Sunday, September 27, 2009

Can Someone Explain to Me When to Use jQuery live() vs. liveQuery() plugin?

Seems the 1.3 live() feature is more limited than the plugin? But will the plugin become deprecated eventually?

This seems to be the best thread so far, but I'll have to head over to IRC perhaps:

Maybe a benchmark on large DOMs comparing the 2 solutions? Anyone interested? If so I'll whip something up.

In any case it seems that the current recommendation is to use live() until you need liveQuery() for some event not supported by live()

Generative shapes and Processing

This might be completely incompatible, but maybe Processing is a good language for "generative bio assay" design.

Some interesting Processing ( work:

Wednesday, September 16, 2009

Wordpress Video Issues to Fix

  1. Right now the short code doesn't have a way to specify only a thumbnail. So if you want a preview image, but NOT the player, you can't do that. Useful for some theme layouts that want to overlay text or something else on top of the preview (like another image, like NEW!)
  • EDIT: Actually there does seem to be a way to do this: get_the_excerpt(). Unfortunately, it inserts the entire HTML element, and some breaks, which is not what I need. I need ONLY the url. I have temporarily added a new function that bascially does the same thing, only returns JUST the URL. Should I make this a template tag? Or should we add an attribute to the short code?
  • 10/25/09 EDIT: OK finally figured this out (mostly). wp_theme_videolink() is something I added to the video.php file of the WP Video project. I will review the code with Hailin and se if we can get it committed. It is basically a version of the wp_add_videolink() that I modified to be for themes, not RSS feeds. Below is a version I used for the eVid theme.
$thumb = wp_theme_videolink();
//Was this : $thumb = get_post_meta($post->ID, 'Thumbnail', $single = true);

  1. There is no way to render the same video in 2 different sizes. For example the eVid theme has a top "Featured Videos" panel which it wants to size large (and widescreen, more later). But the same post can/will appear in the main page. Well, since the theme just dumps the_content(), it uses the same dimensions in both places. So you'd have to hack in a custom meta value to support "featured" vs. "normal", etc. Not elegant. Nicer if the shortcode allowed you to specify a css class and then you could do something like [wpvideo Ay1SIRji class="letterbox"]
  2. Need an option for the shortcode to remove the player elements. Might want to disable some of the controls for various views.
  3. How can you remove/change the Wordpress watermark that the player renders? If it's not already supported, add support for making that dynamic in the shortcode. Not only would someone want to remove it, but they might want their own site logo on it, OR they may want different images depending on category, tag, page, etc.
  4. Need to review/grok how cacheing works. Should cache all thumbnails so loads fast.
  5. Sitemaps --- how to load to Google, Bing, Yahoo

Tuesday, September 15, 2009

SynBio Licensing and SimTK

Met Chris of tonight at Hacker Dojo. Chris is helping on their web site. Very cool site.
Especially interested in :
Might be very useful to carry out simulation after BioBrick part assembly in silico.

Also of interest to the synbiolib discussions on licensing:

Home brew Microfluidics

Home brew Photolithography - large structures - high resolution imagesetter with plastic transparency for a mask
  1. Lateral positioning of the mask and substrate, resist material, and distance between mask and substrate
  2. exposure process of how to transfer patters to the photoresist layer: contact printing or projection printing
  3. development: dissolution or etching of the resist pattern
Are there any home brew or small scale/cost variants of:
  • interfereometric lithography
  • chemical vapor deposition
  • thermal oxidation
  • Sol-Gel deposition
  • Spin coating
  • wet etching
  • chemical or chemical-physical dry etching
What about pattern transfer processes? Steps in general (additive):
  1. deposit functional layer over a substrate
  2. spin coat with photoresist (positive or negative photoresist)
  3. select mask type (dark or clear field)
  4. transfer pattern to the resist layer
  5. etch the structure into the functional layer
  6. wash away photoresist
For lift-off you coat the photoresist directly on the sustrate, put on the mask, develop, but then deposit functional layer OVER the photo resist such that subsequently waashing off the parts with photoresist+functional wash away, but parts with substrate only+functional stay in place.

Sources: Fundamentals and Applications of Microfluidics, Second Ed. Nam-Trung Nguyen, Steven T. Wereley

BioBrick Assay Plan

* in vitro protein expression and interaction analysis
* platform based on a highly parallel and sensitive microfluidic affinity assay
* exhaustively measured the protein-protein interactions of parts (promoter and gene to express) etc.

Monday, September 14, 2009

Microfluidics Notes

Tabeling, Patrick. Circa 2003-2005
Market size for gene chips, lab on chips, sensors, flow controllers, nozzles, valves, pressure measurement, actuators, relays, sata storage, strain sensors $4-8Bln in 2003 USD.
(from DARPA estimates, so how good can those be!!?)

Look at Burns, Johnson, et. al. Science 282, 484 (1998) for (first?) bio lab on a chip paper.

Issues: data acquisition from chip to computer. diagnoses times/latencies

Review Capillary electro-chromatography

Overall architectural considerations:
  • kinematic properties, transport properties, thermodynamic properties, surface tension, vapor pressure, surface accomodation
  • Fluidic interconnects - standards? universal interconnects?
  • pumps and valves - fabrication, integration, elastomers
  • fluid injection = volume vs. sensitivity (if you only have one cell worth of protein, and add fluid you need sensitive sensors
Use cases:
  • Confining molecules for detection
  • kinetics of chemical reactions
  • molecule activitiy
  • intensifying and analyzing role of surfaces in catalytic reactions
  • applying magnetic fields to conotrol reactions
  • labelling molecules
  • biomolecules with NEMS
  • amplification of other than DNA biological structures
  • non-newtonian fluids
Viable marketable serviecs with demand/practical application today
  • sequenced low-nanogram scale bacterial and mammalian DNA
  • support of more efficient PCR prep, see example overview of the issues here:
"Accurate quantification of the sequencing library is essential to achieve high yield and high quality sequencing. Inaccuracy in quantification is addressed by the manufacturers through ‘titration’ runs of the sequencer, which are used to empirically divine the concentration of productive DNA fragments in the sequencing library."

Overview of modern sequencing:
In vitro clonal amplification
As molecular detection methods are often not sensitive enough for single molecule sequencing, most approaches use
an in vitro cloning step to generate many copies of each individual molecule. Emulsion PCR is one method, isolating
individual DNA molecules along with primer-coated beads in aqueous bubbles within an oil phase. A polymerase chain
reaction (PCR) then coats each bead with clonal copies of the isolated library molecule and these beads are
subsequently immobilized for later sequencing. Emulsion PCR is used in the methods published by Marguilis et al.
(commercialized by 454 Life Sciences, acquired by Roche), Shendure and Porreca et al. (also known as "polony
sequencing") and SOLiD sequencing, (developed by Agencourt and acquired by Applied Biosystems).[17][18][19]
Another method for in vitro clonal amplification is "bridge PCR", where fragments are amplified upon primers
attached to a solid surface, developed and used by Solexa (now owned by Illumina). These methods both produce
many physically isolated locations which each contain many copies of a single fragment. The single-molecule method
developed by Stephen Quake's laboratory (later commercialized by Helicos) skips this amplification step, directly
fixing DNA molecules to a surface.[20]
Parallelized sequencing
Once clonal DNA sequences are physically localized to separate positions on a surface, various sequencing approaches
may be used to determine the DNA sequences of all locations, in parallel. "Sequencing by synthesis", like the popular
dye-termination electrophoretic sequencing, uses the process of DNA synthesis by DNA polymerase to identify the
bases present in the complementary DNA molecule. Reversible terminator methods (used by Illumina and Helicos) use
reversible versions of dye-terminators, adding one nucleotide at a time, detecting fluorescence corresponding to that
position, then removing the blocking group to allow the polymerization of another nucleotide. Pyrosequencing (used
by 454) also uses DNA polymerization to add nucleotides, adding one type of nucleotide at a time, then detecting and
quantifying the number of nucleotides added to a given location through the light emitted by the release of attached
"Sequencing by ligation" is another enzymatic method of sequencing, using a DNA ligase enzyme rather than
polymerase to identify the target sequence.[22][18][19] Used in the polony method and in the SOLiD technology offered
by Applied Biosystems, this method uses a pool of all possible oligonucleotides of a fixed length, labeled according to
the sequenced position. Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for
matching sequences results in a signal corresponding to the complementary sequence at that position.

Saturday, September 12, 2009

Vote on Wordpress Video features

Here's a list of feature I already want to add for my own selfish needs, so vote early and vote often:
*Support L10N strings
*more examples of CDN usage (maybe a step by step for S3 integration)
*implement support for Zend JobQueue or Amazon SQS, or some open
source Q --- any recommendation? I typically use ApacheMQ.
*support for players other than Flash (I do a lot of mobile video stuff).
*support for live video casting

If you have others, please add to the comments. I am gearing up for a hack fest on this starting Monday, so let me know what you want!

Friday, September 11, 2009

Wordpress Video 1.0 Released

One issue I hit is that the server for ffmpeg2theora seems to have gone down? Maybe due to traffic from this project? Anyway, I was able to get the source code from:
and from source.

UPDATE: it finally came back up! Got the binary and used it.

To get a fully functional FFMEG from source: Make sure you have libtheora, ogg, vorbis, x264 already built/installed. (TODO: need to see what configure opts vorbis and theora need, just used defaults)

Note: I used --enable-shared on all builds where the README.txt from the plugin did not explicitly give a command.

Also needed, and (NOTE: libgsm has a crappy makefile, so you need to build it shared manually AFTER the initial build. That cost me 30 minutes in the wee hours of the night.)

NOTE: Be sure to use the EXACT snapshot of x264 as documented, else there is a missing symbol and it won't be used. I wonder why such an old version? TODO: look into updating to the latest if some benefit.

Also DON'T USE latest: libdc1394-2.1.2.tar.gz -- but getting config error:
seems to be needed but this header is not available in the latest src. Must have been deprecated.
with ./configure --enable-shared
This required libraw1394 (I used libraw1394-1.2.0.tar.gz to be consistent with the older libdc1394)
Also need:
yum install xorg-x11-devel
(I actually gave up on dc1394 for the moment since my image didn't have X and getting it built from source was a nightmare...just gave up for lack of time...36 hours of no sleep is not good for the body. Give me 2 hours a day and I'm good!

(later that AM...)

For FFMPEG, I had to apply this patch:

For setup, do make sure to set the video-config.php AND the video-lib.php constants. If you get an error email about ffmpeg, it is probably because your ffmpeg is wrong. If you get an error like "doesn't exist" then it is probably because it cannot find the database (I had to grant additional access to a new server, for example.)

When I created a new video (WMV from the "capture thumbnail" button mentioned on the new media shows up once you start playing the video --- nice touch, but to a sleep deprived person like myself, it was a brain teaser...need my 4th Peets today :)

Also, immediately after upload, I tried to create a post with the short code and it failed. This was once; I tried but could not reproduce it...probably a race condition in the processing vs. posting.

Some nice to haves: thumbnail in the media library view, add a "copy shortcut to clipboard" button, or multi-select in the media library view.

Thursday, September 10, 2009

Overview of the Wordpress Video plugin 0.9

Well it's not a plugin, per se, but really set of plugins, and some background tasks, and an overall suggested architecture.

The basic flow so far is:
(Image checked in by Hailin @ Auttomatic)

  1. Register an action (remote_transcode_one_video) so that when the user attaches a file, it fires off an exec() to run video-upload.php
  2. in the transcoder (now we are on another server, most likely) it checks the auth, saves metadata about size, etc. and uses FFMPEG to transcode
  3. now it sends the file to the file server (send_to_fileserver) where it moves the files into the final resting place, and has a placeholder for sending it off to a CDN or other replicant
Basically, it bounces off the user's blog (WPMU) to the transcoder via a post which in turn bounces it off to the file server. I presume all these scripts should have access to the exact same database (or slave relicant) in order to keep the processing steps in synch, and to update the post metadata about where the final resting place of the video is, and the video info on size, etc.

It seems to me that in the best case, it will require a lot of (real-time HTTP) chatter and not very efficient file transfer through all this. Some folks out there are posting about getting evertything working on one box --- which should be very possible, but frankly I'd be more interested in getting it off the blog sever. I think that was the right decision architecturally, even if it means more complexity for the admin. But I wonder if moving the files around serially is the best way. Maybe some sort of queue (Amazon SQS for the message) + an S3 input bucket for the transcoding workload. Then when the transcoding process finishes a file, it moves it into the fileserver "master" bucket, and the fileserver caches pull from that bucket?? I know it will be fairly complex with load balancing, and geographic distribution, so it probably needs more thought that 30 seconds :)

The key point is to make the HTTP chatter asynchronous. Also by putting the messages into a queue, and having the LRPs just pull from the queue, you get more robustness against error. I'm sure there are all sorts of race conditions by simply relying on the simple status messages , i.e. update_video_info( $blog_id, $post_id, $format, $status ). I think having a workflow that can pick up in the case of error, and at least show the admin which ones are in various error states would be nice.

The other option, assuming a smaller site without geographic distribution, is to put it all on NFS servers behind the main server. That way the file transfers are not HTTP based. If you're not on EC2 I can see where this might be a viable alternative. We do this in the colo now. But if you're on EC2, then simply writing to S3 seems to be the way to go.

I think straight away we should implement an S3 option for the file server, use or similar for the encoding such that it writes to your S3 bucket, and then use CloudFront or other CDN for distribution.

If you really want to duplicate the features of, and hack all the ffmpeg options, then let me know and I can set up a high performance transcoder AMI on EC2 with the scripts.

Some other observations:
  • the upload script and the transcode script checks if you have a DATACENTER defined, presumably for load and redundancy; this is a stub, so you would have to add some logic to round robin or randomize or in other ways pick a "transcoder" server and a "fileserver"
  • there is a simple authentication mechanism using a simple md5 salty string to auth to the transcoder -- would be nice to add per user auth to prevent spam or abuse, or to block users who post illegal content -- CERTAINLY users should change this string in production! maybe in the comments we can make that more explicit. Security by obscurity is never the right way to go
  • we are using some standard formats, but there are ffmpeg templates with many more examples, lots for mobile video, etc. we should import these, and just have a list in the options of all template files, or maybe even create the template inside a post, perhaps with some sort of GUI
*For the fileserver: One nice thing might be to combine some of the logic from the S3 or CloudFront plugins.
*for both file server and transcoder: Also, might be nice to incorporate some sort of stats database on usage, RTT, etc
*for both: Might also be nice to check the country of origin from GeoIP/maxmind and pick a mirror based on that
*for the transcoder: How does this differ from Are these complimentary/orthogonal? Are they substitutes?
*for the ffmpeg calls in the transcoder, a lot of the variables are hardcoded --- we should have some way to specify these for different video types in some option set

Monday, September 07, 2009

Some Bio Toolkits

Also to look at:

Saturday, September 05, 2009


Of course we came in steerage!

record id219405
date arrived06-02-1888
nameAntonio Ficcaglia
aka names
gender, ageMale, 12
native countryItaly
city fromU
embarkation portNaples
purposeStaying in the USA
travel compartmentSteerage
ship manifest id81199
ship nameCachemire

record id219406
date arrived06-02-1888
nameMichele Ficcaglia
aka names
gender, ageMale, 41
native countryItaly
city fromU
embarkation portNaples
purposeStaying in the USA
travel compartmentSteerage
ship manifest id81199
ship nameCachemire

It's like Pacino said...

Every time I try to get out, they pull me back in...

Interesting iphone stuff

Got code?
Joe Hewitt's new lib for native iphone -
java to objective-c cross compiler -

Wordpress Plugin for StackOverflow look and feel?

I am thinking this might be a good start? I couldn't find anything like StackEngine for Wordpress or WPMU...

All the hacking I think it will take is to add a link to add to the number, a "vote", and then sort the comments (grouped by threads of course) by number. Add a dash of Ajax and it should be suitable. I'll try to post an example later if anyone's interested (and I actually get to it).

Reading List for This Week (ok, just for fun)

Friday, September 04, 2009

Interview Question For Clojure

Draw, label, and in other ways explain this in terms of Clojure:
"Clojure is based on the idea that immutability and functional
programming are more important contributors to program robustness
than is static typing." - Rich Hickey

Thursday, September 03, 2009

Seeking Clojure

This is just a post of some links and references I went through as I start looking at Clojure during the HackerDojo Clojure Meetup. Some of these were explicitly discussed, and some were just tangents sparked in my mind by the discussion.

Example toy program: n of k marbles problem, how many combinations?
NOTE: I think this was the problem under discussion...there was some ambiguity as to exactly what the problem was :) I thought this should be solved by the standard formula for the binomial coefficient, but maybe I misunderstood the problem?

Other links of interest to me relevant to Clojure (and more generally functional programming languages and parallel programming:
The above are not specific posts mentioned in the meetup...just my list of pertinent articles for your amusement and further reading.

Some toy problems to practice with: