Category Archives: Open Notebook Thoughts

Testing out a Jekyll-based notebook

I am try­ing out Jekyll as an alter­na­tive to Word­Press for pow­er­ing this site and my open lab note­book. If you sub­scribe, the new RSS (atom) feed for the new note­book is at http://carlboettiger.info/atom.xml. I’d love to hear any feed­back, good or bad, about the switch.  A recent post gives my own reflec­tions.  The site’s …

May 3, 2012 – 10:50 am | By Carl | Posted in Open Notebook Thoughts | Comments (0)

Writing reproducibly in the open with knitr

Sweave is some­thing of a gold stan­dard in repro­ducible research. It cre­ates a dynamic doc­u­ment, writ­ten in a mix of LaTeX and R code where the results of the analy­sis (num­bers, fig­ures, tables) are auto­mat­i­cally gen­er­ated from the code and inserted into the result­ing pdf doc­u­ment, mak­ing them easy to update if the data or …

April 7, 2012 – 2:58 pm | By Carl | Posted in Open Notebook Thoughts | Tagged | Comments (5)

Citations in markdown using knitr

I am find­ing myself more and more drawn to mark­down rather then tex/Rnw as my stan­dard for­mat (not least of which is the ease of dis­play­ing the files on github, par­tic­u­larly now that we have auto­matic image upload­ing). One thing I miss from latex is the cita­tion com­mands. (I under­stand these can be pro­vided to …

March 24, 2012 – 9:33 pm | By Carl | Posted in Computation, Open Notebook Thoughts | Tagged | Comments (0)

knitr, github, and a new phase for the lab notebook

I have recently mod­i­fied the basic work­flow of my lab note­book since dis­cov­er­ing knitr. Before, I would write code files which I could track on github, push fig­ures cre­ated by the code to flickr, and then write a note­book entry on word­press describ­ing what I was doing. I’d embed each fig­ure I wanted into the …

March 21, 2012 – 12:13 pm | By Carl | Posted in Open Notebook Thoughts | Tagged | Comments (3)

Citing R packages

I’m not always care­ful in cit­ing all the R pack­ages I use. R actu­ally has some rather nice built-in mech­a­nisms to sup­port this, so I really have no excuse. Here’s some quick exam­ples: To cite the ouch pack­age in pub­li­ca­tions use: Aaron A. King and Mar­guerite A. But­ler (2009), ouch: Ornstein-Uhlenbeck mod­els for phy­lo­ge­netic com­par­a­tive …

March 20, 2012 – 10:02 am | By Carl | Posted in Open Notebook Thoughts | Tagged | Comments (4)

Knitr with flickr and wordpress

It’s amaz­ing how nice it is to work with well-developed soft­ware. It took me about 20 min­utes to extend Yuhui’s inter­face to allow me to upload images through flickr instead of imgur, and embed them into a word­press blog using the short­code from the flickr gallery plu­gin. To do this, I just mod­i­fied the hook …

February 28, 2012 – 2:59 pm | By Carl | Posted in Open Notebook Thoughts | Comments (4)

Using knitr and RWordPress to publish results directly from R

One of the great things about knitr is its flex­i­bil­ity. Here I set knitr up to pub­lish to Word­Press. I will then use RWord­Press to pub­lish the out­put auto­mat­i­cally. I will base the word­press for­mat on the github-flavored mark­down for­mat. I change the markup for out­put and source-code to use the nice code­blocks pro­vided by …

February 27, 2012 – 6:31 pm | By rwordpress | Posted in Open Notebook Thoughts | Comments (8)

Some Collaborative Tools for Science

Ania Truszczyn­ski invited me to give a lit­tle talk on the use of var­i­ous col­lab­o­ra­tive tools for sci­en­tists.  I enjoyed pre­sent­ing this as a chalk-talk, but alas no slides to link so here’s a list of ref­er­ence. Rather than the impos­si­ble attempt to be com­pre­hen­sive, this is restricted to resources I use reg­u­larly and have …

February 6, 2012 – 3:30 pm | By Carl | Posted in Open Notebook Thoughts, Teaching | Comments (0)

Journey to freedom — a code’s tale of open source license migration

My soft­ware wants to be free. It wants to be seen and used and loved by as many peo­ple as pos­si­ble. When first it heard of open source licenses, it set sail to join the com­pany of great soft­ware in the promised land, but find­ing true free­dom has been a tor­tured jour­ney. In the clutches …

January 31, 2012 – 5:58 pm | By Carl | Posted in Open Notebook Thoughts | Comments (3)

Are open lab notebooks considered prior publication?

This ques­tion invari­ably comes up at some point in any dis­cus­sion of open note­book sci­ence.  This con­cern is usu­ally voiced in ref­er­ence to the high-visibility mag­a­zines, which many sci­en­tists seem to assume will have very restric­tive con­di­tions.  A quick read of their poli­cies shows oth­er­wise.  Here are the links to pre-publication poli­cies of major jour­nals, …

January 16, 2012 – 10:47 am | By Carl | Posted in Open Notebook Thoughts | Comments (7)