Karthik Ram @_inundata

Yay Area / ✈ in transit

December 2012

@labroides @CjBayesian @snacktavish I might have to get tattooed on my arm. I’m an expert at it.

via Tweetbot for Mac in reply to labroides

@snacktavish @labroides In that case I don’t feel bad. There is no heat in my lab and I generally work from home anyway. Couch is my lab!

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@snacktavish I once got one that said “seems like a nice guy. honestly I never really came to section. This is my second time”

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Interested in doing more open science in 2013? Apply to the @rOpenSci’s open science challenge. ropensci.org/open-science-c…

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Someday in the future I hope to find out what coreaudiod does with all of my cpu from time to time.

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@jiffyclub @bendmorris That makes more sense. My entire perspective is as an academic.

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@jiffyclub @bendmorris But I wont belabor my point. If you’ve had a more supportive experience doing this, then awesome.

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@jiffyclub @bendmorris thanks for that, I didn’t realize they weren’t funded before.

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@jiffyclub @bendmorris It’s not just lack of incentives but more that these efforts are penalized despite being recognized as important.

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@jiffyclub @bendmorris sure but ipython’s dev team is supported by a large grant. numpy creator was denied tenure. no incentives = hard.

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@bendmorris right, that’s what I mean. It’s very unfortunate that a best practices paper has to be so discouraging.

via Tweetbot for Mac in reply to bendmorris

@bendmorris If it does nothing to advance one’s career (or offer other rewards), time spent on these = career suicide. What do you suggest?

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Open science software is great but don’t waste time on it. Not much funding, sustainability, or career advancement. marker.to/UoxQwV

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“An In-Depth Analysis of a Piece of Shit”
plosntds.org/article/info:d…
oh @PLOS

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Nice article: Ten Simple Rules for the Open Development of Scientific Software
ploscompbiol.org/article/info:d… I struggle with 10 in particular.

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@matthewmccull Since you’re the one who introduced me to asciidoc, thought this package might interest you.
github.com/SublimeText/As…

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@arielwaldman ooh. an open science tumblr. I don’t follow tumblr but this might be the one to get me on board.

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@brookeborel Looks like an eyeless pig with a forked tongue from the thumbnail. :)

via Tweetbot for Mac in reply to brookeborel

Save Publishing is a bookmarklet that grabs tweetable sentences from any web page. savepublishing.com

via Tweetbot for Mac

@ctitusbrown @rmounce @figshare are these raw or intermediate data? @nics allows me to archive files in that range but not openly.

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As an EEID nerd, I highly recommend these awesome (pandemic porn) suggestions from @David_Dobbs slate.com/articles/healt…

via Tweetbot for Mac

hmason I just wrote: Getting Started with Data Science bit.ly/WNpwFT

via Buffer (retweeted on 10:00 AM, Dec 28th, 2012 via Tweetbot for Mac)

@edyong209 I went through an insomnia phase last year. I don’t envy you.

via Tweetbot for Mac in reply to edyong209

Curling up with Python Scripting for Computational Sciences. Great holiday read if you’ve been holding out for something good.

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@steveklabnik @gvwilson bummed it doesn’t have solution for diamond ring scratched my $700 smart phone.

via Tweetbot for Mac in reply to steveklabnik

. @m_holcombe Yeah, don’t know how I’d function without @Pinboard. See here for full run down macdrifter.com/2011/10/pinboa…

via Tweetbot for Mac in reply to m_holcombe

New startup idea: Emaul. Like email but delivered by an impatient lion so it mauls recipients for not responding in a timely manner.

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@distribecology @labroides So true. I suffered through it when it came out because I was on a date.

via Tweetbot for Mac in reply to emhrt_

@m_holcombe I also bookmark to @Pinboard from @tweetbot directly. All content gets crawled and privately cached so I never lose anything.

via Tweetbot for Mac in reply to m_holcombe

@m_holcombe If it’s a long read I send it to my kindle via @readability using the ` key. All articles get compiled into one doc ev 24 hrs

via Tweetbot for Mac in reply to m_holcombe

Going to gracefully address obnoxious reviewer #2’s comments today.

i.imgur.com/n9zw0.gif

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@zachwill I had this exact problem when I shared my account with my sis back in the day. Eventually just bought her an account.

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@emckiernan13 indeed. No reason this needs to be closed access. Come on @PNASNews

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@mrgunn @openscience I meant the @altmetric list. Sorry for not being clear.

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@mrgunn @openscience that’s true. The Mendeley list is clearly on par (with what one would expect) for citations. I should have been clear.

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@openscience @mrgunn Which is neither here not there. All the papers on the list are lulz, Huff Po, or Men’s Health fodder.

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Going through my old @Vimeo favorites. Love this time lapse collection of fog in the bay area.

vimeo.com/15069551

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@se_hampton This is why I love reading through papers in Ecology from the 1920/30s.

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The @NewYorker on the mess of science retractions and how to clean those up. nyr.kr/Tj8Ll3

via Twuffer

@tpoi It’s a non-profit, runs bootcamps all over, volunteer driven. All teaching material is os.

via Tweetbot for Mac in reply to tpoi

@tpoi They teach basic software skills to scientists. I just signed on as an instructor.

via Tweetbot for Mac in reply to tpoi

@MCrucifix You mean github? That’s what most of use to share R code. Or if this is just one/few scripts, use gist.github.com

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@geoffjentry yes, your twitteR package still works.

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@zachwill I <3 @extragrumpycat
Thanks for the heads up on this awesome feed!

via Tweetbot for Mac in reply to femaleproblems

@kara_woo that’s what happens when you reply before clicking on the link.

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@kara_woo So much better than a Christmas birthday.

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erikfrey free idea: expand the Pew Research Center to also study lasers.

via Twitter Web Client (retweeted on 8:07 PM, Dec 24th, 2012 via Tweetbot for Mac)

@medriscoll hopefully before the insanely long and utterly pointless legal disclaimer.

via Tweetbot for Mac in reply to medriscoll

@phylogenomics That place was always closed whenever I stopped by. Finally managed to go there once before I left Davis.

via Tweetbot for Mac in reply to phylogenomics

One of the most consistently amazing blogs this year has been @isDotR great stuff.
is-r.tumblr.com

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victoriastodden My latest blog post “Data access going the way of journal article access? Insist on open data” blog.stodden.net/2012/12/24/dat…

via Twitter Web Client (retweeted on 11:20 AM, Dec 24th, 2012 via Tweetbot for iOS)

nceas Passionate about communicating science? @nceas is seeking an Assoc Director for Communication & Outreach. Apply by 1/21 bit.ly/T1EmVB

via Hootsuite (retweeted on 5:54 PM, Dec 23rd, 2012 via Tweetbot for Mac)

@hylopsar yep. Helps to get whois protection (fills it with junk info).

via Tweetbot for Mac in reply to hylopsar

A hat tip to all the folks running in the Berkeley hills right now. Also, you people are insane.

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@jiffyclub @gvwilson exactly. It’s anything but single point of failure. Also, git repos can have multiple remotes.

via Tweetbot for Mac in reply to jiffyclub

Something less ominous on the (wrong) calendar this evening. pic.twitter.com/SiflX75h

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@JasonStoddard except their markup on everything is at least 2x. Fast shipping is the least they could do.

via Tweetbot for iOS in reply to JasonStoddard

JeanGreasy My Mayan friends, Ixazaluoh and Xpiayoc are always flaking on dates, so I kinda knew this would happen. Typical.

via Twitter Web Client (retweeted on 4:32 PM, Dec 21st, 2012 via Twitter Web Client)

@kara_woo bit the bullet and went with @versionsapp I already use @kaleidoscopeapp so I know they write great software.

via Tweetbot for Mac in reply to kara_woo

Successfully cloned er “checked out” a svn repo and made my first commit without borking everything.

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Awesome and nerdy holiday greetings video from the good folks @digitalsci w/ @figshare
digital-science.com/videos/seasons…

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ASPB Disturbing Employment Trends in NSF Doctorate Recipient Report - Science Careers Blog: blogs.sciencemag.org/sciencecareers…

via Twitter Web Client (retweeted on 2:08 PM, Dec 21st, 2012 via Tweetbot for Mac)

siah SimpleR tricks and tools by Prof Rob Hyndman (one of the core R developers) ow.ly/ghgrd

via Hootsuite (retweeted on 12:38 PM, Dec 21st, 2012 via Tweetbot for Mac)

LouWoodley How do writers take notes while reading? @David_Dobbs @marynmck @BoraZ share their secrets goo.gl/Yr8ww via @notscientific

via Twitter for iPhone (retweeted on 11:28 AM, Dec 21st, 2012 via Tweetbot for Mac)

@msanclem Someone just reminded me that this is the exact plot of Kindergarden Cop.

via Tweetbot for Mac in reply to msanclem

matthewmccull Love Markdown? Wish you could write emails in MD? Merry Christmas: bit.ly/UVTzdi

via @thepaulrayner

via Tweetbot for iOS (retweeted on 10:19 AM, Dec 21st, 2012 via Tweetbot for Mac)

altmetric Curious to read backstory of some of the most shared articles? New top 10 of ’12 post up now altmetric.com/blog/interacti… cc @NatureNews

via Twitter Web Client (retweeted on 10:09 AM, Dec 21st, 2012 via Tweetbot for Mac)

tomjwebb Top job! “@adrg1: If you are a quantitative ecologist with a stats-head we have another 3yr post-doc goo.gl/OcC7T

via Twitter for iPad (retweeted on 10:06 AM, Dec 21st, 2012 via Tweetbot for Mac)

@tomjwebb A good reason why I maintain two twitter accounts. One day I fear I will post to the wrong one.

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@CameronNeylon I don’t envy you. That’s a lot of time spent at airports (and consuming bad airport food).

via Tweetbot for Mac in reply to CameronNeylon

I’m out of coffee and someone stole my NY times. uh, well played, Mayan overlords.

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tjvision Publishing a paper based on supported research? Funds are now available to make that paper . bit.ly/URD0hJ

via TweetDeck (retweeted on 5:59 PM, Dec 20th, 2012 via Tweetbot for iOS)

@mrgunn @jasonpriem @researchremix indeed. You guys have been making some pretty awesome progress lately. Cheers!

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@tomjwebb Yes, everyone from can blame their hangovers ;)

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@tomjwebb big data. I’ll write a longer comment on your blog post.

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. @tomjwebb has a nice write up on the big data for ecology ws. Great except for the confusing misuse of the term scilogs.com/mola_mola/big-…

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colindonihue Sign a petition to protect research from being cut way back at the Field Museum of Natural History, Chicago change.org/petitions/prot…

via Twitter for Mac (retweeted on 10:36 AM, Dec 20th, 2012 via Tweetbot for Mac)

Unfortunately it’s one of those days. So much to write and not enough inspiration. Relevant: youtube.com/watch?v=wb3j2m… (ᔥ @David_Dobbs long ago)

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aivelo More postdoc greatness available @helsinkiuni - @metapopulation group recruits: MT @evoldir: PostDoc: ButterflyGenomics tinyurl.com/cjvvs64

via TweetDeck (retweeted on 8:03 AM, Dec 20th, 2012 via Tweetbot for iOS)

@wesmckinn @zenrhino It’s nearly impossible to publish an R package without some obnoxious response from him.

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mbeisen .@eperlste celebrating papers at Nature is like celebrating Republicans who consent to small tax hikes

via Twitter for iPhone (retweeted on 7:43 PM, Dec 19th, 2012 via Tweetbot for Mac)

Slowly warming up to the new @PLOS design.

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lets_experiment Congrats @elizabethiorns on being named in @nature’s 10 people who mattered this year! nature.com/news/366-days-…

via Twitter Web Client (retweeted on 4:19 PM, Dec 19th, 2012 via Tweetbot for Mac)

. @github’s end of year review. I rarely tweet in support of companies but they’ve supported so much . github.com/blog/1359-the-…
ta

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.@CameronNeylon We fully embrace this at @rOpenSci. marker.to/F9Z0Wr This includes being mindful of licensing (among other issues).

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Moving beyond just open access - time to facilitate reuse. hear hear! nature.com/nature/journal… from @CameronNeylon

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eswillwalker More sad evidence of the American Fall: Field Museum to cut staff and research, refocus mission chicagotribune.com/news/local/bre…

via Twitter for Websites (retweeted on 2:49 PM, Dec 19th, 2012 via Tweetbot for Mac)

@MiriamGoldste I hear you. and you’re totally right about gender ratio in alt-sci. Just look at compass online.

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@mrgunn Never noticed this until now (unless it’s a new feature). Swipe is great.

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@thrawny thanks, I’m nervous but only one way to test the waters.

via Tweetbot for Mac in reply to j_colomb

@kara_woo @versionsapp looks super slick but I’d hate to spend 59 on something I wont use very much.

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gvwilson OH at Mozilla: “Why do you keep trying to make code better? It was working just fine!”

via Twitter Web Client (retweeted on 1:20 PM, Dec 19th, 2012 via Tweetbot for Mac)

wow, @github image diffs are super slick. See github.com/karthikram/art… and look at 4 options below the figs. twitpic.com/bnfuut

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@sjGoring That’s what you get for choosing the Sudanese journal of paleoecology. Oh god I am terrible at this. Better stick w/ day job.

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eperlste If you can’t share your unpublished data for fear of being scooped, you might consider working on something else.

via Twitter for iPhone (retweeted on 10:26 AM, Dec 19th, 2012 via Tweetbot for Mac)

@hylopsar Yes, you can cross list. The option is in your profile. Let me know if it doesn’t work.

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Not enjoying the new @PLOS design as much as the old one. Might just take some getting used to.

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@kara_woo Thanks Kara! This is really helpful.

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Being forced to use SVN for a project. I don’t know SVN at all. Anyone recommend a free osx svn gui?

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@labroides @PLOSONE PNAS did too. I wonder if the Ambra system just got updated.

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ethanwhite A PDF to XML converter, designed for scientific papers, as a web service! pdfx.cs.man.ac.uk Be still my heart. via @Stew @researchremix

via TweetDeck (retweeted on 8:30 AM, Dec 19th, 2012 via Tweetbot for Mac)

There is simply no way to avoid getting Ripleyed.

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Nice to see @rOpenSci’s rAltmetric listed alongside other scientific web services. altmetric.com/blog/altmetric…

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@hylopsar You do know about academic tree, right? academictree.org Add yourself!

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monteiro The first comment here is pure gold: gawker.com/5969658

via Twitter Web Client (retweeted on 10:27 PM, Dec 18th, 2012 via Tweetbot for Mac)

Just learned about ScienceWise (sciencewise.info) a way to comment and annotate papers. Cool!

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@gvwilson It gets better :)

Nice first gist!

via Tweetbot for Mac in reply to gvwilson

@cboettig @noamross you can’t. You have to add that separately. You can save it as a function though.

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@sjGoring I’m on it. But there’s not much going on there.

via Tweetbot for Mac in reply to sjGoring

@Protohedgehog But that sentiment is pervasive throughout the academic community though.

via Tweetbot for Mac in reply to Protohedgehog

@ethanwhite @gvwilson ah bummer. Sorry I misread. Can automate some of it but still requires manual checking. :(

via Tweetbot for Mac in reply to ethanwhite

@openfisheries I don’t know what paper he’s referring to either.

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@labroides Super! @andrewjdyck and I will have much nicer data viz built in by then.

via Tweetbot for Mac in reply to labroides

@labroides Not on the paper. I just wrote the R package for it.

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Want to play around with global FAO fisheries landing data, compare countries and species? Try out our new R package. github.com/ropensci/rfish…

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@gvwilson If you need additional code to pull out the metrics, I can write that out too. Or just paste that list into impactstory.org/create

via Tweetbot for Mac in reply to gvwilson

@gvwilson Here’s how you programatically read the dois out of that file.

gist.github.com/4324375

via Tweetbot for Mac in reply to gvwilson

@gvwilson not at all. I’m generating an example for you. hang on.

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@gvwilson In R grep for doi, save into list, push list through rAltmetric or rImpactStory which will return citations for each one.

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If you access @Impactstory via R, we’ve updated our package to the new API. Grab an API key and update from here: github.com/ropensci/rImpa…

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@Impactstory Just updated rImpactStory to new API. Version available on GitHub. github.com/ropensci/rImpa…

via Tweetbot for Mac in reply to Impactstory

@shaenasaurus me too. But we’re just around the corner and longer days aren’t far away.

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My friend @labroides on how he evaluates PhD applicants in ecology.

labroides.wordpress.com/2012/12/17/ph-…

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@researchremix Not really. This is our full list: ropensci.org/packages/#lite… (the github links work, but not page links).

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@hylopsar @xieyihui @jdleesmiller @writelatex This would be awesome. Some of us are playing around with this (slowly). md over sweave.

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Oy vey MT “@LSU_FISH: Going through CVs of candidates for this job makes me happy I have one already.

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@mrgunn sad that it was also the first thing that caught my eye.

via Tweetbot for Mac in reply to mrgunn

Staying off of twitter for the rest of the day to get some serious science done. If you see me around, yell at me.

i.imgur.com/iEPiw.png

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@sjGoring totally. In fact, that’s my next tweet!

via Tweetbot for Mac in reply to sjGoring

. @gvwilson on why Julia will have a hard time gaining traction. Agreed (I couldn’t even install it).

third-bit.com/blog/archives/…

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The Matthew effect “rich get richer” of career longevity. Early career productivity is a strong predicter
pnas.org/content/108/1/…
@sjGoring

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@sjGoring That’s not very encouraging (at least to me).

via Tweetbot for Mac in reply to sjGoring

@sjGoring We might have data of interest to you at Cal. I’ll try to get you early access to the api when it comes online.

via Tweetbot for Mac in reply to sjGoring

ethanwhite Why do I feel like we’re spending more time worrying about “credit” these days than focusing on just doing the most awesome science we can?

via TweetDeck (retweeted on 8:38 AM, Dec 14th, 2012 via Tweetbot for Mac)

@ficaryl iAnimal? Did Apple sponsor this event?

via Tweetbot for Mac in reply to ficaryl

Paper by @DataONEorg summer intern @richlitt on scientific workflow use now in IDCC. cc/@rkoskela
ijdc.net/index.php/ijdc…

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@sandramchung @mickresearch Perhaps I should be the one to go. I’m 1/16th hobbit on my father’s side.

via Tweetbot for Mac in reply to sandramchung

@mickresearch @sandramchung Awesome. Share the announcement when it comes around?

via Tweetbot for Mac in reply to mickresearch

@KMBTweets @tkb @figshare @PLOS @osf PLOS is doing that? link? Or is this on the wish list?

via Tweetbot for Mac in reply to KMSilverTweets

@eswillwalker Thanks Ellen! That makes sense. Looks like it never ends!

via Tweetbot for Mac in reply to eswillwalker

If you’re an senior assistant prof, associate prof. or above, who writes your rec letters? Your peers?

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@peromhc @labroides Why is a simpsons rerun a bad day? I love those days.

via Tweetbot for Mac in reply to macmanes

@mfenner Also check out @yoavram’s efforts to build one. github.com/yoavram/markx in python. twitpic.com/blp0aa

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@mfenner seems along the lines of my last blog post. math exists via mathjax. md anchors serve as links (see in your own doc).

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@elife_sciences wow, journal looks fantastic! Finally, a journal page that doesn’t look like it’s from 1995. Love the decision letter/resp

via Tweetbot for Mac in reply to eLife

@sandramchung Have you guys considered joining another ecological society?

via Tweetbot for Mac in reply to sandramchung

eperlste The more I learn about overhead and indirect costs, the more Academia reveals itself to be Industry in disguise.

via Twitter for iPhone (retweeted on 8:37 AM, Dec 13th, 2012 via Tweetbot for Mac)

@researchremix haha. We have way too many. Something going on two to three times a week.

via Tweetbot for Mac

@CameronNeylon It is indeed fantastic. I’ve been recommending it to new open science api developers.

via Tweetbot for Mac in reply to CameronNeylon

fperez_org Some more info regarding our Alfred P. Sloan grant in support of IPython development: ipython.org/sloan-grant.ht….

via Twitter Web Client (retweeted on 8:32 AM, Dec 13th, 2012 via Tweetbot for Mac)

Interactive viz of nearest 100k stars.

workshop.chromeexperiments.com/stars/

Mind. Blown. (warning: auto plays sound)

@David_Dobbs

via Tweetbot for Mac

@noahWG No servers are just busy with the entire world desperate for it. Try again in a few.

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@Impactstory Does Heroku rely on AWS as its backend?

via Tweetbot for Mac in reply to Impactstory

@figshare iOS app (doesn’t even have to be native) would be rad too. Share data on the go, copy doi to clipboard. boom.

via Tweetbot for Mac

@melissaterras was it a pre-shortened URL? Twitter doesn’t like that (mostly to prevent spam/virus links).

via Tweetbot for Mac in reply to melissaterras

swcarpentry Would you like us to run a two-day boot camp somewhere in 2013? Please get in touch (and please retweet). info@software-carpentry.org

via Twitter Web Client (retweeted on 2:50 PM, Dec 12th, 2012 via Tweetbot for Mac)

@hylopsar I’d create a package_name.Rd and add a note in there. Methods are based on Bag, D. 2010. Doesn’t have to be *everywhere*.

via Tweetbot for Mac in reply to hylopsar

@abigailamey Definitely coal. and don’t even bother splurging on ‘clean’ coal.

via Tweetbot for Mac in reply to abigailamey

@ethanwhite @distribecology So yes, I’ll echo the same. Context matters. There is no right number.

via Tweetbot for Mac in reply to ethanwhite

@distribecology You could SEO the crap out of your blog and get tons of hits. But it’s all about the attracting right audience.

via Tweetbot for Mac in reply to emhrt_

Ecological importance of oysters. Video from my former marine lab. youtube.com/watch?v=imXxYr…@phylogenomics

via Tweetbot for Mac

carlystrasser .@CalDigLib still looking for good candidates for data publication postdoc. Pass it along! clir.org/fellowships/po… Deadline 31 Dec (not firm)

via TweetDeck (retweeted on 8:29 AM, Dec 12th, 2012 via Tweetbot for Mac)

@carlystrasser @labroides “I can confirm that the person named in this letter may/may not have a pulse.”

via Tweetbot for Mac in reply to carlystrasser

@brembs nice! What is the workshop format? Hands on? How long?

via Tweetbot for iOS in reply to brembs

kristenobacter everyone feels this way, right? RT @marynmck
XKCD: an arrow to the heart (as always) xkcd.com/1146/

via Twitter Web Client (retweeted on 6:00 AM, Dec 12th, 2012 via Tweetbot for iOS)

@ibartomeus I hear ya. Doing that right now and need to rewrite it in Rcpp but feels too daunting.

via Tweetbot for iOS in reply to ibartomeus

mbeisen The masses fight back against UC logo with snarky memes blog.sfgate.com/stew/2012/12/1…

via Twitter for Websites (retweeted on 10:06 PM, Dec 11th, 2012 via Tweetbot for Mac)

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