Team:UCL

Team:UCL/Playingaround3 - 2015.igem.org

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Team:UCL/Playingaround3

The number of microorganisms in human is higher than the number of human cells in our body. Their metabolic activity equals that of and plays crucial role in many key processes such as digestion, drug metabolism, or functioning of the immune system...
Studies in have shown that the gut microbiome is also capable of influencing the chemistry of our , thus regulating our behaviour , anxiety , mood , cognition and pain ...
Being inspired by this emerging research area, UCL 2015 team wants to explore the modulation of the gut bacteria as a strategy for developing novel treatments for mental health disorders. Ultimately, our goal is to harness synthetic biology to make people happy!

Mind the Gut: Abstract

Lorem Ipsum jest tekstem stosowanym jako przykładowy wypełniacz w przemyśle poligraficznym. Został po raz pierwszy użyty w XV w. przez nieznanego drukarza do wypełnienia tekstem próbnej książki. Pięć wieków później zaczął być używany przemyśle elektronicznym, pozostając praktycznie niezmienionym. Spopularyzował się w latach 60. XX w. wraz z publikacją arkuszy Letrasetu, zawierających fragmenty Lorem Ipsum, a ostatnio z zawierającym różne wersje Lorem Ipsum oprogramowaniem przeznaczonym do realizacji druków na komputerach osobistych, jak Aldus PageMaker

W przeciwieństwie do rozpowszechnionych opinii, Lorem Ipsum nie jest tylko przypadkowym tekstem. Ma ono korzenie w klasycznej łacińskiej literaturze z 45 roku przed Chrystusem, czyli ponad 2000 lat temu! Richard McClintock, wykładowca łaciny na uniwersytecie Hampden-Sydney w Virginii, przyjrzał się uważniej jednemu z najbardziej niejasnych słów w Lorem Ipsum – consectetur – i po wielu poszukiwaniach odnalazł niezaprzeczalne źródło: Lorem Ipsum pochodzi z fragmentów (1.10.32 i 1.10.33) „de Finibus Bonorum et Malorum”, czyli „O granicy dobra i zła”, napisanej właśnie w 45 p.n.e. przez Cycerona. Jest to bardzo popularna w czasach renesansu rozprawa na temat etyki. Pierwszy wiersz Lorem Ipsum, „Lorem ipsum dolor sit amet...” pochodzi właśnie z sekcji 1.10.32.

Why are we doing it?
An estimated 450 million people world-wide suffer from mental health problem
By 2030, depression alone is likely to be highest contributon to global burden of disease
According to WHO, in low income countries, depression represents almost as large problem as does malaria

80% of people with severe mental health con-dition do not have access to needed treatment
1 in 5 children suffers from mental health problems. Due to the lack of support, these problems lead to poorer school performance
Fewer than 20% of countries have mental health service organizations that provide community and individual assistance
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//
// SmoothScroll for websites v1.3.8 (Balazs Galambosi)
// Licensed under the terms of the MIT license.
//
// You may use it in your theme if you credit me.
// It is also free to use on any individual website.
//
// Exception:
// The only restriction would be not to publish any
// extension for browsers or native application
// without getting a written permission first.
//
 
(function () {
// Scroll Variables (tweakable)
var defaultOptions = {
 
// Scrolling Core
frameRate : 150, // [Hz]
animationTime : 400, // [px]
stepSize : 120, // [px]
 
// Pulse (less tweakable)
// ratio of "tail" to "acceleration"
pulseAlgorithm : true,
pulseScale : 4,
pulseNormalize : 1,
 
// Acceleration
accelerationDelta : 20, // 20
accelerationMax : 1, // 1
 
// Keyboard Settings
keyboardSupport : true, // option
arrowScroll : 50, // [px]
 
// Other
touchpadSupport : true,
fixedBackground : true,
excluded : ''
};
 
var options = defaultOptions;
 
 
// Other Variables
var isExcluded = false;
var isFrame = false;
var direction = { x: 0, y: 0 };
var initDone = false;
var root = document.documentElement;
var activeElement;
var observer;
var deltaBuffer = [];
var isMac = /^Mac/.test(navigator.platform);
 
var key = { left: 37, up: 38, right: 39, down: 40, spacebar: 32,
pageup: 33, pagedown: 34, end: 35, home: 36 };
 
 
/***********************************************
* SETTINGS
***********************************************/
 
var options = defaultOptions;
 
 
/***********************************************
* INITIALIZE
***********************************************/
 
/**
* Tests if smooth scrolling is allowed. Shuts down everything if not.
*/
function initTest() {
if (options.keyboardSupport) {
addEvent('keydown', keydown);
}
}
 
/**
* Sets up scrolls array, determines if frames are involved.
*/
function init() {
if (initDone || !document.body) return;
 
initDone = true;
 
var body = document.body;
var html = document.documentElement;
var windowHeight = window.innerHeight;
var scrollHeight = body.scrollHeight;
// check compat mode for root element
root = (document.compatMode.indexOf('CSS') >= 0) ? html : body;
activeElement = body;
initTest();
 
// Checks if this script is running in a frame
if (top != self) {
isFrame = true;
}
 
/**
* This fixes a bug where the areas left and right to
* the content does not trigger the onmousewheel event
* on some pages. e.g.: html, body { height: 100% }
*/
else if (scrollHeight > windowHeight &&
(body.offsetHeight <= windowHeight ||
html.offsetHeight <= windowHeight)) {
 
var fullPageElem = document.createElement('div');
fullPageElem.style.cssText = 'position:absolute; z-index:-10000; ' +
'top:0; left:0; right:0; height:' +
root.scrollHeight + 'px';
document.body.appendChild(fullPageElem);
// DOM changed (throttled) to fix height
var pendingRefresh;
var refresh = function () {
if (pendingRefresh) return; // could also be: clearTimeout(pendingRefresh);
pendingRefresh = setTimeout(function () {
if (isExcluded) return; // could be running after cleanup
fullPageElem.style.height = '0';
fullPageElem.style.height = root.scrollHeight + 'px';
pendingRefresh = null;
}, 500); // act rarely to stay fast
};
setTimeout(refresh, 10);
 
// TODO: attributeFilter?
var config = {
attributes: true,
childList: true,
characterData: false
// subtree: true
};
 
observer = new MutationObserver(refresh);
observer.observe(body, config);
 
if (root.offsetHeight <= windowHeight) {
var clearfix = document.createElement('div');
clearfix.style.clear = 'both';
body.appendChild(clearfix);
}
}
 
// disable fixed background
if (!options.fixedBackground && !isExcluded) {
body.style.backgroundAttachment = 'scroll';
html.style.backgroundAttachment = 'scroll';
}
}
 
/**
* Removes event listeners and other traces left on the page.
*/
function cleanup() {
observer && observer.disconnect();
removeEvent(wheelEvent, wheel);
removeEvent('mousedown', mousedown);
removeEvent('keydown', keydown);
}
 
 
/************************************************
* SCROLLING
************************************************/
var que = [];
var pending = false;
var lastScroll = Date.now();
 
/**
* Pushes scroll actions to the scrolling queue.
*/
function scrollArray(elem, left, top) {
directionCheck(left, top);
 
if (options.accelerationMax != 1) {
var now = Date.now();
var elapsed = now - lastScroll;
if (elapsed < options.accelerationDelta) {
var factor = (1 + (50 / elapsed)) / 2;
if (factor > 1) {
factor = Math.min(factor, options.accelerationMax);
left *= factor;
top *= factor;
}
}
lastScroll = Date.now();
}
// push a scroll command
que.push({
x: left,
y: top,
lastX: (left < 0) ? 0.99 : -0.99,
lastY: (top < 0) ? 0.99 : -0.99,
start: Date.now()
});
// don't act if there's a pending queue
if (pending) {
return;
}
 
var scrollWindow = (elem === document.body);
var step = function (time) {
var now = Date.now();
var scrollX = 0;
var scrollY = 0;
for (var i = 0; i < que.length; i++) {
var item = que[i];
var elapsed = now - item.start;
var finished = (elapsed >= options.animationTime);
// scroll position: [0, 1]
var position = (finished) ? 1 : elapsed / options.animationTime;
// easing [optional]
if (options.pulseAlgorithm) {
position = pulse(position);
}
// only need the difference
var x = (item.x * position - item.lastX) >> 0;
var y = (item.y * position - item.lastY) >> 0;
// add this to the total scrolling
scrollX += x;
scrollY += y;
// update last values
item.lastX += x;
item.lastY += y;
// delete and step back if it's over
if (finished) {
que.splice(i, 1); i--;
}
}
 
// scroll left and top
if (scrollWindow) {
window.scrollBy(scrollX, scrollY);
}
else {
if (scrollX) elem.scrollLeft += scrollX;
if (scrollY) elem.scrollTop += scrollY;
}
// clean up if there's nothing left to do
if (!left && !top) {
que = [];
}
if (que.length) {
requestFrame(step, elem, (1000 / options.frameRate + 1));
} else {
pending = false;
}
};
// start a new queue of actions
requestFrame(step, elem, 0);
pending = true;
}
 
 
/***********************************************
* EVENTS
***********************************************/
 
/**
* Mouse wheel handler.
* @param {Object} event
*/
function wheel(event) {
 
if (!initDone) {
init();
}
var target = event.target;
var overflowing = overflowingAncestor(target);
 
// use default if there's no overflowing
// element or default action is prevented
// or it's a zooming event with CTRL
if (!overflowing || event.defaultPrevented || event.ctrlKey) {
return true;
}
// leave embedded content alone (flash & pdf)
if (isNodeName(activeElement, 'embed') ||
(isNodeName(target, 'embed') && /\.pdf/i.test(target.src)) ||
isNodeName(activeElement, 'object')) {
return true;
}
 
var deltaX = -event.wheelDeltaX || event.deltaX || 0;
var deltaY = -event.wheelDeltaY || event.deltaY || 0;
if (isMac) {
if (event.wheelDeltaX && isDivisible(event.wheelDeltaX, 120)) {
deltaX = -120 * (event.wheelDeltaX / Math.abs(event.wheelDeltaX));
}
if (event.wheelDeltaY && isDivisible(event.wheelDeltaY, 120)) {
deltaY = -120 * (event.wheelDeltaY / Math.abs(event.wheelDeltaY));
}
}
// use wheelDelta if deltaX/Y is not available
if (!deltaX && !deltaY) {
deltaY = -event.wheelDelta || 0;
}
 
// line based scrolling (Firefox mostly)
if (event.deltaMode === 1) {
deltaX *= 40;
deltaY *= 40;
}
// check if it's a touchpad scroll that should be ignored
if (!options.touchpadSupport && isTouchpad(deltaY)) {
return true;
}
 
// scale by step size
// delta is 120 most of the time
// synaptics seems to send 1 sometimes
if (Math.abs(deltaX) > 1.2) {
deltaX *= options.stepSize / 120;
}
if (Math.abs(deltaY) > 1.2) {
deltaY *= options.stepSize / 120;
}
scrollArray(overflowing, deltaX, deltaY);
event.preventDefault();
scheduleClearCache();
}
 
/**
* Keydown event handler.
* @param {Object} event
*/
function keydown(event) {
 
var target = event.target;
var modifier = event.ctrlKey || event.altKey || event.metaKey ||
(event.shiftKey && event.keyCode !== key.spacebar);
// our own tracked active element could've been removed from the DOM
if (!document.contains(activeElement)) {
activeElement = document.activeElement;
}
 
// do nothing if user is editing text
// or using a modifier key (except shift)
// or in a dropdown
// or inside interactive elements
var inputNodeNames = /^(textarea|select|embed|object)$/i;
var buttonTypes = /^(button|submit|radio|checkbox|file|color|image)$/i;
if ( inputNodeNames.test(target.nodeName) ||
isNodeName(target, 'input') && !buttonTypes.test(target.type) ||
isNodeName(activeElement, 'video') ||
isInsideYoutubeVideo(event) ||
target.isContentEditable ||
event.defaultPrevented ||
modifier ) {
return true;
}
// spacebar should trigger button press
if ((isNodeName(target, 'button') ||
isNodeName(target, 'input') && buttonTypes.test(target.type)) &&
event.keyCode === key.spacebar) {
return true;
}
var shift, x = 0, y = 0;
var elem = overflowingAncestor(activeElement);
var clientHeight = elem.clientHeight;
 
if (elem == document.body) {
clientHeight = window.innerHeight;
}
 
switch (event.keyCode) {
case key.up:
y = -options.arrowScroll;
break;
case key.down:
y = options.arrowScroll;
break;
case key.spacebar: // (+ shift)
shift = event.shiftKey ? 1 : -1;
y = -shift * clientHeight * 0.9;
break;
case key.pageup:
y = -clientHeight * 0.9;
break;
case key.pagedown:
y = clientHeight * 0.9;
break;
case key.home:
y = -elem.scrollTop;
break;
case key.end:
var damt = elem.scrollHeight - elem.scrollTop - clientHeight;
y = (damt > 0) ? damt+10 : 0;
break;
case key.left:
x = -options.arrowScroll;
break;
case key.right:
x = options.arrowScroll;
break;
default:
return true; // a key we don't care about
}
 
scrollArray(elem, x, y);
event.preventDefault();
scheduleClearCache();
}
 
/**
* Mousedown event only for updating activeElement
*/
function mousedown(event) {
activeElement = event.target;
}
 
 
/***********************************************
* OVERFLOW
***********************************************/
 
var uniqueID = (function () {
var i = 0;
return function (el) {
return el.uniqueID || (el.uniqueID = i++);
};
})();
 
var cache = {}; // cleared out after a scrolling session
var clearCacheTimer;
 
//setInterval(function () { cache = {}; }, 10 * 1000);
 
function scheduleClearCache() {
clearTimeout(clearCacheTimer);
clearCacheTimer = setInterval(function () { cache = {}; }, 1*1000);
}
 
function setCache(elems, overflowing) {
for (var i = elems.length; i--;)
cache[uniqueID(elems[i])] = overflowing;
return overflowing;
}
 
// (body) (root)
// | hidden | visible | scroll | auto |
// hidden | no | no | YES | YES |
// visible | no | YES | YES | YES |
// scroll | no | YES | YES | YES |
// auto | no | YES | YES | YES |
 
function overflowingAncestor(el) {
var elems = [];
var body = document.body;
var rootScrollHeight = root.scrollHeight;
do {
var cached = cache[uniqueID(el)];
if (cached) {
return setCache(elems, cached);
}
elems.push(el);
if (rootScrollHeight === el.scrollHeight) {
var topOverflowsNotHidden = overflowNotHidden(root) && overflowNotHidden(body);
var isOverflowCSS = topOverflowsNotHidden || overflowAutoOrScroll(root);
if (isFrame && isContentOverflowing(root) ||
!isFrame && isOverflowCSS) {
return setCache(elems, getScrollRoot());
}
} else if (isContentOverflowing(el) && overflowAutoOrScroll(el)) {
return setCache(elems, el);
}
} while (el = el.parentElement);
}
 
function isContentOverflowing(el) {
return (el.clientHeight + 10 < el.scrollHeight);
}
 
// typically for <body> and <html>
function overflowNotHidden(el) {
var overflow = getComputedStyle(el, '').getPropertyValue('overflow-y');
return (overflow !== 'hidden');
}
 
// for all other elements
function overflowAutoOrScroll(el) {
var overflow = getComputedStyle(el, '').getPropertyValue('overflow-y');
return (overflow === 'scroll' || overflow === 'auto');
}
 
 
/***********************************************
* HELPERS
***********************************************/
 
function addEvent(type, fn) {
window.addEventListener(type, fn, false);
}
 
function removeEvent(type, fn) {
window.removeEventListener(type, fn, false);
}
 
function isNodeName(el, tag) {
return (el.nodeName||'').toLowerCase() === tag.toLowerCase();
}
 
function directionCheck(x, y) {
x = (x > 0) ? 1 : -1;
y = (y > 0) ? 1 : -1;
if (direction.x !== x || direction.y !== y) {
direction.x = x;
direction.y = y;
que = [];
lastScroll = 0;
}
}
 
var deltaBufferTimer;
 
if (window.localStorage && localStorage.SS_deltaBuffer) {
deltaBuffer = localStorage.SS_deltaBuffer.split(',');
}
 
function isTouchpad(deltaY) {
if (!deltaY) return;
if (!deltaBuffer.length) {
deltaBuffer = [deltaY, deltaY, deltaY];
}
deltaY = Math.abs(deltaY)
deltaBuffer.push(deltaY);
deltaBuffer.shift();
clearTimeout(deltaBufferTimer);
deltaBufferTimer = setTimeout(function () {
if (window.localStorage) {
localStorage.SS_deltaBuffer = deltaBuffer.join(',');
}
}, 1000);
return !allDeltasDivisableBy(120) && !allDeltasDivisableBy(100);
}
 
function isDivisible(n, divisor) {
return (Math.floor(n / divisor) == n / divisor);
}
 
function allDeltasDivisableBy(divisor) {
return (isDivisible(deltaBuffer[0], divisor) &&
isDivisible(deltaBuffer[1], divisor) &&
isDivisible(deltaBuffer[2], divisor));
}
 
function isInsideYoutubeVideo(event) {
var elem = event.target;
var isControl = false;
if (document.URL.indexOf ('www.youtube.com/watch') != -1) {
do {
isControl = (elem.classList &&
elem.classList.contains('html5-video-controls'));
if (isControl) break;
} while (elem = elem.parentNode);
}
return isControl;
}
 
var requestFrame = (function () {
return (window.requestAnimationFrame ||
window.webkitRequestAnimationFrame ||
window.mozRequestAnimationFrame ||
function (callback, element, delay) {
window.setTimeout(callback, delay || (1000/60));
});
})();
 
var MutationObserver = (window.MutationObserver ||
window.WebKitMutationObserver ||
window.MozMutationObserver);
 
var getScrollRoot = (function() {
var SCROLL_ROOT;
return function() {
if (!SCROLL_ROOT) {
var dummy = document.createElement('div');
dummy.style.cssText = 'height:10000px;width:1px;';
document.body.appendChild(dummy);
var bodyScrollTop = document.body.scrollTop;
var docElScrollTop = document.documentElement.scrollTop;
window.scrollBy(0, 1);
if (document.body.scrollTop != bodyScrollTop)
(SCROLL_ROOT = document.body);
else
(SCROLL_ROOT = document.documentElement);
window.scrollBy(0, -1);
document.body.removeChild(dummy);
}
return SCROLL_ROOT;
};
})();
 
 
/***********************************************
* PULSE (by Michael Herf)
***********************************************/
/**
* Viscous fluid with a pulse for part and decay for the rest.
* - Applies a fixed force over an interval (a damped acceleration), and
* - Lets the exponential bleed away the velocity over a longer interval
* - Michael Herf, http://stereopsis.com/stopping/
*/
function pulse_(x) {
var val, start, expx;
// test
x = x * options.pulseScale;
if (x < 1) { // acceleartion
val = x - (1 - Math.exp(-x));
} else { // tail
// the previous animation ended here:
start = Math.exp(-1);
// simple viscous drag
x -= 1;
expx = 1 - Math.exp(-x);
val = start + (expx * (1 - start));
}
return val * options.pulseNormalize;
}
 
function pulse(x) {
if (x >= 1) return 1;
if (x <= 0) return 0;
 
if (options.pulseNormalize == 1) {
options.pulseNormalize /= pulse_(1);
}
return pulse_(x);
}
 
var wheelEvent;
if ('onwheel' in document.createElement('div'))
wheelEvent = 'wheel';
else if ('onmousewheel' in document.createElement('div'))
wheelEvent = 'mousewheel';
 
if (wheelEvent) {
addEvent(wheelEvent, wheel);
addEvent('mousedown', mousedown);
addEvent('load', init);
}
 
})();
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