User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/08/30

From OpenWetWare
Jump to navigationJump to search
Comparative Phylogenetics Main project page
Previous entry      Next entry

Adaptive Dynamics

<html> <a href="" title="analytic_contours1 by cboettig, on Flickr"><img src="" width="480" height="480" alt="analytic_contours1" /></a> </html> Simulation Results (code) <html>

<a href="" title="coexist_sim1 by cboettig, on Flickr"><img src="" width="480" height="480" alt="coexist_sim1" /></a> </html> Analytics (Analytics code)

Notebooks and files

Looking at a better way to get figures into my online notebook. I often run simulations that generate figures which I look at, make some adjustments to the code based on the figure, and then delete or overwrite the figure without uploading it to my notebook, because it isn't "right" or "finished" and uploading takes a lot of clicks, particularly when the code generates 36 figures in a run. Then I discover on some later date that I really want to take another look at the figure. While I usually have the version of the code that generated it saved in github, the codes sometimes take many hours to run, so this isn't very efficient -- it would make much more sense to have everything saved in the notebook. I'm looking into photo hosting sites for figures, as I think these could offer many other benefits as well. Seeing what friendfeed can suggest on this:

<html> <iframe src="" frameborder="0" height="600" width="600" style="border:1px solid #aaa"></iframe> </html>

Exploring Flickr for scientific figures in my notebook

<flickr>4942856122|thumb|m|Image embedded using the mediawiki flickr plugin </flickr>

  • So I've set up a flickr account. First things first: edit settings so default permissions are cc-by. Now time to explore.
  • First concern was for permanent stable links, which it seems are guaranteed even in the free account. Will wait and see if I need the capacity of the pro account, but 100MB/month should be a good start.

Offline/Desktop tools for Flickr

  • One of the most promising things about flickr seems to be the extensive development around it. Several linux native programs support Flickr, including the social netwoking manager, gwibber. Particularly interested in tools that will let me have the automated, command-line upload ability to connect to my notebook. Even if I can automatically get figures into Flickr, I guess there's still the step of getting them into the notebook. I'm beginning to understand more and more why Cameron talks about aggregators so much. Meanwhile, looking at two ubuntu-native tools:
  • DFO, the Desktop flickr organizer for gnome. Looks nice, easy GUI, very polished. However, no longer under active development and not sure if it has command line support. Can be installed with apt-get.

--Carl Boettiger 18:21, 30 August 2010 (EDT) Doesn't seem reliable for uploading, sometimes images don't appear

  • flickrfs -- remote mount your flickr account like a directory. No interface but then acting like a directory means immediate interoperability with command line and other desktop applications. Should make adding/uploading very easy. Uses filename.meta for metadata. Can be installed directly with apt-get.

--Carl Boettiger 18:21, 30 August 2010 (EDT) Unable to actually get the directory to mount with user permissions. Mounts but unable to add with root permissions

  • kflickr: native KDE flickr uploader. Works great, simple and intuitive. Just for uploading though. No obvious command line interface.
  • Nautilus integration works. simple, easy. We'll see about scripting. apt-get able: nautilus-flickr-uploader
  • flickr_upload Yay, an easy to use command-line tool that just works. This looks very promising, able to upload photos and add tags with ease.

<syntaxhighlight lang="bash">

flickr_upload --tag="my_tag" image.jpg


From Flickr to Notebook

  • Can embed flickr using the mediawiki plugin. Note that syntax is a bit picky, no spaces, a few set sizes. Can always embed as above with html, which, unlike photobucket embed, lets you set the image size in the html.

Looking for embedding options for a whole collection. Flickr supports "sets" and other kinds of groups (including tags). Site will make a slideshow of a set but prevents iframe embedding: <syntaxhighlight lang="html4strict">

 <html><iframe height="500px" width="1000px" src="">

</iframe></html> </syntaxhighlight>

Ah, seems to have it's own embedding option linked from its slideshow.

Slideshows can also be created using tags. Replacing every instance of the tag in the embed script with the new tag works to create a slideshow of that tag, making it easy to automate this. So, with a single commandline call I can embed the full 30 likelihood ratio comparisons from a few days ago:

<syntaxhighlight lang="bash"> flickr_upload --tag="LR_anoles" *vs*.png </syntaxhighlight>


<object width="400" height="300"> <param name="flashvars" value="offsite=true&lang=en-us&page_show_url=%2Fphotos%2Fcboettig%2Ftags%2FLR_anoles%2Fshow%2F&page_show_back_url=%2Fphotos%2Fcboettig%2Ftags%2FLR_anoles%2F&user_id=46456847@N08&tags=LR_anoles&jump_to=&start_index="></param> <param name="movie" value=""></param> <param name="allowFullScreen" value="true"></param><embed type="application/x-shockwave-flash" src="" allowFullScreen="true" flashvars="offsite=true&lang=en-us&page_show_url=%2Fphotos%2Fcboettig%2Ftags%2FLR_anoles%2Fshow%2F&page_show_back_url=%2Fphotos%2Fcboettig%2Ftags%2FLR_anoles%2F&user_id=46456847@N08&tags=LR_anoles&jump_to=&start_index=" width="400" height="300"></embed></object> </html>

Adaptive Dynamics Analytics Results

The numerical coexistence time simulations are still running, meanwhile here are the rest of the analytic set (and one simulation that finished). See code for parameters etc.

<html> <object width="400" height="300"> <param name="flashvars" value="offsite=true&lang=en-us&page_show_url=%2Fphotos%2F46456847%40N08%2Fsets%2F72157624718737779%2Fshow%2F&page_show_back_url=%2Fphotos%2F46456847%40N08%2Fsets%2F72157624718737779%2F&set_id=72157624718737779&jump_to="></param> <param name="movie" value=""></param> <param name="allowFullScreen" value="true"></param><embed type="application/x-shockwave-flash" src="" allowFullScreen="true" flashvars="offsite=true&lang=en-us&page_show_url=%2Fphotos%2F46456847%40N08%2Fsets%2F72157624718737779%2Fshow%2F&page_show_back_url=%2Fphotos%2F46456847%40N08%2Fsets%2F72157624718737779%2F&set_id=72157624718737779&jump_to=" width="400" height="300"></embed></object> </html>

More Open Notebook Science discussion

<html> <iframe src="" frameborder="0" height="400" width="600" style="border:1px solid #aaa"></iframe> </html>