony Salvagno
Now I will be turning on the laser and running the software. - Anthony Salvagno
After thoughts: DON'T use the perfusion chambers anymore. It seems there are some weird things going on. I'll use the double-stick tape method from now on. - Anthony Salvagno
Anthony Salvagno
Power Spectrum Analysis
I am doing this alone. Pranav is not here. I don't think he came in today because I do not detect him. - Anthony Salvagno
I hate unzipping. Nothing works when I do it, but every time Koch works with me nothing goes wrong. Now I can barely see the laser spot. I am not doing anything different from what I have previously been doing. - Anthony Salvagno
Pranav must have eliminated back reflections very well. - Anthony Salvagno
Nevermind. Ok so I need to move the trap into solution some because I can't view beads when the trap is in focus now. - Anthony Salvagno
Fuck! It is just one thing after another. I can't take this. I can't find beads now. When I did see beads, the trap was nowhere near the lowest point the bead would diffuse to. This is so fucking annoying. - Anthony Salvagno
ok i finally got everything back in order. Maybe it has something to do with the perfusion chamber. I'll do a little experiment. I will go make some new samples. I will do same concentration as now in the double stick tape chamber. I will do more concentrated in both chambers as well. - Anthony Salvagno
Koch came in and helped me out. We realized that the telescope might be misaligned. Koch adjusted one of the lenses (not the steering lens) and that made it a little better. - Anthony Salvagno
I spent about 15 minutes trying to adjust the mirrors so that the trap looked better. Basically I focus in and out and look at how the light from the trap focuses (its movement). When the trap focuses symmetrically I say job well done. - Anthony Salvagno
After trap alignment, I moved the trap with the steering lens. The Sum signal from the detector wouldn't move no matter what direction you moved the trap. Prior to my adjustment, after Koch's adjustment, the sum signal was stable only in one direction (maybe y?). - Anthony Salvagno
Caveat: The sum would change slightly in x, but only a little bit and I think this will be fixed with more adjustment. - Anthony Salvagno
I'm still not confident in my optics skills so adjustments I make actually make me nervous. It'll come though. - Anthony Salvagno
Anthony Salvagno
i'm doing one final test. i added the feed of this page to my notebook for today and want to see how it handles a post and comments
here is a comment - Anthony Salvagno
one more - Anthony Salvagno
uno mas - Anthony Salvagno
Anthony Salvagno
More Tweezer Power Spectrum Stuff
Evernote providing problems with embed. I'll just work around it. - Anthony Salvagno
Goals for today: 1- realign as best as possible beam expander, 2- do power spectra at different beam expansions (can be set on beam expander itself), 3- kick ass as always - Anthony Salvagno
Droid test - Anthony Salvagno from Android
Ok I've fixed the alignment as best I can. It seems to focus in and out symmetrically instead of the asymmetry you get from a non aligned trap. Time for power analysis. - Anthony Salvagno
I'm having trouble trapping beads - Anthony Salvagno
ok i'm trying again with small beads. After talking with Koch it seems that small beads are easier to trap than large beads. I'll test the theory. - Anthony Salvagno
I can't trap little beads now. Hmmm. Something is wrong with the tweezers and I'll have to work with Pranav to figure it out. - Anthony Salvagno
(SJK Note: Was able to trap after anthony, so must have been bad luck.) - Steve Koch
Anthony Salvagno
for 2nd fit above power at 45mW sum at .78 -
for 2nd fit above power at 45mW sum at .78
for 2nd fit above power at 45mW sum at .78 3rd power at 100mW sum at 1.53 - Anthony Salvagno
Anthony Salvagno
Anthony Salvagno
Anthony Salvagno
Anthony Salvagno
Just got one and love it - Jean-Claude Bradley
Now I'm in the envious early-adopter later-on situation .. my G1 / HTC Dream dev phone is doing just fine, but I'm so tempted to upgrade to a Droid :) - Andrew Perry from Android
I've been in desperate need of a new phone and my old phone does all the things that smart phones do, just very poorly. Now I get to live in the present. - Anthony Salvagno
Can I ask if people considered nexus one at all? - Andrew Su
I did consider the Nexus One, but it is still uncertain if Verizon will be selling it with contract or if Google will just sell a phone compatible with Verizon's network. Also I got the buy one get one droid free deal and split the cost so it worked out cheaper for me in the end. - Anthony Salvagno
Anthony Salvagno
Interesting... I'll have to dig a little deeper. - Anthony Salvagno
Anthony Salvagno
Idk if anyone read this post, but at some point I talk about making shirts for the lab with proceeds going toward lab materials and experiment purchases. I think this is an interesting concept (assuming people buy t-shirts) and I would be willing to do designs for a number of labs wanting their own t-shirt shops. Maybe even some open science/open notebook science shirts... - Anthony Salvagno
Steve Koch
Michael Nielsen Colloquium at U. New Mexico ... Questions still going 40 minutes later!
Show all
In 3.5 years here, I have never seen anything close to this! Props to Michael for coming back here to infuse optism in our department. Props to our department for being so receptive to new ideas. Also, thank you a bunch Michael for the mentions during talk ... many tenure voters listening :) - Steve Koch from email
During the questions grid, someone asked Michael what he thought about big NSF projects for open data (not sure which one he cited exactly, or whether I'm getting the question right). Michael's answer was very enlightening: He cited half a dozen very successful projects that were started very quickly and "lightly": Galaxy Zoo (two weeks?), Polymath (one day), twitter, facebook, etc. He... more... - Steve Koch
Indeed. This an important part of the web 2.0 philosophy that I think is often forgotten in science 2.0 projects. A large percentage of projects are going to fail, but if you have spent a large grant on a project then you cannot easily just shut it down. Also, it is easier to argue for funding for something that is already partially successful. - Matt Leifer
The Q&A was very exciting and the shoutouts made me proud to be both an open scientist and in KochLab. It was great having Michael here and I look forward to the next FriendFeed/open science talk we can host. - Anthony Salvagno
Sorry to say, no. We never do that at our colloquium, and it didn't occur to me to think about it. My bad. - Steve Koch
Graham, I think you had the right idea -- it's just our physics department weekly invited talk. We have funding to fly them in and host them for a day. As opposed to the Gordon page you linked to, our seminar is completely open to the public, and there's no non-disclosure agreement. Every department I've been to is the same for the weekly colloquium. I don't think there'd be objections... more... - Steve Koch
Glad I was able to make it, Steve. It was a pleasure to meet you in person! - Michael Nielsen
On funding / doing things in a lightweight way: more examples are the arXiv (first live version was done on a timescale of weeks), and even GenBank, which got started on a shoestring. It's true that some successful projects require lots of funding - the Sloan Digital Sky Survey is an outstanding example. But there most of the money is being spent on the instrument and infrastructure,... more... - Michael Nielsen
Steve Koch
Really great methods video by Andy and Anthony! -
Really great methods video by Andy and Anthony!
Until very recently I didn't even know they'd made these videos! I had nothing to do with this video and I have to say it's very well done. I'm looking forward to the day we find out it helped out another lab somewhere around the world! - Steve Koch from Bookmarklet
I love making these movies in many ways (too many to list). If file sharing was easy I would offer services to all people although I guess there is DVD and thumb drives. I think JC Bradley and others would get use out of my services. Was the music awkward and made you regret living this time? - Anthony Salvagno
BTW I can now make my PCR video. Which I will in due time. - Anthony Salvagno
No, the music was surprising and great :) - Steve Koch
Yea I wanted to keep it low key just for some added sound. - Anthony Salvagno
Thanks. I like music in the background, as just talking is quiet and boring. The presentation we made for you was weird but fun. I've been trying to get it right ever since. I think I have 2 successes and that one failure so far. - Anthony Salvagno
very nice - if you put a few of these together you might be able to submit them to JoVE - since you are doing all the editing maybe they would give you a fee waiver for making it OA - Jean-Claude Bradley
Great idea, Jean-Claude! Andy/Ant, I like that idea. Even without the JoVE possibility, I liked the idea of a start-to-finish gliding motility assay procedure video. I especially like it since it's such a finicky assay and I've seen many people have inconsistent results with it, but you have it working very well. Working with Emmalee may be a good way to do some of the filming. Could... more... - Steve Koch
Yea I could make that happen. I've been wanting to do stuff like this for a while as seen in other KochLab/my youtube videos. JoVE isn't such a big deal. If we do it fine, but I think Youtube or Vimeo could reach a much larger audience (even though JoVE is open access). - Anthony Salvagno
OA means you can do both remember - get yourself a DOI _and_ an audience ;-) - Cameron Neylon
Sure thing... remember "Sharing is caring!" - Anthony Salvagno
A good reason for using JoVE as well is that you can get a peer reviewed paper out of it - Jean-Claude Bradley
This is true and a good reason! - Anthony Salvagno
I'd forgotten that Andy already had a really nice short article for this process. The video just takes it to "11" : - Steve Koch
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