Karthik Ram @_inundata

Yay Area / ✈ in transit

October 2012

@Drew_Lab So true. We have let those humanities PhDs dominate the barista job market for so long. Time to bring it back to the sciences!

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@researchremix So appropriate because Random house just acquired Penguin.nytimes.com/2012/10/30/bus…

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RT @xieyihui: a statistician is a data scientist who does not know he is a data scientist because he never reads twitter

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@xieyihui @eddelbuettel @hadleywickham brilliant. I’ll go with this definition.

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@eperlste it’s dreary out so I’ll skip driving across the bay and party tomorrow instead.

via Tweetbot for iOS in reply to eperlste

@eperlste right. But looks like @jasonpriem won’t get there till 10 and a couple of others I know canceled. Might also wait till 2mrow.

via Tweetbot for iOS in reply to eperlste

@eperlste I’ll try to make it out there tonight since my earlier plans got canceled. What time you folks getting there?

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@researchremix Was going to ask if you & @jasonpriem were going. I can’t get there till 830 but might skip if all the cool kids don’t go.

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@labroides unfortunately most papers are just that. COME ON PEOPLE TELL ME MORE DEETS ABOUT THIS COOL SHIT SO I CAN DO IT.

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Either DM or email me your idea at karthik dot ram at gmail.

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Ecology & Evolution peeps interested in data sharing/open science, drop me a note if you want to contribute an article. library.queensu.ca/ojs/index.php/…

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my attempt at creating an image labels for ggplot2 legend.
stackoverflow.com/a/13148768/313…

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@naupakaz @ethanwhite @tpoi pandoc foo.tex -o foo.txt. This generally works.

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@jaimedash @noamross still better than nothing. Cover the other $250 for PLOSone.

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@jonesor I use it all the time. Solarized is now part of every syntax highlighting tool.

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@yoavram awesome! I’ve been needing a good slide for explaining the need for DVCS. This is perfect!

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I always worry about Markdown’s future. But after reading this I’m a little more optimistic. codinghorror.com/blog/2012/10/t…

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@boudicca Thanks for organizing last night and for the drinks!

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rmounce Anyone interested in or might well be interested in our new paper biomedcentral.com/1756-0500/5/574

via TweetDeck (retweeted on 8:31 AM, Oct 25th, 2012 via Tweetbot for iOS)

@rich_ rnorm(99999999999999999) should heat your processor enough and get the fans going to dry that up.

via Tweetbot for iOS in reply to rich_

@Stew neat. On a related note, I’m hoping to wrap up rAltmertic this week and demo it at the PLOS ALM next week.

via Tweetbot for iOS in reply to Stew

duffy_ma I’m looking for a technician/lab manager for my aquatic/disease ecology lab! Job ad: umjobs.org/job_detail/756…

via Twitter Web Client (retweeted on 8:24 AM, Oct 25th, 2012 via Tweetbot for iOS)

jonesor When I say “Earl Grey” you say “yes please”… When I say “Ooh” you say “long”ryoutube.com/watch?v=eELH0i…Yn6D

via OS X (retweeted on 8:20 AM, Oct 25th, 2012 via Tweetbot for iOS)

hollybik Moving towards workflow schemes for scientific analyses (e.g. iPython notebook) - will enable transparency and reproducibility

via Twitter Web Client (retweeted on 11:24 PM, Oct 24th, 2012 via Tweetbot for iOS)

jasonpriem If you’re in the Bay Area, don’t miss the first hackathon Nov 3-4 at @PLOS! altmetricshackathon2012.eventbrite.com

via TweetDeck (retweeted on 8:42 PM, Oct 24th, 2012 via Tweetbot for iOS)

ReaderMeter Inspiring crowd and talks at the kick off meetup of bay area , thanks to @boudicca and @codeforamerica for being such great hosts

via Twitter for iPhone (retweeted on 8:38 PM, Oct 24th, 2012 via Tweetbot for iOS)

@gangleton @zachwill we’re going to Azucar lounge after a short panel session.

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@gangleton @zachwill will do. I see you people on the other side!

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@gangleton @zachwill open data meetup group. 3 ten minute talks but the plan is to go to a bar nearby after it ends.

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None of the folks I know at @codeforamerica are at their open data meetup. Looking at @zachwill and Serena.

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@brookeborel much better realizing you’ve been writing all day but haven’t eaten.

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hmason Yay @github! githubarchive.org is amazing data to play with.

via Twitter Web Client (retweeted on 3:01 PM, Oct 24th, 2012 via Tweetbot for iOS)

@datatelling @shashashasha ah right. I’ve heard this elsewhere too. But the company is also quite young.

via Tweetbot for iOS in reply to datatelling

@davidwhogg @github @openscience that would be brilliant and I’d love to see that day. But, baby steps.

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davidwhogg we should be able to submit papers to the and to by just giving a “git clone” command (cc @github)

via Twitter Web Client (retweeted on 12:35 PM, Oct 24th, 2012 via Tweetbot for iOS)

@datatelling @shashashasha I’m sure people have faded away from Github but do you mean no one intentionally deleted their acct?

via Tweetbot for iOS in reply to datatelling

Drew_Lab Slides from the lecture on the up on @figshare. Feel free to share (acknowledgements appreciated) shar.es/c4XBV

via Twitter for Websites (retweeted on 12:14 PM, Oct 24th, 2012 via Tweetbot for iOS)

@KTInvasion So 2 to a bazillion measurements can be referenced by 1 variable. You can slide, dice, transform, facet, whatever by that 1 var.

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@KTInvasion You can collapse a dataset with bazillion individuals x bazillion measurements on each into a bazillion x 3 dataset.

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@KTInvasion because it is easier to slice and apply functions to long shaped data that wide shaped data. 1 col vs n cols.

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@KTInvasion A is easier for data entry. B is easier for transforming data, applying functions and making faceted plots. R makes A->B easy.

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@hadleywickham @rstudioapp Looks pretty neat! Bootstrap?

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matthewmccull On Git 1.8.0, the default behavior changed:

“git push will warn about upcoming change until you set this var.”

bit.ly/T6O1tb

via Tweetbot for iOS (retweeted on 7:55 AM, Oct 22nd, 2012 via Tweetbot for iOS)

victoriastodden I’m co-organizing a conf on reproducibility in science in Dec - Peter Norvig and GitHub’s @timothyclem keynoting. Woot! icerm.brown.edu/tw12-5-rcem

via Twitter Web Client (retweeted on 1:44 PM, Oct 20th, 2012 via TweetDeck)

xkcd charts in d3. dan.iel.fm/xkcd/
my nerdy side is pleased.

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hadleywickham ggmcmc: new package for visualising mcmc results with ggplot2: xavier-fim.net/packages/ggmcm…, by Xavier Fernández-i-Marín

via Echofon (retweeted on 9:14 AM, Oct 18th, 2012 via TweetDeck)

victoriastodden Open source tool to visualize your python scripts, communicate and better understand code: pythontutor.com from pgbovine.net

via Twitter Web Client (retweeted on 11:46 AM, Oct 17th, 2012 via TweetDeck)

@CMastication More cores not always = faster computation. For work that I do, it levels of at 96.

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@CMastication Seems completely silly. The IO transfer across that many cores will negate any added benefit of that much power.

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One of the many joys of working from home. Coding/writing in my back yard. pic.twitter.com/FxyZW9Td

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@ethanwhite Love their work too. I need to connect with @fperez_org and talk about some python /R image analysis ideas.

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@researchremix @ORCID_Org I’m always embarrassed by all of my code all the time. So, I’m like way way ahead of my peers, right?

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Downloading 150 gigs of simulation data from @NICS high performance storage system. Data transfer speed makes it look like black magic.

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A vintage photo of E.B. White composing a tweet. freecabinporn.com/post/337097906…
But srsly, this is one way to finish that manuscript.

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@DavidJohnGibson @figshare @ORCID_Org Don’t listen to @ethanwhite This mean you are now the protagonist in the new Susan Orlean book.

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@recology_ @rstudioapp But how? embed it inside the gui?

via TweetDeck in reply to sckottie

@Impactstory @researchremix Are all your new API changes done? Can I hack away again?

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@duffy_ma Darwin had impostor syndrome long before it was cool! Mention that in your lecture, @labroides!

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@datatelling What’s your panel about? Is there a link to it?

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@SeemaSheth Awesome! Thanks for the heads up!

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SO BADASS –>> @hadleywickham: @joshua_ulrich nice! I’m working on better profr vis with d3, like had.co.nz/profr/d3/profr…

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@maximolly @datatelling congrats! this is great.

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@carlystrasser People were complaining that I look nothing like the Inundata logo. :)

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@fonnesbeck @ucfagls @recology_ @ethanwhite Nice to render md correctly on GH for web display. html requires gh-pages which confuses ppl.

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@ucfagls @recology_ @ethanwhite @fonnesbeck @EliSwede The only downside is Github md != pandoc md for tables. :(

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smart people -> @iEvoBio: Introducing the iEvoBio 2013 Committee: @kcranstn @Laura_Kubatko @hdeus @trayc7 @carlystrasser @Dr_Bik @ncellinese

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hadleywickham new version of httr, web APIs made easy web in , blog.rstudio.org/2012/10/14/htt…

via Echofon (retweeted on 4:19 PM, Oct 14th, 2012 via Tweetbot for iOS)

@moclanmomo The article is OA but the journal made a mistake. Grab a pre-print here: ropensci.org/resources/ (bottom of page)

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@IHStreet @Pettorelli +1. Seriously contemplating leaving academia in the next year. Hoping to find another way to keep doing science.

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@distribecology @recology_ I think I win this round of hipsterest coffee shop. pic.twitter.com/b7SxyUhw

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@IHStreet @Pettorelli agreed. But the problem is so pervasive in STEM that we are reaching a breaking point.

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@distribecology There is one guy here at the arbor cafe with a Sony Vaio. We’re all giving him dirty looks.

via TweetDeck in reply to emhrt_

Many more @rOpenSci packages are either on CRAN or will soon get there. Look at all the green on this page! ropensci.org/packages/

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@recology_ @ethanwhite @fonnesbeck @EliSwede Anyone know if pandoc supports multi-markdown tables? I also hate lack of tables in mdown.

via TweetDeck in reply to sckottie

birbigs I want to live in the Quiet Car of life.

via TweetDeck (retweeted on 5:02 PM, Oct 13th, 2012 via Twitter Web Client)

I really wish @TweetDeck would let you mute folks for various lengths of time like @tweetbot

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Fun fact: I begin nearly all weekends with a todo list titled “Fires burning” as immortalized in this painting. bukk.it/shitsonfire.jpg

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. @recology_ is a R machine. Two packages off to CRAN the same day!

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Great perspective on work-life balance and gender inequality in academia by @Pettorelli sciencecareers.sciencemag.org/career_magazin…
couldn’t agree more.

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rOpenSci ritis, our wrapper to the Integrated Taxonomic Information Service (or ITIS) was just sent to CRAN, code: bit.ly/HyWEsx

via TweetDeck (retweeted on 1:56 PM, Oct 13th, 2012 via TweetDeck)

@msanclem @MiriamGoldste Can I blurb the book? “Total…garbage”. or maybe I should save that for Miriam’s garbage patch book.

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@Impactstory Will there be altpetizers at this event? maybe some altisanal beer?

via Tweetbot for Mac in reply to Impactstory

@MiriamGoldste I always use Frontier when I travel to/from CO. I like them a lot.

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eperlste If the victors of the Tenure Games have no incentive to change and everyone else gets killed, how does academia evolve?

via Twitter for iPhone (retweeted on 12:45 PM, Oct 13th, 2012 via Tweetbot for iOS)

@duffy_ma I get science done at a much slower pace and I don’t even have a baby.

via TweetDeck in reply to duffy_ma

@melissaterras Love it. I bet Governor mittens will give us all professor jobs.

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The myth of making tenure (or finding a TT job) is now officially folklore. …miainchildrenspicturebooks.tumblr.com/post/335104222…

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@recology_ @fonnesbeck But every once in a while you get a group of collabs all on the same page.

via TweetDeck in reply to sckottie

If you ever have to ftp a git managed project, here is a neat little tool for that: github.com/resmo/git-ftp

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@kwren88 wow, @GrunerDaniel gets the red carpet. Never seen anyone listed alone on a tweet.

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Note: Don’t ever mess with @MiriamGoldste. Here’s why: youtu.be/l5P4ZiBzoQg?t=…

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The first paper on an @rOpenSci package is out! Check out @cboettig and Duncan’s Treebase paper onlinelibrary.wiley.com/doi/10.1111/j.…

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Met some awesome peeps from @IFTTT at the @github meetup. More nerding.

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A girl just asked me how often I rebase my commits. What the hell I don’t even…WTF @github

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Someone at the @github meetup offered me a R consulting job at 240/hr. holy shit.

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I’m at a @github meetup. Can’t handle. So. Much. Nerd.

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@ethanwhite (wrong handle). FYI, I used our arXiv paper as an example of collaborative writing for a Cal talk. inundata.org/ecolunch/#GitH…

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@ethanwhile FYI, I used our arXiv paper as an example of collaborative writing for a Cal ecolunch talk. inundata.org/ecolunch/#GitH…

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@GrunerDaniel wow, Dan. a bit surprised to see you on Twitter.

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ReaderMeter Join us on October 24 at Code for America HQ for the inaugural Open Data Bay Area meetup meetup.com/Open-Data-Bay-…

via OS X (retweeted on 1:34 PM, Oct 11th, 2012 via TweetDeck)

Rejected manuscripts eventually do find better homes. sciencemag.org/content/early/…

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@eperlste Sure you don’t want another hit? I’ll sell you some 52.28 for cheap.

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@arielwaldman Feeling the same way in the east bay. Fighting it with upbeat music and not looking out the window.

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PLOSALM Hackathon, Nov 3 in SF. Hosted by @Impactstory, @PLOSALM. Spread the word & come join us in the fun! altmetricshackathon2012.eventbrite.com

via Twitter Web Client (retweeted on 1:19 PM, Oct 11th, 2012 via TweetDeck)

This is exactly where I need to go, far away from the internet, to get a bunch of writing done. –-> freecabinporn.com/post/333655334…

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@duffy_ma and look how fancy you turned out! Well done on the interview!

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@ethanwhite @recology_ Good call. They announced it a year after I started using it. Scott should apply. They take calls 4 times a year.

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@ethanwhite @recology_ Of course they said that! They need to justify keeping their jobs! ;)

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@recology_ @ethanwhite I sunk in over 2K of personal funds on EC2 early on. Uni should share cost of large clusters, thro NSF and open it up

via TweetDeck in reply to sckottie

@ethanwhite @recology_ agreed. This is silly. HPC centers are not fragile. I know way more about this than my last two PIs combined.

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@revodavid A true nerd would have sent this at 13:14:15 ;)

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@ethanwhite Cool, I didn’t notice it posted elsewhere. I was lamenting earlier that I couldn’t comment directly on your arXiv version.

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@ethanwhite If you guys revise it, I’d be happy to help edit/cut down the revision.

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@recology_ Looks really amazing. Cool work.

via TweetDeck in reply to sckottie

@zachwill You people are working on an API for rising sun? I love that brewery. +1

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@ethanwhite Just read your arXiv paper. Looks great but your section on VCS describes only centralized ones, not distributed ones like Git.

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@phdpqc @trashbird1240 Great, thanks! Now I have to write the authors and old fashioned email.

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Am i missing something or is it not possible to comment on a arXiv pre-pub?

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@mrgunn and not a peep in Berkeley. At least this was a reminder to bring my laundry in.

via Tweetbot for iOS in reply to mrgunn

@jasonpriem Glad R is on your brain and you also seem to be rubbing shoulders with Kanye!

via Tweetbot for Mac in reply to jasonpriem

@ESA_org You really need to move on from Allen Press. The system is broken and the longer you wait, the harder it’ll get.

via Tweetbot for Mac in reply to ESA_org

@datatelling Indeed, I’m finally excited that NSF recognizes more of my work.

via TweetDeck in reply to datatelling

@recology_ Love the package but what an unfortunate name.

via Tweetbot for Mac in reply to sckottie

@recology_ It will show updates on all the ones your watching, all orgs you’re a member of, and any issues assigned to you.

via TweetDeck in reply to sckottie

@recology_ @prismatic I really like QuickHub for mac for that same reason. I can easily see activity, create repos, etc. from my menu bar.

via TweetDeck in reply to sckottie

@labroides It’s quite impressive with all those sideways people. Are you at the Hogwarts library?

via Tweetbot for Mac in reply to labroides

@JacquelynGill I don’t list them contributed talks in detail since it is just cv padding. I condense those into one sentence with links.

via Tweetbot for Mac in reply to JacquelynGill

markus_eichhorn 3yr research fellowships at Uni of Nottingham, with up to £25k p.a. grant bit.ly/RprCc3. Keen ecologists get in touch!

via TweetDeck (retweeted on 7:42 AM, Oct 8th, 2012 via Tweetbot for Mac)

@hadleywickham nice! looking fwd to it. Is there a major new feature in the update?

via Tweetbot for Mac in reply to hadleywickham

Loving oh my zsh to keep track of branches and commit status from my terminal prompt. pic.twitter.com/gmIOW1v7

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@Impactstory nice! I’m giving a talk on Monday and added impactstory.it Still have enough time to update it!

via Tweetbot for iOS in reply to Impactstory

Just finished my slides for a Monday talk on a Friday. Not sure I’m ok with being so organized.

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@ninamehta pamfax.biz/en/ worked well for me the last few times i had to deal with a fax machine.

via TweetDeck in reply to ninamehta

researchremix It’s official! Now NSF biosketches “may include… publications, data sets, software, patents, and copyrights” and more nsf.gov/pubs/2013/nsf1…

via Twitter Web Client (retweeted on 11:03 AM, Oct 5th, 2012 via Tweetbot for iOS)

datadryad After 14-Jan-2013, NSF biosketches to list “products” incl. datasets, software, &etc and not just pubs is.gd/km8oao h/t @ethanwhite:

via TweetDeck (retweeted on 9:57 AM, Oct 5th, 2012 via TweetDeck)

noamross A script I wrote to remove annoying cover pages from PDFs: goo.gl/M4pNu @_inundata

via Adium (retweeted on 9:26 AM, Oct 5th, 2012 via Tweetbot for Mac)

@tpoi @phdpqc @ethanwhite Looks good to me. Added a minor comment to improve readability.

via Tweetbot for Mac in reply to tpoi

@tmccormick @arielwaldman If your twitter is public, then the favs rss feed can be linked to anything (evernote, instapaper) via @IFTTT

via TweetDeck in reply to tmccormick

@arielwaldman solution. Archive your Stellar rss feed (i.e. your favorites) to Instapaper while that is still available.

via TweetDeck in reply to arielwaldman

@arielwaldman But I’m also bummed to lose all the @IFTTT Twitter triggers.

via TweetDeck in reply to arielwaldman

@arielwaldman Nope. Any service that does it would violate the new TOS. To archive, bufffer + kipp is an option to archive your own.

via TweetDeck in reply to arielwaldman

Hey Journals, thanks for adding that coversheet to every PDF! Super helpful infomation and I love spending more time at the printer!

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@gigi_rose offline PDFs - yes. Their mobile app is not so great though (or at least the last time I tried using it).

via TweetDeck in reply to gigi_rose

@phdpqc @ethanwhite Centralized would be awesome. Would also be a great way to track and reward people who contribute their time.

via TweetDeck in reply to phdpqc

@distribecology you are right (i have too many versions of python on this machine). Still a great piece of software though.

via TweetDeck in reply to emhrt_

@distribecology Works for me with 2.7.2 You should post on the Sublime forum. sublimetext.com/forum/ Pretty sure someone will suggest a fix

via TweetDeck in reply to emhrt_

Pro tip: Need a really clean house and all chores completed? Get yourself a hard deadline.

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openscience Choose a PDF to upload knowminer.at:8080/code-demo/inde… Demo of metadata + entity extraction from scientific PDFs ty @_krisjack

via TweetDeck (retweeted on 5:32 PM, Oct 4th, 2012 via TweetDeck)

Sublime Text is by far the best editor I’ve ever used. Such a pleasure for coding and general writing (in markdown). tutsplus.com/course/improve…

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@p_schulthess If you need a syntax highlighter for non wp-blogs there are many options.

via Tweetbot for Mac in reply to hellopascal

@p_schulthess On inundata.org? Some outdated plugin called wp-syntax. I need to find time to switch away from wp to Jekyll.

via Tweetbot for Mac in reply to hellopascal

Great interview with Ethan Perlstein. nature.com/naturejobs/sci…

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mbeisen if prop 37 passes, i’m going to sue organic farmers and ask them to prove prehistoric farmers didn’t use “recombinant DNA techniques”

via Twitter Web Client (retweeted on 10:13 PM, Oct 3rd, 2012 via Tweetbot for iOS)

@trashbird1240 @ethanwhite @phdpqc @tpoi How much does Gitorious cost? Does it have a userbase like Github? Git repos can be self-hosted.

via TweetDeck in reply to JoelJAdamson

@ttso I’ve fixed it. Do an update and you’ll see total counts gone from the plot. Also added support for other doc types.

via Tweetbot for Mac in reply to ttso

@ttso Thanks, I realized that. I’ll fix it in the next update.

via Tweetbot for Mac in reply to ttso

@cjlortie It already exists. I need to write a tool to upload data to @DataUpCDL once i figure out their software.

via Tweetbot for Mac in reply to cjlortie

DataONEorg A new tool in the DataONE ITK: DataUp bit.ly/D1DataUpPR. Released today by CDL, Microsoft, DataONE and… fb.me/2egRyiM3X

via Facebook (retweeted on 5:11 PM, Oct 2nd, 2012 via Tweetbot for Mac)

ethanwhite Grading workflow for my @swcarpentry class: 1. Update student’s repository 2. Execute/read code 3. Comments in text file 4. Commit comments

via Twitter Web Client (retweeted on 5:07 PM, Oct 2nd, 2012 via Tweetbot for Mac)

@cjlortie @DataUpCDL I have the exact same issues with using it. Will have to wait for @DataONEorg goodies.

via Tweetbot for Mac in reply to cjlortie

@jebyrnes I suspect that the Q will get you numerous upvotes but no actual answers.

via Tweetbot for Mac in reply to jebyrnes

@ttso Thanks for posting that issue. appreciate it!

via Tweetbot for Mac in reply to ttso

@jebyrnes not a geom. Should be a theme. So .. + theme_xkcd()

via Tweetbot for Mac in reply to jebyrnes

@jebyrnes and now I see you already posted one for R.

via Tweetbot for Mac in reply to jebyrnes

@jebyrnes haha. I woke up and marveled at the SE thread too. Nerds do alike.

via Tweetbot for Mac in reply to jebyrnes