diff --git a/1research.md b/1research.md
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--- /dev/null
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+---
+layout: page
+title: Research
+permalink: /research/
+---
+
+# Projects
+
+## Knowledge Graphs
+
+**Building High-quality Knowledge Graphs.** Using and developing Knowledge Graph technologies and methods to structured data and to connect them to existing biological knowledge. These structures facilitate analysis and interpretation of complex data. We are contributing to a groundbreaking field by developing tools and methods to build, assess and investigate Knowledge Graphs and applying them to solve challenges in biology and health.
+
+
+
+ MicW2Graph
+
In this project, we investigated the microbiome of the wastewater treatment (WWT) process to build MicW2Graph, an open-source knowledge graph that integrates metagenomic and metatranscriptomic information with their biological context, including biological processes, environmental and phenotypic features, chemical compounds, and additional metadata. We developed a workflow to collect meta-omics datasets from MGnify and infer potential interactions among microorganisms through microbial association networks. MicW2Graph enables the investigation of research questions related to WWT, focusing on aspects such as microbial connections, community memberships, and potential ecological functions.
+
The following figure shows the general workflow of the MicW2Graph project:
KGBioGraphy is a manually-curated knowledge graph that contains information of the data sources and usecases of published biological/biomedical knowledge graphs (BKGs). Currently, there are 69 BKGs summarized within KGBioGraphy. Each BKG within KGBioGraphy is represented by an ego network, linking the BKG to its publication, data sources (e.g., databases and ontologies), node and relationship types it contains, and usecases.
+
We incorporated the open access BKG publications and KGBioGraphy into a corrective Retrievcal-Augmented Generation (RAG) model which provides a large language model (LLM) with a context-rich prompt to improve LLM response performance. Coming soon: Users will soon be able to interact with the KG-BioGraphy RAG through a streamlit interface and API.
+
The following is a flow diagram of the Retrieval-Augmented Generation (RAG) model and KG-BioGraphy:
(B) A vector database (DB) comprising vector representations of text snippets from the publications included in the review.
+
(C) KG-BioGraphy Neo4j DB.
+
(D) The retrieved contexts are used to query 1) the LLM and 2) the KG-BioGraphy DB to generate a text and subgraph response, respectively, which is outputed to the user.
+
This figure was created on Biorender.com.
+
+
+------------------------
+
+## Graph Machine Learning
+
+**Developing and Applying Novel Methods on Graphs.** Unleashing the power of Machine Learning on Graphs, a cutting-edge approach to extracting valuable insights from network data. We explore how this fusion of machine learning and graph theory helps to recognize patterns, generate predictions, and discovering new knowledge across a multitude of applications, including biological and medical networks.
+
+------------------------
+
+## Microbial Communities
+
+**Exploring Microbial Communities and their Environments.** Integrating multiple biological resources to unravel the assembly, interaction and adaptation mechanisms of microbial networks, offering insights into their functions and inpact on ecosystems, and how changes affect those communities.
+
+
+
+
+
+
+------------------------
+
+## Multimodal Data
+
+**Implementing tools to process, integrate, and analyse multimodal data.** Diving into the benefits of harmonising multimodal data that converge to provide a comprehensive view of complex biological systems. Specifically we are interested in high-throughput multi-omics data generated using Mass spectrometry technology (proteomics and metabolomics) and metaomics data (metagenomics and metaproteomics).
+
+------------------------
+
+## Open Science
+
+**Data Science Democratisation.** Focusing on data literacy training as a means to reduce inequality, and promoting open science by making all research, data content, and software open and accessible.
+
+
+****
+****
+
+
+# Publications
+
+Ayala-Ruano, S., Webel, H., & Santos, A. (2025). _VueGen: Automating the generation of scientific reports_. bioRxiv. [https://doi.org/10.1101/2025.03.05.641152](https://doi.org/10.1101/2025.03.05.641152)
\ No newline at end of file
diff --git a/2ds_platform.md b/2ds_platform.md
new file mode 100644
index 00000000000..edd2561287f
--- /dev/null
+++ b/2ds_platform.md
@@ -0,0 +1,27 @@
+---
+layout: page
+title: DS Platform
+permalink: /data-science-platform/
+---
+
+# Data Science Platform
+
+
+ Supporting and Promoting Data Science
+
+
+The primary objective of the Data Science Platform (DSP) is to make data science more accessible and inclusive across the Centre and the DTU community.
+
+The DSP is built on four pillars: **support, education, innovation, and tool development**
+
+- **Support** provide researchers and core functions at the Centre with assistance in areas such as statistics, programming, analytics, and machine learning. DSP will adopt a collaborative approach to understand the research questions and then provide the best assistance. This collaboration will be defined as consultancy, training, or implementation, depending on the needs. Whenever possible, DSP will prioritize consultancy and training to empower researchers, especially young ones, to learn data science skills that are crucial for their careers.
+
+- **Education** develop a training program focused on data science literacy, guiding researchers through different levels to become data-aware and proficient in data science. The training program includes initiatives such a data science club that holds periodic meetings to help researchers develop their data literacy skills, data science and bioinformatics workshops, and pop-up meetings to present trending technologies.
+
+- **Innovation** seeks to introduce researchers to new computational biology methods and technologies, and modernize the data science landscape at the Centre. This pillar aims to help researchers stay ahead of the curve by learning the latest technologies and techniques.
+
+- **Tool development** aims to transform the outputs of the other pillars into standard tools that can be shared across the Centre and open sourced for the entire community to use. This will create a comprehensive set of tools easily accessible to researchers.
+
+## Data Science Platform Notes
+
+We have our own notes repository which you can find at [biosustain.github.io/dsp_notes/](https://biosustain.github.io/dsp_notes/). It contains technical notes related to our work and links to our teaching materials.
diff --git a/3tools.md b/3tools.md
new file mode 100644
index 00000000000..f470ced6e24
--- /dev/null
+++ b/3tools.md
@@ -0,0 +1,123 @@
+---
+layout: page
+title: Tools
+permalink: /tools/
+---
+
+
+ Clinical Knowledge Graph - CKG
+
Integrating and Interpreting MS-based Proteomics Data
+
The Clinical Knowledge Graph (CKG) is a graph database with millions of nodes and relationships representing experimental data, databases, and scientific literature. Further, CKG is an open-source platform that allows easy expansion with new databases and experimental data types and it includes statistical and machine learning tools for faster proteomics analysis.
+
We are currently working on a new version that will be more flexible and generalizable. Stay tuned!
Understanding host-parasite interactions is vital for tackling infectious diseases. Due to the challenges in experimental identification, we propose a computational method to predict protein interactions between human and 18 eukaryotic parasites. Our approach leverages an orthology-based transfer of interactions, focusing on parasite secretomes and human membrane proteins. We also filter the host proteome based on the parasites' specific tissue tropisms. In this version, we added cell-type specific expression annotations to provide further resolution of the host-parasite predicted interactions and we support interactions with structural information.
+
Giardia intestinalis Predicted PPI
+
+
+
+
+
+ Analytics Core (Acore) Library
+
Acore, short for analytics core, is an open-source Python library to preprocess and analyse multi-omics data. It includes functionality related to preprocessing, e.g. for data normalization, missing value imputation or feature selection, and functionality for statistical data analysis, e.g. an analysis of covariance.
+
Acore is designed to be user-friendly and flexible, allowing users to easily apply different analysis strategies, testing effects of choosing specific steps.
VueGen is a tool that automates the creation of reports from bioinformatics outputs, allowing researchers with minimal coding experience to communicate their results effectively. With VueGen, users can produce reports by simply specifying a directory containing output files, such as plots, tables, networks, Markdown text, HTML components, and API calls, along with the report format. Supported formats include documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), Jupyter notebooks and Streamlitweb applications.
+
An overview of the VueGen workflow is shown in the figure below:
VueGen offers various implementation options for both non-technical and experienced users. It is available as a Python package, Docker image, nf-core module, and cross-platform desktop application with a user-friendly interface, making it accessible and customizable for different user needs and expertise levels.
+
The documentation is available at vuegen.readthedocs.io, where you can find detailed information of the package’s classes and functions, installation and execution instructions, and case studies to demonstrate its functionality.
+
+
+
+
+ FermentDB
+
A Standard Data Model for Precision Fermentation
+
+ FermentDB is a platform for bioprocess data Integration, Analysis and Visualization.
+ It is designed to address key challenges in precision fermentation by establishing a community standard for biofoundries. It streamlines the integration of high-throughput bioprocess data, supporting the development and scaling of biosustainable production processes.
+ As an open-source database, FermentDB addresses the main obstacles related to FAIR data principles. By providing a standardized data model, it offers the scientific community a powerful computational tool for bioprocess data integration.
+ It also supports the upscaling of research through descriptive analytics for fermentation monitoring, enabling more efficient scaling of biomanufacturing and reducing time to market for new bioproducts.
+ By enabling seamless integration of new datasets from collaborators, including omics data and in silico testing and optimization, FermentDB reduces time and resource demands and accelerates innovation in biomanufacturing.
+
+
A graphical image of FermentDB workflow is shown in the figure below:
gdbcore is a python library that can take your tables and transform them into graph databases in Networkx, graph-tool or Neo4j (v4). gdbcore is available for installation from PyPI.
+
We are currently improving the project and the documentation. Stay tuned!
+
+
+
+
diff --git a/4education.md b/4education.md
new file mode 100644
index 00000000000..d32370b85ce
--- /dev/null
+++ b/4education.md
@@ -0,0 +1,76 @@
+---
+layout: page
+title: Education
+permalink: /education/
+---
+
+The Multi-omics Network Analytics group and the Data Science Platform at [DTU Biosustain](https://www.biosustain.dtu.dk/) have come together to offer a diverse range of courses designed to empower students with essential data science skills and familiarize them with both internal and external tools we have developed.
+
+We are strong advocates of open science, and as part of that commitment, we make sure to share all the course materials on our [GitHub repository](https://github.com/Multiomics-Analytics-Group). This means that you will have access to comprehensive resources that aim to enhance the learning experience.
+
+Our courses are designed typically following a short-training format, ranging from single lectures to a few days of intensive, hands-on instruction. Explore our course offerings and contribute or provide feedback!
+
+# Courses
+
+## Protein Language Models [[link]](https://github.com/Multiomics-Analytics-Group/course_protein_language_modeling)
+
+
+
+An up-to-date course at the intersection of language models and the complex world of proteins! This course provides an overview of the current state of the art of Protein Language Models (pML), which are revolutionizing research, discovery, and innovation in the field of molecular biology.
+
+**Objectives**
+
+- Gain a comprehensive understanding of the synergy between language models and protein data
+- Equip students with the skills to leverage pre-trained models and fine-tuning for bioinformatics applications
+- Explore cutting-edge use cases and discover how protein language models are shaping the future of molecular biology
+- Understand the current limitations of the field and be prepared to tackle bioinformatics challenges
+
+-----------------------
+
+## Networks to Study Microbes [[link]](https://github.com/Multiomics-Analytics-Group/networks_to_study_microbes)
+
+
+
+The goal of the course is to provide an introduction to the use of networks in microbiology. The students will receive an overview of the field of computational microbiology with special emphasis on data standardization* and data sources, and how to use graph structures to solve biological questions. Further, the students will get a hands on introduction to Python programming language and its scientific libraries.
+
+**Objectives**
+
+- Use multiple data sources for studying microbes in different biological contexts
+- Build networks, visualize and analyse them using different tools
+- Use Python to extract, transform and analyse different data structures
+
+> **_NOTE:_** Some of the course content is in Spanish, but we are working on an english version. Coming out soon!
+
+-----------------------
+
+## Leveraging Existing Biological Data and Making Sense of it [[link]](https://github.com/Multiomics-Analytics-Group/course_synthetic_biology_data)
+
+This course is designed to introduce students to the essential skills required to fully utilize available resources. Further, this course provides an overview of how networks can be used to integrate and analyse these data.
+
+**Objectives**
+
+- Understand the fundamental principles of open science and its impact on research and collaboration
+- Explore the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles to ensure your data is valuable and widely usable
+- Dive into ontologies and structured data, and learn how to apply them effectively
+- Discover diverse data sources and learn how to generate and find open data
+- Explore the graphs and networks as powerful visual representation of complex data
+
+-----------------------
+
+## Introduction to Knowledge Graphs [[link]](https://github.com/Multiomics-Analytics-Group/course_knowledge_graphs)
+
+An introduction to the fascinating world of Knowledge Graphs and their vital role in the field of biology. This course explores fundamental concepts, practical applications, and significance of Knowledge Graphs in understanding complex biological systems. Whether you're a biologist, data enthusiast, or simply curious about the intersection of knowledge representation and biology, this course is your gateway to how to leverage interconnected biological data.
+
+**Objectives**
+- Familiarize with graph-based representations and their applications in biology
+- Understand the principles and structure of Knowledge Graphs, enabling you to work with diverse biological data
+- Gain insight into data standards and graph databases in creating effective Knowledge Graphs
+- Explore real-world examples to inspire innovative approaches to biological research
+- Learn practical analysis techniques to harness the power of Knowledge Graphs for insightful discoveries in biology
+
+## Data Science Platform Trainings
+
+The Data Science platform has strong commitment to advancing the education of our researcher fellows in Data Science topics. To that end, we are organizing courses about different data-types handled and produced at DTU - Biosustain (during May), and about data science aspects in general (during November). Furthermore, we are also co-organizing with DTU - Bioengineering the Data Science Club on monthly basis.
+
+An overview of the technical trainings offered by the Data Science Platform can be found
+at [biosustain.github.io/dsp_notes/trainings](https://biosustain.github.io/dsp_notes/trainings).
diff --git a/5people.md b/5people.md
new file mode 100644
index 00000000000..4e0f7f3ceef
--- /dev/null
+++ b/5people.md
@@ -0,0 +1,284 @@
+---
+layout: page
+title: People
+permalink: /people/
+---
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Meet The Team
+
+
+
Multi-omics Network Analytics (MoNA)
+
+
+
+
+
+
Alberto Santos
+
Director, Informatics Platform
+
Group Lead
+
albsad@dtu.dk
+
+
+
+
+
+
+
+
+
Angel L. Phanthanourak
+
PhD Student
+
anglup@dtu.dk
+
+
+
+
+
+
+
+
+
Sebastian Ayala Ruano
+
Research Assistant
+
asaru@dtu.dk
+
+
+
+
+
+
+
+
+
+
+
+
Txell Amigo
+
Research Assistant
+
txeami@dtu.dk
+
+
+
+
+
+
+
+
+
Marco Reverenna
+
PhD Student
+
marcor@dtu.dk
+
+
+
+
+
+
+
+
+
Jui-Tse Ko
+
PhD Student
+
juik@dtu.dk
+
+
+
+
+
+
+
+
+
+
+
+
+
Alexander Zubov
+
PhD Student
+
alzub@dtu.dk
+
+
+
+
+
+
+
+
+
Binhuan Sun
+
PhD Student
+
binsun@dtu.dk
+
+
+
+
+
+
+
+
+
Edir Sebastian Vidal Castro
+
MSc Student & Student Assistant
+
s243564@dtu.dk
+
+
+
+
+
+
+
+
Data Science Platform
+
+
+
+
+
+
Albert Pallejà Caro
+
Team Lead Data Science Platform
+
apca@dtu.dk
+
+
+
+
+
+
+
+
+
Jakob B. Jespersen
+
Data Scientist
+
jbeje@dtu.dk
+
+
+
+
+
+
+
+
+
Henry Webel
+
Senior Data Scientist
+
heweb@dtu.dk
+
+
+
+
+
+
+
+
+
+
+
+
+
Juliana Assis
+
Senior Data Scientist
+
jasge@dtu.dk
+
+
+
+
+
+
+
+
+
Sebastian Schulz
+
Senior Data Scientist
+
sebschu@dtu.dk
+
+
+
+
+
+
+
diff --git a/6contact.md b/6contact.md
new file mode 100644
index 00000000000..beabfd93a4b
--- /dev/null
+++ b/6contact.md
@@ -0,0 +1,26 @@
+---
+layout: page
+title: Contact
+permalink: /contact/
+---
+
+# Address
+
+Building 220, Kemitorvet
+
+2800 Kgs. Lyngby, Denmark
+
+Phone: +45 45 25 80 00
+
+Email: albsad@biosustain.dtu.dk
+
+# Map
+
+
+
+# DTU Links
+
+- [**Multi-omics Network Analytics group**](https://www.biosustain.dtu.dk/research/research-groups/multi-omics-network-analytics-alberto-santos-delgado)
+
+- [**Data Science Platform**](https://www.biosustain.dtu.dk/informatics/data-science-platform)
+
diff --git a/README.md b/README.md
index 26fe63f0534..6c57728da55 100644
--- a/README.md
+++ b/README.md
@@ -1,118 +1,167 @@
-# Hyde
+# MoNA website
+
+This website was created using [jekyll](https://jekyllrb.com/) and [GitHub Pages](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/about-github-pages-and-jekyll).
+
+Jekyll is a static site generator that takes care of updating a site template with contents of our chosing, which we can provide via markdown files.
+
+The site template is [Hyde (see repo for more details)](https://github.com/poole/hyde) with some of our own modifications.
+
+Included are instructions for how to update the team website with a focus on the content rather than styling.
+
+- [MoNA website](#mona-website)
+ - [Directory organization](#directory-organization)
+ - [MUST READ - how jekyll works](#must-read---how-jekyll-works)
+ - [Home page (default) vs. all other pages](#home-page-default-vs-all-other-pages)
+ - [Updating website content](#updating-website-content)
+ - [(OPTIONAL) Previewing changes locally](#optional-previewing-changes-locally)
+ - [Updating an existing page](#updating-an-existing-page)
+ - [Adding a page (example)](#adding-a-page-example)
+ - [Updating side nav links](#updating-side-nav-links)
+ - [Updating the styling ](#updating-the-styling)
+ - [Original Author](#original-author)
+ - [License](#license)
+
+
+## Directory organization of Repo
+
+(only highlighting folders and files relevant to updating site)
+
+```bash
+/
+├── index.md
+├── 1research.md
+├── 2ds_platform.md
+├── 3people.md
+├── 4tools.md
+├── 5education.md
+├── 6contact.md
+├── README.md
+├── _config.yml
+├── _includes/
+│ ├── head.html
+│ └── sidebar.html
+├── _layouts/
+│ ├── default.html
+│ └── page.html
+├── _site/
+└── public/
+ ├── assets/
+ └── css/
-Hyde is a brazen two-column [Jekyll](http://jekyllrb.com) theme that pairs a prominent sidebar with uncomplicated content. It's based on [Poole](http://getpoole.com), the Jekyll butler.
-
-
-
-
-## Contents
-
-- [Usage](#usage)
-- [Options](#options)
- - [Sidebar menu](#sidebar-menu)
- - [Sticky sidebar content](#sticky-sidebar-content)
- - [Themes](#themes)
- - [Reverse layout](#reverse-layout)
-- [Development](#development)
-- [Author](#author)
-- [License](#license)
-
-
-## Usage
-
-Hyde is a theme built on top of [Poole](https://github.com/poole/poole), which provides a fully furnished Jekyll setup—just download and start the Jekyll server. See [the Poole usage guidelines](https://github.com/poole/poole#usage) for how to install and use Jekyll.
-
-
-## Options
-
-Hyde includes some customizable options, typically applied via classes on the `` element.
-
-
-### Sidebar menu
-
-Create a list of nav links in the sidebar by assigning each Jekyll page the correct layout in the page's [front-matter](http://jekyllrb.com/docs/frontmatter/).
-
-```
----
-layout: page
-title: About
----
-```
-
-**Why require a specific layout?** Jekyll will return *all* pages, including the `atom.xml`, and with an alphabetical sort order. To ensure the first link is *Home*, we exclude the `index.html` page from this list by specifying the `page` layout.
-
-
-### Sticky sidebar content
-
-By default Hyde ships with a sidebar that affixes it's content to the bottom of the sidebar. You can optionally disable this by removing the `.sidebar-sticky` class from the sidebar's `.container`. Sidebar content will then normally flow from top to bottom.
-
-```html
-
-
-
- ...
-
-
-
-
-
-
- ...
-
-
```
-### Themes
-
-Hyde ships with eight optional themes based on the [base16 color scheme](https://github.com/chriskempson/base16). Apply a theme to change the color scheme (mostly applies to sidebar and links).
-
-
-
-There are eight themes available at this time.
-
-
-
-To use a theme, add anyone of the available theme classes to the `` element in the `default.html` layout, like so:
-
-```html
-
- ...
-
-```
-
-To create your own theme, look to the Themes section of [included CSS file](https://github.com/poole/hyde/blob/master/public/css/hyde.css). Copy any existing theme (they're only a few lines of CSS), rename it, and change the provided colors.
-
-### Reverse layout
-
-
-
-Hyde's page orientation can be reversed with a single class.
-
-```html
-
- ...
-
-```
-
-
-## Development
-
-Hyde has two branches, but only one is used for active development.
-
-- `master` for development. **All pull requests should be submitted against `master`.**
-- `gh-pages` for our hosted site, which includes our analytics tracking code. **Please avoid using this branch.**
-
-
-## Author
-
+## MUST READ - how jekyll works
+
+1. How jekyll knows to work its magic on a markdown or html file is based on the file's [YAML front matter block](https://jekyllrb.com/docs/front-matter/).
+
+ e.g.,
+ ```
+ ---
+ layout: page
+ title: About
+ permalink: /about/
+ ---
+ ```
+- **no front matter = not included in the website** (e.g., jekyll knows not to include this README.md you are reading because there is no front matter)
+
+2. Main takeaway: To update the **contents of the website** you will only need to add/remove/update the markdown files with front matter in the main directory. (e.g., [3people.md](3people.md)) More instructions in [Updating website content](#updating-website-content).
+
+- **Do not alter the files in `_includes`, `_layouts` for now.**
+
+
+#### Home page (default) vs. all other pages
+
+- How jekyll knows to work its magic on a markdown or html file is based on the file's [YAML front matter block](https://jekyllrb.com/docs/front-matter/).
+
+- Currently, there are 2 page layouts (templates) used in our site:
+ - `default` via */_layouts/default.html*
+ - `page` via */_layouts/page.html`*
+
+- The way that the styling is merged with the markdown files is via `layout` in the front matter:
+ e.g.,
+ ```
+ ---
+ layout: page
+ title: About
+ permalink: /about/
+ ---
+ ```
+- `layout: page` is to be used for almost all of the pages you want included in the site
+- `layout: default` is only used for the home page [index.md](index.md) because it has some additional formatting + appears as the first option in the top menu bar
+ >From the Hyde repo: "**Why require a specific layout?** Jekyll will return *all* pages, including the `atom.xml`, and with an alphabetical sort order. To ensure the first link is *Home*, we exclude the `index.md` page from this list by specifying the `default` layout."
+
+
+## Updating website content
+
+- To update the contents of the website you will only need to add/remove/update markdown files in the main directory.
+- To incorporate images or any other files into the site please put them in `/public/assets/`
+
+#### (OPTIONAL) Previewing changes locally
+If you want to test/preview the site locally as you make changes
+
+1. [install jekyll](https://jekyllrb.com/docs/installation/)
+2. in your terminal cd into the site's repo
+3. then run `jekyll serve --watch`
+4. open the url in `Server address: ...`
+5. To preview your changes don't forget to save your file and refresh the browser.
+
+#### Updating an existing page
+
+1. Clone this repository
+2. Create a branch from the 'master' branch of THIS repository (not the poole/hyde one)
+3. In the main directory, open the markdown file you want to update e.g. [3people.md](3people.md)
+4. make whatever changes to the content you want
+5. save the file
+6. push the changes to your branch
+7. Make a pull request for your branch into the **MoNA's `Master` branch** (:warning: NOT poole/hyde) then jekyll will take care of the rest
+
+(it's that easy :smiley:)
+
+
+#### Adding a page (example)
+Let's say you want to add a 'Contact' page and it should appear as the last option on the top menu bar
+
+1. Steps 1-3 in [Updating an existing page](#updating-an-existing-page)
+2. Create a markdown file in the root directory. Since pages are sorted alphabetically, if you want the Contact page to be last in the menubar of the website, prefix the markdown filename with a '9' or 'z' for example
+3. In the markdown file, the front matter should look like this:
+
+ ```
+ ---
+ layout: page
+ title: Contact
+ permalink: /contact/
+ ---
+ ```
+ - the layout should be 'page', to tell jekyll to use the page.html layout
+ - the title is what will be used in the top menu bar
+ - assigning a permalink will overwrite the default of using the ugly filename (e.g., `... .github.io/contact/` instead of `... .github.io/9contact/`)
+
+4. Underneath the front matter include whatever content you would like. You can add formatting to the file using markdown or html syntax.
+5. Steps 5-7 in [Updating an existing page](#updating-an-existing-page)
+
+
+#### Updating side nav links
+- similar steps to those in [Updating an existing page](#updating-an-existing-page)
+- However, the file that needs to be updated is `/_includes/sidebar.html`
+- Look for the `sidebar-nav-item` tags
+
+
+## Updating the styling
+**:warning: Dangerous territory**
+
+- Recall that the site template is [Hyde (see repo for more details)](https://github.com/poole/hyde) with some of our own modifications.
+- Updates to formating is done in the 3 directories: `/_includes/` `/_layouts/` and `/public/`
+- Requires HTML and CSS
+
+
+## Original Author
+[Please see hyde repo for more details](https://github.com/poole/hyde)
**Mark Otto**
-
-
-
## License
-
Open sourced under the [MIT license](LICENSE.md).
<3
diff --git a/_config.yml b/_config.yml
index 3e2f2432dd5..d37ff626e22 100644
--- a/_config.yml
+++ b/_config.yml
@@ -1,26 +1,22 @@
# Dependencies
-markdown: redcarpet
highlighter: pygments
# Permalinks
permalink: pretty
-relative_permalinks: true
# Setup
-title: Hyde
-tagline: 'A Jekyll theme'
-description: 'A brazen two-column Jekyll theme that pairs a prominent sidebar with uncomplicated content. Made by @mdo.'
-url: http://hyde.getpoole.com
-baseurl: /
+title: MoNA
+tagline: 'Multi-omics Network Analytics Group'
+description: 'Multi-omics Network Analytics Group'
+url: 'http://multiomics-analytics-group.github.io'
+baseurl: ''
-author:
- name: 'Mark Otto'
- url: https://twitter.com/mdo
+# author:
+# name: 'Mark Otto'
+# url: https://twitter.com/mdo
-paginate: 5
+# paginate: 5
# Custom vars
-version: 2.1.0
-
github:
- repo: https://github.com/poole/hyde
+ repo: https://github.com/Multiomics-Analytics-Group
diff --git a/_includes/head.html b/_includes/head.html
index e2b070e242a..0451d2bb9da 100644
--- a/_includes/head.html
+++ b/_includes/head.html
@@ -15,14 +15,14 @@
-
-
-
+
+
+
-
-
+
+
diff --git a/_includes/sidebar.html b/_includes/sidebar.html
index 586f47b2d74..e9a3ac153e8 100644
--- a/_includes/sidebar.html
+++ b/_includes/sidebar.html
@@ -1,36 +1,52 @@
- Download
- GitHub project
- Currently v{{ site.version }}
-
+ {% comment %}
+ The code below dynamically generates a sidebar nav of pages with
+ `layout: page` in the front-matter. See readme for usage.
+ {% endcomment %}
-
diff --git a/_posts/2012-02-06-whats-jekyll.md b/_posts/2012-02-06-whats-jekyll.md
deleted file mode 100644
index a6d28b59212..00000000000
--- a/_posts/2012-02-06-whats-jekyll.md
+++ /dev/null
@@ -1,12 +0,0 @@
----
-layout: post
-title: What's Jekyll?
----
-
-[Jekyll](http://jekyllrb.com) is a static site generator, an open-source tool for creating simple yet powerful websites of all shapes and sizes. From [the project's readme](https://github.com/mojombo/jekyll/blob/master/README.markdown):
-
- > Jekyll is a simple, blog aware, static site generator. It takes a template directory [...] and spits out a complete, static website suitable for serving with Apache or your favorite web server. This is also the engine behind GitHub Pages, which you can use to host your project’s page or blog right here from GitHub.
-
-It's an immensely useful tool and one we encourage you to use here with Hyde.
-
-Find out more by [visiting the project on GitHub](https://github.com/mojombo/jekyll).
\ No newline at end of file
diff --git a/_posts/2012-02-07-example-content.md b/_posts/2012-02-07-example-content.md
deleted file mode 100644
index 7dc8108543b..00000000000
--- a/_posts/2012-02-07-example-content.md
+++ /dev/null
@@ -1,138 +0,0 @@
----
-layout: post
-title: Example content
----
-
-
-
- Howdy! This is an example blog post that shows several types of HTML content supported in this theme.
-
-
-Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. *Aenean eu leo quam.* Pellentesque ornare sem lacinia quam venenatis vestibulum. Sed posuere consectetur est at lobortis. Cras mattis consectetur purus sit amet fermentum.
-
-> Curabitur blandit tempus porttitor. Nullam quis risus eget urna mollis ornare vel eu leo. Nullam id dolor id nibh ultricies vehicula ut id elit.
-
-Etiam porta **sem malesuada magna** mollis euismod. Cras mattis consectetur purus sit amet fermentum. Aenean lacinia bibendum nulla sed consectetur.
-
-## Inline HTML elements
-
-HTML defines a long list of available inline tags, a complete list of which can be found on the [Mozilla Developer Network](https://developer.mozilla.org/en-US/docs/Web/HTML/Element).
-
-- **To bold text**, use ``.
-- *To italicize text*, use ``.
-- Abbreviations, like HTML should use ``, with an optional `title` attribute for the full phrase.
-- Citations, like — Mark otto, should use ``.
-- Deleted text should use `` and inserted text should use ``.
-- Superscript text uses `` and subscript text uses ``.
-
-Most of these elements are styled by browsers with few modifications on our part.
-
-## Heading
-
-Vivamus sagittis lacus vel augue rutrum faucibus dolor auctor. Duis mollis, est non commodo luctus, nisi erat porttitor ligula, eget lacinia odio sem nec elit. Morbi leo risus, porta ac consectetur ac, vestibulum at eros.
-
-### Code
-
-Cum sociis natoque penatibus et magnis dis `code element` montes, nascetur ridiculus mus.
-
-{% highlight js %}
-// Example can be run directly in your JavaScript console
-
-// Create a function that takes two arguments and returns the sum of those arguments
-var adder = new Function("a", "b", "return a + b");
-
-// Call the function
-adder(2, 6);
-// > 8
-{% endhighlight %}
-
-Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa.
-
-### Gists via GitHub Pages
-
-Vestibulum id ligula porta felis euismod semper. Nullam quis risus eget urna mollis ornare vel eu leo. Donec sed odio dui.
-
-{% gist 5555251 gist.md %}
-
-Aenean eu leo quam. Pellentesque ornare sem lacinia quam venenatis vestibulum. Nullam quis risus eget urna mollis ornare vel eu leo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Donec sed odio dui. Vestibulum id ligula porta felis euismod semper.
-
-### Lists
-
-Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus.
-
-* Praesent commodo cursus magna, vel scelerisque nisl consectetur et.
-* Donec id elit non mi porta gravida at eget metus.
-* Nulla vitae elit libero, a pharetra augue.
-
-Donec ullamcorper nulla non metus auctor fringilla. Nulla vitae elit libero, a pharetra augue.
-
-1. Vestibulum id ligula porta felis euismod semper.
-2. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.
-3. Maecenas sed diam eget risus varius blandit sit amet non magna.
-
-Cras mattis consectetur purus sit amet fermentum. Sed posuere consectetur est at lobortis.
-
-
-
HyperText Markup Language (HTML)
-
The language used to describe and define the content of a Web page
-
-
Cascading Style Sheets (CSS)
-
Used to describe the appearance of Web content
-
-
JavaScript (JS)
-
The programming language used to build advanced Web sites and applications
-
-
-Integer posuere erat a ante venenatis dapibus posuere velit aliquet. Morbi leo risus, porta ac consectetur ac, vestibulum at eros. Nullam quis risus eget urna mollis ornare vel eu leo.
-
-### Images
-
-Quisque consequat sapien eget quam rhoncus, sit amet laoreet diam tempus. Aliquam aliquam metus erat, a pulvinar turpis suscipit at.
-
-
-
-
-
-### Tables
-
-Aenean lacinia bibendum nulla sed consectetur. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
-
-
-
-
-
Name
-
Upvotes
-
Downvotes
-
-
-
-
-
Totals
-
21
-
23
-
-
-
-
-
Alice
-
10
-
11
-
-
-
Bob
-
4
-
3
-
-
-
Charlie
-
7
-
9
-
-
-
-
-Nullam id dolor id nibh ultricies vehicula ut id elit. Sed posuere consectetur est at lobortis. Nullam quis risus eget urna mollis ornare vel eu leo.
-
------
-
-Want to see something else added? Open an issue.
diff --git a/_posts/2013-12-28-introducing-hyde.md b/_posts/2013-12-28-introducing-hyde.md
deleted file mode 100644
index 98e8a0c446d..00000000000
--- a/_posts/2013-12-28-introducing-hyde.md
+++ /dev/null
@@ -1,37 +0,0 @@
----
-layout: post
-title: Introducing Hyde
----
-
-Hyde is a brazen two-column [Jekyll](http://jekyllrb.com) theme that pairs a prominent sidebar with uncomplicated content. It's based on [Poole](http://getpoole.com), the Jekyll butler.
-
-### Built on Poole
-
-Poole is the Jekyll Butler, serving as an upstanding and effective foundation for Jekyll themes by [@mdo](https://twitter.com/mdo). Poole, and every theme built on it (like Hyde here) includes the following:
-
-* Complete Jekyll setup included (layouts, config, [404](/404), [RSS feed](/atom.xml), posts, and [example page](/about))
-* Mobile friendly design and development
-* Easily scalable text and component sizing with `rem` units in the CSS
-* Support for a wide gamut of HTML elements
-* Related posts (time-based, because Jekyll) below each post
-* Syntax highlighting, courtesy Pygments (the Python-based code snippet highlighter)
-
-### Hyde features
-
-In addition to the features of Poole, Hyde adds the following:
-
-* Sidebar includes support for textual modules and a dynamically generated navigation with active link support
-* Two orientations for content and sidebar, default (left sidebar) and [reverse](https://github.com/poole/lanyon#reverse-layout) (right sidebar), available via `` classes
-* [Eight optional color schemes](https://github.com/poole/hyde#themes), available via `` classes
-
-[Head to the readme](https://github.com/poole/hyde#readme) to learn more.
-
-### Browser support
-
-Hyde is by preference a forward-thinking project. In addition to the latest versions of Chrome, Safari (mobile and desktop), and Firefox, it is only compatible with Internet Explorer 9 and above.
-
-### Download
-
-Hyde is developed on and hosted with GitHub. Head to the GitHub repository for downloads, bug reports, and features requests.
-
-Thanks!
diff --git a/about.md b/about.md
deleted file mode 100644
index 9b2605bb4ce..00000000000
--- a/about.md
+++ /dev/null
@@ -1,30 +0,0 @@
----
-layout: page
-title: About
----
-
-
- Hey there! This page is included as an example. Feel free to customize it for your own use upon downloading. Carry on!
-
-
-In the novel, *The Strange Case of Dr. Jeykll and Mr. Hyde*, Mr. Poole is Dr. Jekyll's virtuous and loyal butler. Similarly, Poole is an upstanding and effective butler that helps you build Jekyll themes. It's made by [@mdo](https://twitter.com/mdo).
-
-There are currently two themes built on Poole:
-
-* [Hyde](http://hyde.getpoole.com)
-* [Lanyon](http://lanyon.getpoole.com)
-
-Learn more and contribute on [GitHub](https://github.com/poole).
-
-## Setup
-
-Some fun facts about the setup of this project include:
-
-* Built for [Jekyll](http://jekyllrb.com)
-* Developed on GitHub and hosted for free on [GitHub Pages](https://pages.github.com)
-* Coded with [Sublime Text 2](http://sublimetext.com), an amazing code editor
-* Designed and developed while listening to music like [Blood Bros Trilogy](https://soundcloud.com/maddecent/sets/blood-bros-series)
-
-Have questions or suggestions? Feel free to [open an issue on GitHub](https://github.com/poole/issues/new) or [ask me on Twitter](https://twitter.com/mdo).
-
-Thanks for reading!
diff --git a/index.html b/index.html
deleted file mode 100644
index 743a0808990..00000000000
--- a/index.html
+++ /dev/null
@@ -1,37 +0,0 @@
----
-layout: default
-title: Home
----
-
-
\ No newline at end of file
diff --git a/index.md b/index.md
new file mode 100644
index 00000000000..543949b283e
--- /dev/null
+++ b/index.md
@@ -0,0 +1,183 @@
+---
+layout: default
+title: Home
+---
+
+# Vision
+
+Getting a holistic view of biological systems and their context to understand their complexity and provide new insights and applications that can benefit human and environmental health.
+
+
+
+
+
+
+
+
+
+
+
+
+
+>
+
+
+
+
+
+
+We focus on **Multimodal Data**, processing and analyzing diverse types such as mass spectrometry (proteomics, metabolomics) and metaomics (metagenomics, metatranscriptomics, metaproteomics), tackling complex biological problems.
+
+A key component is developing **High-quality Knowledge Graphs** that connect data, allowing integration and interpretation of these data and we use **Graph Machine Learning** to extract insights, revealing patterns and generating predictions from graph structures.
+
+We apply these technologies to explore and understand **Microbial Communities** and their environments, unraveling assembly, interaction, adaptation, and impact, spanning ecology to biotech.
+
+Further, we're strong advocates of **Open Science**, adhering to open principles for our generated data, training, and software, aiming to reduce inequality and promote accessibility by democratizing data science.
\ No newline at end of file
diff --git a/public/Gi_network.html b/public/Gi_network.html
new file mode 100644
index 00000000000..5385a02645d
--- /dev/null
+++ b/public/Gi_network.html
@@ -0,0 +1,163 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/public/apple-touch-icon-144-precomposed.png b/public/apple-touch-icon-144-precomposed.png
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diff --git a/public/cluster_8.html b/public/cluster_8.html
new file mode 100644
index 00000000000..16385a225ac
--- /dev/null
+++ b/public/cluster_8.html
@@ -0,0 +1,343 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 
+
+
+ 
+ 
+ 
+ 
+ 
+ 
+
+An up-to-date course at the intersection of language models and the complex world of proteins! This course provides an overview of the current state of the art of Protein Language Models (pML), which are revolutionizing research, discovery, and innovation in the field of molecular biology.
+
+**Objectives**
+
+- Gain a comprehensive understanding of the synergy between language models and protein data
+- Equip students with the skills to leverage pre-trained models and fine-tuning for bioinformatics applications
+- Explore cutting-edge use cases and discover how protein language models are shaping the future of molecular biology
+- Understand the current limitations of the field and be prepared to tackle bioinformatics challenges
+
+-----------------------
+
+## Networks to Study Microbes [[link]](https://github.com/Multiomics-Analytics-Group/networks_to_study_microbes)
+
+
+
+The goal of the course is to provide an introduction to the use of networks in microbiology. The students will receive an overview of the field of computational microbiology with special emphasis on data standardization* and data sources, and how to use graph structures to solve biological questions. Further, the students will get a hands on introduction to Python programming language and its scientific libraries.
+
+**Objectives**
+
+- Use multiple data sources for studying microbes in different biological contexts
+- Build networks, visualize and analyse them using different tools
+- Use Python to extract, transform and analyse different data structures
+
+> **_NOTE:_** Some of the course content is in Spanish, but we are working on an english version. Coming out soon!
+
+-----------------------
+
+## Leveraging Existing Biological Data and Making Sense of it [[link]](https://github.com/Multiomics-Analytics-Group/course_synthetic_biology_data)
+
+This course is designed to introduce students to the essential skills required to fully utilize available resources. Further, this course provides an overview of how networks can be used to integrate and analyse these data.
+
+**Objectives**
+
+- Understand the fundamental principles of open science and its impact on research and collaboration
+- Explore the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles to ensure your data is valuable and widely usable
+- Dive into ontologies and structured data, and learn how to apply them effectively
+- Discover diverse data sources and learn how to generate and find open data
+- Explore the graphs and networks as powerful visual representation of complex data
+
+-----------------------
+
+## Introduction to Knowledge Graphs [[link]](https://github.com/Multiomics-Analytics-Group/course_knowledge_graphs)
+
+An introduction to the fascinating world of Knowledge Graphs and their vital role in the field of biology. This course explores fundamental concepts, practical applications, and significance of Knowledge Graphs in understanding complex biological systems. Whether you're a biologist, data enthusiast, or simply curious about the intersection of knowledge representation and biology, this course is your gateway to how to leverage interconnected biological data.
+
+**Objectives**
+- Familiarize with graph-based representations and their applications in biology
+- Understand the principles and structure of Knowledge Graphs, enabling you to work with diverse biological data
+- Gain insight into data standards and graph databases in creating effective Knowledge Graphs
+- Explore real-world examples to inspire innovative approaches to biological research
+- Learn practical analysis techniques to harness the power of Knowledge Graphs for insightful discoveries in biology
+
+## Data Science Platform Trainings
+
+The Data Science platform has strong commitment to advancing the education of our researcher fellows in Data Science topics. To that end, we are organizing courses about different data-types handled and produced at DTU - Biosustain (during May), and about data science aspects in general (during November). Furthermore, we are also co-organizing with DTU - Bioengineering the Data Science Club on monthly basis.
+
+An overview of the technical trainings offered by the Data Science Platform can be found
+at [biosustain.github.io/dsp_notes/trainings](https://biosustain.github.io/dsp_notes/trainings).
diff --git a/5people.md b/5people.md
new file mode 100644
index 00000000000..4e0f7f3ceef
--- /dev/null
+++ b/5people.md
@@ -0,0 +1,284 @@
+---
+layout: page
+title: People
+permalink: /people/
+---
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+  MoNA 1.png)
+ 
+
+
+