Anthony Salvagno › Comments

I should also forward kudos to Michael Nielsen, as Alex recently read his book "reinventing discovery..." and was inspired to ask this question. - Steve Koch

I would LOVE to talk to this person about library school, science librarianship, and data curation. LOVE LOVE. dorothea.salo@gmail.com - RepoRat

I was in his same position about 3-4 years ago and now I feel like I'm in a position to make an impact, so I'd be happy to talk to him as well. I believe you have my email, so feel free to pass it along. - Mr. Gunn

Thanks Repo & MrGunn -- Hopefully Alex will contact you if he wants. If you're comfortable, I was also hoping for some really great public discussion on this thread. I think we'd learn a lot from it! - Steve Koch

Software development is another possible career path to explore. After all, those labs & libraries & startups will need people with both good science knowledge and good software skills to help build those open systems. - John Dupuis

Btw, I get science people contacting me occasionally to talk about library careers and I definitely tell them it's something worth exploring. - John Dupuis

Well, the library school I teach at (U Wisconsin-Madison) is launching a science-librarianship track. For data curation specifically, we probably aren't the place to go; Illinois and UNC-CH are. (Illinois has a well-regarded distance-ed program; I don't know what UNC-CH does.) That said, I do my best, and I have former students doing well -- frex, one is at the National Library of... more... - RepoRat

If he doesn't have any particular research interest -- if there are no research questions that keep him up at night -- then he should avoid grad school, at least until he finds such an obsession. Grad school is no place for a human being and the only way to make it worthwhile is if you are there because you have found your vocation. With similar reasoning, unless something "clicks" and he discovers that kind of connection with librarianship (/other field), I'd avoid rushing into library (/other) school. - Bill Hooker

At the end of undergrad, one is very young -- my usual advice is to go out and try a few things. E.g. get a job as a research assistant; if he's really brave, apply for every such position he can find and bring up Open Science in the interview. Are there library internships? Entrepreneurial avenues are more difficult to square with an Open Foo approach unless you are in the driver's seat -- starting your own company and taking your own risks. - Bill Hooker

I guess all of this depends on his personal situation -- married, kids, etc? If he can travel freely for work and can afford to spend a few years not worrying too much about making ends meet, it will be a lot easier for him to knock around a bit and gather intel for a better decision making process. - Bill Hooker

Library school is a professional program; one escapes with a master's. (Going on for a Ph.D in LIS is a mug's game, I agree.) So the calculus Bill is talking about is just a tiddy bit different -- but it's STILL important. Opportunity cost is not to be sneezed at. - RepoRat

"Grad school is no place for a human being" - Bill Hooker. This is going in my next presentation. :) What is he interested in in physics? If it is theoretical, I might be able to advise him on possible people to work with. - Andrew Lang

first: find some scientists who are interested in open science. it's not the no-brainer you'd think it could be. - henry

I think the algorithmic handling of data provides good perspectives for people with an open science slant, and so does the creation of interesting citizen science projects and of open educational resources from open access, open source and open science materials. I am testing those waters myself and will gladly respond to any questions about that. - Daniel Mietchen

Henry's point is what I was clumsily getting at when I said "bring up OS in the interview". You can still count on both hands (and maybe a foot) the number of labs where OS or ONS is openly on the menu, so he may have to make rather than find an opportunity. - Bill Hooker

Thank you everyone for the good thoughts! Hopefully Alex will join the thread (I encouraged him to join FriendFeed to do so). Ironically, I'm at an e-science conference that prevents me from having wifi or cell coverage during most of the day! - Steve Koch

Perhaps they have a different idea about the "e" in e-science. Wonder what that may be. - Daniel Mietchen

Hey all, this is Alexander. I wasn't expecting such immediate results from contacting Dr. Koch, but this is great. I had thought along the lines of software/online tools and entrepreneurship, but not about library school. In terms of research interest, I've switched to applied mathematics from physics - I think that modeling ability will be increasingly important in the future. I also... more... - Alexander Barron

If I expand on what Bill was saying - if you want to make an impact in open science then there is the looooooooooooong game...actually getting into research and hoping to make a small difference along the way and a gradually bigger difference as you get there. This is tough, and unless you have a real burning passion for research then I'd advise against that (and I'm effectively tenured faculty so take this with as much or as little salt as you wish!). - Cameron Neylon

The shorter route is getting into a place, generally a company, startup, or resource like a library where you can make a real difference today. In terms of data handling and modelling there is real potential in the "library space" today. Most librarie aren't realising it but the folks around here can definitely tell you what the options are (and aren't at the moment). Equally there are... more... - Cameron Neylon

Re libraries: frankly, what most of us who do this in libraries now are doing is making the case for what we do so that we can be given resources and time to do it. If schmoozing isn't your thing, wait a few years for libraries to catch up -- or take your MLS straight into a research context (which is happening!). - RepoRat

Alex: I am currently at a conference with two UNM peeps from the Library, both are heavily involved in using computation / software / online tools for "connected science." When we return I can put you in touch with them, particularly Rob Olendorf, and you could get an idea for the potential the Library has to make a huge impact on ALL areas of research--by enabling the kinds of things... more... - Steve Koch

I have a couple of friends, one with and one without a PhD, who went from bio research to library school. I can put you in touch if you want to collect different perspectives. - Bill Hooker

Heard a LOT of caution at dinner about pursuing MLS degree without science degree as far as hiring concerned.lots of competition and biases that won't go away soon. - Steve Koch from Android

I'm not having ANY trouble placing students with science backgrounds. And I don't even run a whole data-curation program! (It should be said that my students are pretty badass.) - RepoRat

To clarify, I meant without advanced (PhD) science degrees, which I think Repo inferred. Sooooo, there's disagreement. At least at first, it seems that those of us with science PhDs working in research view it as a long road to slow change. But even some (not all) of those in Library (with or without science PhD) view science/research as a good path. One person at dinner pointed out... more... - Steve Koch

It seems to me that in order to get open science moving at more than a snail's pace, some preliminary system has to be made. Open science has to be at least somewhat viable as an alternative to "old" science. People need an incentive to offset, at least partially, opportunity cost ("publish or perish"). I've seen a few science majors veer off from science when graduating after seeing... more... - Alexander Barron

It sounds to me like you'd benefit from talking with some people like Carl Boettiger, Mark Hahnel, and perhaps some people at Mendeley who are close to your career stage, but a bit further along. Mr. Gunn (above) is at Mendeley, but I think those others haven't appeared on this thread yet. Your thoughts are well-aligned with Michael Nielsen and others as far as the incentive system goes... more... - Steve Koch

I've been thinking about this a lot lately and would love to brainstorm a project that gets us to the open science tipping point faster. Currently I'm trying to figure out how social media and the web can be used as instant reward. Basically getting hits to your open notebook would (hopefully) give you the same feeling of reward as reads on a published paper. And I know I've been getting much satisfaction from the hits in my notebook. - Anthony Salvagno

Ant: Alex is still around campus I think and would probably enjoy meeting you. Also agree about rewards. You and I and others get tons of personal rewards. Many of those will continue, such as the reward from doing science better by sharing. Others are transient, such as recognition because it's new will fade as open science practices take over. But the _official_ rewards are still... more... - Steve Koch

Can u include any more info for ur dossier? I can give you the analytics for my notebook. - Anthony Salvagno from Android

After reading this, I'll ad a section to my CV: 'peer-reviewed methods' right after 'peer-reviewed original research'. This new section will also have download stats to our software at http://buridan.sourceforge.net (as soon as our paper describing that package is out). - Björn Brembs

"Use as many metrics to back up your contributions as you can." Anyone have metrics they'd want to help make their open science case that they can't easily get to now? - Heather Piwowar

@Ant: Yes! Dan was extraordinarily helpful with advice and letter for me. He's one of many generous, helpful, and successful open scientists out there & why I know regardless of my own tenure decision, open science contributions will be rewarded. Fundamentally, it makes for much, much higher impact science and since most scientists want that, the reward system will come around. - Steve Koch

@Heather the system you've been working on is great! Every tool that is developed in the coming years needs metrics. As Nielsen points out in his book, many of the most successful endeavors (such as the Mathworks competition and fold.it) provide instant feedback and scoring. Some very important features of those successes are (1) numerical score, (2) instant scoring, and (3) EASY... more... - Steve Koch

Steve, very useful, thanks. Nope, total-Impact doesn't have any relative metrics yet, we're trying to figure out the best way to do it... - Heather Piwowar

Agreed. - Graham Steel

See also: http://friendfeed.com/treeofl... - Bill Hooker

Yeah, I wondered about that. I think Anthony means something like "let the cat out of the bag". - Bill Hooker

Hey Bill, here's a response to you from the other thread: Hey Bill -- I've read a lot of those studies. Heavy water tends to stabilize biomolecules and biomolecular aggregates. Microtubules are very susceptible to this stabilization, and thus heavy water toxicity to eukaryotes resembles anti-mitotic drugs such as taxol that stabilize microtubules and prevent cell division. Lewis'... more... - Steve Koch

I think by "jump the shark" he meant I don't have any awesome idea to mention yet. I don't think there's a cat in the bag--a reliable metric is something he's searching for. - Steve Koch

Presumably [D+] depends on pH? Perhaps an organism adapted to low pH might be more susceptible -- or the effect of pH on any organism or system might be altered by D levels? - Bill Hooker

You can D-replace prokaryotes... what would happen if you did that for 100, or 100 million, generations, then switched 'em back to regular water? Can you H-replace 'em using D-depleted water? I'm trying to come up with ways to adapt some enzyme or other to D, wondering if you could get it sensitive enough that adding D to a system using that enzyme would act as a switch... - Bill Hooker

(P.S. have I mentioned how awesome this project is? Because it is seriously awesome. This is what I thought it would be like to be a scientist, when I was a kid and had no concept of grants and reviews and tenure and all that shit. Following this project in an Open notebook makes me feel like a kid again.) - Bill Hooker

yes pD (i.e. -log[D]) depends on pH, although that is an even bigger can of worms than I think I realized until now. Because D-O is a stronger bond than D-H, the pD of pure D2O is about 7.4 (see, e.g. http://www.madsci.org/posts...). So even though the ratio of D to H in "normal" water is 1/6600-ish, the ratio of free D to free H is even lower.... more... - Steve Koch

Well, that big problem aside (I don't think it accounts for our results, since heavy-oxygen water also showed a gliding speed affect. I hope), I am still so confused that I am losing confidence that adjusting the "pL" that way is "correct." Furthermore, I am not even sure there is a "correct" way to do it, since H->D affects different bonds differently. I am thinking that for Anthony's... more... - Steve Koch

I love your idea about using acidophiles to amplify an effect of deuterium-depletion! (http://en.wikipedia.org/wiki...) Although I am too confused to know whether it would amplify or attenuate the affect. There must be plants that are acidophilic (I remember as a kid someone telling me that pine trees make the soil more acidic to fight off competitor plants...not sure if that is true). I would love a reason to study cactuses or archaea :) - Steve Koch

And thank you Bill for saying the project is awesome and for your encouragement and ideas since the start! I share your sentiment and feel like a kid scientist again too--whether we can do it and still get tenure (me) and money (us) remains to be seen, but I decided WTF, but probably wouldn't have pursued it without your interest. When we publish in PLoS ONE you should be a co-author if... more... - Steve Koch

Sorry, I'm late to the show, but all this notebooking has actually made me less accessible than I want to be. Also sorry for my improper use of jumping the shark. I meant it as you all interpreted it and not as it is actually defined. Oops! - Anthony Salvagno

Also thanks everyone for your great suggestions and comments! This project and my new notebook has raised my spirits to levels beyond my imagination. Like Bill and Steve stated I feel like a kid again too (even though I'm relatively young) and I get to report on really cool basic science that surprisingly hasn't been very deeply investigated. This project is literally like "I wonder what would happen if..." and then we get to see! Very exciting stuff. - Anthony Salvagno

What do you mean? Do you mean link to documents in each Google Doc that I link to through twitter? - Anthony Salvagno

I mean if I happen to find that particular doc and I don't know about your project it isn't clear what the context is. If you had a link to a page explaining how all these small docs are connected it would provide the context. - Jean-Claude Bradley

I see what you mean. Right now I wouldn't know how to effectively do it because Docs doesn't have very good connectivity with itself. I'm just tweeting everything to hopefully get them google indexed. I could have one document that links all the stuff in the project. Or I could have a folder for each experiment and put all relevent documents in that folder. Then have a note that... more... - Anthony Salvagno

JC, is that permanent, or just to bootstrap the journal in the first three years? - Egon Willighagen

Egon - good question - I didn't get the impression that it was temporary but Cameron might know more - Jean-Claude Bradley

Ironically, I have found that Google Docs are not indexed well (if at all?) by Google. Were you not getting good indexing on your wiki? - Jean-Claude Bradley

I actually was, but some things are too tedious to link through and Google Docs allows me to do things much faster. It helps that I'm always logged in there and I use them to set up my reactions and other little things. Yea the reason I'm tweeting my notes is because Google doesn't index Google Docs (although some pages from like two years ago said they enabled that. I read somewhere... more... - Anthony Salvagno

When you say GoogleDocs are you talking about the word processor? If you mean Google Spreadsheets then I agree their functionality cannot be duplicated with a wiki. - Jean-Claude Bradley

I too love Albuquerque. Never been there myself, but my good friends from the band, Prefab Sprout put Albuquerque on the global map with:- http://www.youtube.com/watch... CHORUS #hotdog #jumpingfrog #Albuquerque [caveat, this one was probably filmed in the UK, but so what] - Graham Steel

I used to hate Albuquerque, but I've slowly grown to at least not hate it. I met my girlfriend here so it can't be that bad. Also that post is what people from here say about this place. SMH. - Anthony Salvagno

Graham, if you ever make it out here, you definitely have at least one place to stay! Ant and I will take you out for beers every night. Or morning, if you're on Scotland time, which would be perfect. - Steve Koch

Can I have this in writing? Oooh, I already have !!!! - Graham Steel

What do you mean by conscious? I think if we make AI's that we can interact with they might have emotions, like robots that act as pets. They could just be algorithms that give the impression of emotions though. - Anthony Salvagno

By conscious I mean ability to feel pain, not just mimic the behavior of organic life forms in pain - Jean-Claude Bradley

I just liked the imported from detroit part. - Anthony Salvagno from email

You will like it more once they get the robocop statue. - Steve Koch

BTW what was the giant metal arm? - WarLord

Joe Lewis, http://en.wikipedia.org/wiki... http://www.flickr.com/photos... - Steve Koch

Thanks Graham. It would be nice for this stuff to get out to people who don't already know of tools like this, so I'll take all the help I can get! - Anthony Salvagno

Wordpress would not accept the file in embed terms, so am uploading it to YTube, linking to the source, but of course. - Graham Steel

ok, i was going to upload to youtube as well. - Anthony Salvagno

"Your file has been uploaded. We are now processing the video..." url is http://www.youtube.com/watch... - Graham Steel

Why is it 7min long? lol. - Anthony Salvagno

At least you didn't sing this time... - Graham Steel

ouch... - Anthony Salvagno

But in all seriousness, I think it added the movie twice to the same file, because my move was a little over 3 mins. Unless you remixed the end of it... - Anthony Salvagno

well, let's see, am about to blog it. - Graham Steel

Hey guys- sorry for being late to the party here. Graham, the embed code can be a bit finicky- you need to paste the code into the "HTML" tab in wordpress- it won't work if you paste it in the "Visual" tab. Really sorry for the inconvenience! I don't know when that started happening- it used to be fine in both tabs. - Alan Marnett

WP seems to be a bit clunky generally. Got there in the end, so it's cool. http://www.science3point0.com/mcblawg... - Graham Steel

Hey Graham, thanks for the help. It seems the video and audio from the movie are not linked very well via your youtube upload of the benchfly download and may be a source for the extra length. I'm uploading the video to youtube now and you can try embedding that when it's done. I'll send the link. - Anthony Salvagno

I think the video will be here when processing finishes: http://www.youtube.com/watch... - Anthony Salvagno

Thanks Graham- if you guys are having trouble with the YT situation, you may want to try embedding the BenchFly vid into the HTML tab in wordpress- may eliminate the problem or at least let you know if it was a problem with the download/upload process. - Alan Marnett

I'm not sure that without the resource Google can provide that that will take off either. Still too niche and very hard to build a good enough interface. Anyway will try to blog later when I have time... - Cameron Neylon

I think its our last best hope... - Benjamin Tseng

So you think we need to crash and burn four times before we'll get there? ;-) - Cameron Neylon from twhirl

I've seen a lot of comments this morning about Wave's demise, but can't see anything official from Google either on the Wave site or on their developer blogs. Was there a press release or something I've missed? (EDIT: see http://googleblog.blogspot.com/2010...) - Dan Hagon

Having just run a Webinar on the topic of Wave, I have spent some time recently looking at the tool. I think the concept behind Wave was entirely sound. The interface however was simply not intuitive, not in the way that (for example) Twitter's interface is. The system clearly worked well for certain populations (programmers, engineers, etc.) -- those who are spatially or... more... - Jill O'Neill

We used to fairly regularly do a 2-stage PCR for introducing tricky site-directed mutants. This involved using the products of 2 PCR reactions in the 1st stage as the template for the 2nd stage reaction. It usually worked great (more effective than the QuickChange kits for making the mutants, although a bit more time-consuming) - Jason Winget

(1) yes; (2) depends -- if you use the same primers again, it's rather like adding enzyme and doing more cycles -- and as you'd expect, the noise comes up faster than the signal in many (most?) cases. But if you nest the primer pairs, or at least use one nested primer, it should be OK. - Bill Hooker

P.S. Wikipedia is surprisingly bad on "nested PCR", avoid. - Bill Hooker

The reason I wanted to use it was in case of damaged template DNA and I figured doing it like this was a way to have a template strand that has no nicks or structural damage in it. Sequence modifications are ok in my application and I only really care about length and integrity. Thanks for all the insight! - Anthony Salvagno

@Bill: What is nested PCR? My capabilities lie only in basic PCR. - Anthony Salvagno

Yea, thanks for the condolences though. I won't let it stop my open-ness though! - Anthony Salvagno

that's bad shit, sorry to learn about this. - Graham Steel

Bummer. I hope the perp gets genital chiggers. - Bill Hooker

Ha @ Bill! That must mean you're left handed, trying to reduce chance of contaminants falling from your hand into the unused tips ;) - Steve Koch

I used to do it in order like that, and I was pretty anal about it. I got bored and then started doing the designs. I'm anal about those too. - Anthony Salvagno

Graham you can do it too. - Anthony Salvagno

Well, you can count me in then :) - Graham Steel

Awesome! - Anthony Salvagno

Great idea, Ant. As an example, I would love to see a professional-style video about the ONS Solubility challenge, showing live screenshots of the wiki, google docs, lulu, etc. And with comments from Jean-Claude, Andy, and others. (Apologies if that video already exists :) ) - Steve Koch

Off the top of head. On a regular basis (once or twice a fortnight) I check out YouTube and Vimeo for any new content about Open Science and spread the word about any new good stuff. Afaik, these are two resources that are very popular in general content of anything terms - LOL. I hadn't come across BenchFly until today, but it does seem like a much better niche 'target audience' video... more... - Graham Steel

As Anthony and I talked about, I think this would be a lot of fun to put together and I'd be happy to help out in any way possible. I think the BenchFly audience would find this really useful and would be interested in trying out the resources that are featured. - Alan Marnett

Ding ding. Absolutely, Alan (hello). Thank you for getting involved in this !! - Graham Steel

beam shape looks like an oval (fatter in one direction then the other). we are cleaning the slide and the lenses to make sure it isn't the oil - Anthony Salvagno

we captured a bead and are doing analysis at different power levels - Anthony Salvagno

after some time the focus of the trap moved (as it usually does) and some of my data is in this new position. that probably influenced bad data. - Anthony Salvagno

also I've noticed that at high power levels the corner frequency shifts and that the fit isn't very good making my measurements very inaccurate. - Anthony Salvagno

all of a sudden, all the beads stuck to the surface. I can't find a single free floating bead. It was very sudden too. I was actually trying to grab a free bead (which at the time there were NO stuck beads), next thing I know every bead is stuck to the surface. - Anthony Salvagno

part 2 of tethering, diluted beads 1:800 - Anthony Salvagno

there is an indicator on the software that says input saturated. what does this mean? - Anthony Salvagno