Exabyte-io · timurbazhirov · Oct 9, 2025 · Oct 9, 2025 · Oct 9, 2025 · Oct 9, 2025
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diff --git a/lang/en/docs/index.md b/lang/en/docs/index.md
@@ -1,42 +1,52 @@
-# Mat3ra Documentation
-
-[**Mat3ra**](https://platform.mat3ra.com) is a cloud-native accessible and collaborative platform for materials modeling from the atomic scale. Our platform makes it easier for scientists, engineers, and researchers to **design new materials** and **predict their properties** using *first-principles* approaches and *AI/ML* techniques. 
-
-First-principles approach does not require any knowledge of experimental observations, instead solely takes into account the atomistic description of material (e.g., constituent atoms, crystal structure, lattice constant, etc.) to compute desired properties thanks to [Density Functional Theory](https://en.wikipedia.org/wiki/Density_functional_theory){:target='_blank'} and its numerical implementations. When enough data is present, the AI/ML techniques can be applied to discover trends and accelerate predictions. Our platform also helps users collaborate, share and gather obtained knowledge with others. 
-
-The present documentation explains how the platform works in detail.
+Mat3ra is a platform for materials modeling from the atoms up. This documentation explains how to use the platform to
+design new materials and predict their properties using physics-based and AI/ML models powered by cloud HPC.
 
+!!!note "Migrating to the New Platform (Q4 2025)"
+    Existing users: see [Migrating to the New Platform](migrating-to-new-platform.md) for timelines and guidance.
 
 ## Quick start
 
-You can skip straight to our tutorial summarizing [first steps](getting-started/run-first-simulation/web-interface.md). There you will learn how to set up and run [density functional theory](models-directory/dft/overview.md) calculation to obtain [electronic band structure](properties-directory/non-scalar/bandstructure.md) of silicon, a semiconducting material widely used in making electronic chips.
-
+- [Run your first simulation (web)](getting-started/run-first-simulation/web-interface.md)
+- [Run your first CLI job](getting-started/run-first-simulation/cli-job.md)
+- [Content highlights](getting-started/content-highlights.md)
+
+## Popular topics
+
+- **Access the platform**: [Platform access guide](tutorials/platform-access.md)
+- **Jobs via CLI**: [Overview](jobs-cli/overview.md) · Batch scripts
+  ([Overview](jobs-cli/batch-scripts/overview.md),
+  [General structure](jobs-cli/batch-scripts/general-structure.md),
+  [Directives](jobs-cli/batch-scripts/directives.md),
+  [Working directory](jobs-cli/batch-scripts/directories.md),
+  [Apptainer & Modules](jobs-cli/batch-scripts/apptainer.md),
+  [Samples](jobs-cli/batch-scripts/sample-scripts.md))
+- **Remote connection**: [SSH](remote-connection/ssh.md) · [Web Terminal](remote-connection/web-terminal.md) ·
+  [Remote Desktop](remote-connection/remote-desktop.md)
+- **Data locations and quotas**: [Data on disk: directories](data-on-disk/directories.md) ·
+  [Quotas](data-on-disk/quotas.md)
+- **Clusters**: [Overview](infrastructure/clusters/overview.md) ·
+  [Cluster-101 (free tier)](infrastructure/clusters/cluster-101.md) ·
+  [AWS](infrastructure/clusters/aws.md) · [Azure](infrastructure/clusters/azure.md) ·
+  [GCP](infrastructure/clusters/google.md)
+- **Materials**: [Overview](materials/overview.md) · [Import from files](materials/import-from-files.md)
+- **Models**: [DFT overview](models-directory/dft/overview.md)
+- **Properties**: [Overview](properties/overview.md) · [Band structure](properties-directory/non-scalar/bandstructure.md)
+- **Workflows**: [Overview](workflows/overview.md) · [Designer](workflow-designer/overview.md)
+- **REST API**: [Overview](rest-api/overview.md)
 
 ## Searching
 
-If you are looking for a specific topic of interest, please use the search box on top to quickly locate relevant pages.
-
-The [Links](#links) section below lists resources containing more in-depth explanations about what we are building and why[^1] and example case studies[^2].
-
+Use the search box at the top to quickly find specific topics across the documentation.
 
-## Contents
-
-The navigation bar on the left serves as the table of contents for the whole documentation while the table of contents on the right lists content headers under the current page. You may click on any top-level items on the left sidebar to expand the corresponding section. The [content highlights page](getting-started/content-highlights.md) has a brief overview of various features available in Mat3ra platform and links to them.
+## How this site is organized
 
+The left sidebar is the global table of contents. Click any top-level item to expand sections. For a high-level tour of
+major features, see [Content highlights](getting-started/content-highlights.md).
 
 ## Support
 
-We reply to support requests within 24 hours. Our team can be contacted during working hours Pacific Time through:
-
-- Email: <a href="mailto:support@mat3ra.com" target="_blank">support@mat3ra.com</a>
-- Phone: +1 (510) 473-7770
-- Via web widget: click **Support** button at the bottom of our <a href="https://platform.mat3ra.com" target="_blank">web application</a>.
-
-!!! tip "Let us hear your feedback"
-    In case you find that something is missing or if you still have questions after reading this documentation, please <a class="text-muted" href="mailto:support@mat3ra.com" target="_blank">contact us</a>.
-
-
-## Links
+We respond to support requests within 24 hours during working hours (Pacific Time). See
+[Help & Support](other/support.md) for ways to get assistance.
 
-[^1]: [What is materials discovery cloud, article](https://www.linkedin.com/pulse/how-we-design-world-tomorrow-what-materials-discovery-timur-bazhirov)
-[^2]: [Mat3ra: case studies](https://mat3ra.com/case-studies)
+!!! tip "Help us improve"
+    If something is missing or unclear, please open the [Help & Support](other/support.md) page and get in touch.
diff --git a/lang/en/docs/migrating-to-new-platform.md b/lang/en/docs/migrating-to-new-platform.md
@@ -1,32 +1,44 @@
-# Migrating to the New Mat3ra Platform (Q4 2025)
+# Migrating to The New Platform (Q4 2025)
 
 > Last updated Oct 7, 2025.
 
-We are excited to announce the immediate availability of the new iteration of the Mat3ra platform. This is a significant upgrade over previous monthly releases and introduces new infrastructure, compute options, and improvements to the overall user experience.
+We are excited to announce the immediate availability of the new iteration of the Mat3ra platform. This is a significant
+upgrade over previous monthly releases and introduces new infrastructure, compute options, and improvements to the
+overall user experience.
 
-!!! note "Important": For a smooth transition, both the old and the new platform versions will remain operational through the end of 2025. See the timeline below.
+!!!note "Important": For a smooth transition, both the old and the new platform versions will remain operational
+through the end of 2025. See the timeline below.
 
 ---
 
 ## What’s New
 
-- **Free compute tier (cluster-101)**
-  - A new always-available free tier via `cluster-101`.
-  - Read more: [Free Tier and Community Access](other/community-programs.md) and [Cluster-101](infrastructure/clusters/cluster-101.md).
+### Free compute tier (cluster-101)
 
-- **New cloud infrastructure setup**
-  - Google Cloud Platform via `cluster-001` — see [GCP clusters](infrastructure/clusters/google.md)
-  - Amazon Web Services via `cluster-002` — see [AWS clusters](infrastructure/clusters/aws.md)
-  - Microsoft Azure via `cluster-003` — see [Azure clusters](infrastructure/clusters/azure.md)
-  - Updated set of instance types across providers, including larger CPU and GPU options
+A new always-available free tier via `cluster-101`. Read
+more: [Free Tier and Community Access](other/community-programs.md)
+and [Cluster-101](infrastructure/clusters/cluster-101.md).
 
-- **Operating system upgrade**
-  - Base OS updated to RHEL 9 across the new platform infrastructure
+### New cloud infrastructure setup
 
-- **Apptainer-based application deployment**
-  - Modernized packaging and runtime isolation for scientific applications
-  - See: [Jobs via Command Line](jobs-cli/overview.md) for updated CLI usage and examples
-  - We welcome contributions for additional applications your workflows require
+As below:
+
+- Google Cloud Platform via `cluster-001` — see [GCP clusters](infrastructure/clusters/google.md)
+- Amazon Web Services via `cluster-002` — see [AWS clusters](infrastructure/clusters/aws.md)
+- Microsoft Azure via `cluster-003` — see [Azure clusters](infrastructure/clusters/azure.md)
+- Updated set of instance types across providers, including larger CPU and GPU options
+
+### Operating system upgrade
+
+Base OS updated to RHEL 9 across the new platform infrastructure
+
+### Apptainer-based application deployment
+
+As below:
+
+- Modernized packaging and runtime isolation for scientific applications
+- See: [Jobs via Command Line](jobs-cli/batch-scripts/apptainer.md) for updated CLI usage and examples
+- We welcome contributions for additional applications your workflows require
 
 ---
 
@@ -43,28 +55,30 @@ You can sign in to the new platform with the same credentials you use for the cu
 
 ## Migration Timeline
 
-- **Now → Oct 31, 2025**
-  - Both old and new platforms are live. You can explore and begin migrating at your convenience.
+- **Now → Oct 31, 2025**:
+    - Both old and new platforms are live. You can explore and begin migrating at your convenience.
 
 - **On/after Nov 1, 2025**
-  - `https://platform.mat3ra.com` will route to the new platform
-  - The old platform will remain accessible at `https://platform-old.mat3ra.com`
-  - Equivalent routing changes will apply to related URLs (docs, login)
+    - `https://platform.mat3ra.com` will route to the new platform
+    - The old platform will remain accessible at `https://platform-old.mat3ra.com`
+    - Equivalent routing changes will apply to related URLs (docs, login)
 
 - **On/after Jan 1, 2026**
-  - Only the new platform will remain available
+    - Only the new platform will remain available
 
 ---
 
 ## What Gets Migrated Automatically
 
-- Application data stored in the platform database (entities, metadata, workflows, settings) is migrated automatically.
+Application data stored in the platform database (entities, metadata, workflows, settings) is migrated automatically.
 
 ## What Does NOT Migrate Automatically
 
-- Runtime files and bulk data stored on disk do not migrate automatically. Due to updated infrastructure libraries and layout in the new environment, data migration from legacy cluster homes and shares is handled on a case-by-case basis.
+Runtime files and bulk data stored on disk do not migrate automatically. Due to updated infrastructure libraries and
+layout in the new environment, data migration from legacy cluster homes and shares is handled on a case-by-case basis.
 
-> Tip: Review data locations under [Data on Disk > Directory Structure](data-on-disk/directories.md) and [Infrastructure > Login Node Directories](infrastructure/login/directories.md) to plan your migration.
+> Tip: Review data locations under [Data on Disk > Directory Structure](data-on-disk/directories.md)
+> and [Infrastructure > Login Node Directories](infrastructure/login/directories.md) to plan your migration.
 
 ---
 
@@ -78,15 +92,12 @@ You can sign in to the new platform with the same credentials you use for the cu
 
 ## CLI and Environment Modules with Apptainer
 
-See examples of module loading, `$EXEC_CMD`, and containerized execution in: [Apptainer and Environment Modules](jobs-cli/batch-scripts/apptainer.md)
-
-### Using in job scripts
-
-As below:
-
-```
+See examples of module loading, `$EXEC_CMD`, and containerized execution
+in: [Apptainer and Environment Modules](jobs-cli/batch-scripts/apptainer.md)
 
-## Contact and Support
+## Contact Support
 
-- For migration help (data movement, cluster selection, workflow updates), contact your Mat3ra representative or reach us via Support Widget in the platform header or `support@mat3ra.com`.
-- If you require a specific application or environment, please let us know — we welcome contributions and requests to expand supported software.
+- For migration help (data movement, cluster selection, workflow updates), contact your Mat3ra representative or reach
+  us via Support Widget in the platform header or `support@mat3ra.com`.
+- If you require a specific application or environment, please let us know — we welcome contributions and requests to
+  expand supported software.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -86,7 +86,7 @@ theme:
         primary: deep purple
         accent: deep purple
     logo: "images/logo/logo-white.png"
-    favicon: "images/logo/favicon.ico"
+    favicon: "images/logo/favicon.svg"
     icon:
         edit: material/pencil
         repo: fontawesome/brands/github
@@ -121,7 +121,7 @@ plugins:
 
 nav:
     - Home: index.md
-    - Migrating to New Platform, Q4.2025: migrating-to-new-platform.md
+    - Migrating to New Platform:                         migrating-to-new-platform.md
 
 # INTRODUCTION
     - Getting Started: