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− | {{EMW_Street_Bio}}
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| + | <title>Biota Beats - by EMW Streetbio</title> |
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− | <h3>★ ALERT! </h3> | + | <h1 id="logo"><a href="https://2016.igem.org/Team:EMW_Street_Bio"></a></h1> |
− | <p>This page is used by the judges to evaluate your team for the<a href="https://2016.igem.org/Judging/Awards"> Best Software Tool award</a>. </p>
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| + | <li><a href="concept.html">Concept</a></li> |
| + | <li> |
| + | <a href="https://2016.igem.org/Team:EMW_Street_Bio/Hardware">Hardware</a> |
| + | <ul> |
| + | <li><a href="https://2016.igem.org/Team:EMW_Street_Bio/Hardware/Incubator">Incubator</a></li> |
| + | <li><a href="https://2016.igem.org/Team:EMW_Street_Bio/Hardware/Records">Microbiome Records</a></li> |
| + | </ul> |
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| + | <li><a href="https://2016.igem.org/Team:EMW_Street_Bio/Wetware">Culturing</a></li> |
| + | <li class="active"><a href="https://2016.igem.org/Team:EMW_Street_Bio/Software">Sonification</a></li> |
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| + | <!-- Features 2 --> |
| + | <div class="wrapper"> |
| + | <header class="major special"> |
| + | <h2>Sonification</h2> |
| + | </header> |
| + | <section class="container"> |
| + | <article class="row"> |
| + | <p>How can microbes be sonified? Once inoculated, our microbiome records were imaged utilizing an |
| + | open-source camera to generate 2D images. We developed several approaches to generate sound and |
| + | music from these images, with a principal question in mind: how is the sound meaningful from a |
| + | biological perspective?</p> |
| | | |
− | <p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p> | + | <p>Ultimately, we focused on three forms of data that could be extracted from the images of our |
− | </div> | + | records: microbe location, density, and cluster size. Given the design of our records, we could add |
| + | an additional layer of information by having different segments of each record correspond to |
| + | organisms swabbed from different parts of the body. With our incubator and camera, we could also |
| + | take time-lapse images, adding a time parameter. Based on these inputs, we developed several |
| + | algorithms to convert these data streams to sound and music. </p> |
| + | </article> |
| + | <article class="row"> |
| + | <header class="special"> |
| + | <h4>Background</h4> |
| + | </header> |
| | | |
| + | <p><u>Sonification:</u> the use of non-speech audio to convey information or perceptualize data.</p> |
| | | |
| + | <p>Auditory perception has advantages in temporal, spatial, amplitude, and frequency resolution that |
| + | open |
| + | possibilities as an alternative complement to visualisation techniques.</p> |
| | | |
| + | <p>There is prior work sonifying algae data, star data, and microbial data into music by various |
| + | methods. |
| + | For example, scientists looked for patterns in readings from blue-green algae samples collected in |
| + | the |
| + | western English Channel then transformed the data into musical notes: |
| + | <a href="http://www.livescience.com/23626-microbe-music-algae-songs.html"> |
| + | http://www.livescience.com/23626-microbe-music-algae-songs.html</a>. |
| + | The tune "Bloom" illustrates how some |
| + | algae species bloom occasionally and become more abundant for short periods of time. They had lower |
| + | abundance of microbe correspond to lower notes, and chord progression was related to day length, |
| + | chlorophyll concentration in the water, and other physical parameters.</p> |
| | | |
| + | <p>Here astronomers converted star data from NASA's Kepler telescope into reggae songs: |
| + | <a href="http://www.space.com/16119-stars-reggae-music-kepler-telescope.html?_ga=1.215947806.863416596.1474217560.">link</a>. |
| + | </p> |
| | | |
| | | |
− | <div class="column full_size"> | + | <p>Then a team converted RNA sequences and protein 3D structure into sound: |
− | <p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.</p> | + | <a href="http://victoriashennan.com/Anthropocene-Microbial-Music">link</a>.</p> |
| | | |
| + | </article> |
| + | </section> |
| + | <section class="container"> |
| + | <header class="special"> |
| + | <h3>Making</h3> |
| + | </header> |
| + | <article class="row"> |
| + | <p>Based on inspiration from the previous sonification projects, the sonification software was designed |
| + | using prior image processing techniques. First, a Gaussian filter reduces the image noise, and the |
| + | image |
| + | is converted to a black-and-white binary image. The location of the center of each cluster and the |
| + | size |
| + | of each cluster are stored. Based on this information, the density of each area on the plate is |
| + | computed.</p> |
| | | |
− | <h5> Inspiration </h5> | + | <p>Each image is mapped to a coordinate system, and the colony location correlates to musical notes, or |
− | <p> | + | pitches. Then density of the colonies corresponds to background music. Granular Synthesis is a |
− | Here are a few examples from previous teams:
| + | method by |
− | </p> | + | which sounds are broken into tiny grains that are redistributed and reorganized to form other |
− | <ul> | + | sounds. |
− | <li><a href="https://2013.igem.org/Team:TU-Munich/Results/Software">TU Munich 2013</a></li> | + | Here the concept of granular synthesis is used with the density data.</p> |
− | <li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</a></li> | + | |
− | <li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li> | + | <p>In the first attempt, shape and size of the colonies was to correlate to different scale types: |
− | </ul> | + | major, |
| + | natural minor, melodic minor, pentatonic,and chromatic. However, a classifier with only five groups |
| + | brings more ambiguities. Thus, it was switched to FM synthesis. FM synthesis stands for frequency |
| + | modulation synthesis; the timbre (tone quality) of a waveform is changed by adjustingits frequency |
| + | with |
| + | a modulator frequency that is also in the audio range, resulting in a more complex waveform. This |
| + | new |
| + | tone can be described as "gritty" if it is a thick and dark timbre. For synthesizing harmonic |
| + | sounds, |
| + | the modulating signal must have a harmonic relationship to the original carrier signal.</p> |
| + | |
| + | <p>With two types of culture plates, the program can be used to compare the sonification results from |
| + | each. |
| + | With a timelapse video for 2-3 days of the culture plates, it is also possible to listen to the |
| + | sound |
| + | change as the microorganisms grow.</p> |
| + | |
| + | <p>Setup for camera module:</p> |
| + | |
| + | <span class="image 8u -2u 12u(mobile)"><img |
| + | src="https://static.igem.org/mediawiki/2016/b/b7/T--EMW_Street_Bio--images_yixiao1.jpg" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 8u -2u 12u(mobile)"><img |
| + | src="https://static.igem.org/mediawiki/2016/0/08/T--EMW_Street_Bio--images_yixiao2.jpg" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/0/00/T--EMW_Street_Bio--images_yixiao3.jpg" |
| + | alt=""/></span> |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/c/c6/T--EMW_Street_Bio--images_yixiao31.jpg" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/1/13/T--EMW_Street_Bio--images_yixiao4.png" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/1/18/T--EMW_Street_Bio--images_yixiao5.png" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/d/d4/T--EMW_Street_Bio--images_yixiao6.png" |
| + | alt=""/></span> |
| + | |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/4/4b/T--EMW_Street_Bio--images_yixiao7.png" |
| + | alt=""/></span> |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/2/20/T--EMW_Street_Bio--images_yixiao8.png" |
| + | alt=""/></span> |
| + | <span class="image 6u"><img |
| + | src="https://static.igem.org/mediawiki/2016/f/f8/T--EMW_Street_Bio--images_yixiao9.png" |
| + | alt=""/></span> |
| + | |
| + | </article> |
| + | </section> |
| + | <section class="container"> |
| + | <header class="special"> |
| + | <h3>Creating Audio files from the Microbiome.</h3> |
| + | </header> |
| + | <article> |
| + | <span class="image 8u -2u 12u(mobile)"><img |
| + | src="https://static.igem.org/mediawiki/2016/a/a5/T--EMW_Street_Bio--images_yixiao_ex1.jpg" |
| + | alt=""/>Mapping Method from Microbiome to Music. 5 discrete areas are shown and sonified.</span> |
| + | |
| + | <span class="image 8u -2u 12u(mobile)"><img |
| + | src="https://static.igem.org/mediawiki/2016/8/8e/T--EMW_Street_Bio--images_yixiao_ex2.png" |
| + | alt=""/>Squares of Distances from Colony Clusters to the Center in each area. Each cluster is assigned with a rhythmic sound by a different musical instrument.</span> |
| + | |
| + | <p>Each numbered audio file corresponds to the sonification of 4 out of 5 discrete areas shown above.</p> |
| + | <audio controls> |
| + | <source src="https://static.igem.org/mediawiki/2016/9/9a/T--EMW_Street_Bio--images_sound1.mp3" |
| + | type="audio/mp3"> |
| + | Your browser does not support the audio element. |
| + | </audio> |
| + | <audio controls> |
| + | <source src="https://static.igem.org/mediawiki/2016/e/e5/T--EMW_Street_Bio--images_sound2.mp3" |
| + | type="audio/mp3"> |
| + | Your browser does not support the audio element. |
| + | </audio> |
| + | <audio controls> |
| + | <source src="https://static.igem.org/mediawiki/2016/7/74/T--EMW_Street_Bio--images_sound3.mp3" |
| + | type="audio/mp3"> |
| + | Your browser does not support the audio element. |
| + | </audio> |
| + | <audio controls> |
| + | <source src="https://static.igem.org/mediawiki/2016/3/38/T--EMW_Street_Bio--images_sound4.mp3" type="audio/mp3"> |
| + | Your browser does not support the audio element. |
| + | </audio> |
| + | <audio controls> |
| + | <!--<source src="https://static.igem.org/mediawiki/2016/9/9a/T--EMW_Street_Bio--images_sound1.mp3" type="audio/mp3">--> |
| + | <!--Your browser does not support the audio element.--> |
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| + | </article> |
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