Nature and Technology

Beginner's Tutorial to RubyAMF with RESTful Rails

2007-10-09T15:57:00.000-07:00

Update Dec. 9, 2007: I decided to get my own domain and to use Wordpress instead of Blogger so this blog has moved. The new address is panscendo.com. Any new updates to this tutorial will be here

Update Nov. 29, 2007: Tutorial now current for Rails 2.0 RC2 and RubyAMF 1.5

RubyAMF is a flash remoting gateway that allows a Rails backend to communicate with a Flex frontend. The marriage allows rapid development of rich internet applications. This tutorial goes over the basic steps of creating a RESTful Rails project that has a HTML and Flex frontend and data persistence via MySQL database.

Rails

Setting up the Rails Project

Create a new rails project by first opening a command prompt and then changing the working directory to your rails project directory. Once there type the following command to create a rails project called "rubyamf"

> rails rubyamf

Now that we have a project created we need to install RubyAMF by using the rails installer. To do this you must first move into the rubyamf directory and then run the ruby plugin installer script


> cd rubyamf
rubyamf> ruby script/plugin install http://rubyamf.googlecode.com/svn/trunk/rubyamf

Note: If you receive a error like this: "Missing the Rails 1.99.0 gem. Please 'gem install -v=1.99.0 rails', update your RAILS_GEM_VERSION setting in config/environment.rb for the Rails version you do have installed, or comment out RAILS_GEM_VERSION to use the latest version installed." then you just need to commet out the the line specified by the error. Since Rails 2.0 is still being developed it isn't actually 1.99.0 but 1.99.blah.

Connecting Rails to your Database

Since we want to be able to save our data we need to create a database to store said data. Open up a command prompt again and, assuming MySQL is already running, type:

> mysql -u root -p
Enter password:
mysql> create database rubyamf;

Good, now we need to tell Rails how to communicate with the database we just created. Open up the config/database.yml file and edit the text to look like this:

development:
 adapter: mysql
 endocing: utf8
 database: rubyamf
 username: root
 password: yourpassword
 host: localhost

Creating a REST controller

We now have a Rails project that is able to talk to a database. Cool! Now what we need to do is create a controller that issues the commands. Rails allows us to do this with a little beauty command called "scaffold_resource." When we run it we always follow it with an uppercase singular noun and a series of name value pairs. The noun is the name of the Rails model, or the database table, and the name:value pairs are the names of the column in the table and their datatype. Lets try it out; open up that command prompt once again, make the rubyamf directory the active dir and then issue the following command:

rubyamf> ruby script/generate scaffold Message text:string

Note: "scaffold_resource" has been changed to "resource" in Rails 2.0.

Among other things you now have two important files; messages_controller.rb which Flex and RubyAMF will communicate with, and a migrate file (called 001_create_messages.rb) that we will run to create the database table.

Lets do the latter right now. In the command prompt type this:

rubyamf> rake db:migrate  Making Sure it all Works
 We're basically finished with rails for now. But before we call it good lets just make sure that it is running smoothly (and so we can look in awe of what we just did).
 Boot up your rails server:
 rubyamf> ruby script/serverNow open up your favorite browser and make sure that RubyAMF is running by going to http://localhost:3000/rubyamf/gateway.  You should see something like the following image.
  If you do not get the above image and instead get prompted to download an AMF file you need to edit the app/controllers/rubyamf_controller.rb file.  Open it up and change:
amf_response = if request.env['CONTENT_TYPE'].to_s.match(/x-amf/) 
    headers['Content-Type'] = "application/x-amf"
    RailsGateway.new.service(request.raw_post) #send the raw data throught the rubyamf gateway and create the response
  else 
    welcome_screen_html # load in some stub html
  end
send_data(amf_response, :type => 'application/x-amf')To:
amf_response = if request.env['CONTENT_TYPE'].to_s.match(/x-amf/) 
    content_type  = "application/x-amf"
    RailsGateway.new.service(request.raw_post) #send the raw data throught the rubyamf gateway and create the response
  else 
    content_type = "text/html"
   welcome_screen_html # load in some stub html
  end
send_data(amf_response, :type => content_type, :disposition=>'inline')Note: If you use the rubyamf controller fix suggested on the RAMF blog it will brake your application (thanks goes to Quest4 for figuring this one out).  The above code is not official so use it at your own risk.
Now make sure our Messages controller is working by pointing your browser to http://localhost:3000/messages and witnessing this:
So far so good. Now what we need to do is to add some data into the database so our Flex app has something to retrieve.  Lets do that by clicking the "New Message" link at http://localhost:3000/messages, typing a short message (this tutorial uses "Hello World"), and press the "Create" button.  *Bam* you just added a new Message to the database.
Enough of Rails, lets dive into Flex
Flex
Setting up the Flex Project
Boot up Adobe Flex and create a new project. I named mine rubyamf for consistency but you could name it something else (like planctomyces). Click the "Next" button, not the "Finish" button.  Set the output folder to the "bin" dir (you'll probably have to create this) in the "public" dir of your rails project.  That is, \rubyamf\public\bin.  Press "Next." Now make sure that your output folder URL is set to: http://localhost:3000/bin.  Press "Finish." You now have a shiny new Flex project.
  Adding services-config.xml
 We need to create an XML file that will point your Flex project in the direction of your Rails project.  This is called the "services-config.xml" file and it needs to be placed in the same folder as your MXML file.  Create a new file via File > New > File and name it "services-config.xml"
 Now for the code.  Open up "services-config.xml" and add this code:
<?xml version="1.0" encoding="UTF-8"?>
 <services-config>
  <services>
   <service id="rubyamf-flashremoting-service" class="flex.messaging.services.RemotingService" messageTypes="flex.messaging.messages.RemotingMessage">
    <destination id="rubyamf">
     <channels>
      <channel ref="rubyamf"/>
     </channels>
     <properties>
      <source>*</source>
     </properties>
    </destination>
   </service>
  </services>
  <channels>
   <channel-definition id="rubyamf" class="mx.messaging.channels.AMFChannel">
    <endpoint uri="http://localhost:3000/rubyamf/gateway" class="flex.messaging.endpoints.AMFEndpoint"/>
   </channel-definition>
  </channels>
 </services-config>Now we tell Flex to include "services-config.xml" when it compiles the application.  To do this we need to add a command to the flex compiler.  Do this by Project > Properties > Flex Compiler and adding -services "services-config.xml" to the "Additional compiler arguments" field.
Creating the UI
Now the fun part.  Here's the Flex UI code to paste into the MXML file:
<?xml version="1.0" encoding="utf-8"?>
 <mx:Application xmlns:mx="http://www.adobe.com/2006/mxml" layout="vertical">
  <mx:TextArea id="resultTxt"
   width="80%" height="30%" />
  <mx:Button id="getMessage"
   label="Get Messages" />
  <mx:TextArea id="createTxt"
   width="80%" height="30%" />
  <mx:Button id="createMessage"
   label="Create Message" />
 </mx:Application>The above should look something like this:
The above is pretty and all but it's like a mannequin; looks good but it has no function.  Lets give it a purpose and turn it into a real live lady.  We'll do this by adding the RemoteObject code.
Between the <mx:Application> and <mx:TextArea /> tags add this:
 <mx:Script>
  <![CDATA[
   import mx.rpc.events.ResultEvent;
   import mx.rpc.events.FaultEvent;
   import mx.rpc.Fault;

   private function onFault(e:FaultEvent):void
   {
    resultTxt.text = e.fault.faultString;
   }
   private function onResult(e:ResultEvent):void
   {
    resultTxt.text = e.message.toString();
   }
  ]]>
 </mx:Script>
 
 <mx:RemoteObject id="messageService" fault="onFault(event)" 
  source="MessagesController" destination="rubyamf">
  <mx:method name="index" result="onResult(event)" />
  <mx:method name="create" result="onResult(event)" />
 </mx:RemoteObject>RemoteObject is where the magic occurs.  This particular instance we chose to call id="messageService"
  source="MessagesController" is the name of the rails controller we want to communicate with.  The actual name needs to be exactly the same as the ruby class name (open up app/controllers/messages_controller.rb)
  destination="rubyamf" maps to the channel-definition in the services-config.xml file we created earlier (which then points Flex to the rubyamf remoting endpoint).
The two <mx:method /> tags map to two of the methods in the MessagesController class.
 
 To call our methods we'll update the "click" event handlers of the two buttons in our UI. Add click="messageService.index.send();" to the "getMessage" button and click="messageService.create.send({text: createTxt.text});" to the "createMessage" button.
 <mx:Button id="getMessage"
  label="Get Messages"
  click="messageService.index.send();" />
  
 <mx:Button id="createMessage"
  label="Create Message" 
  click="messageService.create.send({text: createTxt.text});" />Back to Rails
 Tweaking messages_controller.rb
 We're almost finished. All we have to do now is explain to our rails controller about AMF. We'll be polite and speak it's native language; ruby.  Open up app/controllers/messages_controller.rb and add "format.amf { render :amf => @messages }" to the respond_to block of the index method.
 def index
     @messages = Message.find(:all)

     respond_to do |format|
       format.html # index.rhtml
       format.xml  { render :xml => @messages.to_xml }
       format.amf { render :amf => @messages }
     end
 endThe respond_to block tells our controller to act differently when different mediums are attempting to work with it.  If a browser calls the index method the controller will spit out HTML but now if the Flash Player requests something the controller will spit out AMF.  Perfect!
 Updating the create method is a bit trickier.  We add an if statement to check if AMF was sent, and if so, do some tricky stuff.
 def create
  if is_amf
   @message = Message.new({:text => params[0][:text]})
  else
   @message = Message.new(params[:message])
  end
 ...Note: params[0][:text] was suggested by Peter Armstrong - thanks!
Then we add some code to the respond_to block that tells the controller to speak AMF if it's talking to the flash player.
 ...
  respond_to do |format|
    if @message.save
         flash[:notice] = 'Message was successfully created.'
         format.html { redirect_to message_url(@message) }
         format.xml  { head :created, :location => message_url(@message) }
   format.amf  { render :amf => "Message Saved" }
       else
         format.html { render :action => "new" }
         format.xml  { render :xml => @message.errors.to_xml }
   format.amf  { render :amf => @message.errors }
       end
     end
   endWhew!  That's it.  We can test the app now.
 Testing... (in awe)
 First we need to start our server (or restart it).
 rubyamf> ruby script/server Compile and run your Flex project.  It should be running from the URL "http://localhost:3000/bin/rubyamf.html." Click on "Get Messages" and you should see something like this:
  Type a message into the second text area ("We received data from RubyAMF, can we send data to it?").  Press the button and you should see:
  Finished!
 
Yee-haw! By using the powers of RubyAMF we have just grabbed data from a database and written some right back at speeds much faster than XML or JSON. Plus, we still get a HTML front end for those types that fear flash.



DNA Painter
2007-10-07T20:46:00.000-07:00
DNA Painter is a small application that reads a nucleotide sequence and outputs an image.  The logic behind it is pretty simple.  I coded it while being influenced by ideas of cellular automata although it, technically, is not implementing those ideas.

The program works by reading a nucleotide string (A, T, C, or G) and applying logic to the current character.  Each nucleotide gives the program a different and simple instruction.
A: Move one pixel down and add some red to the current color
T: Move one pixel right and add some green to the current color
C: Move one pixel up and add some blue to the current color
G: Move one pixel left and do something wacky (I think the current build right now just darkens the pixel)
In Actionscript 3.0 a pixel is a 32 bit number with 8 bits corresponding to the Alpha (transparency), Red, Green, and Blue values respectively.  By mapping the RGB values to certain nucleotides I'll get at least 3 colors per image.  Since chances are good that certain pixels will be painted on more than once the combination of two or more RGB values will result in a different color (red + blue = magenta, etc).  This means that any image, given a long enough nucleotide sequence, will result in a multitude of color.

Application

Although I created DNA Painter as an expression of art through computation and science one use of DNA Painter is the creation of visual representations of genes.  The application can output an image based off of, say, the aldolase gene of three different mammalian species so the relative divergence of the gene can be seen.  Yes, I realize that using some sort of bioinformatic statistical analysis on the actual DNA string will be much better.  But it's not cool you see, and in this world we need cooo-oool.

Notes on usage
Some things to think about while playing around with the program:
A long red line in an image means the mapped gene has a long series of A (adenine) and a long green horizontal line means T (thymine) and so on.
A stair step in the image is a sequence of alternating nucleotides
Increasing the bitmap size will show a more accurate picture of the gene.  This is because the drawing wraps when it reaches an edge of the bitmap.  So a larger bitmap means less overlap so less "noise".
The five available genes that are embedded in the application are all human genes


More Info on the genes
GDF9
ZNF7
CEACAM6
BAAT
LGALS8
Further Development

Although I would like to make the images prettier by applying filters and other effects I think I would like to focus more on the application of the program rather than the aesthetics.  It would be nice to remove the wrap effect so each gene or sequence will be a consistent image no matter the bitmap size.  This will allow the user to zoom in and out (and pan).  It'll allow the visualization of repeating sections of nucleotides that can be shown to exist across related genes.  Furthermore, by applying the application to mRNA we could break down each image to a series of codons.

Now that I think about it we could create a catalog of common DNA sequences.  Whoa!


Exposed: Crows using tools
2007-10-05T12:39:00.000-07:00



The Behavioural Ecology Research Group of Oxford has recently published a paper in Science detailing tool use by New Caledonian crows, Corvus moneduloides, by attaching miniature cameras to their tail feathers.

Both Sciam and BBC News cover the story.  BBC News links to the videos but if you want to avoid the 30 sec advertisements I suggest you go straight to the source.


Free college lectures
2007-10-04T20:25:00.000-07:00
Ah yes, get your quality learnings right here - all for free.  UC Berkeley has uploaded a series of lectures to youtube on various topics including biology, physics, and chemistry.  There will be more to come.

So far, in the biology realm, there is only Integrative Biology 131.  The lectures I browsed are very good and I look forward to more.  Be a lobbyist and help get some lectures on evolution and/or ecology up.

This page lists the lectures by class: http://youtube.com/profile?user=ucberkeley

Update: I found out that Berkeley has been uploading webcasts and podcasts of their lectures since 2005.  This semester they have a total of 45 classes.  Here is the class list.  To watch or listen to achieved lectures change the number following "semesterid=" in the URL to a previous semester (changing it to "1" will give you Spring 2005's class list).  There are some semesters with no classes and others with only a few.


Scientists Ask Congress To Fund $50 Billion Science Thing
2007-09-29T10:22:00.000-07:00



According to the scientists, the electromagnetic science-maker will make atoms move and spin around very quickly, though spectators at the hearing said afterward they could not account for how one could get some atoms to move around faster than other ones if everything is made of atoms anyway. In addition, the scientists said that the device would be several miles in circumference, which puzzled onlookers who had long assumed that atoms were tiny. Despite these apparent inconsistencies, the scientists, in Rep. Gordon's words, appeared "very smart-sounding" and confident that their big spinner would solve some kind of problem they described.

- via The Onion

The above article is a stunningly good satire on the difficulties of scientific journalism and thus the way the public views scientific funding and research.


Encyclopedia of Life
2007-09-19T21:23:00.000-07:00
Comprehensive, collaborative, ever-growing, and personalized, the Encyclopedia of Life is an ecosystem of websites that makes all key information about life on Earth accessible to anyone, anywhere in the world. Our goal is to create a constantly evolving encyclopedia that lives on the Internet, with contributions from scientists and amateurs alike. To transform the science of biology, and inspire a new generation of scientists, by aggregating all known data about every living species. And ultimately, to increase our collective understanding of life on Earth, and safeguard the richest possible spectrum of biodiversity.

I get goosebumps every time I watch the promo video for the Encyclopedia of Life.  It was launched back in May and I haven't heard anything about it since then.  If E. O. Wilson pulls this off it could be the best thing to hit the internet.  Ever.

 


Cordyceps Fungi vs Ants
2007-09-18T21:17:00.000-07:00
Cordyceps is a type of fungi that parasitizes insects and some arthropods.  BBC's Planet Earth had a clip on a type of ant that, when parasitized, is 'brainwashed' (the ants perception of pheromones is screwed) into climbing up a tall structure.  The fruiting body consumes the ant's brain and grows out of its head.  The result is a mystical ant-unicorn chimera.  

Is this a case of extreme co-evolution or just a sort of unintended effect (much like many plants have chemicals that evolved for self-defense but work in such a way that we just have to use them recreationally)?  I'll do some sleuthing in the near future.

fungi growth on insect! [youtube]



Find more info here.


Enemies of Reason
2007-09-16T20:50:00.000-07:00
Richard Dawkins, the head-cheese of atheism, has recently broaden his attacks to superstition vs reason instead of religion vs science.  In his two part series titled Enemies of Reason Dawkins argues that religion and pseudo-scientific health care are a result of poor reasoning and that both tax human society.

I highly recommend the series.  I've embedded them on this blog for your convenience.  It is now easier to watch the two episodes than turning on your tv.  So, ummm, don't turn on your tv.

Slaves to Superstition



The Irrational Health Service




Randomness and Free Will
2007-09-08T04:07:00.000-07:00
For the past few days I have been interested in the history of life on Earth.  One question that is sure to arise when dealing with such things is if we restart the system (from the big bang) will intelligent life arise again.  More specifically, will humans always be the victors on the top of the evolutionary tree.  Will we truly be the king of the mountain?

I think that the above question begs another.  Is there true randomness in nature or are there definite causes and effects?  For different outcomes to occur in a system that is initiated with the same values for each variable there needs to be randomness.  If the evolution of intelligent life is inevitable then it would have to be the end of a long string of causes and effects occurring in a world that lacks randomness.

Nature is all about regularly occurring phenomenon.  The laws of physics must work in such a way that a certain set of causes will produce an effect.  Science, at its foundation, requires the 'necessity' of a certain effect from a certain cause (science of course does not dictate how the world works but only finds the best way of explaining it.  So far it has worked really well).  There are plenty of terms like "random" in scientific models, such as the "stochasticity" or how the "electron cloud"  but these are random in the sense that they are uncertain.  There are so many variables affecting the model that we just say it is random.  But of course it is not truely random.

So we do not see any randomness in nature.  What does this mean about free will?  Unless we conjure up some sort of spiritual tinkerer to bless our minds with something outside of the physical world then we must accept that our thoughts and actions are predestined.  We are part of the same laws that govern everything else in the world and if those laws lack randomness then we must as well.

It seems that the actions you choose to take when you're 80 years old are predictable from the moment you are conceived.  Well, actually, they are predictable from the moment the universe began.

Update:Hmmmm.... Determinism


Sword Fern, Polystichum munitum
2007-08-30T09:30:00.000-07:00

Sword Fern.  Photo taken near middle fork snoqualmie river, WA.

Although the above sword fern may look and act almost exactly like another in nearby Oregon it has hints of once being on the track to becoming a different species.  A paper by Soltis et al. (1996) looked at chloroplast DNA of the sword fern, among other plants, and found that there is a significant difference between populations in the north (Alaska to central Oregon) and populations in the south (central Oregon to northern California).

Genetic isolation of a once uniform population does not occur easily.  For two populations to emerge from one there must be some sort of isolating mechanism that prevents the exchange of genetic material.  Isolation allows the two populations to diverge genetically through genetic drift and selection without sharing the changes.

Soltis et al. (1996) suggested that the isolating mechanism was extensive glaciation which occurred in the Pleistocene (the famous Ice Age).  Because plants have an extremely difficult time growing on moving rivers of ice the sword fern population was cleaved and left with, at least, one northern refugium and one southern refugium.  The two populations were left to go about their own business and respond to their own local environment.

Today the glaciers are mostly gone and the northern and southern populations are allowed to fill the gap.  Genetic material is being transferred between the two and the differences will most likely blur but there will always be the hint of what once could have been a new and noble species.

Sources

Soltis, D., Gitzendanner, M., Strenge, D., Soltis, P. (1996) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America.  Plant Systematics and Evolution (206) 353-373.  http://www.springerlink.com/content/v15m72k6238462p3/


Lunar Eclipse
2007-08-25T12:10:00.000-07:00
Tuesday morning people in the western hemisphere and eastern Asia will be able to view the second lunar eclipse of 2007.  A lunar eclipse occurs when the Earth comes between the sun and the moon.  The Earth prevents sunlight from hitting the moon so a shadow is cast.

Here's a simulation of a lunar eclipse created by E-Lad.

 


SciVee
2007-08-23T08:21:00.000-07:00
It is often difficult to communicate scientific findings to both the scientific community and the general public.  This is because journals are numerous, expensive, and often difficult to digest.  In an attempt to remedy this problem SciVee has launched.

From the FAQ, "SciVee is about the free and widespread dissemination and comprehension of science."  It's a video service, kind of like youtube, but smart.  SciVee has the support of PloS, an online, free, peer-reviewed, journal.  It works by having scientists submit their paper and accompany it with a short video presentation explaining what their paper is addressing.  It's neat.  It's a step towards getting science out to the masses.

Right now there seems to be a shortage of content but check it out anyways.


Meadow Vole, Microtus pennsylvanicus
2007-08-21T20:20:00.000-07:00

Baby meadow vole, taken near Rochester, WA.

A paper by Pierce et al. (2005) titled Food-deprivation-induced changes in sexual behavior of meadow voles, Microtus pennsylvanicus addresses one small aspect of the complex conditions which determine vole reproduction.  The research found that short-term food availability has an impact on reproduction of meadow voles.

The researches basically withheld food from male and female voles and observed the changes in sexual behavior.  The females were more sensitive to brief (6-12 hr) and moderate (18-24 hr) pauses in food than the males.  Females must expend more resources on carrying babies than males do with expending semen so it makes sense that females are more sensitive to a decrease in important resources such as food.

Sources

Pierce, A. Ferkin, M. Williams, T. 2005. Food-deprivation-induced changes in sexual behavior of meadow voles, Microtus pennsylvanicus. Animal behaviour 70(2): 339-348.


Fractals in Nature
2007-08-12T08:25:00.000-07:00
The morphology of plants is structured in such a way that repetitive patterns occur.  This is termed modular organization and is a method of defining certain repetitive structures of a plant.  If we consider a single instance of a leaf or a branch as a module then we can reduce a (very) simplified tree to being just a collection of these two components.  If we are in need of representing a tree programmically then realizing the above makes things much easier.  Even more interesting Ferra et al. (2005) states that “in some cases, the modules are arranged into compound, recursively nested, fractal-like structures, with similar patterns appearing at different scales.”



Ferra et al. mentioned that many plants have fractal-like structures.  So what are they?  Fractals are statistically self-similar structures, which, according to Mandelbrot (1982), is “when each piece of a shape is geometrically similar to the whole, both the shape and the cascade that generate it are called self-similar.”  To see this graphically it'll help to refer to the picture of the fern.  Each pinnule (the smallest 'leaf') of the fern is geometrically similar to each pinna which is geometrically similar to the entire fern.  Nature repeats and beauty is a result.

Below is a flash application that I created by modifying code written by Matt Pearson (2007).  The tree is composed of a 'trunk' and a 'leaf' both of which are laid down by a recursive function.  Click it to randomly generate a new tree.



Sources

[1] B. B. Mandelbrot. The fractal geometry of nature. W. H. Freeman, San Francisco, 1982.
[2] Ferrao P., Godin C., Prusinkiewicz P. Toward a quantification of self-similarity in plants. Fractals, 2005. http://algorithmicbotany.org/papers/similar.fractals2005.pdf
[3] Pearson, M. Fractals in ActionScript 3 - A Flash Tutorial. zenbullets.com. 2007. http://zenbullets.com/blog/?page_id=80
[4] http://www.flickr.com/photos/roddh/156854158/