Team:Vanderbilt/SoftwareProjectSubPageBuilder

From 2014.igem.org

(Difference between revisions)
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var p = createP("The final device will consist of a PDMS slab with microfluidic geometries embedded on the bottom of the slab. Fluids can be run through the device by either directly pipetting them through the inlet or by affixing microfluidic tubing with 1/16” OD to the inlet and pumping fluids in using a fluid pump such as a syringe pump or peristaltic pump.");
var p = createP("The final device will consist of a PDMS slab with microfluidic geometries embedded on the bottom of the slab. Fluids can be run through the device by either directly pipetting them through the inlet or by affixing microfluidic tubing with 1/16” OD to the inlet and pumping fluids in using a fluid pump such as a syringe pump or peristaltic pump.");
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         leftPageBuilder.appendChild(head);
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         document.getElementById("left_page").appendChild(head);
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         leftPageBuilder.appendChild(list);
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         document.getElementById("left_page").appendChild(list);
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         leftPageBuilder.appendChild(p);
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         document.getElementById("left_page").appendChild(p);
     };
     };
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         document.getElementById("right_page").appendChild(img1);
         document.getElementById("right_page").appendChild(img1);
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    };
 
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    subPage.createCollaborationsLeft = function() {
 
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        var head = document.createElement("header");
 
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        head.appendChild(document.createTextNode("Results and Directions"));
 
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        var text = "In addition to our own wetware project, our team led fruitful collaborations with a total of three" +
 
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            " other iGEM teams. First, we played a major role in assisting Vanderbilt's microfluidic division with the b" +
 
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            "iological aspect of their project. We prepared the biobrick parts they tested in their microfluidic device" +
 
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            ", including transforming the E. coli they used to study their quorum-sensing fluorescent oscillator circui" +
 
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            "t. Second, we provided feedback to Vanderbilt's software division about their own project involving a prog" +
 
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            "ram to aid in the manipulation of genetic sequences. We used the program as if it were for a real project " +
 
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            "and gave them suggestions on how to make their program easier to use and more useful to biologists. ";
 
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        var p1 = subPage.createP(text);
 
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        var building = subPage.createPhoto("http://parts.igem.org/wiki/images/9/9c/Vanderbilt_Yellow_square.png", "Ravenwood High School", 250, 250, "Ravenwood High School");
 
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        building.style.float = "left";
 
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        building.style.margin = "1%";
 
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        text = "Last but not least, we provided significant assistance and guidance to the Ravenwood Raptors high schoo" +
 
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        "l iGEM team. In a series of conversations with Dr. Amanda Benson, we planned a smaller scale version of our ow" +
 
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        "n project that involved only a single terpene synthase gene. After visiting the high school and presenting our" +
 
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        " idea, the students voted to choose it for their project. We also provided the primers and sage genomic DNA te" +
 
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        "mplate they used in their experiments. ";
 
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        var p2 = subPage.createP(text);
 
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        leftPageBuilder.appendChild(head);
 
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        leftPageBuilder.appendChild(p1);
 
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        leftPageBuilder.appendChild(building);
 
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        leftPageBuilder.appendChild(p2);
 
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    };
 
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    subPage.createCollaborationsRight = function() {
 
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        var header = document.createElement("header");
 
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        header.appendChild(document.createTextNode("References"));
 
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        var text1 = "1. USDA Industrial Uses Reports. Essential Oils Widely Used in Flavors and Fragrances. September 1995.";
 
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        var text2 =
 
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            "2. Ajikumar PK, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G. Terpenoids: opportunities for biosynth" +
 
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            "esis of natural product drugs using engineered microorganisms. Mol Pharm. 2008;5(2):167-90.";
 
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        var text3 =
 
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            "3. Dudareva N, Klempien A, Muhlemann JK, Kaplan I. Biosynthesis, function and metabolic engineering of plant " +
 
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            "volatile organic compounds. New Phytol. 2013;198(1):16-32.";
 
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        var text4 =
 
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            "4.Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia " +
 
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            "coli for production of terpenoids. Nat Biotechnol. 2003;21(7):796-802.";
 
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        var p1 = subPage.createP(text1);
 
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        var p2 = subPage.createP(text2);
 
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        var p3 = subPage.createP(text3);
 
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        var p4 = subPage.createP(text4);
 
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        p1.style.fontStyle = "italic";
 
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        p2.style.fontStyle = "italic";
 
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        p3.style.fontStyle = "italic";
 
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        p4.style.fontStyle = "italic";
 
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        rightPageBuilder.appendChild(header);
 
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        rightPageBuilder.appendChild(p1);
 
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        rightPageBuilder.appendChild(p2);
 
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        rightPageBuilder.appendChild(p3);
 
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        rightPageBuilder.appendChild(p4);
 
     };
     };
     return subPage;
     return subPage;
}
}

Revision as of 22:13, 26 January 2015

function SoftwareProjectSubPageBuilder() {

   var subPage = new SubPageBuilder();
   subPage.maxSubPage = 4;
   subPage.getMaxSubPage = function() {
       return subPage.maxSubPage;
   };
   subPage.createSubPage = function (subPageNum) {
       switch(subPageNum){
           case 1:
               subPage.createPage1Left();
               subPage.createPage1Right();
               break;
           case 2:
               subPage.createPage2Left();
               subPage.createPage2Right();
               break;
           case 3:
               subPage.createPage3Left();
               subPage.createPage3Right();
               break;
           case 4:
               subPage.createPage4Left();
               subPage.createPage4Right();
               break;
       }
   };
   subPage.createPage1Left = function() {
       var head = document.createElement("header");
       head.appendChild(document.createTextNode("Developing low cost, easy-to-design microfluidic device fabrication method"));
       var text = "Our team utilized a unique microfluidic development process that emphasizes low cost and rapid prototyping. Through the use of open source design software and cheap manufacturing methods we were able to fabricate microfluidic devices in a cost and time efficient manner. It is our hope that these methods can be utilized by other iGEM teams who are interested in incorporating microfluidics into their projects without the hassle of complex design and fabrication techniques.";
       var p1 = subPage.createP(text);
       var head2 = document.createElement("header");
       head2.appendChild(document.createTextNode("Microfluidic Computer Aided Design (CAD)"));
       text = "Several programs were used by members on the team to design and ultimately fabricate microfluidic devices. Initially, traditional computer aided design software packages were used such as AutoCAD and Solidworks. These packages provide advanced features which designers can wield to make complex devices with varying functions such as mixing and trapping cells. Alternative software packages were explored such as the open source vector graphics software Inkscape which proved to be easy to use in the design of a microfluidic device. Inkscape is an open source analogue to Adobe Illustrator, a common vector graphics editing software. Inkscape is easy to use and with a few online tutorials, ideas for microfluidic designs can be turned into realities.";
       var p2 = subPage.createP(text);
       document.getElementById("left_page").appendChild(head);
       document.getElementById("left_page").appendChild(p1);
       document.getElementById("left_page").appendChild(head2);
       document.getElementById("left_page").appendChild(p2);
   };
   subPage.createPage1Right = function() {
       var img1 = subPage.createPhoto("VU_MF_Photo_1.JPG", "Vacuum used in fabricating microfluidic devices made of PDMS", 487, 519, "Vacuum used in fabricating microfluidic devices made of PDMS");
       img1.style.position = "relative";
       img1.style.margin = "auto";
       img1.style.marginBottom = "1em";
       var img2 = subPage.createPhoto("VU_MF_Photo_1_%281%29.JPG", "Material used in fabrication", 487, 578, "Material used in fabrication");
       img2.style.position = "relative";
       img2.style.margin = "auto";
       img2.style.marginBottom = "1em";
       document.getElementById("right_page").appendChild(img1);
       document.getElementById("right_page").appendChild(img2);
   };
   subPage.createPage2Left = function() {
       var head = document.createElement("header");
       head.appendChild(document.createTextNode("Microfluidic Prototyping using a Vinyl Cutter"));
       var text = "In order to rapidly prototype microfluidic devices of different geometries and designs, our team explored fabrication techniques that bypassed the complicated photolithography process that is standard for microfluidic devices in research laboratories. Photolithography has the benefit of achieving very fine resolution and fine details for pinpoint fluid manipulation, but it is detracted from its lengthy creation process. The time scale from device design to fabrication of a working device using photolithography is on the order of 2-3 days and uses a variety of expensive and highly technical equipment that is not readily accessible to many iGEM teams. ";
       var p1 = subPage.createP(text);
       text = "Our team focused on bypassing the entire photolithography process by using a commercially available arts and crafts vinyl cutter (Silhouette) to produce device masters. Arts and crafts vinyl cutters are typically used to craft complex shapes and figures for use in decorations. A vinyl cutter has a resolution on the order of 250 microns which means that the devices made using this technique are considerably larger than those made using standard photolithography techniques. While the devices obtained from vinyl cutting are larger, for many synthetic biology applications this is not an issue. For the purpose of E. chrono, the size of the channels simply affected the total amount of fluid needing to be pumped into the device.";
       var p2 = subPage.createP(text);

text = "As mentioned previously, the main benefit of using a vinyl cutter is the rapid production of microfluidic masters. A vinyl cutter is able to take a device design to a master and ultimately a device in roughly an hour. By simplifying and speeding up the design and fabrication process, vinyl cutting can allow iGEM teams with no microfluidic knowledge to rapidly develop their own devices for testing. Using an open source design software such as Inkscape allows a team to rapidly formulate and then test a microfluidic device within an afternoon.";

       var p3 = subPage.createP(text);
       leftPageBuilder.appendChild(head);
       leftPageBuilder.appendChild(p1);
       leftPageBuilder.appendChild(p2);
       leftPageBuilder.appendChild(p3);
   };
   subPage.createPage2Right = function() {
       var img1 = subPage.createPhoto("VU_MF_Photo_2.JPG", "", 240, 325, "");
       img1.style.marginRight = "1em";

var img2 = subPage.createPhoto("VU_MF_Photo_2_%281%29.JPG", "", 240, 325, "");

       img2.style.marginLeft = "1em";
       rightPageBuilder.appendChild(img1);
       rightPageBuilder.appendChild(img2);
   };
   subPage.createPage3Left = function() {
       var head = document.createElement("header");
       head.appendChild(document.createTextNode("Converting a Design to a Vinyl Master"));
       var list = document.createElement("ol");

var arr = [["Import the design for microfluidic device into Silhouette Studio, the vinyl cutting software used to make designs. Note: for Design process, see Microfluidic Device Design instructions"], ["With device inside Silhouette, check to make sure dimensions are within the vinyl cutter resolution limits. No feature of the device should be smaller than 250 microns, this rule applies predominantly to channel widths."], ["Place vinyl paper inside printer and load the paper in place"], ["Place the blade setting to 2"], ["On the right hand side there is are several options for vinyl cutting, click Include Edges and then submit the job to be printed."], ["Once the device is cut onto a vinyl sheet, using a razor blade peel away the surrounding vinyl so that only the cut out is left"], ["With tweezers and razor blade, pick up the cutout and place on a glass slide"], ["Flatten the cutout onto the glass slide, this creates the “master” with which microfluidic devices can be manufactured"]];

subPage.addMultLI(list, arr);

       leftPageBuilder.appendChild(head);
       leftPageBuilder.appendChild(list);
   };
   subPage.createPage3Right = function() {
       var img1 = subPage.createPhoto("VU_MF_Photo_3_%281%29.JPG", "Vinyl Cutter", 421, 571, "Vinyl Cutter");
       img1.style.margin = "auto";
       img1.style.marginBottom = "1em";
       document.getElementById("right_page").appendChild(img1);
   };
   subPage.createPage4Left = function() {
       var head = document.createElement("header");
       head.appendChild(document.createTextNode("Fabricating a PDMS device using a Vinyl Master"));
       var list = document.createElement("ol");

var arr = [["Prepare a PDMS solution with 10:1 ratio of PDMS to epoxy and mix well"], ["Pour the PDMS mixture on top of the master, making sure that the PDMS spreads out over the whole petri dish and covers the master evenly."], ["Place the petri dish with PDMS inside a vacuum chamber and suction the chamber for 20 minutes to allow the air bubbles inside the PDMS to flow out"], ["Once the bubbles have been removed from the PDMS, place the Petri dish in a warm incubator to cure for 8 hours or overnight. "], ["In order to remove the device, a razor blade or scalpel can be used to cut out the device from the surrounding PDMS inside the petri dish."], ["The vinyl master can be removed from the bottom of the device and either thrown away or reused for fabrication of more devices"], ["Take a 1/16” OD syringe tip and use it to “punch” a hole inside the microfluidic inlet channel and inside the microfluidic outlet channel"], ["Once the device holes have been punched, the device can be plasma bonded to a glass slide or coverslip by treating the bottom of the microfluidic device (where the channels are open) with a plasma wand or plasma oven for 45 seconds and then bonding to a plasma treated glass slide."]];

subPage.addMultLI(list, arr);

var p = createP("The final device will consist of a PDMS slab with microfluidic geometries embedded on the bottom of the slab. Fluids can be run through the device by either directly pipetting them through the inlet or by affixing microfluidic tubing with 1/16” OD to the inlet and pumping fluids in using a fluid pump such as a syringe pump or peristaltic pump.");

       document.getElementById("left_page").appendChild(head);
       document.getElementById("left_page").appendChild(list);
       document.getElementById("left_page").appendChild(p);
   };
   subPage.createPage4Right = function() {
       var img1 = subPage.createPhoto("VU_MF_Photo_3.JPG", "Microfluidic Device", 487, 649, "Microfluidic Device");
       img1.style.margin = "auto";
       img1.style.marginBottom = "1em";
       document.getElementById("right_page").appendChild(img1);
   };
   return subPage;

}