Revision as of 22:52, 13 October 2014

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Welcome to the TU Darmstadt iGEM Team Wiki-Pages 2014

We dedicated the this year's project to find a new approach to produce Anthocyanines, a class of plant pigments, in Escherichia coli (E. coli).

Anthocyanine not only stains blossoms in blue, violet or red but also is enclosed in fruits and is valued for its antioxidant effect as well as the ability to lower the risks for cancer.

In the our technological approach, the anthocyanin dye is utilised to build a so-called “Grätzel cells”. This electrochemical dye-sensitised solar cell use the produced dye instead of a silica semiconductor material for the absorption of light. The objective was to investigate an innovative approach for a sustainable energy source; wherever and whenever needed.

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+// An html parser written in JavaScript
+// Based on http://ejohn.org/blog/pure-javascript-html-parser/
+(function() {
+    var supports = (function() {
+        var supports = {};
+        var html;
+        var work = this.document.createElement('div');
+        html = "<P><I></P></I>";
+        work.innerHTML = html;
+        supports.tagSoup = work.innerHTML !== html;
+        work.innerHTML = "<P><i><P></P></i></P>";
+        supports.selfClose = work.childNodes.length === 2;
+        return supports;
+    })();
+    // Regular Expressions for parsing tags and attributes
+    var startTag = /^<([\-A-Za-z0-9_]+)((?:\s+[\w\-]+(?:\s*=\s*(?:(?:"[^"]*")|(?:'[^']*')|[^>\s]+))?)*)\s*(\/?)>/;
+    var endTag = /^<\/([\-A-Za-z0-9_]+)[^>]*>/;
+    var attr = /([\-A-Za-z0-9_]+)(?:\s*=\s*(?:(?:"((?:\\.|[^"])*)")|(?:'((?:\\.|[^'])*)')|([^>\s]+)))?/g;
+    var fillAttr = /^(checked|compact|declare|defer|disabled|ismap|multiple|nohref|noresize|noshade|nowrap|readonly|selected)$/i;
+    var DEBUG = false;
+    function htmlParser(stream, options) {
+        stream = stream || '';
+        // Options
+        options = options || {};
+        for(var key in supports) {
+            if(supports.hasOwnProperty(key)) {
+                if(options.autoFix) {
+                    options['fix_'+key] = true;//!supports[key];
+                }
+                options.fix = options.fix || options['fix_'+key];
+            }
+        }
+        var stack = [];
+        var append = function(str) {
+            stream += str;
+        };
+        var prepend = function(str) {
+            stream = str + stream;
+        };
+        // Order of detection matters: detection of one can only
+        // succeed if detection of previous didn't
+        var detect = {
+            comment: /^<!--/,
+            endTag: /^<\//,
+            atomicTag: /^<\s*(script|style|noscript|iframe|textarea)[\s>]/i,
+            startTag: /^</,
+            chars: /^[^<]/
+        };
+        // Detection has already happened when a reader is called.
+        var reader = {
+            comment: function() {
+                var index = stream.indexOf("-->");
+                if ( index >= 0 ) {
+                    return {
+                        content: stream.substr(4, index),
+                        length: index + 3
+                    };
+                }
+            },
+            endTag: function() {
+                var match = stream.match( endTag );
+                if ( match ) {
+                    return {
+                        tagName: match[1],
+                        length: match[0].length
+                    };
+                }
+            },
+            atomicTag: function() {
+                var start = reader.startTag();
+                if(start) {
+                    var rest = stream.slice(start.length);
+                    // for optimization, we check first just for the end tag
+                    if(rest.match(new RegExp("<\/\\s*" + start.tagName + "\\s*>", "i"))) {
+                        // capturing the content is inefficient, so we do it inside the if
+                        var match = rest.match(new RegExp("([\\s\\S]*?)<\/\\s*" + start.tagName + "\\s*>", "i"));
+                        if(match) {
+                            // good to go
+                            return {
+                                tagName: start.tagName,
+                                attrs: start.attrs,
+                                content: match[1],
+                                length: match[0].length + start.length
+                            };
+                        }
+                    }
+                }
+            },
+            startTag: function() {
+                var match = stream.match( startTag );
+                if ( match ) {
+                    var attrs = {};
+                    match[2].replace(attr, function(match, name) {
+                        var value = arguments[2] || arguments[3] || arguments[4] ||
+                            fillAttr.test(name) && name || null;
+                        attrs[name] = value;
+                    });
+                    return {
+                        tagName: match[1],
+                        attrs: attrs,
+                        unary: !!match[3],
+                        length: match[0].length
+                    };
+                }
+            },
+            chars: function() {
+                var index = stream.indexOf("<");
+                return {
+                    length: index >= 0 ? index : stream.length
+                };
+            }
+        };
+        var readToken = function() {
+            // Enumerate detects in order
+            for (var type in detect) {
+                if(detect[type].test(stream)) {
+                    if(DEBUG) { console.log('suspected ' + type); }
+                    var token = reader[type]();
+                    if(token) {
+                        if(DEBUG) { console.log('parsed ' + type, token); }
+                        // Type
+                        token.type = token.type || type;
+                        // Entire text
+                        token.text = stream.substr(0, token.length);
+                        // Update the stream
+                        stream = stream.slice(token.length);
+                        return token;
+                    }
+                    return null;
+                }
+            }
+        };
+        var readTokens = function(handlers) {
+            var tok;
+            while(tok = readToken()) {
+                // continue until we get an explicit "false" return
+                if(handlers[tok.type] && handlers[tok.type](tok) === false) {
+                    return;
+                }
+            }
+        };
+        var clear = function() {
+            var rest = stream;
+            stream = '';
+            return rest;
+        };
+        var rest = function() {
+            return stream;
+        };
+        if(options.fix) {
+            (function() {
+                // Empty Elements - HTML 4.01
+                var EMPTY = /^(AREA|BASE|BASEFONT|BR|COL|FRAME|HR|IMG|INPUT|ISINDEX|LINK|META|PARAM|EMBED)$/i;
+                // Elements that you can| intentionally| leave open
+                // (and which close themselves)
+                var CLOSESELF = /^(COLGROUP|DD|DT|LI|OPTIONS|P|TD|TFOOT|TH|THEAD|TR)$/i;
+                var stack = [];
+                stack.last = function() {
+                    return this[this.length - 1];
+                };
+                stack.lastTagNameEq = function(tagName) {
+                    var last = this.last();
+                    return last && last.tagName &&
+                        last.tagName.toUpperCase() === tagName.toUpperCase();
+                };
+                stack.containsTagName = function(tagName) {
+                    for(var i = 0, tok; tok = this[i]; i++) {
+                        if(tok.tagName === tagName) {
+                            return true;
+                        }
+                    }
+                    return false;
+                };
+                var correct = function(tok) {
+                    if(tok && tok.type === 'startTag') {
+                        // unary
+                        tok.unary = EMPTY.test(tok.tagName) || tok.unary;
+                    }
+                    return tok;
+                };
+                var readTokenImpl = readToken;
+                var peekToken = function() {
+                    var tmp = stream;
+                    var tok = correct(readTokenImpl());
+                    stream = tmp;
+                    return tok;
+                };
+                var closeLast = function() {
+                    var tok = stack.pop();
+                    // prepend close tag to stream.
+                    prepend('</'+tok.tagName+'>');
+                };
+                var handlers = {
+                    startTag: function(tok) {
+                        var tagName = tok.tagName;
+                        // Fix tbody
+                        if(tagName.toUpperCase() === 'TR' && stack.lastTagNameEq('TABLE')) {
+                            prepend('<TBODY>');
+                            prepareNextToken();
+                        } else if(options.fix_selfClose &&
+                            CLOSESELF.test(tagName) &&
+                            stack.containsTagName(tagName)) {
+                            if(stack.lastTagNameEq(tagName)) {
+                                closeLast();
+                            } else {
+                                prepend('</'+tok.tagName+'>');
+                                prepareNextToken();
+                            }
+                        } else if (!tok.unary) {
+                            stack.push(tok);
+                        }
+                    },
+                    endTag: function(tok) {
+                        var last = stack.last();
+                        if(last) {
+                            if(options.fix_tagSoup && !stack.lastTagNameEq(tok.tagName)) {
+                                // cleanup tag soup
+                                closeLast();
+                            } else {
+                                stack.pop();
+                            }
+                        } else if (options.fix_tagSoup) {
+                            // cleanup tag soup part 2: skip this token
+                            skipToken();
+                        }
+                    }
+                };
+                var skipToken = function() {
+                    // shift the next token
+                    readTokenImpl();
+                    prepareNextToken();
+                };
+                var prepareNextToken = function() {
+                    var tok = peekToken();
+                    if(tok && handlers[tok.type]) {
+                        handlers[tok.type](tok);
+                    }
+                };
+                // redefine readToken
+                readToken = function() {
+                    prepareNextToken();
+                    return correct(readTokenImpl());
+                };
+            })();
+        }
+        return {
+            append: append,
+            readToken: readToken,
+            readTokens: readTokens,
+            clear: clear,
+            rest: rest,
+            stack: stack
+        };
+    }
+    htmlParser.supports = supports;
+    htmlParser.tokenToString = function(tok) {
+        var handler = {
+            comment: function(tok) {
+                return '<--' + tok.content + '-->';
+            },
+            endTag: function(tok) {
+                return '</'+tok.tagName+'>';
+            },
+            atomicTag: function(tok) {
+                console.log(tok);
+                return handler.startTag(tok) +
+                    tok.content +
+                    handler.endTag(tok);
+            },
+            startTag: function(tok) {
+                var str = '<'+tok.tagName;
+                for (var key in tok.attrs) {
+                    var val = tok.attrs[key];
+                    // escape quotes
+                    str += ' '+key+'="'+(val ? val.replace(/(^|[^\\])"/g, '$1\\\"') : '')+'"';
+                }
+                return str + (tok.unary ? '/>' : '>');
+            },
+            chars: function(tok) {
+                return tok.text;
+            }
+        };
+        return handler[tok.type](tok);
+    };
+    htmlParser.escapeAttributes = function(attrs) {
+        var escapedAttrs = {};
+        // escape double-quotes for writing html as a string
+        for(var name in attrs) {
+            var value = attrs[name];
+            escapedAttrs[name] = value && value.replace(/(^|[^\\])"/g, '$1\\\"');
+        }
+        return escapedAttrs;
+    };
+    for(var key in supports) {
+        htmlParser.browserHasFlaw = htmlParser.browserHasFlaw || (!supports[key]) && key;
+    }
+    this.htmlParser = htmlParser;
+})();
 </script>
-<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js" type="text/javascript"></script>
 <script src="typo3conf/ext/sf_banners/Resources/Public/Js/HtmlParser.js?1412482268" type="text/javascript"></script>
 <script src="typo3conf/ext/sf_banners/Resources/Public/Js/Postscribe.js?1412482268" type="text/javascript"></script>

Team:TU Darmstadt/wiki/

From 2014.igem.org

Revision as of 22:52, 13 October 2014

The Project

Data, more data!

The People

Welcome to the TU Darmstadt iGEM Team Wiki-Pages 2014