Merge branch 'main' of https://github.com/prophetdb-openlab/prophetdb…

….org

docs/assets/overrides/main.html

@@ -12,10 +12,10 @@
 
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-  data-lang="en" crossorigin="anonymous" async>
+<script src="https://giscus.app/client.js" data-repo="yjcyxky/prophetdb.org" data-repo-id="R_kgDOJ1s3Vw"
+  data-category="Q&A" data-category-id="DIC_kwDOJ1s3V84CXj9H" data-mapping="pathname" data-strict="0"
+  data-reactions-enabled="1" data-emit-metadata="1" data-input-position="top" data-theme="preferred_color_scheme"
+  data-lang="en" data-loading="lazy" crossorigin="anonymous" async>
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 <script>

docs/assets/stylesheets/extra.css

@@ -65,7 +65,7 @@ iframe[style^="background"] {
 }
 
 .showcase-container a .image {
-  height: 100%;
+  /* height: 100%; */
   margin: 10px;
 }
 
@@ -86,57 +86,57 @@ iframe[style^="background"] {
   color: black;
 }
 
-.card {
+.member-card {
   display: flex;
   flex-direction: row;
   justify-content: space-between;
   margin-bottom: 20px;
-  width: 33%;
+  /* width: 33%; */
   height: 230px;
   margin-right: 20px;
   border: 1px solid #e7e7e7;
   border-radius: 4px;
   padding: 5px;
 }
 
-.card .left {
+.member-card .left {
   display: flex;
   flex-direction: column;
   justify-content: flex-start;
   align-items: center;
 }
 
-.card .left img {
+.member-card .left img {
   width: 150px;
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   border-radius: 50%;
 }
 
-.card .right {
+.member-card .right {
   font-size: 16px;
   margin-left: 20px;
-  text-align: right;
+  text-align: left;
 }
 
-.card .left .name {
+.member-card .left .name {
   font-size: 20px;
   font-weight: bold;
   text-align: center;
   margin: 5px 0;
 }
 
-.card .left .position {
+.member-card .left .position {
   font-size: 16px;
   text-align: center;
 }
 
 /* media */
 @media screen and (max-width: 768px) {
-  .card .right {
+  .member-card .right {
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   }
 
-  .card .left {
+  .member-card .left {
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@@ -146,11 +146,11 @@ iframe[style^="background"] {
 }
 
 @media (min-width: 768px) and (max-width: 1024px) {
-  .card .right {
+  .member-card .right {
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   }
 
-  .card .left {
+  .member-card .left {
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   }
 
@@ -160,15 +160,20 @@ iframe[style^="background"] {
 }
 
 @media (min-width: 1024px) and (max-width: 1280px) {
-  .card .right {
+  .member-card .right {
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   }
 
-  .card .left {
+  .member-card .left {
     width: 100%;
   }
 
   .showcase-container a {
     width: 30%;
   }
+}
+
+.member-card {
+    flex: 0 0 calc(50% - 10px);
+    margin: 5px;
 }

docs/platform.md

@@ -5,14 +5,26 @@ hide:
 
 ## 🖥️ Open-Source Projects from Our Lab
 
-### A Platform for Drug Repurposing, Disease Mechanism, Toxicological Mechanism and Biomarker Screening
+### Knowledge Curation and Databases
+
+<img src="https://raw.githubusercontent.com/yjcyxky/prophetdb.org/master/docs/assets/images/prophet-studio-kg-editor.png" width="100%" />
+
+| Title | Description| Open Source Repo | Feedback |
+|--|--|--|--|
+| [Prophet Studio](https://prophet-studio.3steps.cn/) | A data labeling and annotation tool for biomedical publications. | [GitHub Repo](https://github.com/yjcyxky/prophet-studio) | [Post an Issue](https://github.com/yjcyxky/prophet-studio/issues) |
+| [GuideScoper](https://biosolver.cn/) | Find the Best sgRNAs and Design top-scoring guide RNAs for gene knockout | [GitHub Repo](https://github.com/yjcyxky/cell-guider) ||
+| [GlioMarker](http://gliomarker.prophetdb.org/#/home) | An integrated Database for Knowledge Exploration of Diagnostic Biomarkers in Gliomas | [GitHub Repo](https://github.com/yjcyxky/gliomarker) ||
+
+### A Platform for Drug Repurposing, Disease Mechanism, and Biomarker Screening
+
+<img src="https://raw.githubusercontent.com/yjcyxky/prophetdb.org/master/docs/assets/images/biomedgps.png" width="100%" />
 
 Such as Knowledge Graph, Omics Data Analyzer, QC Tools, Data Repo for BioMedical Models, DL Models etc.
 
-|Title | Language | Description|
-|--|--|--|
-| [BioMedGPS](https://github.com/yjcyxky/biomedgps) | Rust, TypeScript, Python | A knowledge graph system with graph neural network for drug repurposing, disease mechanism and biomarker screening.|
-| [Chat Publications](https://github.com/yjcyxky/chat-publications) | Python | Ask questions and get answers from publications.|
+|Title | Language | Description| Feedback |
+|--|--|--|--|
+| [BioMedGPS](https://github.com/yjcyxky/biomedgps) | Rust, TypeScript, Python | A knowledge graph system with graph neural network for drug repurposing, disease mechanism and biomarker screening.| [Post an Issue](https://github.com/yjcyxky/biomedgps/issues) |
+| [Chat Publications](https://github.com/yjcyxky/chat-publications) | Python | Ask questions and get answers from publications.| |
 
 ### Online Quality Assessment Platform for Multi-omics Data
 
@@ -29,14 +41,6 @@ Such as Knowledge Graph, Omics Data Analyzer, QC Tools, Data Repo for BioMedical
 | [BioMiner Indexd](https://github.com/yjcyxky/biominer-indexd) | Rust | Index engine for biomedical data files. We epect it will be a indexing engine for indexing high quality data, such as clinical data (EHR), multi-omics data, whole slide image, etc. |
 | [PreQC Pack](https://github.com/yjcyxky/preqc-pack) | Rust | A quality assessment tool for high throughput sequence data. |
 
-### Knowledge Curation and Databases
-
-| Title | Description| Open Source Repo |
-|--|--|--|
-| [Prophet Studio](https://prophet-studio.3steps.cn/) | A data labeling and annotation tool for biomedical publications. | [GitHub Repo](https://github.com/yjcyxky/prophet-studio) |
-| [GuideScoper](https://biosolver.cn/) | Find the Best sgRNAs and Design top-scoring guide RNAs for gene knockout | [GitHub Repo](https://github.com/yjcyxky/cell-guider) |
-| [GlioMarker](http://gliomarker.prophetdb.org/#/home) | An integrated Database for Knowledge Exploration of Diagnostic Biomarkers in Gliomas | [GitHub Repo](https://github.com/yjcyxky/gliomarker) |
-
 ## 📁 Collections
 
 | Title | Description |

docs/projects.md

@@ -5,6 +5,15 @@ hide:
 
 # 📝 Ongoing Research Projects - 2023
 
+## Introduction
+
+<div style="position: relative; width: 100%; 
+    padding-top: calc(100% * 720 / 1280); 
+    border: 2px black solid;">
+  <iframe src="//player.bilibili.com/player.html?aid=364614495&bvid=BV1S94y187ev&cid=1296306181&p=1" scrolling="no" border="0" frameborder="no" framespacing="0" allowfullscreen="true" style="position: absolute; width: 100%; height: 100%; top: 0;">
+  </iframe>
+</div>
+
 ## Curation - Building Your Own Knowledge Graph
 
 ### 🧑‍🔬 Curation of BioMedical Knowledges for Chemotherapy-induced Thrombocytopenia (CIT)

docs/team_members.md

@@ -8,20 +8,32 @@ hide:
 
 <!-- Add several div tags which contains four elements for each div tag. Four elements are picture, name, position and description. And the description item must be placed on the right, other items are placed on the left. -->
 
-<div style="display: flex; flex-direction: row;">
-  <div class="card">
+<div style="display: flex; flex-direction: row; flex-wrap: wrap;">
+  <div class="member-card">
     <div class="left">
       <img src="/assets/images/jingchengyang.jpeg" />
       <div>
         <div class="name">Jingcheng Yang</div>
-        <div class="position">Post Doc</div>
+        <div class="position">Post-doc Fellow</div>
       </div>
     </div>
     <div class="right">
-      PostDoc, Fudan University. He is interested in drug repurposing, knowledge graph, and machine learning.
+      Post-doc Fellow, Harvard Medical School & MGH, Fudan University. He has earned a Ph.D. in Genetics from Fudan University. Prior to this, he was a cardiothoracic surgeon. Now, he focuses on integrating multi-omics data and knowledge graphs and conducts deep-learning heterogeneous network methods for network medicine to discover rare disease mechanisms and potential treatments. <a href="https://github.com/yjcyxky">Github</a> >>> <a href="https://www.researchgate.net/profile/Jingcheng-Yang-4">Research Gate</a>
     </div>
   </div>
-  <div class="card">
+  <div class="member-card">
+    <div class="left">
+      <img src="/assets/images/penghaoxu.jpg"/>
+      <div>
+        <div class="name">Penghao xu</div>
+        <div class="position">Post-doc Fellow</div>
+      </div>
+    </div>
+    <div class="right">
+      Post-doc Fellow, Georgia Tech. He has earned a Ph.D. in Bioinformatics from Georgia Tech in 2022. Prior to this, he received a Master’s degree in Computational Sciences and Engineering from Georgia Tech in 2019, and a Bachelor’s degree in Biological Sciences from Fudan University in 2017. His research area include Bioinformatics, Genomics, Data analysis, and Machine Learning. <a href="https://github.com/xph9876">Github</a> >>> <a href="https://www.linkedin.com/in/penghao-xu-24111914b/">Linkedin</a>
+    </div>
+  </div>
+  <div class="member-card">
     <div class="left">
       <img src="/assets/images/zihanran.png"/>
       <div>
@@ -30,19 +42,31 @@ hide:
       </div>
     </div>
     <div class="right">
-      PhD, Fudan University. Her research interests focus on the health effects and toxicological mechanisms of pollutant exposure, knowledge graph and multi-omics data integration and analysis.
+      She has earned a Ph.D. from Fudan University. She focuses on the health effects and toxicological mechanisms of pollutant exposure, knowledge graph and multi-omics data integration and analysis.
+    </div>
+  </div>
+  <div class="member-card">
+    <div class="left">
+      <img src="/assets/images/fengzhu.png"/>
+      <div>
+        <div class="name">Feng Zhu</div>
+        <div class="position">Ph.D...</div>
+      </div>
+    </div>
+    <div class="right">
+      He is currently pursuing a Ph.D. at Fudan University. His research focuses on the development of CRISPR libraries and gene-editing cell libraries, as well as target and drug screening based on these technologies.
     </div>
   </div>
-  <div class="card">
+  <div class="member-card">
     <div class="left">
       <img src="/assets/images/yechaohuang.png"/>
       <div>
         <div class="name">Yechao Huang</div>
-        <div class="position">PhD</div>
+        <div class="position">Research Scientist</div>
       </div>
     </div>
     <div class="right">
-      Ph.D. at the School of Life Sciences, Fudan University. His research focuses on genomic structural variations in the human genome and population genetics.
+      He has earned a Ph.D. at the School of Life Sciences, Fudan University. He focuses on genomic structural variations in the human genome and population genetics.
     </div>
   </div>
 </div>

docs/tutorials/prophet-studio/T001-文献标注.md

@@ -1,3 +1,8 @@
+---
+hide:
+  - navigation
+---
+
 ## 网站网址
 
 Prophet Studio: [https://prophet-studio.3steps.cn/](https://prophet-studio.3steps.cn/)

mkdocs.yml

@@ -72,7 +72,4 @@ nav:
   - Publications: publications.md
   - 'Team Members': team_members.md
   - 'Contact Us': contact.md
-  - 'FAQs': faqs.md
-  - 'Tutorials':
-    - 'Prophet Studio':
-      - 'T001-文献标注': './tutorials/prophet-studio/T001-文献标注.md'
+