Anthony Salvagno › Comments

I'm always looking for the chance to whip out Illustrator and flex my pen tool! - Anthony Salvagno

Sure - as long as clicking on the logo leads to ONSclaims page for an explanation more logos would be fine - Jean-Claude Bradley

I'm currently doing a mash-up of this one.... - Graham Steel

What does that entail? - Anthony Salvagno

Music. I opted for Daft Punk:- http://steelgraham.posterous.com/koch-la... - Graham Steel

Now that is awesome and hilarious. Thanks for that! - Anthony Salvagno

Andy, Anthony, Graham, that made my night. I am still laughing! Jean-Claude, thanks for that link, I'm going to look into it. - Steve Koch

Hey, glad you guys liked this ;-) I've only got basic editing s/ware and my PC was playing up when I mixed this one. I pretty much chose a random effect and liked how it auto-generated the colour visuals. Also thought Robot Rock was a cool choice of music. I love playing about with things like this. - Graham Steel

Plus it goes with our little robot on the fridge. - Anthony Salvagno

and you can order that latte with amazing accuracy. - Mickey Schafer

Please delete this post - it could be infectious. All it takes is for a few undergraduates to get wind of this and you could tip over the whole apple cart. - Jeremy Leipzig

Too late, don't tell my PI (Steve Koch) but I'm leaving the lab now. I knew I didn't have to work for free for a chance to be successful! - Anthony Salvagno

with or without a frothy introduction... - Mickey Schafer

Why do mathematicians need PhDs? Discussion from diybio.org: http://groups.google.com/group... - Mackenzie Cowell

@Mark, another idea before its time: http://testingtfv.blogspot.com/2007... - Steve Koch

Is your data licensed as CC0? - Steve Koch

Maybe I shouldn't incite that argument on this thread. But very cool data. - Steve Koch

That looks great, Anthony. Bookmarked and I will keep an eye on this :)) Nice one, mate. - Graham Steel

Did you html tag that? - Anthony Salvagno

nice Anthony! - Jean-Claude Bradley

If people have ideas for a good t-shirt design but are not going to use them in the contest, maybe they could share them here. I will start by giving an idea for a graphic: lots of individual stick figure scientists standing on individual cubes ("data") of various sizes. In the center, a *giant* human or robot figure made up of cubes like the individual ones and a bunch of stick figure scientists *standing on his shoulders*. Please feel free to use this idea or any variation of it. - Lisa Green

And what a fantastic prize !! A neat tool for this kind of stuff is http://www.zazzle.com/create (although there are many others out there of course). No log-in required until saving ideas. - Graham Steel

ooh I have a long standing idea but I need a graphic designer to work with...actually its probably simple enough that I can mock it up myself but it could do with some attention from someone who knows that they're doing :-) - Cameron Neylon

I could work with you Cameron. I would love to submit an image, but have drawing block right now. Let me know your idea and/or show me your simple mock up and let me see what I can do. - Anthony Salvagno

Also @Lisa or anyone else who knows, can you submit more than one design? I had an idea over the weekend of a globe with a string of binary circling it in a double helix pattern. I thought it wasn't that good and didn't do anything with it, but now I think it seems ok. What do others think? - Anthony Salvagno

@Anthony You may submit as many designs as you like. - Lisa Green

@Neil We are changing that! There will be a blog post on Science Commons tomorrow announcing the rule change. We've decided to make it open to anyone, but if the winner is not in the US we may work out a different prize. - Lisa Green

hurrah for internationalism! - Rob Syme

Hurrah indeed! Rule change is official http://sciencecommons.org/weblog... - Lisa Green

Anthony has been drumming up some collaborators and is having fun. Made me _finally_ realize, though, the irony in having a prize for a single individual in a logo design contest for ScienceCommons! Not a big deal, though, teams can nominate someone to be their traveler--and Anthony would be a good nominee :) - Steve Koch

Ha--good point Steve. But sharing a hotel room can be awkward for teams. Not to mention airplane seats. - Hope Leman

Here's Carl's friendfeed: http://friendfeed.com/cboettig - Steve Koch

Carl says that KochLab students' ONS on OWW partly inspired him to start his own open notebooks. That makes me happy! Props to Carl & Anthony, Larry, Andy, Brian, ... - Steve Koch

One of us! One of us! :-) :-) This makes me very happy. - Bill Hooker

"I'm an Open Scientist and this is what I do!" I agree with Bill. This makes me very happy! - Anthony Salvagno

nice! Are these examples of theoretical notebooks? http://en.wikipedia.org/wiki... - Jean-Claude Bradley

I added his two notebooks under the theory section. As I understand it, it's theory + computational modeling. Computational modeling can be in either in my opinion--the kind of results generated are probably more like lab experiments than theory. So, probably there's need for far more than two categories. Plus, that section of notebooks examples is getting too big! That's a good thing,... more... - Steve Koch

Thanks for adding Steve. I think computational is more closely related to theoretical since there isn't a clear tradition of what constitutes an "experiment" and how to record it like there is in experimental sciences. I don't think the Wikipedia editors will allow the creation of a separate page just for examples of ONS but we certainly can put them at the end if some more examples get collected. - Jean-Claude Bradley

I'm surprised that wikipedia editors have been harassing you, Jean-Claude! I've started many articles of questionable significance and never had anyone mark them for deletion. (For example: http://en.wikipedia.org/wiki...) Someday I think the article would have to be changed to "notable open notebook science practitioners," but I don't see why we... more... - Steve Koch

Carl, you should pipe in on whether your computational work is more similar to theory or experiment! I think the whole spectrum of science is much harder to put into categories than Jean-Claude or I expect. I see computational as "experiment" often. For example, I collaborate with some people doing molecular dynamics (MD) simulations. It surprising how much like experiments it is.... more... - Steve Koch

Steve - it was actually not that easy to get the ONS entry on Wikipedia to not be deleted or redirected - it took 2 tries and lots of documentation to appease the editors - see the discussion page. I guess you don't know how it will play out until you try. - Jean-Claude Bradley

Sounds like an overly-aggressive guy was obsessed with deleting your article? No rush for anything, but if you think it'd be better with a sub-page of practitioners, I'll create the page someday. - Steve Koch

Steve - I think it is actually much more difficult to capture the information for computational experiments because it is so easy to generate immense amounts of data. If every tweak is "an experiment" you would end up spending more time documenting what you do than actually doing work. When we did docking we did approach documenting it like a physical experiment so that there is enough... more... - Jean-Claude Bradley

Interesting, Jean-Claude. And I hadn't been thinking of the legal definition (and I also don't feel like thinking about that now :) ). The MD simulations I was thinking of actually took significant time on a supercomputer for each tweak (I think). So, that would be practical to record everything and treat it as an experiment. Clearly, though, as you say there are cases where it would be... more... - Steve Koch

And perhaps another dimension for how much tacit knowledge there is. I think tacit knowledge may be what I had in mind when I said computational science may be easier to do as ONS. Certainly there is tacit knowledge in computational science. But listening to John Hogenech at ScienceOnline2010, I learned that it's possible for one group to exactly replicate another group's computations,... more... - Steve Koch

For Andy's gliding motility assays in our lab, I'd rate it (1) solidly in experiment, (2) low/moderate amounts of information (GBs of image data), (3) moderate/high amounts of tacit knowledge. (Or tacit knowledge that is difficult to capture. Maybe that's what the 3rd dimension is: how difficult to capture the tacit knowledge) - Steve Koch

Interesting discussion! In my mind they are both. In the phyologenetics notebook, I am trying to extend the theory of comparative methods beyond linear models. This field is moving very quickly, and it's no use to suggest new theory without providing software that implements it, or no one will be able to use it. I also find that saving all the data from all the runs I do can be... more... - Carl Boettiger

The reason I mention the legal definition of a lab notebook is that it leads to an expectation in the scientific community that students will be trained to record their experiments in a fairly consistent way. Perhaps I have the wrong impression here but it seems that there is not a standard way to record computational/theoretical work. [In fact as a postdoc I wanted to change the format... more... - Jean-Claude Bradley

Carl - one of the benefits I'm finding from the researchers who keep Open Notebooks is learning how science is done in different fields and different groups. This is something that has traditionally been difficult to assess because notebooks are traditionally very private. Over time we're gathering data that will prove handy for discovering how the scientific process actually works - as opposed to the ideal of hypothesis -> experiment design and execution -> evaluation which is widely taught. - Jean-Claude Bradley

Jean-Claude, that's an excellent point. I've also found that most of my colleagues in wet labs are taught to keep lab notebooks in a rather precise way. I know of only a few theorists in my department who keep any kind of regular notebook, and I've never had that kind of instruction or even encouragement. In computational sciences I'm surprised how few scientists use version management... more... - Carl Boettiger

Swine Flu doesn't have the timelessness and staying power that T4 and E. coli do. You picked well. - Steve Koch

I have coli and rhinovirus on my desk but I agree. That t4 is a must have... - Cameron Neylon from Android

This is the first of hopefully many designs. I want to do the one that Lisa Green mentioned here (http://ff.im/fdN6S) and then I have a couple other ideas. Any ideas that people won't make, don't have time for, etc and want to see made let me know and we can work something out (time permitting of course). Critique away (as my blog says). - Anthony Salvagno

looks like i need to trademark that tag line :) - Anthony Salvagno

"I am an Open Scientist and this is what I do" Yo Bubba. That is a well well cool tag line and I would most definately consider using it, if I were you !! - Graham Steel

Agree on the tag line. I do like how delighted the scientist on the left is. - Steve Koch

Also, in an utterly amazing coincidence, Walter Jessen did single-molecule studies of nucleosome occupancy on PHO5 promoter a few years ago. Your project remains complementary, but it's a really good paper that I had read in the past year (and highlighted a bunch--check my references/transcription directory). But I hadn't connected any dots to know that he was the author! http://www.ncbi.nlm.nih.gov/pubmed... - Steve Koch

Suggested tagline for kochlab.com: "We pronounce it "Cook""! :-) - Bill Hooker

Steve - I'm not sure that buying and maintaining a domain name is necessary - http://salvagno.blogspot.com/ is free and available - Jean-Claude Bradley

I'm not sure either, Jean-Claude. Walter was adamant, though, so I guess I'll keep thinking about it. - Steve Koch

We also already own the kochlab.org domain so the fee is not a problem. I have been thinking of improving the site because that sort of thing is right up my alley, but I'm not sure of blogging on anthony.kochlab.org. I'd rather just post data and papers and other important stuff there. - Anthony Salvagno

Nice! How long did it take you guys to script it? The descriptions were very accurate, and easy to follow (though I guess I'm at an advantage). The instances of singing and the very first audio bit were reprehensible and made me sorry to be alive...thank you for making them so brief :) - Steve Koch

For my part I think I spent 10 minutes writing it up. I had known what I was going to say for the most part, but I wanted to write it down so I wouldn't fumble my words so much. Listening to it again last night, the music and singing is awkward, but adds a fun-loving touch. I also agree and happy that we kept it short. I also didn't want to live... - Anthony Salvagno

Andy/Anthony. Thanks very much for putting this together for me. By means of the background to this, I'm going to be doing a series of interviews for Next Generation Science and I've been in touch with Steve Koch in this regard. Koch Lab have agreed to take part in an interview and I asked for some pointers as I was interested to learn a bit more about the work they do in preparation for the interview. What a cool way to reply. As to Anthony's vocal talents............. - Graham Steel

Oh man. This is priceless. The 8 bit soundtrack is what really ties the whole thing together. The science is almost trumped by the 8 bit awesomeness! - Andy Maloney

Quite, Andy. I use OS Audacity for all my Dig recordings/remixes:- http://audacity.sourceforge.net/ And before I went digital, I had muchas fun with this 4 track analog machine http://steelgraham.posterous.com/fostex-... which produced results such as D.N.A (Demo Version) http://www.macjams.com/song... - Graham Steel

We used audacity for the addition of music because I'm still learning Adobe Soundbooth. Which is what we used for the recordings. As for my vocal talents... err I wasn't trying! - Anthony Salvagno

"As for my vocal talents... err I wasn't trying!" Does that mean that you CAN hactually sing, Anthony? Wasn't aware of Soundbooth ($199) and being Scottish, I'll stick with Audacity - LOL - Graham Steel

I agree with that, but I got the boss to pay for this through UNM. We got a bunch of programs from the Creative Suite for like $300 or something. Illustrator, Photoshop, and Premier Pro being the ones I use the most (and a lot recently) as you may well be aware. - Anthony Salvagno

Cool !! Getting back OT, in terms of Penrose and consciousness, whilst I never assume anything, are you guys referring to this guy (who I hadn't come across)? http://en.wikipedia.org/wiki... - Graham Steel

Yes Andy is referring to that guy, but jokingly. - Anthony Salvagno

Phew !! - Graham Steel

FUNNY - Graham Steel

OT - Possibly a long shot, but was it "Don't eat yellow snow"? #zappa - Graham Steel

I thought it was in response to http://twitpic.com/wxy5s ? And YES: I love it :) - Steve Koch

We usually don't put music to our experimental videos but that is a nice twist (our JoVE video does have music though http://www.jove.com/index...) - Jean-Claude Bradley

I spoke with Andy a while ago saying that I would like to publish in video form. The way the JoVE video is broken up is EXACTLY how I imagined I would do it (table of contents on the side for quick navigation). Do you do your videos in your own lab or do you outsource? I'm very interested in knowing the workflow because I love what you did there. Thanks for showing me that! - Anthony Salvagno

NICE - @J-C thanks to this http://supportpcs.co.uk/index... I've been experimenting in Dalek-ian terms. http://www.divshare.com/downloa... or http://www.divshare.com/downloa... - Graham Steel

thanks Graham - that was pretty spooky! - Jean-Claude Bradley

Did you give Camtasia a try? - Jean-Claude Bradley

Not yet. I haven't put much effort into the making of. I do think I will give it a try for my actual talk. Have you ever used Cam Studio? It's free and does the same thing (supposedly) as Camtasia and I was just wondering about the comparison. - Anthony Salvagno

I've tried to use CamStudio over the years but always had a problem with the output in a format suitable for uploading. Camtasia allows you to edit audio and video and output to many different formats. But recently I've been uploading FLV files directly to SciVee - which gives me high resolution and tiny file size. I think CamStudio outputs FLV - maybe try that and let me know? - Jean-Claude Bradley

I bet zoho is better than Google Docs. Slideshare? - Steve Koch

I thought about slideshare. I just figured it was easier to upload to google since I will have like 30 iterations of the talk by then. I guess I can post my practice talk at that time. - Anthony Salvagno

Worth taking a look at Zoho (or actually maybe even Office Live). Google version of powerpoint is awful. - Steve Koch

It is awful but in Zoho can you do an online presentation the same way as GDocs? If you upload a presentation from elsewhere GDocs is usually olk - Cameron Neylon

I use a BlackBerry to tweet & follow up with laptop but wonder whether a netbook would be easier--saw lots of them at the last conference I was at. Longer battery life and takes less time to type tweets than BlackBerry or iPhone (I'm guessing on some of these things...). - Mary Canady

I have blogger setup for my phone and I have a full qwerty on my phone so I just use that. - Anthony Salvagno

Welcome Geoff, I listen to the Nature podcast every week! I use my ultraportable and my iPhone usually. - Björn Brembs

Laptop running twhirl and Firefox - good wireless connection. If video streaming I take a reasonably good quality logitech webcam which has done me proud mostly. Try to avoid using the phone, especially when overseas - interface is clunky and o/s data is very expensive. - Cameron Neylon

A laptop since I tend to cover as much of the talk as possible when microblogging, so almost constant typing + some web browsing to find links. But I think a netbook would be ideal for that scenario with the added benefit of being less obtrusive and more portable; all I really need is Firefox. - Shirley Wu

Has anyone tried skype via hand-held? I wonder how that would work? - Jim Hardy

Jim, I have. works if you have a decent wifi connection - Deepak Singh

Laptop with Tweetdeck and Firefox; I also tend to take more complete notes for each presentation in a text editor for later consumption/blogging. - Daniel MacArthur

Carrier pigeons :) Actually, I do use Pidgin to IM directly to Friendfeed. - Iddo Friedberg

Laptop, for me. - Maxine

I used to use my laptop but now I use the iPhone - has Twitter, Friendfeed, Evernote, Skype, Safari, ReQall for voicenotes, Birdhouse for emailing/tweeting notes and camera etc. Had to get a little portable charger for it though or the juice runs out by lunchtime >.< - Sally Church

Laptop - I hate typing on smaller things. Hoping to convert to Palm Pre someday (the keyboard on my old Palm was acceptable). I've seen a lot of iPhones for FFing and twittering. - Heather