1<!DOCTYPE html> 2<html> 3 <head> 4 <link rel="stylesheet" href="/assets/bootstrap/css/bootstrap.min.css" /> 5 <link rel="stylesheet" href="/assets/swiper/swiper-bundle.min.css" /> 6 <link rel="stylesheet" href="/styles.css" /> 7 8<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-2" /> 9<meta name="title" content="SYNTHIA Insight 10: Using Synthetic Data to Build Trust in Cancer Genomics Tools" /> 10<meta name="description" content="Insight featuring Stella (Styliani-Christina) Fragkouli from CERTH. " /> 11<meta name="robots" content="index, follow" /> 12<meta property="og:title" content="SYNTHIA Insight 10: Using Synthetic Data to Build Trust in Cancer Genomics Tools" /> 13<meta property="og:description" content="Insight featuring Stella (Styliani-Christina) Fragkouli from CERTH. " /> 14<meta property="og:image" content="https://www.ihi-synthia.eu/img/2646_7270_SYNTHIA_Insight_10.jpg" /> 15<link rel="image_src" href="https://www.ihi-synthia.eu/img/2646_7270_SYNTHIA_Insight_10.jpg" /> 16 17<meta name="resource-type" content="document" /> 18<meta name="classification" content="document" /> 19<meta name="page-topic" content="all, alle," /> 20<meta name="publisher" content="ihi-synthia.eu" /> 21<meta name="canonical" content="https://www.ihi-synthia.eu/news/synthia-insight-10-using-synthetic-data-to-build-trust-in-cancer-genomics-tools" /> 22<link rel="shortcut icon" href="/img/2635_6643_fav.png" />
23<script src="//ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js"></script>
23 24<!-- RES cmsFunctions.min.js -->
24<script>var randomnumber = Math.floor(Math.random()*11000000); 25var is_mobile = false; 26var is_waypoint = false; 27 28var Cms = function(siteID) { 29 this.siteID = siteID; 30}; 31 32// 33// ***** AUTOCOMPLETE ***** 34// 35Cms.prototype.setAutocomplete = function(config) { 36 var siteID = this.siteID; 37 $( "#" + config.termDiv ).val( config.defaultText ); 38 $( "#" + config.termDiv ).focus(function() { 39 if ($(this).val() == config.defaultText) { 40 $(this).val(''); 41 } 42 }); 43 if (config.shopSearch == null) { 44 config.shopSearch = ""; 45 } 46 $( "#" + config.termDiv ).autocomplete({ 47 source: function(request, response) { 48 $.ajax({ 49 url: "/cgi-bin/itworx/lib/hirbox/ajax_search.cgi", 50 dataType: "json", 51 data: { 52 'term': request.term, 53 'siteID': siteID, 54 'showCategoryName': config.showCategoryName, 55 'showColumnName': config.showColumnName, 56 'language': config.language, 57 'categoryID': config.categoryID.join(','), 58 'columnID': config.columnID.join(','), 59 'shopSearch': config.shopSearch 60 }, 61 success: function(data) { 62 response(data); 63 } 64 }); 65 }, 66 minLength: 1, 67 select: function( event, ui ) { 68 //document.location.href = ui.item.id + "?mit=" + encodeURI($( "#mit" ).val()); 69 document.location.href = ui.item.id; 70 } 71 }); 72 73 $('form[name="' + config.form + '"]').submit(function(event){ 74 event.preventDefault(); 75 if (config.noSubmit != true) { 76 if ($( "#" + config.termDiv ).val() == config.defaultText) { 77 $( "#" + config.termDiv ).val('*'); 78 } 79 80 var cats = new Array(); 81 var catsUrl = ""; 82 for (var x = 0; x < config.categoryID.length; x++) { 83 cats.push("CATEGORY=" + config.categoryID[x]); 84 } 85 if (cats.length > 0) { 86 catsUrl = "&" + cats.join("&"); 87 } 88 89 var cols = new Array(); 90 var colsUrl = ""; 91 for (var x = 0; x < config.columnID.length; x++) { 92 cols.push("COLUMN=" + config.columnID[x]); 93 } 94 if (cols.length > 0) { 95 colsUrl = "&" + cols.join("&"); 96 } 97 document.location.href = "/?autocomplete=1&mit=" + $( "#" + config.termDiv ).val() + "&SHOPTEXT=" + $( "#" + config.termDiv ).val() + "&SHOPSEARCH=" + config.shopSearch + "&nyelv=" + config.language + "&view=rv&tID=" + config.templateColumnID + "&DOSEARCH=1&SEARCHFULLTEXT=mit" + catsUrl + colsUrl; 98 } 99 }); 100}; 101 102// 103// ***** stickyHeader ***** 104// 105function stickyHeader(config) { 106 // Do our DOM lookups beforehand 107 var nav_container = $("." + config.navContainerClass); 108 var nav = $("nav"); 109 var top_spacing = 0; 110 var waypoint_offset = 0; 111 112 nav_container.waypoint(function(direction) { 113 if (direction == 'down') { 114 nav_container.css({ 'height':nav.outerHeight() }); 115 nav.stop().addClass("sticky").css("top", config.offset-nav.outerHeight()); 116 } else { 117 nav_container.css({ 'height':'auto' }); 118 nav.stop().removeClass("sticky").css("top",nav.outerHeight()+waypoint_offset); 119 } 120 }, { 121 offset: function() { 122 return -nav.outerHeight()-waypoint_offset; 123 } 124 } 125 ); 126}; 127 128/* WAYPOINT BASED IMAGE LOADER */ 129function waypointImageLoader() { 130 $('.waypointImageLoader').waypoint(function() { 131 var w = ""; 132 var h = ""; 133 var t = ""; 134 if ( parseFloat($(this).width()) > 0 ) { 135 w = "width='" + $(this).width() + "'"; 136 } 137 if ( parseFloat($(this).height()) > 0 ) { 138 h = "height='" + $(this).height() + "'"; 139 } 140 if ($(this).attr("title") != undefined) { 141 t = $(this).attr("title"); 142 } 143 $(this).html( "<img src='" + $(this).attr("data") +"' " + w + " " + h + " alt='" + t +"' title='" + t +"' />" ); 144 }, { 145 triggerOnce: true, 146 offset: $.waypoints('viewportHeight') - 50 147 //'bottom-in-view' 148 } 149 ); 150 is_waypoint = true; 151} 152 153// 154// ***** PAGE PRINT ***** 155// 156Cms.prototype.printPage = function (elem, config) { 157 if (config.width == undefined) { 158 config.width = 600; 159 } 160 if (config.height == undefined) { 161 config.height = 400; 162 } 163 var mywindow = window.open('', 'cmsPrintWindow', 'height=' + config.height + ',width=' + config.width);
164 mywindow.document.write('<html><head><title>' + config.title + '</title>'); 165 /*optional stylesheet*/ //mywindow.document.write('<link rel="stylesheet" href="main.css" type="text/css" />'); 166 mywindow.document.write('</head><body >'); 167 if (config.prepend != undefined) { 168 mywindow.document.write( config.prepend ); 169 } 170 mywindow.document.write( $(elem).html() ); 171 if (config.append != undefined) { 172 mywindow.document.write( config.append ); 173 } 174 mywindow.document.write('</body></html>'); 175 176 if (config.debug == undefined) { 177 //mywindow.setTimeout(function(){ mywindow.print(); mywindow.close(); }, 1000); 178 mywindow.print(); 179 } 180 181 return true; 182}; 183 184// 185// ***** FILE UPLOADER ***** 186// 187var fileUploader = function(config) { 188 this.config = config; 189 this.fields = {}; 190}; 191 192fileUploader.prototype.getForm = function(params) { 193 var html = ""; 194 var config = this.config; 195 var obj = this; 196 var uploader; 197 this.fields[params.container] = 0; 198 199 if (params.id == '') { 200 document.getElementById(params.container).innerHTML = '<input type="file" name="' + params.container + 'File" />'; 201 return false; 202 } 203 204 if (params.secure == undefined) { 205 params.secure = 0; 206 } 207 208 var extArray = new Array(); 209 if (params.extensions != '') { 210 extArray = params.extensions.split(","); 211 } 212 213 var uploadTxt = config.uploadTxt; 214 var downloadTxt = "<img src='http://static.itworx.hu/jquery-fileuploader/download-icon.png' border='0' hspace='2' align='absmiddle'> " + config.downloadTxt; 215 if (params.type == "doc") { 216 if (params.uploadTxt != undefined) { 217 uploadTxt = params.uploadTxt; 218 } 219 } 220 if (params.type == "image") { 221 uploadTxt = config.uploadImageTxt; 222 if (params.uploadImageTxt != undefined) { 223 uploadTxt = params.uploadImageTxt; 224 } 225 } 226 if (params.downloadTxt != undefined) { 227 downloadTxt = "<img src='http://static.itworx.hu/jquery-fileuploader/download-icon.png' border='0' hspace='2' align='absmiddle'> " + params.downloadTxt; 228 } 229 230 if (params.defaultFile == '') { 231 uploader = new qq.FineUploader({ 232 element: document.getElementById(params.container), 233 multiple: false, 234 debug: false, 235 forceMultipart: true, 236 inputName: 'qqfile', 237 request: { 238 endpoint: "/", 239 params: { 240 doFileUpload: 1, 241 cmsAjaxCall: 1, 242 field: params.field, 243 ID: params.id 244 } 245 }, 246 messages: { 247 typeError: config.uploadErrorTxt + params.extensions 248 }, 249 retry: { 250 preventRetryResponseProperty: 'preventRetry' 251 }, 252 validation: { 253 allowedExtensions: extArray 254 }, 255 text: { 256 uploadButton: "<img src='http://static.itworx.hu/jquery-fileuploader/upload-icon.png' border='0' hspace='2' align='absmiddle'> " + uploadTxt 257 }, 258 callbacks: { 259 onSubmit: function(id, fileName) { 260 $("#" + params.container).hide(); 261 }, 262 onComplete: function(id, fileName, responseJSON) { 263 obj.fields[params.container] = 1; 264 if (config.downloadTxt == '') { 265 config.downloadTxt = responseJSON.file; 266 } 267 if (params.type == "doc") { 268 if (params.secure == 1) { 269 document.getElementById(params.container).innerHTML = "<a href='/?view=userdocstreamer&guid=" + responseJSON.file + "'>" + downloadTxt + "</a> - <img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + responseJSON.file + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> "; 270 } else { 271 document.getElementById(params.container).innerHTML = "<a href='/" + params.folder + "/" + responseJSON.file + "'>" + downloadTxt + "</a> - <img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + responseJSON.file + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> "; 272 } 273 } 274 if (params.type == "image") { 275 if (params.secure == 1) { 276 document.getElementById(params.container).innerHTML = "<img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' vspace='6' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + responseJSON.file + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> <br/><img src='/?view=userdocstreamer&guid=" + responseJSON.file + "' border='1' hspace='4' />"; 277 } else { 278 document.getElementById(params.container).innerHTML = "<img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' vspace='6' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + responseJSON.file + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> <br/>
278<img src='/" + params.folder + "/" + responseJSON.file + "' border='1' hspace='4' />"; 279 } 280 } 281 $("#" + params.container).fadeIn(); 282 }, 283 onError: function(id, fileName, responseJSON) { 284 //this.reset(); 285 } 286 } 287 }); 288 } 289 290 if (params.defaultFile != '') { 291 this.fields[params.container] = 1; 292 if (config.downloadTxt == '') { 293 config.downloadTxt = params.defaultFile; 294 } 295 if (params.type == "doc") { 296 if (params.secure == 1) { 297 $("#" + params.container).html("<a href='/?view=userdocstreamer&guid=" + params.defaultFile + "'>" + downloadTxt + "</a> - <img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + params.defaultFile + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> "); 298 } else { 299 $("#" + params.container).html("<a href='/" + params.folder + "/" + params.defaultFile + "'>" + downloadTxt + "</a> - <img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + params.defaultFile + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> "); 300 } 301 } 302 if (params.type == "image") { 303 if (params.secure == 1) { 304 $("#" + params.container).html("<img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + params.defaultFile + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> <br/><img src='/?view=userdocstreamer&guid=" + params.defaultFile + "' border='1' vspace='6' />"); 305 } else { 306 $("#" + params.container).html("<img src='http://static.itworx.hu/jquery-fileuploader/remove-icon.png' border='0' hspace='2' align='absmiddle'> <a href='javascript:void(0)' onclick='" + config.name + ".removeFile(\"" + params.defaultFile + "\", " + JSON.stringify(params, null, 2) + ");'>" + config.deleteTxt + "</a> <br/><img src='/" + params.folder + "/" + params.defaultFile + "' border='1' vspace='6' />"); 307 } 308 } 309 } 310 311}; 312 313fileUploader.prototype.removeFile = function (guid, params) { 314 var obj = this; 315 var config = this.config; 316 if (confirm(config.deleteConfirmTxt)) { 317 $("#cms-root").load( 318 "/", 319 { 320 cmsAjaxCall: 1, 321 removeUploadedFile: 1, 322 field: params.field, 323 ID: params.id, 324 guid: guid, 325 r: randomnumber 326 }, 327 function() { 328 $("#" + params.container).html(''); 329 params.defaultFile = ""; 330 obj.fields[params.container] = 0; 331 obj.getForm(params); 332 } 333 ); 334 } 335}; 336 337fileUploader.prototype.getState = function (container) { 338 return this.fields[container]; 339}; 340 341function LimitAttach(file, ext) { 342 //console.log(file + ", " + ext); 343 var extArray = new Array(); 344 extArray = ext.split(","); 345 allowSubmit = false; 346 if (!file) { 347 return; 348 } 349 while (file.indexOf("\\\\") != -1) { 350 file = file.slice(file.indexOf("\\\\") + 1); 351 ext = file.slice(file.indexOf(".")).toLowerCase(); 352 for (var i = 0; i < extArray.length; i++) { 353 //console.log(ext + " vs " + extArray[i]); 354 if (extArray[i] == ext) { 355 allowSubmit = true; 356 break; 357 } 358 } 359 } 360 if (allowSubmit){ 361 return true; 362 } else { 363 return false; 364 } 365}; 366 367function checkExtenstion(fileName, validExtensions) { 368 var fileNameExt = fileName.substr(fileName.lastIndexOf('.') + 1); 369 if ($.inArray(fileNameExt, validExtensions) == -1){ 370 return false; 371 } 372 return true; 373} 374 375// ########################################## 376// cookies 377function cookieMessage(config) { 378 var name = "#" + config.div; 379 var cl = readCookie("cookieLaw"); 380 if (cl == null) { 381 var menuYloc = null; 382 var offsetTemp = 0; 383 var message = 'A weboldalunkon cookie-kat használunk, hogy a legjobb felhasználói élményt nyújthassuk. Az adatvédelemrõl bõvebben <a href="' + config.articleUrl + '">itt olvashat</a>.'; 384 var closeMessage = 'Rendben'; 385 if (config.language == 'en') { 386 message = 'We use cookies to improve your experience on our site. To find out more, read our <a href="' + config.articleUrl + '">cookie policy</a>.'; 387 closeMessage = 'Yes, I agree'; 388 } 389 if (config.language == 'nl') { 390 message = 'Om onze website optimaal te laten functioneren gebruiken wij cookies. Voor meer informatie zie ons <a href="' + config.articleUrl + '">Cookiebeleid.</a>'; 391 closeMessage = 'Akkoord'; 392 } 393 if (config.language == 'de') { 394 message = 'Diese Website verwendet Cookies, um bestimmte Funktionen zu ermöglichen und das Angebot zu verbessern. Indem Sie hier fortfahren, stimmen Sie der Nutzung von Cookies zu. Weitere Informationen zu Cookies erhalten Sie in unserer <a href="' + config.articleUrl + '">Datenschutzerklärung</a>'; 395 closeMessage = 'Ich stimme zu'; 396 } 397 398 // custom message 399 if (customCookieText != undefined) { 400 if (customCookieText != "") { message = customCookieText; } 401 } 402 if (customCookieButton != undefined) { 403 if (customCookieButton != "") { closeMessage = customCookieButton; } 404 } 405 406 if (config.preprend == undefined) { 407 config.preprend = "body"; 408 } else {
409 config.preprend = "#" + config.preprend; 410 } 411 if (config.zindex == undefined) { 412 config.zindex = 1; 413 } 414 if (config.barColor == undefined) { 415 config.barColor = "#000"; 416 } 417 418 var c = "cookieMessage"; 419 if (config.addClass != undefined) { 420 c = c + " " + config.addClass; 421 } 422 $(name).html('<div align="center" class="' + c + '">' + message + ' <span id="close_message" style="cursor:pointer"><span class="cookieButton" style="background-color: #a0b800;border-color: #a0b800!important;color: #fff!important;text-transform: uppercase;padding: 3px 15px;border-radius: 2px;margin-left: 4px;">' + closeMessage + '</span></span></div>'); 423 $(".cookieMessage").css('background-color', config.barColor); 424 $(".cookieMessage").css('color', '#ccc'); 425 $(".cookieMessage").css('padding', '5px 5px 5px 25px'); 426 $(".cookieMessage").css('text-align', 'center'); 427 $(".cookieMessage").css('z-index', config.zindex); 428 429 /*menuYloc = parseInt($(name).css("bottom").substring(0,$(name).css("bottom").indexOf("px"))) 430 $(window).scroll(function () { 431 offset = (-1*($(document).scrollTop()+menuYloc)+"px"); 432 $(name).css("bottom", offset); 433 });*/ 434 435 $(config.preprend).prepend( $(name).html() ); 436 $(name).html(); 437 $(name).hide(); 438 439 $('#close_message').click(function() { 440 createCookie("cookieLaw", 1, 90); 441 $('.cookieMessage').fadeOut(); 442 443 // update consent configuration 444 console.log("update consent configuration"); 445 gtag('consent', 'update', { 446 'analytics_storage': 'granted', 447 'ad_storage': 'granted', 448 'ad_personalization': 'granted', 449 'ad_user_data': 'granted', 450 'functionality_storage': 'granted', 451 'personalization_storage': 'granted', 452 'security_storage': 'granted', 453 }); 454 }); 455 } else { 456 $(name).hide(); 457 } 458}; 459 460function createCookie(name,value,days,hours) { 461 var expires; 462 if (days > 0) { 463 var date = new Date(); 464 date.setTime(date.getTime()+(days*24*60*60*1000)); 465 expires = "; expires="+date.toGMTString(); 466 } else { 467 if (days == 0) { 468 var date = new Date(); 469 date.setTime(date.getTime()+(10000)); 470 expires = "; expires="+date.toGMTString(); 471 } else { 472 expires = ""; 473 } 474 } 475 document.cookie = name+"="+value+expires+"; path=/"; 476}; 477 478function createCookieMins(name,value,mins) { 479 var expires; 480 var date = new Date(); 481 date.setTime(date.getTime()+(mins*60*1000)); 482 expires = "; expires="+date.toGMTString(); 483 document.cookie = name+"="+value+expires+"; path=/"; 484}; 485 486function readCookie(name) { 487 var nameEQ = name + "="; 488 var ca = document.cookie.split(';'); 489 for(var i=0;i < ca.length;i++) { 490 var c = ca[i]; 491 while (c.charAt(0)==' ') { 492 c = c.substring(1,c.length); 493 } 494 if (c.indexOf(nameEQ) == 0) { 495 return c.substring(nameEQ.length,c.length); 496 } 497 } 498 return null; 499}; 500 501function eraseCookie(name) { 502 createCookie(name,"",-1); 503}; 504 505/* VALIDATORS */ 506function isValidUrl(url){ 507 var RegExp = /^(([\w]+:)?\/\/)(([\d\w]|%[a-fA-f\d]{2,2})+(:([\d\w]|%[a-fA-f\d]{2,2})+)?@)?([\d\w][-\d\w]{0,253}[\d\w]\.)+[\w]{2,4}(:[\d]+)?(\/([-+_~.\d\w]|%[a-fA-f\d]{2,2})*)*(\?(&?([-+_~.\d\w]|%[a-fA-f\d]{2,2})=?)*)?(#([-+_~.\d\w]|%[a-fA-f\d]{2,2})*)?$/; 508 if(RegExp.test(url)) { 509 return true; 510 } else { 511 return false; 512 } 513}; 514 515function isValidEmail(email){ 516 if (email.length == 0) { 517 return false; 518 } 519 if (!email.match(/[a-zA-Z0-9_\-][a-zA-Z0-9_\-\.]*[a-zA-Z0-9_\-]*[@][a-zA-Z0-9_\-]+([\.][a-zA-Z0-9_\-]+)*[\.][a-zA-Z]{2,10}$/)) { 520 return false; 521 } 522 return true; 523}; 524 525/* url param extractor */ 526function getURLParameter(name) { 527 return decodeURI( 528 (RegExp(name + '=' + '(.+?)(&|$)').exec(location.search)||[,""])[1] 529 ); 530}; 531 532/* HELPERS */ 533function getCheckedValue(radioObj) { 534 if(!radioObj) 535 return ""; 536 var radioLength = radioObj.length; 537 if(radioLength == undefined) 538 if(radioObj.checked) 539 return radioObj.value; 540 else 541 return ""; 542 for(var i = 0; i < radioLength; i++) { 543 if(radioObj[i].checked) { 544 return radioObj[i].value; 545 } 546 } 547 return ""; 548}; 549 550/* MOBILE check */ 551if( /Android|webOS|iPhone|iPad|iPod|BlackBerry|Windows Phone/i.test(navigator.userAgent) ) { 552 is_mobile = true; 553}; 554 555/* BROWSER_ERROR handler */ 556function addWindowErrorHandler() {
557 window.onerror = function (message, url, lineNumber, columnNumber, error) { 558 var trace = ''; 559 console.log('Error: ' , error); 560 try {trace = error.stack;} catch (e) {trace = '';} 561 try {$.ajax({method: "POST",url: 'https://developer.webmark-solutions.nl/cgi-bin/_sysadmin/browser_alert.php', 562 data: {s: url, m: message, l: lineNumber, c: columnNumber, t: trace} 563 }).done(function (data) {console.log('Response: ', data);}); 564 } catch (e) {console.log('Unhandled ERROR');} finally {return true;} 565 }; 566}; 567 568/* SCROLL TO TOP */ 569if (window.jQuery) { 570 $(".scrolltop").click(function(e) { 571 e.preventDefault(); 572 $("html,body").animate({scrollTop: $("body").offset().top}, "fast"); 573 }); 574}; 575</script>
575 576<!-- RES --> 577<!-- RES navigator/navigator-bootstrap5.js -->
577<script>// create drop down menu from json using bootsrap 578 579function createMenu_bootstrap5(params) { 580 var menuID = Math.floor(Math.random()*1000001); 581 var menuHTML = '<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent' + menuID + '" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">\n<span class="navbar-toggler-icon"></span>\n</button>\n'; 582 var kickbackActivate = 0; 583 menuHTML = menuHTML + '<div class="collapse navbar-collapse" id="navbarSupportedContent' + menuID + '">\n'; 584 menuHTML = menuHTML + "<ul class=\"navbar-nav\">\n"; 585 for(var x = 0; x < params.menuJson.length; x++) { 586 var response = parseMenuItemBootstrap5(params.menuJson[x], menuHTML, params.param1, params.tID, params.nID, params.gID, params.regformID, false); 587 menuHTML = response[0]; 588 kickbackActivate = response[1]; 589 } 590 menuHTML = menuHTML + "</ul>\n</div>\n"; 591 //console.log(menuHTML); 592 593 $("#" + params.id).html(menuHTML); 594} 595 596function parseMenuItemBootstrap5(menuItem, menuHTML, allowKickbackActivate, tID, nID, gID, regformID, isDropDown) { 597 var activeClass = ""; 598 var kickbackActivate = 0; 599 if (menuItem.href == null) { 600 menuItem.href = "javascript:void(0)"; 601 } 602 // if no ID defined try the url 603 if ((tID == '') && (nID == '') && (gID == '') && (regformID == '')) { 604 if (menuItem.href == document.location.pathname) { 605 activeClass = "active"; 606 kickbackActivate = 1; 607 } 608 } else { 609 var i = menuItem.key.split(":"); 610 if ((i[0] == "column") && (i[1] == tID)) { 611 activeClass = "active"; 612 kickbackActivate = 1; 613 } 614 if ((i[0] == "page") && (i[1] == nID)) { 615 activeClass = "active"; 616 kickbackActivate = 1; 617 } 618 if ((i[0] == "gallery") && (i[1] == gID)) { 619 activeClass = "active"; 620 kickbackActivate = 1; 621 } 622 if ((i[0] == "regform") && (i[1] == regformID)) { 623 activeClass = "active"; 624 kickbackActivate = 1; 625 } 626 } 627 628 menuItem.title = unescape(menuItem.title); 629 630 var randomnumber = Math.floor(Math.random()*1000001); 631 632 if (menuItem.children != undefined) { 633 if (menuItem.href == "") { menuItem.href = "#"; } 634 var key = menuItem.key.replace(":", ""); 635 var dropdownID = Math.floor(Math.random()*1000001); 636 menuHTML = menuHTML + '<li class="nav-item dropdown" data-href="' + menuItem.href + '" id="' + key + '" data-key="' + menuItem.key +'">'; 637 menuHTML = menuHTML + ' <a class="nav-link dropdown-toggle" href="#" data-href="' + menuItem.href + '" id="navbarDropdown' + dropdownID + '" role="button" data-bs-toggle="dropdown" aria-expanded="false">' + menuItem.title + '</a>\n'; 638 menuHTML = menuHTML + ' <ul class="dropdown-menu" aria-labelledby="navbarDropdown' + dropdownID + '">\n'; 639 640 for(var x = 0; x < menuItem.children.length; x++) { 641 var response = parseMenuItemBootstrap5(menuItem.children[x], menuHTML, allowKickbackActivate, tID, nID, gID, regformID, true); 642 menuHTML = response[0]; 643 kickbackActivate = response[1]; 644 if ((kickbackActivate == 1) && (allowKickbackActivate == 1)) { 645 menuHTML = menuHTML.replace("id='level" + randomnumber + "'", "id='level" + randomnumber + "'" + " class=\"active\""); 646 } 647 } 648 menuHTML = menuHTML + "</ul>\n"; 649 menuHTML = menuHTML + "</li>\n"; 650 } else { 651 // menu links 652 if (isDropDown) { 653 menuHTML = menuHTML + "<li id='level" + randomnumber + "'>\n"; 654 menuHTML = menuHTML + "<a href='" + menuItem.href + "' class='dropdown-item " + activeClass + "'>" + menuItem.title + "</a>\n"; 655 } else { 656 menuHTML = menuHTML + "<li class='nav-item' id='level" + randomnumber + "'>\n"; 657 menuHTML = menuHTML + "<a href='" + menuItem.href + "' class='nav-link " + activeClass + "'>" + menuItem.title + "</a>\n"; 658 } 659 } 660 661 var key = menuItem.key.replace(":", ""); 662 //console.log(menuItem.key); 663 menuHTML = menuHTML.replace("id='level" + randomnumber + "'", "id='" + key + "' data-key='" + menuItem.key + "'"); 664 menuHTML = menuHTML + "</li>\n"; 665 return [menuHTML, kickbackActivate]; 666}</script>
666 667<!-- RES --> 668<!-- RES navigator/navigator-simplerenderer.js -->
668<script>function createMenu_simplerenderer(params){var menuHTML="";var kickbackActivate=0;menuHTML=menuHTML+"<ul>\n";for(var x=0;x<params.menuJson.length;x++){var response=parseMenuItem(params.menuJson[x],menuHTML,params.param1,params.tID,params.nID,params.gID,params.regformID);menuHTML=response[0];kickbackActivate=response[1]}menuHTML=menuHTML+"</ul>\n";$("#"+params.id).html(menuHTML)}function parseMenuItem(menuItem,menuHTML,allowKickbackActivate,tID,nID,gID,regformID){var activeClass="";var kickbackActivate=0;if(menuItem.href==null){menuItem.href="javascript:void(0)"}if((tID=='')&&(nID=='')&&(gID=='')&&(regformID=='')){if(menuItem.href==document.location.pathname){activeClass=" class=\"current\"";kickbackActivate=1}}else{var i=menuItem.key.split(":");if((i[0]=="column")&&(i[1]==tID)){activeClass=" class=\"current\"";kickbackActivate=1}if((i[0]=="page")&&(i[1]==nID)){activeClass=" class=\"current\"";kickbackActivate=1}if((i[0]=="gallery")&&(i[1]==gID)){activeClass=" class=\"current\"";kickbackActivate=1}if((i[0]=="regform")&&(i[1]==regformID)){activeClass=" class=\"current\"";kickbackActivate=1}}menuItem.title=unescape(menuItem.title);var randomnumber=Math.floor(Math.random()*1000001);menuHTML=menuHTML+"<li"+activeClass+" id='level"+randomnumber+"'>\n";menuHTML=menuHTML+"<a href='"+menuItem.href+"'>"+menuItem.title+"</a>\n";if(menuItem.children!=undefined){menuHTML=menuHTML+"<ul>\n";for(var x=0;x<menuItem.children.length;x++){var response=parseMenuItem(menuItem.children[x],menuHTML,allowKickbackActivate,tID,nID,gID,regformID);menuHTML=response[0];kickbackActivate=response[1];if((kickbackActivate==1)&&(allowKickbackActivate==1)){menuHTML=menuHTML.replace("id='level"+randomnumber+"'","id='level"+randomnumber+"'"+" class=\"current\"")}}menuHTML=menuHTML+"</ul>\n"}var key=menuItem.key.replace(":","");menuHTML=menuHTML.replace("id='level"+randomnumber+"'","id='"+key+"'");menuHTML=menuHTML+"</li>\n";return[menuHTML,kickbackActivate]}</script>
668 669<!-- RES --> 670<!-- RES jquery-swipebox/jquery.swipebox.min.js -->
vendor: 13,172 bytes, lines 670-671
670<script>/*! 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class="container py-4 py-lg-5 position-relative"> 777 <nav aria-label="breadcrumb"> 778 <ol class="breadcrumb"> 779 <li class="breadcrumb-item"><a href="/">Home</a></li> 780 <li class="breadcrumb-item"><a href="/news/">News</a></li> 781 <li class="breadcrumb-item active" aria-current="page">SYNTHIA Insight 10: Using Synthetic Data to Build Trust in Cancer Genomics Tools</li> 782 </ol> 783 </nav> 784 785 <h1 class="xxl-font mb-lg-4 font-weight-600 color-3 mt-3 mt-lg-5">SYNTHIA Insight 10: Using Synthetic Data to Build Trust in Cancer Genomics Tools</h1> 786 <p class="s-font color-1 mb-1"><b></b></p> 787 <p class="s-font color-3 mb-3 event-date" data-d1="2026-08-23" data-d2="0-00-00">23 August 2026</p> 788 <div class="row"> 789 <div class="col-12"> 790 <div class="m-font font-weight-300 article-text"><hr /> 791<p>Welcome to SYNTHIA Insight – a series of focused content pieces that bring the science behind SYNTHIA to life. Through interviews with our project partners, we explore views, visions and expertise in synthetic data. Each edition offers an accessible window into the objectives of SYNTHIA and the progress of our work – helping to engage the wider community, spark dialogue, and promote understanding of SYNTHIA’s mission and impact. We invite you to connect with the minds shaping the future of synthetic data.</p> 792 793<hr /> 794<p><strong>In SYNTHIA Insight nr. 10, we reintroduce <span style="color:#8e44ad;">Stella (Styliani-Christina) Fragkouli</span>, Research Associate at the<span style="color:#8e44ad;"> Centre for Research and Technology Hellas (CERTH)</span>. In this edition, Stella discusses the motivation and findings behind the publication published in the Frontiers in Bioinformatics, titled:<span style="color:#8e44ad;"> </span><a href="/publications/synth4bench-synthetic-data-generation-for-benchmarking-tumor-only-somatic-variant-calling-algorithms"><span style="color:#8e44ad;">Synth4bench: Generating Synthetic Data for Benchmarking Tumor-Only Somatic Variant Calling Algorithms.</span></a></strong></p> 795 796<hr /> 797<p>The study explores an important application of synthetic data in cancer genomics: creating reliable ground truth datasets that allow researchers to evaluate the computational tools used to identify genetic mutations.</p> 798 799<p>Cancer develops through the accumulation of genetic alterations, including somatic mutations that arise in cells during a person's lifetime. Accurately identifying these variants is therefore an important part of understanding cancer genomics. However, different c
799omputational algorithms can analyse the same sequencing data and produce different results. This creates a fundamental challenge: if the true variants within a real-world dataset are not fully known, how can researchers determine which algorithm is giving the most accurate answer?</p> 800 801<p>Synth4bench addresses this challenge by using synthetic genomics data as a known ground truth. Because researchers control what has been generated, they know which variants are present before asking an algorithm to detect them. This makes it possible to systematically compare algorithms, understand why their results differ, and explore which tools may be better suited to different scenarios.</p> 802 803<hr /> 804<p>Watch the video interview:</p> 805 806<div><iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen="" frameborder="0" height="315" referrerpolicy="strict-origin-when-cross-origin" src="https://www.youtube.com/embed/jLFkGSt_YUU?si=DDmnY9KnOOomJrtY" title="YouTube video player" width="560"></iframe></div> 807 808<div> </div> 809 810<div> 811<hr /> 812<p><span style="color:#8e44ad;"><strong>When Different Algorithms Give Different Answers</strong></span></p> 813 814<p>A central challenge explored in the study is the disagreement between tools used for somatic variant calling. As Fragkouli explains, different algorithms have different mathematical foundations and make different assumptions about the data. As a result, even when they receive exactly the same dataset, their outputs can differ.</p> 815 816<p><span style="color:#2980b9;">“Algorithms that are given the same data produce different results.”</span> This becomes particularly problematic when working with real-world data. If three algorithms produce three different sets of variants with relatively little overlap, researchers face a difficult question: which one is closest to the truth? <span style="color:#2980b9;">“At the end of the day, the question is: which one is telling the truth?”</span> Fragkouli explains.<span style="color:#2980b9;"> “And you cannot tell that because you don't know what's inside your data.”</span> The scarcity of high-quality datasets with known ground truth has long made the robust benchmarking of variant calling tools difficult. Synth4bench was developed to help overcome this limitation by bringing synthetic data generation, variant calling and benchmarking together within one pipeline.</p> 817 818<hr /> 819<p><span style="color:#8e44ad;"><strong>Creating a Ground Truth with Synthetic Data</strong></span></p> 820 821<p>Synthetic data changes the benchmarking process because the researchers generating the dataset already know what it contains. <span style="color:#2980b9;">“Synthetic data gives us the opportunity to have well-characterized datasets. We know what is there before asking the algorithm to make the report, so then we can actually benchmark the algorithm against the ground truth,”</span> Fragkouli explains. Synth4bench generates controlled next-generation sequencing datasets and compares the results produced by different variant callers against this predefined ground truth. The researchers can also systematically change characteristics of the sequencing data, such as sequencing depth and read length, while keeping other parameters unchanged. This allows them to investigate how individual characteristics of a dataset influence an algorithm's behaviour.<br /> 822This controlled environment provides something that is extremely difficult to achieve with complex real-world datasets: the ability to isolate individual factors and observe how algorithms respond to them.</p> 823 824<hr /> 825<p><span style="color:#8e44ad;"><strong>There Is No One-Size-Fits-All Algorithm</strong></span></p> 826 827<p>Using Synth4bench, the researchers evaluated five widely used variant callers – Mutect2, FreeBayes, VarDict, VarScan2 and LoFreq. The analysis revealed considerable differences in their performance, with results influenced by the type of variant being detected as well as sequencing characteristics such as read length and depth. For Fragkouli, one of the most interesting findings was not simply that the algorithms disagreed, but what that disagreement tells us about the way these tools model complex biological processes. Different algorithms have different <span style="color:#2980b9;">“mathematical hearts”</span>, as she describes them. Some rely on Bayesian inference, others on different statistical approaches, and each weighs components of the data differently. This means that algorithms developed with different assumptions may perform better or worse depending on the research question and type of data being analysed.</p> 828 829<p><span style="color:#2980b9;">“Different algorithms are better for different scenarios,” </span>Fragkouli explains.<span style="color:#2980b9;"> “It is very important for researchers to know that if you want this type of variant, then this tool works better – or if you want this scenario, go for that tool.” </span>
829Rather than identifying a universal winner, the results therefore underline the importance of choosing and optimizing tools according to the specific research context. The paper concludes that there is no single solution that performs best across every scenario, and that both sequencing optimization and caller selection are important for maximizing sensitivity and reliability.</p> 830 831<hr /> 832<p><span style="color:#8e44ad;"><strong>Why Some Genetic Variants Remain Harder to Detect</strong></span></p> 833 834<p>The publication also highlighted the particular difficulty of detecting insertions and deletions, or indels – variants in which small numbers of DNA bases are inserted into or removed from the genome. Across the benchmarking experiments, indels remained more challenging to identify reliably than single nucleotide variants (SNVs).</p> 835 836<p>Fragkouli explains that this is partly due to their more complex nature. Unlike a single nucleotide change, an insertion or deletion can occur in different forms and involve different numbers of bases, creating greater variability for algorithms to interpret. The findings are consistent with previous benchmarking research, but Synth4bench provides a controlled environment in which researchers can examine these difficulties more systematically. In doing so, the study also points towards opportunities for further research into how computational models represent the complex mutational processes underlying cancer.</p> 837 838<hr /> 839<p><span style="color:#8e44ad;"><strong>Beyond Privacy: Another Role for Synthetic Data</strong></span></p> 840 841<p>Synthetic data is frequently discussed in healthcare because of its potential to support data access and use while protecting patient privacy. Synth4bench demonstrates another important application: using synthetic data as a scientific benchmarking resource.<span style="color:#2980b9;"> “Synthetic data is a great tool when we talk about algorithm development as well as modelling processes,” </span>Fragkouli explains. Because synthetic datasets can be generated with known characteristics and in large volumes, they can help researchers develop, test and compare algorithms where suitable real-world data may be limited. They can also be used to investigate how computational systems respond to specific data characteristics before those systems are ultimately evaluated against real-world data. This illustrates how synthetic data can support research at different stages, from algorithm development and data augmentation to benchmarking and validation, while helping researchers better understand the strengths and limitations of the tools they use.</p> 842 843<hr /> 844<p><span style="color:#8e44ad;"><strong>Connecting to SYNTHIA's Mission</strong></span></p> 845 846<p>Within SYNTHIA, this work contributes to the broader goal of developing and validating synthetic data approaches that can support trustworthy healthcare research. While the researchers behind Synth4bench are primarily involved in SYNTHIA's hematological use cases, the benchmarking approach itself has wider relevance across the project, where genomic data can play an important role across different disease areas.</p> 847 848<p><span style="color:#2980b9;">“Our work is very relevant to everyone that is involved in the precision medicine pipeline because we look into the algorithms involved there,”</span> Fragkouli explains. <span style="color:#2980b9;">“At the end of the day, our work is to shed light into trusting algorithms within healthcare.” </span>Ultimately, Synth4bench expands the story of what synthetic data can enable. Its value is not limited to generating alternatives to sensitive real-world datasets. By providing controlled ground truth, synthetic data can also help researchers ask whether the computational tools analysing healthcare data are behaving as expected, and understand where and why they may fail.</p> 849 850<p>For Fragkouli, achieving that goal ultimately depends on collaboration. Algorithm developers, bioinformaticians, biologists and medical researchers bring different expertise to the same healthcare challenges. <span style="color:#2980b9;">“We have to collaborate with each other and combine our different backgrounds, and we have to go hand in hand in order to produce good results that will help patients, doctors and everyone involved in healthcare.” </span>By bringing these perspectives together, work such as Synth4bench can contribute to more transparent, reproducible and trustworthy computational methods, supporting SYNTHIA's wider ambition to advance the responsible use of synthetic data in precision medicine.</p> 851 852<hr /> 853<p>Listen to the podcast:</p> 854 855<ul> 856 <li><a href="https://open.spotify.com/episode/0VPjoz1ojRymuEmp9hzfiM?si=DNKgSVpjSzuFobtz5eWmPQ" target="_blank">Click here to open our podcast on Spotify ></a></li> 857</ul> 858 859<p><br /> 860For the full publication:</p> 861 862<ul> 863 <li><a href="/publications/synth4bench-synthetic-data-generation-for-benchmarking-tumor-only-somatic-variant-calling-algorithms">Click here to open ></a></li> 864</ul> 865 866<hr /> 867<p> </p> 868</div> 869 870<p> </p> 871 872<p> </p> 873 874<p> </p> 875 876<p> </p> 877 878<p> </p> 879 880<p> </p> 881 882<p> </p> 883 884<p> </p> 885</div> 886 <div> </div> 887 </div> 888 </div> 889 </div> 890</section>
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