update

Author: jarochi

docs/fibrea.html

@@ -607,7 +607,7 @@
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/conferences.html"> 
-<span class="menu-text">Presentations</span></a>
+<span class="menu-text">Conferences etc.</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/theses.html"> 
@@ -846,37 +846,64 @@ <h2 class="anchored" data-anchor-id="consortium">Consortium</h2>
 <p>
 Leads molecular grammar development and overall coordination. Expertise in protein informatics, machine learning for amyloids and peptides and FAIR/DOME-compliant data workflows.
 </p>
+Leader:
+<div>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="subsite/fig/ppl/mb.jpeg" title="Michał Burdukiewicz" class="img-fluid figure-img"></p>
+<figcaption>Michał Burdukiewicz</figcaption>
+</figure>
+</div>
+</div>
 </div>
 <div class="partner-card">
 <div class="partner-name">
-University of Copenhagen (DK)
+Vilnius University (LT)
 </div>
 <div class="partner-role">
-WP2 Leader
+WP4 Leader
 </div>
 <div class="pill">
-<i class="bi bi-mesh"></i> Coarse-grained simulations
+<i class="bi bi-droplet-half"></i> Aggregation assays
+</div>
+<div class="pill">
+<i class="bi bi-badge-3d"></i> cryo-EM / TEM / AFM
 </div>
 <p>
-Developers of CALVADOS and world leaders in protein folding and aggregation modeling. Provide physics-based constraints and structural descriptors for CFAMs.
+Experimental amyloid specialists performing biophysical characterization, structural validation and independent reproducibility checks.
 </p>
+Leader:
+<div>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="subsite/fig/fibrea/DariusS.png" title="Darius Šulskis" class="img-fluid figure-img"></p>
+<figcaption>Darius Šulskis</figcaption>
+</figure>
+</div>
+</div>
 </div>
 <div class="partner-card">
 <div class="partner-name">
-Vilnius University (LT)
+University of Copenhagen (DK)
 </div>
 <div class="partner-role">
-WP4 Leader
-</div>
-<div class="pill">
-<i class="bi bi-droplet-half"></i> Aggregation assays
+WP2 Leader
 </div>
 <div class="pill">
-<i class="bi bi-badge-3d"></i> cryo-EM / TEM / AFM
+<i class="bi bi-mesh"></i> Coarse-grained simulations
 </div>
 <p>
-Experimental amyloid specialists performing biophysical characterization, structural validation and independent reproducibility checks.
+Developers of CALVADOS and world leaders in protein folding and aggregation modeling. Provide physics-based constraints and structural descriptors for CFAMs.
 </p>
+Leader:
+<div>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="subsite/fig/fibrea/KDVS-KRESTEN.jpg" title="Kresten Lindorff-Larsen" class="img-fluid figure-img"></p>
+<figcaption>Kresten Lindorff-Larsen</figcaption>
+</figure>
+</div>
+</div>
 </div>
 <div class="partner-card">
 <div class="partner-name">
@@ -891,6 +918,15 @@ <h2 class="anchored" data-anchor-id="consortium">Consortium</h2>
 <p>
 Experts in curli-based nanomaterials and biofilm engineering. Optimize host strains, codon usage, fermentation and purification for CFAM production.
 </p>
+Leader:
+<div>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="subsite/fig/fibrea/urartu_seker_wp1.jpg" title="Urartu Özgür Şafak Şeker" class="img-fluid figure-img"></p>
+<figcaption>Urartu Ozgur Safak Seker / Urartu Özgür Şafak Şeker</figcaption>
+</figure>
+</div>
+</div>
 </div>
 <div class="partner-card">
 <div class="partner-name">
@@ -905,6 +941,15 @@ <h2 class="anchored" data-anchor-id="consortium">Consortium</h2>
 <p>
 Focus on functional CFAMs carrying fluorescent and enzymatic modules. Demonstrate catalytic CFAMs and FRET-based co-assembly.
 </p>
+Leader:
+<div>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="subsite/fig/fibrea/JaviGP.jpeg" title="Javier Garcia Pardo" class="img-fluid figure-img"></p>
+<figcaption>Javier Garcia Pardo</figcaption>
+</figure>
+</div>
+</div>
 </div>
 </div>
 <hr>

docs/index.html

@@ -456,7 +456,7 @@
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/conferences.html"> 
-<span class="menu-text">Presentations</span></a>
+<span class="menu-text">Conferences etc.</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/theses.html"> 

docs/index_projects.html

@@ -453,7 +453,7 @@
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/conferences.html"> 
-<span class="menu-text">Presentations</span></a>
+<span class="menu-text">Conferences etc.</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./subsite/theses.html"> 

docs/search.json

@@ -732,7 +732,7 @@
     "href": "fibrea.html#consortium",
     "title": "Functional Interfaces and Biomolecular Rules for Engineered Amyloids",
     "section": "Consortium",
-    "text": "Consortium\n\nFIBREA unites complementary expertise across bioinformatics, simulations, amyloid biology and synthetic biology.\n\n\n\n\nMedical University of Białystok (PL)\n\n\nCoordinator · WP1 and WP6 Leader\n\n\n Computational design\n\n\n Project management\n\n\nLeads molecular grammar development and overall coordination. Expertise in protein informatics, machine learning for amyloids and peptides and FAIR/DOME-compliant data workflows.\n\n\n\n\nUniversity of Copenhagen (DK)\n\n\nWP2 Leader\n\n\n Coarse-grained simulations\n\n\nDevelopers of CALVADOS and world leaders in protein folding and aggregation modeling. Provide physics-based constraints and structural descriptors for CFAMs.\n\n\n\n\nVilnius University (LT)\n\n\nWP4 Leader\n\n\n Aggregation assays\n\n\n cryo-EM / TEM / AFM\n\n\nExperimental amyloid specialists performing biophysical characterization, structural validation and independent reproducibility checks.\n\n\n\n\nBilkent University – UNAM (TR)\n\n\nWP3 Leader\n\n\n Curli expression systems\n\n\nExperts in curli-based nanomaterials and biofilm engineering. Optimize host strains, codon usage, fermentation and purification for CFAM production.\n\n\n\n\nAutonomous University of Barcelona (ES)\n\n\nWP5 Leader\n\n\n Functional amyloids\n\n\nFocus on functional CFAMs carrying fluorescent and enzymatic modules. Demonstrate catalytic CFAMs and FRET-based co-assembly."
+    "text": "Consortium\n\nFIBREA unites complementary expertise across bioinformatics, simulations, amyloid biology and synthetic biology.\n\n\n\n\nMedical University of Białystok (PL)\n\n\nCoordinator · WP1 and WP6 Leader\n\n\n Computational design\n\n\n Project management\n\n\nLeads molecular grammar development and overall coordination. Expertise in protein informatics, machine learning for amyloids and peptides and FAIR/DOME-compliant data workflows.\n\nLeader:\n\n\n\n\nMichał Burdukiewicz\n\n\n\n\n\n\nVilnius University (LT)\n\n\nWP4 Leader\n\n\n Aggregation assays\n\n\n cryo-EM / TEM / AFM\n\n\nExperimental amyloid specialists performing biophysical characterization, structural validation and independent reproducibility checks.\n\nLeader:\n\n\n\n\nDarius Šulskis\n\n\n\n\n\n\nUniversity of Copenhagen (DK)\n\n\nWP2 Leader\n\n\n Coarse-grained simulations\n\n\nDevelopers of CALVADOS and world leaders in protein folding and aggregation modeling. Provide physics-based constraints and structural descriptors for CFAMs.\n\nLeader:\n\n\n\n\nKresten Lindorff-Larsen\n\n\n\n\n\n\nBilkent University – UNAM (TR)\n\n\nWP3 Leader\n\n\n Curli expression systems\n\n\nExperts in curli-based nanomaterials and biofilm engineering. Optimize host strains, codon usage, fermentation and purification for CFAM production.\n\nLeader:\n\n\n\n\nUrartu Ozgur Safak Seker / Urartu Özgür Şafak Şeker\n\n\n\n\n\n\nAutonomous University of Barcelona (ES)\n\n\nWP5 Leader\n\n\n Functional amyloids\n\n\nFocus on functional CFAMs carrying fluorescent and enzymatic modules. Demonstrate catalytic CFAMs and FRET-based co-assembly.\n\nLeader:\n\n\n\n\nJavier Garcia Pardo"
   },
   {
     "objectID": "fibrea.html#work-packages",
@@ -1315,19 +1315,12 @@
     "section": "",
     "text": "LIMAD: Large-scale identification of microorganism products impacting amyloid diseases\nPI: Valen\nFunding agency: National Science Center Poland\nProgramme: Miniatura 9\nGrant ID: 2025/09/X/NZ7/00600\nStart date: 21 Aug 2025\nDuration: 12 months\nBudget: PLN49,999.00\nProtein aggregation and amyloid deposits are hallmarks of neurodegenerative diseases such as Alzheimer’s (AD) and Parkinson’s (PD). Emerging evidence suggests that microbial proteins can influence the misfolding of human amyloidogenic proteins (notably Aβ42 and α-synuclein), potentially via the gut–brain axis. LIMAD aims to systematically uncover microbial proteins with amyloid potential and evaluate their ability to interact with and promote aggregation of Aβ42 and α-synuclein.\n\n\n\n🔍 Systematic review of microbes linked to Alzheimer’s & Parkinson’s\n\n🧬 Screening microbial proteins for amyloid potential\n\n🤖 Using ML & structural biology to test cross-interactions with Aβ42 & α-synuclein\n\n🧪 Generating new hypotheses for microbial contributions to neurodegeneration\n\n🎯 Identifying potential drug targets and prevention strategies"
   },
-  {
-    "objectID": "subsite/publications.html#section",
-    "href": "subsite/publications.html#section",
-    "title": "Publications",
-    "section": "",
-    "text": "Our colaborators and former members manuscripts"
-  },
   {
     "objectID": "subsite/team/jc.html",
     "href": "subsite/team/jc.html",
     "title": "Jarosław (Jarek) Chilimoniuk",
     "section": "",
-    "text": "📝 Bio\n\n👨‍🔬 I am a passionate researcher with experience in laboratory work 🧪, bioinformatics 🖥️, and administrative tasks 📑. My main focus is on amyloids 🌀, both in vivo 🧬 and in silico 🖥️, as well as data curation 📊 and analysis 📉. I specialize in developing and deploying Shiny apps 📱 for interactive data visualization, making complex biological data more accessible and user-friendly.\n🔍 I love exploring new approaches and experimenting with fresh ideas 💡. Trying different methods often gives me a new perspective 👀 on challenges, helping me overcome roadblocks 🚧 and push my research forward.\n🌍 I am highly mobile and enjoy working in different countries ✈️. Experiencing how various scientific communities tackle university challenges 🏛️, research struggles 🧑‍🔬, and work culture differences 🤝 gives me valuable insights and broadens my approach to problem-solving.\n🎲🎮📚🛹 Board games, computer games, books, and skateboarding? That’s life, that’s love! Whether strategizing over a game, getting lost in a great book, or cruising on my skateboard, I believe in balancing work with the things that bring joy and inspiration.\n⚡ With expertise in wet lab experiments 🏺, computational analysis 🤖, and project management 📋, I thrive at the intersection of biology 🧪 and informatics 💻, combining data-driven insights with hands-on scientific exploration. Always eager to learn, innovate, and collaborate 🤝, I am driven by curiosity and a passion for discovery 🚀\n\n\n📱 Contact\n\n    \n\n\n🚀 Research stays\n\n\n\n\n\n\n\n\n\n💻🧫 Experience\n\n\n\n\n\n\n\n\n\n🎓 Education\n\n\n University of Wrocław\n\n\nBioTechNan - Program of Interdisciplinary Environmental PhD Studies KNOW in the area of Biotechnology and Nanotechnology\n\n2018-10-01 - 2023-07-06 PhD thesis: Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB 📍 Wrocław, Poland\n\n Brandenburg University of Technology Cottbus-Senftenberg\n\n\nExchange studies, German Academic Exchange Service scholarship, Biotechnology\n\n2020-10-01 - 2021-09-30 📍 Senftenberg, Germany\n\n University of Wrocław\n\n\nMolecular Biology\n\n2017-10-01 - 2018-09-30 📍 Wrocław, Poland\n\n University of Warsaw\n\n\nBiotechnology, specialization in Molecular Biology\n\n2013-10-01 - 2015-08-13 MSc thesis: Disposal of hardly biodegradable feedstock wastes in methane fermentation process 📍 Warsaw, Poland\n\n University of Warsaw\n\n\nBiotechnology\n\n2010-10-01 - 2013-09-06 BSc thesis: Localization of hSUV3 protein and γ-tubulin at different developmental stages of the human umbilical cord blood-derived neural stem cell line (HUCB-NSC) 📍 Warsaw, Poland\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻\n\n\n\n\n\n\n\n\n\n📖 Publications\n\n\n\n\n\n\n\n\n\n🧑🏻‍🔬 Other activities\n\n\nAssociation of Wrocław R Users (STWUR) meetings co-organizer - R language workshops\nCo-organizer of WhyR? 2019 Conference in Warsaw\nCo-organizer of WhyR? 2018 Conference in Wrocław\nCEO of PhD Bioinformatics Club at University of Wrocław, 2017-2023"
+    "text": "Jarosław (Jarek) Chilimoniuk\n\n\nData Scientist · R & Quarto · Analytics\n\n\n ·  ·  ·  · \n\n\nDownload PDF \n\n\n\n📝 Bio\n\n👨‍🔬 I am a passionate researcher with experience in laboratory work 🧪, bioinformatics 🖥️, and administrative tasks 📑. My main focus is on amyloids 🌀, both in vivo 🧬 and in silico 🖥️, as well as data curation 📊 and analysis 📉. I specialize in developing and deploying Shiny apps 📱 for interactive data visualization, making complex biological data more accessible and user-friendly.\n🔍 I love exploring new approaches and experimenting with fresh ideas 💡. Trying different methods often gives me a new perspective 👀 on challenges, helping me overcome roadblocks 🚧 and push my research forward.\n🌍 I am highly mobile and enjoy working in different countries ✈️. Experiencing how various scientific communities tackle university challenges 🏛️, research struggles 🧑‍🔬, and work culture differences 🤝 gives me valuable insights and broadens my approach to problem-solving.\n🎲🎮📚🛹 Board games, computer games, books, and skateboarding? That’s life, that’s love! Whether strategizing over a game, getting lost in a great book, or cruising on my skateboard, I believe in balancing work with the things that bring joy and inspiration.\n⚡ With expertise in wet lab experiments 🏺, computational analysis 🤖, and project management 📋, I thrive at the intersection of biology 🧪 and informatics 💻, combining data-driven insights with hands-on scientific exploration. Always eager to learn, innovate, and collaborate 🤝, I am driven by curiosity and a passion for discovery 🚀\n\n\n📱 Contact\n\n    \n\n\n🚀 Research stays\n\n\n\n\n\n\n\n\n\n💻🧫 Experience\n\n\n\n\n\n\n\n\n\n🎓 Education\n\n\n University of Wrocław\n\n\nBioTechNan - Program of Interdisciplinary Environmental PhD Studies KNOW in the area of Biotechnology and Nanotechnology\n\n2018-10-01 - 2023-07-06 PhD thesis: Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB 📍 Wrocław, Poland\n\n Brandenburg University of Technology Cottbus-Senftenberg\n\n\nExchange studies, German Academic Exchange Service scholarship, Biotechnology\n\n2020-10-01 - 2021-09-30 📍 Senftenberg, Germany\n\n University of Wrocław\n\n\nMolecular Biology\n\n2017-10-01 - 2018-09-30 📍 Wrocław, Poland\n\n University of Warsaw\n\n\nBiotechnology, specialization in Molecular Biology\n\n2013-10-01 - 2015-08-13 MSc thesis: Disposal of hardly biodegradable feedstock wastes in methane fermentation process 📍 Warsaw, Poland\n\n University of Warsaw\n\n\nBiotechnology\n\n2010-10-01 - 2013-09-06 BSc thesis: Localization of hSUV3 protein and γ-tubulin at different developmental stages of the human umbilical cord blood-derived neural stem cell line (HUCB-NSC) 📍 Warsaw, Poland\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻\n\n\n\n\n\n\n\n\n\n📖 Publications\n\n\n\n\n\n\n\n\n\n🧑🏻‍🔬 Other activities\n\n\nAssociation of Wrocław R Users (STWUR) meetings co-organizer - R language workshops\nCo-organizer of WhyR? 2019 Conference in Warsaw\nCo-organizer of WhyR? 2018 Conference in Wrocław\nCEO of PhD Bioinformatics Club at University of Wrocław, 2017-2023"
   },
   {
     "objectID": "subsite/team/jp.html",

docs/site_libs/wordcloud2-0.0.1/hover.js

@@ -0,0 +1,129 @@
+// create element
+function newlabel(el){
+  var newDiv = document.createElement("div");
+  var newSpan = document.createElement("span");
+  newDiv.id = 'wcLabel';
+  newSpan.id = "wcSpan";
+  el.appendChild(newDiv);
+  document.getElementById("wcLabel").appendChild(newSpan);
+}
+
+// hover function
+function cv_handleHover(item, dimension, evt) {
+  var el = document.getElementById("wcLabel");
+  if (!item) {
+    el.setAttribute('hidden', true);
+
+    return;
+  }
+
+  el.removeAttribute('hidden');
+  // console.log(evt.srcElement.offsetLeft);
+
+  el.style.left = dimension.x + evt.srcElement.offsetLeft + 'px';
+  el.style.top = dimension.y + evt.srcElement.offsetTop + 'px';
+  el.style.width = dimension.w + 'px';
+  el.style.height = dimension.h + 'px';
+
+  this.hoverDimension = dimension;
+
+  document.getElementById("wcSpan").setAttribute(
+    'data-l10n-args', JSON.stringify({ word: item[0], count: item[1] }));
+  document.getElementById("wcSpan").innerHTML =item[0]+":" + item[1];
+
+}
+
+function updateCanvasMask(maskCanvas) {
+    var ctx = maskCanvas.getContext('2d');
+    var imageData = ctx.getImageData(
+        0, 0, maskCanvas.width, maskCanvas.height);
+    var newImageData = ctx.createImageData(imageData);
+
+    var toneSum = 0;
+    var toneCnt = 0;
+    for (var i = 0; i < imageData.data.length; i += 4) {
+        var alpha = imageData.data[i + 3];
+        if (alpha > 128) {
+            var tone = imageData.data[i]
+                + imageData.data[i + 1]
+                + imageData.data[i + 2];
+            toneSum += tone;
+            ++toneCnt;
+        }
+    }
+    var threshold = toneSum / toneCnt;
+
+    for (var i = 0; i < imageData.data.length; i += 4) {
+        var tone = imageData.data[i]
+            + imageData.data[i + 1]
+            + imageData.data[i + 2];
+        var alpha = imageData.data[i + 3];
+
+        if (alpha < 128 || tone > threshold) {
+            // Area not to draw
+            newImageData.data[i] = 0;
+            newImageData.data[i + 1] = 0;
+            newImageData.data[i + 2] = 0;
+            newImageData.data[i + 3] = 0;
+        }
+        else {
+            // Area to draw
+            // The color must be same with backgroundColor
+            newImageData.data[i] = 255;
+            newImageData.data[i + 1] = 255;
+            newImageData.data[i + 2] = 255;
+            newImageData.data[i + 3] = 255;
+        }
+    }
+
+    ctx.putImageData(newImageData, 0, 0);
+    console.log(maskCanvas.toDataURL());
+}
+
+
+
+//mask function
+function maskInit(el,x){
+  console.log(1)
+  str = x.figBase64;
+  //console.log(str)
+  var newImg = new Image();
+  newImg.src = str;
+  newImg.style.position = 'absolute';
+  newImg.style.left = 0;
+  // console.log(el.clientHeight);
+  newImg.width = el.clientWidth;
+  newImg.height = el.clientHeight;
+  // maskCanvas = init(el, x, newImg);
+  vvalue = 128
+
+  ctx = el.firstChild.getContext('2d');
+
+                ctx.drawImage(newImg, 0, 0, canvas.width, canvas.height);
+                updateCanvasMask(ctx);
+
+
+
+
+
+            WordCloud(el.firstChild, { list: listData,
+                  fontFamily: x.fontFamily,
+                  fontWeight: x.fontWeight,
+                  color: x.color,
+                  minSize: x.minSize,
+                  weightFactor: x.weightFactor,
+                  backgroundColor: x.backgroundColor,
+                  gridSize: x.gridSize,
+                  minRotation: x.minRotation,
+                  maxRotation: x.maxRotation,
+                  shuffle: x.shuffle,
+                  shape: x.shape,
+                  rotateRatio: x.rotateRatio,
+                  ellipticity: x.ellipticity,
+                  clearCanvas: false,
+                  drawMask: true,
+                  hover: x.hover || cv_handleHover,
+                  abortThreshold: 3000
+                  });
+}
+