@sandramchung That’s an age old trick! A great way to get someone to contribute.
@elizabethiorns @MarkHahnel Tim O Reilly is also attending (I think) so It’ll be a party all around. :)
@elizabethiorns @MarkHahnel Mark will be here for scifoo!
tpoi [Blog] Data sharing and preprints in ecology bit.ly/11V8p7g
Banyan - a GitHub for science. Looks a lot like GitHub itself.
bit.ly/16jf6FA
@carlystrasser are you one of the cool kids?
@tomjwebb The registration fees are also quite insane.
Reproducibility and reciprocity
bit.ly/18kfz75
gawbul pyEnsemblRest will be the first package for @pyOpenSci, a blatant rip of @rOpenSci, but for #Python instead of #Rstats ;)
David_Hillis Congrats to Marc Feldman, Joan Strassmann, Sally Otto, Brian Charlesworth, Ian Baldwin & Nancy Knowlton on election to NAS! Go Evol!
@DrewPurves how about @Protohedgehog?
frank_burdon #PLOSONE: Is ecology becoming a problem-solving science? - trends in ecological research during the last 3 decades dx.plos.org/10.1371/journa…
karmel_a GithubPages + Jekyll = My dissertation will be televised, internet style. Amazing how easy+pretty versus when I started web-devel 7 yrs ago!
MSURabbott Interested in improving access to the worlds scientific resources? @ScienceExchange is hiring developers! Find me floating around #railsconf
@hspter @kara_woo with you on this one too. Real sugar or gtfo. One of my many nicknames is Sugar K. Because I love sugar so much.
@BrunaLab @skmorgane gmail has been doing a fantastic job of sending really important email to spam lately. Have you checked there?
@hspter +1
@hspter agreed. They are all weird. I can’t do coffee without sugar.
LettersOfNote An editor is a person who knows more about writing than writers do but who has escaped the terrible desire to write. pic.twitter.com/W6osqHYyR2
@eddelbuettel is there a Rcpp book in the works?
@kaythaney Congrats! Looking forward to hearing more.
@labroides you will be, my friend.
That comma was really important.
@labroides you will be my friend.
@labroides and we covered three centuries of environmental history in one evening.
@labroides it was. I felt like a fish out of water taking about my research.
Everyone at the party is a well known author and dropped off copies of their books at my house today. #youngpersonfail.
Went to a birthday party for my 90 year old landlord and his octogenarian friends. Tried to teach them flip cup and failed. 1/2
@zentree No idea. Took me the longest time to figure out after becoming a mac user.
I’ve reached the point where there are no more easy keybindings for my text editor.
⌥ + ⌃ + ⇧ + 5 + A + Z + rub belly clockwise.
A call to share code in the astrophysics community. 87% don’t.
bit.ly/YcbDG9
@eldromedario @recology_ You can also use ggsubplot to add in that inset. If you post some code, I can help you get it right.
@eldromedario @recology_ Fairly easy to do. Combine geom_line and geom_bar, adjust scales and inset second plot with a viewport.
@cjlortie @ScienceExchange has a reproducibility initiative. bit.ly/12NUPor
@cjlortie Heather is @researchremix
@IanMulvany Looking forward to that day.
Friday night: A false sense of excitement that the weekend is coming up when in fact both days will be no different than any other.
ryneches I think it should be a law that if you are a restaurant in an airport, you cannot put local time restrictions on "breakfast."
@adaptive_plant Cool. All my ST resources if interested: bit.ly/120V3EW
Blog post by @tpoi bit.ly/120V3ES
miah_ GitHub Offers Free Private Repositories for Women Learning Open Source Software bit.ly/14lR10F
@hspter haha yes. I thought I was crazy.
@adaptive_plant I also like iAwriter on a mac. But mostly write in ST2 with the markdown focus package.
@adaptive_plant Sublime Text all the way down. Use it for everything these days. bit.ly/14lX0T7 bit.ly/14lX0CS
@researchremix @jasonpriem Show her the ImpactStory report! Change in visitors, blog mentions, and bookmarks since last visit w/ conf int
dancohen Zooniverse has open sourced their code for crowdsourcing scientific & cultural data blog.zooniverse.org/2013/04/16/gal… Planet Hunters, Old Weather, etc.
@Cmdr_Hadfield Looks like a snapping turtle!
@ethanwhite Right now it feels like DATA ALL THE THINGS!
In case there weren’t enough web based markdown editors, here’s one more: bit.ly/181QwIy
GBIF Congrats to @rOpenSci - won Best Overall App in @USGS Earth Science Data awards for TaxaViewer usgs.gov/newsroom/artic…, uses #gbif + others
“Five years on, my job hangs by a thread, my future somewhat questionable” I'm a scientist, and that's why I drink
bit.ly/181Pv3b
@tomjwebb I’m a moleskine addict and have sources here. If you’re really in need of a particular kind, I can get it for you.
@ToriHerridge @tomjwebb I’m partial to the gridded one. Or plain. Good for doodling.
@natekontny @mfenner happy to help with this. My email is firstname.lastname at gmail.
@skmorgane Congrats! This is awesome.
Ira Glass on the secret of success (for creative work but also applies elsewhere) bit.ly/YX3EYJ
@doc_becca I hope the kid submitted the paper as a scratch off. A+
@NKSBarker You’ve seen the new @PLOSBiology paper, right? bit.ly/ZjhtV0
@tpoi @ctitusbrown Came to Berkeley early on but missed the chance. Been dying to see it.
phylogenomics WTF - I hate how #PLOS publication system completely screws up any figure w/ embedded text by conversion to TIFF plosone.org/article/info%3…
@noamross @cboettig I just scrolled down to “Sharing Notes” here bit.ly/17lh32i and realized you can’t cleanly push it.
@vijay_ivaturi Awesome! Are you teaching, helping, organizing or attending?
noamross FasteR! HigheR! StrongeR! - My guide to speeding up #Rstats for busy people noamross.net/blog/2013/4/25…
Some of my Twitter outrage is best captured by this → i.imgur.com/VTHcWsA.jpg ↬ @zachwill
@noamross No but you can ref lines in the issues (just need to change .md ext to something else). Issues aren’t available offline anyway.
@zachwill haha, love it.
@noamross Yes afaik (weird, I know). I wish it were everywhere.
@noamross Purely on GitHub. It’s sort of their value added service on top of a free platform. It’s good but makes git less decentralized.
@noamross It either remains in issues or on top of a commit.
@noamross b) Click on any commit (like this: bit.ly/YWrHag) and then hover over line numbers to add a comment.
@noamross a) Reference line numbers by appending to URL like so: bit.ly/ZLmcyl
@recology_ @cboettig @thePeerJ It’s a Github thing. Markdown is rendered automatically. So you can ref lines. So add *any other* extension.
@tmkeesey why not just clone? Forking serves the purpose of having one’s own copy to build upon, or to contribute back.
@mfenner Have you seen DraftIn? bit.ly/Z0hisD
✔ markdown
✔ VC (although not transparent)
✔ collaboration
✔ diffs
✔ not geeky.
@mfenner 1K barely covers any salary. There are no material costs involved in building something like this unlike expt work.
@mfenner @recology_ @tmkeesey Agreed 100% Happy to build one but not without funding. markx was a prototype of the idea.
@recology_ @tmkeesey Issues are usually fine. Analogous to a std. review. People rarely edit your ms directly but that’s what forks do.
@recology_ @tmkeesey Mine had two pull requests with edits from random people which were actually great.
@tmkeesey @recology_ No forking needed. Just post comments and feedback as issues. See bit.ly/UvWgpg
@recology_ @thePeerJ You can’t do that with Github for plain text. Only code. So markdown etc doesn’t work.
@ekansa thorn on my side too. Happy to throw in some % of my grant into a collective pot to fix this.
SteveMartinToGo I believe it was Socrates who said, “When someone favorites your Tweet the nanosecond you send it, they are a bot.”
@gingi0 There are still people around who use CVS? o_O
@thePeerJ That’s awesome because I’m a huge fan/user of SO. The system forces people to articulate comments better. I’ve felt that myself.
@shaenasaurus Not in a cv for a traditional academic job though.
@shaenasaurus If it’s relevant to the job. I’m sitting through a machine learning class now. Would mention it if necessary.
@recology_ What do you think of the article?
@sjGoring hah I hate that too. I never use twitter via the browser but when I do, I have to start at a user page. Glad it’s not just me.
@cboettig which one broke? fishbase?
@Stew @altmetric Love the email alerts! Just noticed that @NCI_NCIP tweeted my recent paper. Wouldn’t have noticed otherwise.
@DrLabRatOry I nodded without even reading the article. I did bookmark it for later though. /sad
smfrogers Nice piece for us by @kaythaney about @DataKindUK "Doing good with data: why DataKind is launching in the UK" bit.ly/10BQ6rZ
Cities of science. Wired article by @arbesman
bit.ly/Y5vret
Boston and Berkeley!
Nature paper: bit.ly/Y5vtCV
Nice work @ElDon78! bit.ly/10e0DSX
@recology_ R kernel hacking.
@figshare Mac uploader bug. Cannot tab from username field to password field in login screen.
@recology_ @yoavram yeah. We’re talking about native support. Julia was just done. If you guys want to help with R integration let me know.
@recology_ I might work on it with @fperez_org. We talked about it last night.
aloraine205 @sjGoring Right on. I love #knitr and #RStudio. Everyone in my lab is using them now and we are 10x more productive.
@ctitusbrown @noamross Use email from your own domain on gmail and when it goes away point it elsewhere and then RYO or pay for what’s avail
@ctitusbrown @noamross Sure, any free product can be sunset anytime. But do you have to roll your own everything?
@catallman Awesome! Happy to talk to you about it at scifoo. I’m an instructor at @swcarpentry
@flimsin A few more: bit.ly/ZN0tTH
@flimsin Thanks for putting that list together! We can’t add directly to it, can we?
@flimsin You should also add @jennifergardy to the list.
@ctitusbrown @noamross Boomerang is a paid service. Fremium model.
profjsb BitTorrentSync (once it includes git-style versioning) fosters the reproducible research dream: persistent decentralized #bigdata storage
schuyler OH: "I think Mad Men is about to hit UNIX timestamp zero."
wiseio "If Big Data can’t fit hand-in-glove with usability & workflow... big data will be empty data crunching." @billwise
allthingsd.com/20130423/big-d…
@gvwilson I’ve been managing GitHub issues via CLI. You might find it useful too bit.ly/11A7gTB
The magic citations tools in @papersapp works beautifully with @sublimehq. So thrilled at the moment.
@Impactstory you guys got a shout out here (see last page): bit.ly/ZjhtV0
@figshare @rmflight I should have done that. I put the figshare link inline with the text but will add to citations next time.
@MikeTaylor @mbeisen When I heard about embargoes early in grad school it never made sense to me. Didn’t Q it because of impostor synd.
@rmflight @figshare I have (sort of). Not Bioinf but another BMC journal. I just threw a figshare link in the article.
An Introduction to Social Media for Scientists. by @Dr_Bik and @MiriamGoldste in @PLOSBiology
bit.ly/ZjhtV0
@vsbuffalo @pathogenomenick @lexnederbragt @BioMickWatson Agreed. Without Hacker News and my Github stream I’d be lost.
@David_Dobbs Just found out you’ll be at #scifoo. Looking forward to finally meeting you!
@MarkHahnel excited to see you there too. :)
Just saw the participant list for #scifoo. Star struck would be a huge understatement.
Notes from Nature looks fantastic! Transcribe labels from museums in my building!
bit.ly/10x3Xjk
@GrunerDaniel First student finishing? Congrats!
Three Years of Sun in Three Minutes
youtube.com/watch?v=piuKlp…
@davidjayharris @hspter I guess Tweetbot really knows how to get people to click on things! i.imgur.com/DO8PVif.png
@hspter The thumbnail just has ING. I was, like, they, like, really save their money, and stuff.
@profjsb Slate is on it. slate.me/12Cnixm
@hylopsar You realize that you shouldn’t keep your sole copy of *anything* on a cloud hosted platform, right? esp one your not paying for.
@arbesman They’ve been doing this for some time (at least a year). Obviously not everywhere but major locations.
rOpenSci We just won the USGS Earth Sciences Data Challenge! Thanks for all your support.
applifyingusgsdata.challenge.gov/submissions
@msanclem Don’t blame you.
@GrunerDaniel I appreciate you getting back to me so quickly. Feel free to contact w/ further Qs.
--
<long useless confidentiality notice>
@msanclem Wanna trade? We got 85F weather here.
Want: A option to favorite emails (like Twitter) in lieu of acknowledgement.
I’d be so thankful not to have “sounds good” emails anymore.
@kara_woo Sorry. Classes are actually $1.75 discounted from $25. Excel error.
omearabrian Please let folks know: RT I am looking for a postdoc to work on #phylogeography and #speciesdelimitation in #rstats: brianomeara.info/ad
counternotions What "academic freedom" asks former Harvard professor now at Google. bit.ly/15zpDwd
zentree @_inundata I once put my cat in the acknowledgments. He was much more helpful than the reviewers.
@dfflanders hear hear.
Acknowledgements: unhelpful comments from one obnoxious anonymous reviewer made me question my life and journal choices. Supported by NSFDEB
@papersapp I’m almost ready to switch over but you are missing one key feature. auto-bibtex export (available in Mendeley). In the works?
jamescrabtree This really is an outstanding headline - pic.twitter.com/gYUwTCl8gA
Spreadsheets, Retractions, and Bias bit.ly/XYF12N
A former UCL postdoc captures the atmosphere of the British museum in this delightful mix.
bit.ly/15yz3rW
So perfect for writing.
Open Access at Berkeley.
bit.ly/13Fb3D3
<3 Cal.
timoreilly “Science sucks at getting better at science” Great observation made at iAnnotate conference bit.ly/14C5JB5 via @naypinya
@Dr_Bik It’s already picnic day? Damn time sure flies.
@sjGoring feel better dude. Sending good mojo your way.
If you're feeling stressed/burnt out from this week, grab a drink and watch Bob Ross paint some happy trees.
@hspter or a drink.
@adaptive_plant @zotero Sounds awesome. I’d much rather have these features in an open environment.
@adaptive_plant So far Papers is winning. It seems to match papers really well, even arXiv.
@revodavid Thanks David. I love that dog and animal videos are taking up more screen space than code (given the weeks’ mood).
@victoriastodden Looks like we need more such SNAFUs before people really start paying attention to the reproducibility problem.
@adaptive_plant Trying both out for a month to see which one to go with. Zotero desktop does not feel intuitive (yet).
@Impactstory I'm rooting for you kids.
@Impactstory congrats!
@David_Dobbs I move the rest which is worth the extra trouble because I don’t end up with tax returns and other forms in my library.
@David_Dobbs Regular expressions to match the use of doi or journal specific patterns. Some use the word “full”. Catches ~95%.
@David_Dobbs I use Hazel heavily. It moves pdfs to watch folders from anywhere if it looks like an academic PDF.
@David_Dobbs Looks like second option works too!
@David_Dobbs Thanks David! First Q was more important.
Papersapp Q. Can it automatically monitor a folder and grab PDFs that show up? Can it organize PDFs and delete originals (like iTunes)?
The Huffington Post cannot make headline fonts any bigger. It’s that kind of morning.
omearabrian I am looking for a postdoc to work on #phylogeography and #speciesdelimitation in #rstats: brianomeara.info/ad
@soozaphone I read it. wow, just wow. I need another lie down.
@GrunerDaniel @duffy_ma Here’s my secret. media.tumblr.com/3f3ad7e26f09c8… Lots of filing away, deleting, quick replies, and todo items.
@Protohedgehog means altmetrics. ALM specifically refers to article level metrics.
@jhamrick It is. I just want this all to end.
@hspter me too. :(
@jhamrick What a shit week overall. I hate it.
@emilysdarling @carlystrasser I also second that you drive up north.
@recology_ I got access denied on both links. So what is the awesome part?
@minrk I hope to get one of these someday. kck.st/15pRcYP
I really hope I live to be age XX.
reut.rs/15pQCKE
@distribecology @cboettig you just need to remove the proxy part before the url.
@phylorich Yep. I will gladly spend a bazillion hours doing this after you accept my god damned paper. For now just take the PDF.
@tomjwebb me too :) That’s why I zoom in on the text on my laptop/tablet.
@tomjwebb Same thing with double spaced lines. I don’t really need it anymore. I’m going to annotate the PDF.
@JacquelynGill @sjGoring Not sure I entirely agree with your argument. Will post a comment.
@katejjeffery Love it. Brilliant.
# THE FIGURES AND PUT THE LEGENDS BESIDE THEM, SO THAT I DON’T HAVE TO KEEP SCROLLING BACK AND FORTH THROUGH THE PDF
bit.ly/11idvv6
Meter maids everywhere just suck.
bit.ly/17JjUTE
sesync Postdoc opp @ #SESYNC, apply deadline May 1 bit.ly/YlKRom Social, environmental, or cyberinfrastructure synthesis research #phdchat
@distribecology super easy. just ask.
@hspter Does Etsy have an SF office? Are they looking for an ecologist/data/stats nerd who also likes animals?
@hspter I bet everyone at Etsy gets their choice of office animal companion. /jealous.
@sjGoring Not to worry Simon. The one for academia is a drab gray page with “best viewed in Netscape 4.0” at the bottom.
twoeightnine Beginning to think that getting your news a day later on a piece of paper really was the way to go.
Some perks of working in industry. bit.ly/XICmYB
@xieyihui That’s a long dash (also known as EM dash).
@covert I have several such playlists. You've also seen musicforprogramming.net right?
@phylorich @phdpqc I live dangerously in R and also take the slow lane to enjoy the view.
I kid but you’re right.
@BrunaLab So you don’t do invited talks further north? ;)
@weiwei82 Congrats YiWei & Wilmers lab!