biovisualize/index.html

## index.html
<!DOCTYPE html>
<html>
<head>
<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js"></script>
<script type="text/javascript" src="svg_slides.js"></script>

<script type="text/javascript">

    // There are probably better ways of loading the SVG, but this is one example I found

    d3.xml("test.svg", "image/svg+xml", function(xml) {
        var importedNode = document.importNode(xml.documentElement, true);
        d3.select("body").node().appendChild(importedNode);

        svg=d3.select("body").select("svg")
            .attr("height","100%")
            .attr("width","100%");
        slides = svg_slides(svg,1500);

        // Lets test the slide scales - put a bouncing ball on slide id 3
        s = slides[3];
        circle = svg.append("svg:circle")
            .attr("cx",s.scale_x(500)).attr("cy",s.scale_y(500))
            .attr("r",20)
            .style("fill","steelblue");

        next = 500;

        function bounce() {
            next = -next;
            circle.transition().duration(2500).attr("cx",s.scale_x(500+next))
            .each("end",bounce);
        }

        bounce();
    });

</script>
</head>
<body></body>
</html>

## svg_slides.js
/*  This is a basic attempt to use d3 to process transitional slides from SVG files (i.e. Inkscape)
    The main objective here was to keep everything as simple as possible

    To create a slide, simply create a rectangle in inkscape where you set the object ID to "slide_" + a number
    This number can be either integer or float, so "slide_1","slide_2" and "slide_3.56" all work.

    The script sorts the slide-numbers and transitions between slides based on the final sorted order.

    It is easy to add slides into a pre-existing ordering, simply by chosing a floating number in the middle of the two
    Example: If we want to add slide between "slide_2" and "slide_3" we simply add a rectancle called "slide_2.5"

    Keyboard definitions:
        Right arrow:    next slide
        Left arrow:     previous slide
        Home:           first slide
        End:            last slide

    Please be aware that you need to remove any layer transition is the svg file (or put the layer transition to 0,0)

    Each slide has a scale_x and scale_y functions that have pre-set range to the slide boundaries and a default
    domain of [0,1000], allowing the user to position objects easily onto each slide.


    ziggy.jonsson.nyc@gmail.com
*/


function svg_slides(svg,delay) {
    var slides={},
        slide = 0,
        delay = delay ? delay : 3500;

    svg.attr("preserveAspectRatio","xMidYid meet");

    rects = svg.selectAll("rect")[0];

    for (i=0;i<rects.length;i++) {
        id = rects[i].id;
        console.log(id);
        if (id.slice(0,6)=='slide_') {
            slides[id.slice(6)]=rects[i]
            rects[i].scale_x = d3.scale.linear().range([rects[i].x.baseVal.value,rects[i].x.baseVal.value+rects[i].width.baseVal.value]).domain([0,1000]);
            rects[i].scale_y = d3.scale.linear().range([rects[i].y.baseVal.value,rects[i].y.baseVal.value+rects[i].height.baseVal.value]).domain([0,1000]);
            }

    }

    keys = Object.keys(slides).sort();
    slides.keys = keys;

    function next_slide()  {
        svg.transition().duration(delay).attr("viewBox",slides[keys[slide]].x.baseVal.value+" "+slides[keys[slide]].y.baseVal.value+" "+slides[keys[slide]].width.baseVal.value+" "+slides[keys[slide]].height.baseVal.value);
    }

    d3.select("body").on("touchmove", function() { if(slide<keys.length-1) {slide++; console.log(slide);}});

    d3.select(window).on("keydown", function() {
        switch (d3.event.keyCode) {
          case 37: {if (slide>0) {slide=slide-1; console.log(slide);next_slide()};break}
          case 39: {if(slide<keys.length-1) {slide++; console.log(slide);next_slide()};break}
          case 36: {slide = 0;next_slide();break}
          case 35: {slide = keys.length -1; next_slide();break}
        }

     });

    // Start with the first slide
    next_slide();
    return slides
}

## test.svg
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<svg
   xmlns:osb="http://www.openswatchbook.org/uri/2009/osb"
   xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:cc="http://creativecommons.org/ns#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:svg="http://www.w3.org/2000/svg"
   xmlns="http://www.w3.org/2000/svg"
   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
   width="1052.36"
   height="744.09003"
   id="svg2"
   version="1.1"
   inkscape:version="0.48.2 r9819"
   sodipodi:docname="test2.svg">
  <defs
     id="defs4">
    <linearGradient
       id="linearGradient3779"
       osb:paint="solid">
      <stop
         style="stop-color:#ffffff;stop-opacity:1;"
         offset="0"
         id="stop3781" />
    </linearGradient>
  </defs>
  <sodipodi:namedview
     id="base"
     pagecolor="#ffffff"
     bordercolor="#666666"
     borderopacity="1.0"
     inkscape:pageopacity="0.0"
     inkscape:pageshadow="2"
     inkscape:zoom="0.98994949"
     inkscape:cx="520.12813"
     inkscape:cy="80.053504"
     inkscape:document-units="px"
     inkscape:current-layer="layer1"
     showgrid="false"
     inkscape:window-width="1280"
     inkscape:window-height="972"
     inkscape:window-x="-8"
     inkscape:window-y="-8"
     inkscape:window-maximized="1"
     showguides="false" />
  <metadata
     id="metadata7">
    <rdf:RDF>
      <cc:Work
         rdf:about="">
        <dc:format>image/svg+xml</dc:format>
        <dc:type
           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
        <dc:title />
      </cc:Work>
    </rdf:RDF>
  </metadata>
  <g
     inkscape:label="Layer 1"
     inkscape:groupmode="layer"
     id="layer1"
     transform="translate(0,0)">
    <rect
       style="fill:none;stroke:none"
       id="slide_6"
       width="927.06183"
       height="746.22504"
       x="78.847794"
       y="298.08136"
       inkscape:label="#rect3777" />
    <flowRoot
       xml:space="preserve"
       id="flowRoot3789"
       style="font-size:40px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
         id="flowRegion3791"><rect
           id="rect3793"
           width="213.64726"
           height="115.66247"
           x="356.58386"
           y="571.02448" /></flowRegion><flowPara
         id="flowPara3795" /></flowRoot>    <text
       xml:space="preserve"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="361.63461"
       y="578.09558"
       id="text3797"
       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3799"
         x="361.63461"
         y="578.09558" /></text>
    <flowRoot
       xml:space="preserve"
       id="flowRoot3801"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
         id="flowRegion3803"><rect
           id="rect3805"
           width="183.34268"
           height="110.6117"
           x="376.7869"
           y="574.56006" /></flowRegion><flowPara
         id="flowPara3807" /></flowRoot>    <flowRoot
       xml:space="preserve"
       id="flowRoot3867"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
         id="flowRegion3869"><rect
           id="rect3871"
           width="15.657365"
           height="8.586297"
           x="266.1752"
           y="263.43304" /></flowRegion><flowPara
         id="flowPara3873" /></flowRoot>    <flowRoot
       xml:space="preserve"
       id="flowRoot3910"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
         id="flowRegion3912"><rect
           id="rect3914"
           width="195.96959"
           height="97.479721"
           x="313.65237"
           y="366.4686" /></flowRegion><flowPara
         id="flowPara3916" /></flowRoot>    <flowRoot
       xml:space="preserve"
       id="flowRoot3927"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
         id="flowRegion3929"><rect
           id="rect3931"
           width="200.01021"
           height="107.58125"
           x="311.12698"
           y="360.91275" /></flowRegion><flowPara
         id="flowPara3933" /></flowRoot>    <rect
       style="fill:#ffffff;stroke:#000000;stroke-width:1.23192263"
       id="slide_1"
       width="213.13286"
       height="152.40985"
       x="283.69193"
       y="534.05963"
       inkscape:label="#rect2985" />
    <rect
       style="fill:#ffffff;stroke:#000000"
       id="slide_2.1"
       width="251.42857"
       height="151.42857"
       x="588.08197"
       y="630.68048"
       inkscape:label="#rect2987" />
    <rect
       style="fill:#ffffff;stroke:#000000;stroke-width:0.95687521"
       id="slide_3"
       width="234.32884"
       height="150.04312"
       x="265.50507"
       y="744.45441"
       inkscape:label="#rect2989" />
    <text
       xml:space="preserve"
       style="font-size:18px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="353.49954"
       y="765.80719"
       id="text3005"
       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3007"
         x="353.49954"
         y="765.80719">Slide 3</tspan></text>
    <text
       xml:space="preserve"
       style="font-size:18px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="678.60321"
       y="661.50439"
       id="text3005-1"
       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3007-7"
         x="678.60321"
         y="661.50439">Slide 2</tspan></text>
    <text
       xml:space="preserve"
       style="font-size:18px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="357.95425"
       y="566.61926"
       id="text3005-8"
       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3007-8"
         x="357.95425"
         y="566.61926">Slide 1</tspan></text>
    <text
       xml:space="preserve"
       style="font-size:2px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="634.71777"
       y="744.79596"
       id="text3879"
       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         x="634.71777"
         y="744.79596"
         id="tspan3883">Random scribble</tspan></text>
    <rect
       style="opacity:0;fill:none;stroke:#000000;stroke-width:1.32380044;stroke-opacity:1"
       id="slide_2.2"
       width="75.437637"
       height="32.00108"
       x="605.07025"
       y="736.82806"
       inkscape:label="#rect3887" />
    <path
       sodipodi:type="arc"
       style="opacity:0;fill:none;stroke:#000000;stroke-width:0.2;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
       id="path3957-5-1"
       sodipodi:cx="124.75384"
       sodipodi:cy="184.64114"
       sodipodi:rx="2.0203052"
       sodipodi:ry="1.5152289"
       d="m 126.77414,184.64114 a 2.0203052,1.5152289 0 1 1 -4.04061,0 2.0203052,1.5152289 0 1 1 4.04061,0 z"
       transform="translate(503.74816,513.5077)" />
    <path
       style="fill:none;stroke:#000000;stroke-width:0.2;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
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       id="path3157"
       inkscape:connector-curvature="0" />
    <text
       xml:space="preserve"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
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       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3947-6-0-2"
         x="641.77338"
         y="692.36462">Here is a bullet point (1) </tspan></text>
    <text
       xml:space="preserve"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
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         sodipodi:role="line"
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         x="641.77338"
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    <text
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       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
       x="641.59479"
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       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3955-3-8-1"
         x="641.59479"
         y="713.63916">Here is the final point </tspan></text>
    <path
       transform="translate(306.04281,306.32951)"
       sodipodi:type="arc"
       style="fill:#000080;fill-opacity:1;stroke:#000080;stroke-width:0.80000001;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
       id="path3059-2-6"
       sodipodi:cx="330.625"
       sodipodi:cy="383.43362"
       sodipodi:rx="1.1607143"
       sodipodi:ry="1.25"
       d="m 331.78571,383.43362 a 1.1607143,1.25 0 1 1 -2.32142,0 1.1607143,1.25 0 1 1 2.32142,0 z" />
    <path
       transform="translate(306.1321,317.04381)"
       sodipodi:type="arc"
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    <path
       transform="translate(306.31067,327.93671)"
       sodipodi:type="arc"
       style="fill:#000080;fill-opacity:1;stroke:#000080;stroke-width:0.80000001;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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       xml:space="preserve"
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       sodipodi:linespacing="125%"><tspan
         sodipodi:role="line"
         id="tspan3947-6-0-6"
         x="335.70218"
         y="603.79321">Press right-arrow for next slide</tspan></text>
    <text
       xml:space="preserve"
       style="font-size:6px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"
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         sodipodi:role="line"
         id="tspan3951-4-4-8"
         x="335.70218"
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    <text
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         sodipodi:role="line"
         id="tspan3955-3-8-2"
         x="335.52359"
         y="625.06775">END for last slide and HOME for first slide</tspan></text>
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       sodipodi:type="arc"
       style="fill:#000080;fill-opacity:1;stroke:#000080;stroke-width:0.80000001;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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    <path
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       sodipodi:type="arc"
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    <path
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	<!DOCTYPE html>
	<html>
	<head>
	<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js"></script>
	<script type="text/javascript" src="svg_slides.js"></script>

	<script type="text/javascript">

	// There are probably better ways of loading the SVG, but this is one example I found

	d3.xml("test.svg", "image/svg+xml", function(xml) {
	var importedNode = document.importNode(xml.documentElement, true);
	d3.select("body").node().appendChild(importedNode);

	svg=d3.select("body").select("svg")
	.attr("height","100%")
	.attr("width","100%");
	slides = svg_slides(svg,1500);

	// Lets test the slide scales - put a bouncing ball on slide id 3
	s = slides[3];
	circle = svg.append("svg:circle")
	.attr("cx",s.scale_x(500)).attr("cy",s.scale_y(500))
	.attr("r",20)
	.style("fill","steelblue");

	next = 500;

	function bounce() {
	next = -next;
	circle.transition().duration(2500).attr("cx",s.scale_x(500+next))
	.each("end",bounce);
	}

	bounce();
	});

	</script>
	</head>
	<body></body>
	</html>
	/* This is a basic attempt to use d3 to process transitional slides from SVG files (i.e. Inkscape)
	The main objective here was to keep everything as simple as possible

	To create a slide, simply create a rectangle in inkscape where you set the object ID to "slide_" + a number
	This number can be either integer or float, so "slide_1","slide_2" and "slide_3.56" all work.

	The script sorts the slide-numbers and transitions between slides based on the final sorted order.

	It is easy to add slides into a pre-existing ordering, simply by chosing a floating number in the middle of the two
	Example: If we want to add slide between "slide_2" and "slide_3" we simply add a rectancle called "slide_2.5"

	Keyboard definitions:
	Right arrow: next slide
	Left arrow: previous slide
	Home: first slide
	End: last slide

	Please be aware that you need to remove any layer transition is the svg file (or put the layer transition to 0,0)

	Each slide has a scale_x and scale_y functions that have pre-set range to the slide boundaries and a default
	domain of [0,1000], allowing the user to position objects easily onto each slide.


	ziggy.jonsson.nyc@gmail.com
	*/


	function svg_slides(svg,delay) {
	var slides={},
	slide = 0,
	delay = delay ? delay : 3500;

	svg.attr("preserveAspectRatio","xMidYid meet");

	rects = svg.selectAll("rect")[0];

	for (i=0;i<rects.length;i++) {
	id = rects[i].id;
	console.log(id);
	if (id.slice(0,6)=='slide_') {
	slides[id.slice(6)]=rects[i]
	rects[i].scale_x = d3.scale.linear().range([rects[i].x.baseVal.value,rects[i].x.baseVal.value+rects[i].width.baseVal.value]).domain([0,1000]);
	rects[i].scale_y = d3.scale.linear().range([rects[i].y.baseVal.value,rects[i].y.baseVal.value+rects[i].height.baseVal.value]).domain([0,1000]);
	}

	}

	keys = Object.keys(slides).sort();
	slides.keys = keys;

	function next_slide() {
	svg.transition().duration(delay).attr("viewBox",slides[keys[slide]].x.baseVal.value+" "+slides[keys[slide]].y.baseVal.value+" "+slides[keys[slide]].width.baseVal.value+" "+slides[keys[slide]].height.baseVal.value);
	}

	d3.select("body").on("touchmove", function() { if(slide<keys.length-1) {slide++; console.log(slide);}});

	d3.select(window).on("keydown", function() {
	switch (d3.event.keyCode) {
	case 37: {if (slide>0) {slide=slide-1; console.log(slide);next_slide()};break}
	case 39: {if(slide<keys.length-1) {slide++; console.log(slide);next_slide()};break}
	case 36: {slide = 0;next_slide();break}
	case 35: {slide = keys.length -1; next_slide();break}
	}

	});

	// Start with the first slide
	next_slide();
	return slides
	}
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	<svg
	xmlns:osb="http://www.openswatchbook.org/uri/2009/osb"
	xmlns:dc="http://purl.org/dc/elements/1.1/"
	xmlns:cc="http://creativecommons.org/ns#"
	xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
	xmlns:svg="http://www.w3.org/2000/svg"
	xmlns="http://www.w3.org/2000/svg"
	xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
	xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
	width="1052.36"
	height="744.09003"
	id="svg2"
	version="1.1"
	inkscape:version="0.48.2 r9819"
	sodipodi:docname="test2.svg">
	<defs
	id="defs4">
	<linearGradient
	id="linearGradient3779"
	osb:paint="solid">
	<stop
	style="stop-color:#ffffff;stop-opacity:1;"
	offset="0"
	id="stop3781" />
	</linearGradient>
	</defs>
	<sodipodi:namedview
	id="base"
	pagecolor="#ffffff"
	bordercolor="#666666"
	borderopacity="1.0"
	inkscape:pageopacity="0.0"
	inkscape:pageshadow="2"
	inkscape:zoom="0.98994949"
	inkscape:cx="520.12813"
	inkscape:cy="80.053504"
	inkscape:document-units="px"
	inkscape:current-layer="layer1"
	showgrid="false"
	inkscape:window-width="1280"
	inkscape:window-height="972"
	inkscape:window-x="-8"
	inkscape:window-y="-8"
	inkscape:window-maximized="1"
	showguides="false" />
	<metadata
	id="metadata7">
	<rdf:RDF>
	<cc:Work
	rdf:about="">
	<dc:format>image/svg+xml</dc:format>
	<dc:type
	rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
	<dc:title />
	</cc:Work>
	</rdf:RDF>
	</metadata>
	<g
	inkscape:label="Layer 1"
	inkscape:groupmode="layer"
	id="layer1"
	transform="translate(0,0)">
	<rect
	style="fill:none;stroke:none"
	id="slide_6"
	width="927.06183"
	height="746.22504"
	x="78.847794"
	y="298.08136"
	inkscape:label="#rect3777" />
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	xml:space="preserve"
	id="flowRoot3789"
	style="font-size:40px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans"><flowRegion
	id="flowRegion3791"><rect
	id="rect3793"
	width="213.64726"
	height="115.66247"
	x="356.58386"
	y="571.02448" /></flowRegion><flowPara
	id="flowPara3795" /></flowRoot> <text
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	y="578.09558"
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