Revise and expand BrainSTEM documentation pages

Updated index.md to clarify site purpose, community involvement, and support options. Expanded webinterface.md with new sections for Import Tool and Two-Factor Authentication. Significantly enhanced dashboard.md and user-profile.md with detailed component descriptions, navigation tips, and role explanations to improve user onboarding and understanding of platform features.

Author: petersenpeter

docs/index.md

@@ -6,21 +6,23 @@ has_children: false
 has_toc: false
 ---
 
-# BrainSTEM Documentation
+# BrainSTEM Documentation & Support
 {: .no_toc}
 {: .fs-9 }
 
-A collaborative electronic lab notebook for experimental neuroscience.
+Documentation, tutorials, and support resources for BrainSTEM.
 {: .fs-6 .fw-300}
 
 [Get started now](#getting-started){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2} [Visit BrainSTEM.org](https://www.brainstem.org/){: .btn .fs-5 .mb-4 .mb-md-0}
 
 ![website screenshot](/assets/images/website_screenshot_v2.jpg)
 
-## Introduction
+## About BrainSTEM
 {: .no_toc}
 
-BrainSTEM (Brain Structured Experimental Metadata) is a collaborative electronic lab notebook designed specifically for experimental neuroscience. It captures and organizes a comprehensive range of electrophysiological, imaging, and behavioral data through a modular, standardized data model that can be extended to accommodate future data types.
+This site provides comprehensive documentation and support for BrainSTEM (Brain Structured Experimental Metadata) – a collaborative electronic lab notebook designed specifically for experimental neuroscience. BrainSTEM captures and organizes electrophysiological, imaging, and behavioral data through a modular, standardized data model that can be extended to accommodate future data types.
+
+Whether you're running a small lab or managing large-scale collaborative projects, BrainSTEM provides the infrastructure to organize, share, and access your experimental data with standardized metadata and reproducible workflows.
 
 ### Key Features
 
@@ -31,7 +33,7 @@ BrainSTEM (Brain Structured Experimental Metadata) is a collaborative electronic
 - **Customizable Interface**: Web-based interface tailored for neuroscience research workflows
 - **Standardized Metadata**: Consistent data annotation using controlled vocabularies and taxonomies
 
-BrainSTEM is ready for public use, and encourage researchers to create an account and begin exploring the platform. Your feedback helps us advance and shape the future of collaborative neuroscience data management.
+BrainSTEM is ready for public use, and we encourage researchers to create an account and begin exploring the platform. Your feedback helps us advance and shape the future of collaborative neuroscience data management.
 
 [Data Model]({{"/datamodel/"|absolute_url}}){: .btn .fs-5 .mb-4 .mb-md-0 .mr-4} [Web Interface]({{"/webinterface/"|absolute_url}}){: .btn .fs-5 .mb-4 .mb-md-0 .mr-4} [API]({{"/api/"|absolute_url}}){: .btn .fs-5 .mb-4 .mb-md-0 .mr-4} [API Tools]({{"/api-tools/"|absolute_url}}){: .btn .fs-5 .mb-4 .mb-md-0 .mr-4}
 
@@ -51,32 +53,33 @@ Explore advanced features including:
 - Public data sharing and collaboration
 - Resource and taxonomy submission
 - Project and group management
-- API integration for programmatic access
+- Setting up lab infrastructure
 
 [Get Started Tutorial]({{ "/tutorials/get_started/"|absolute_url}}){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2}
 [View All Tutorials]({{ "/tutorials/"|absolute_url}}){: .btn .fs-5 .mb-4 .mb-md-0 .mr-2}
 
-## Join Our Pilot Program
+## Join Our Community
 
-We're actively seeking research groups to participate in the BrainSTEM pilot program. As a pilot user, you'll help shape the future of collaborative neuroscience data management while gaining early notice of new features.
+We're actively seeking research groups to join the BrainSTEM community. As an active user, you'll help shape the future of collaborative neuroscience data management while gaining early notice of new features.
 
 ### Benefits of Joining
-- **Early Access**: Get to know about new features and capabilities first
+- **Stay Informed**: Get early notice about new features and capabilities
 - **Direct Impact**: Your feedback directly influences platform development
-- **Collaborative Network**: Connect with other forward-thinking research groups
-- **Support**: Dedicated support during your onboarding and beyond
+- **Dedicated Support**: Assistance during onboarding and beyond
 
-If you're committed to advancing open science and interested in becoming a pilot user, we'd love to hear from you.
+If you're committed to advancing open science and interested in joining the BrainSTEM community, we'd love to hear from you.
 
-[Join Pilot Program](https://docs.google.com/forms/d/e/1FAIpQLSctFj4ek5Ib-1FQoi9KeGzCkg6o-cuM26oggNu8FYeKRqNpwg/viewform){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0}
+[Join the Community](https://docs.google.com/forms/d/e/1FAIpQLSctFj4ek5Ib-1FQoi9KeGzCkg6o-cuM26oggNu8FYeKRqNpwg/viewform){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0}
 
 ## Support and Community
 
 ### Get Help
-For technical support, bug reports, and feature requests:
+We're here to assist you with any questions or issues:
+
+- **[GitHub Issues](https://github.com/brainstem-org/brainstem_support/issues)**: Report bugs and technical problems
+- **[GitHub Discussions](https://github.com/brainstem-org/brainstem_support/discussions)**: Ask questions, request features, and engage with the community
+- **[Contact Form](https://brainstem.org/#Get-in-touch)**: For account-specific issues and direct support
 
-- **[GitHub Issues](https://github.com/brainstem-org/brainstem_support/issues)**: Report bugs and technical issues
-- **[GitHub Discussions](https://github.com/brainstem-org/brainstem_support/discussions)**: General questions, feature requests, and community discussion
 
 ### Contributing
 BrainSTEM thrives on community input. Whether you're reporting bugs, suggesting enhancements, or participating in discussions, your contribution helps improve the platform for all users.

docs/webinterface.md

@@ -17,5 +17,7 @@ The interface consists of several main components:
 - [__List Views__]({{"webinterface/list-view"|absolute_url}}): Table views showing individual models with flexible sorting and filtering
 - [__Single Entry Views__]({{"webinterface/single-entry-view"|absolute_url}}): Detailed pages showing comprehensive information about specific entries
 - [__User Profile__]({{"webinterface/user-profile"|absolute_url}}): Personal settings and preferences
+- [__Import Tool__]({{"webinterface/import-tool"|absolute_url}}): Bulk data import using CSV templates
+- [__Two-Factor Authentication__]({{"webinterface/two-factor-authentication"|absolute_url}}): Enhanced account security setup
 
 Each of these components is described in detail in the following sections.

docs/webinterface/dashboard.md

@@ -6,16 +6,77 @@ nav_order: 1
 ---
 
 # Dashboard
+{: .no_toc}
 
-The dashboard provides an overview of your research data in BrainSTEM, displaying:
+## Overview
 
-- __Projects__: Your recent projects with total project count
-- __Subjects__: Recently added or modified subjects
-- __Sessions__: Your most recent sessions
-- __Cohorts__: Recent subject cohorts
-- __Collections__: Recent session collections
-- __Strain Statistics__: Most commonly used strains
-- __Consumable Statistics__: Most commonly used consumables
+The dashboard is your landing page in BrainSTEM, providing quick access to your recent research activity and frequently used resources. Click on any item to navigate to its detail page.
 
 ![dashboard_v2](/assets/images/dashboard_v2.png)
-*The BrainSTEM dashboard interface*
+*The BrainSTEM dashboard interface*
+
+## Dashboard Components
+
+### Projects
+
+Shows your most recently edited projects.
+
+- Click on **project names** to navigate to project details
+- View **total count** of projects you can access
+
+### Subjects
+
+Displays recently edited subjects.
+
+- Click on **subject names** to view full details and history
+- Check **last modified** date to track recent updates
+
+### Sessions
+
+Shows your most recent experimental sessions for immediate access to ongoing work.
+
+- Click on **session names** to view full session details
+- Check **last modified** date to track recent updates
+
+### Cohorts
+
+Lists recently created subject cohorts (groups of subjects with shared characteristics).
+
+- Click on **cohort names** to see member subjects
+- Useful for organizing treatment groups, littermates, or subjects by experimental condition
+
+### Collections
+
+Displays recent session collections (groups of related sessions).
+
+- Click on **collection names** to view included sessions
+- Useful for accessing multi-day experiments or related session groups
+
+### Statistics
+
+#### Strain Statistics
+{: .no_toc}
+
+The most commonly used animal strains across all users.
+
+- View frequency of strain usage in your research
+- Click on strain names to filter and see all subjects of that strain
+- Useful for colony management and planning breeding strategies
+
+#### Consumable Statistics
+{: .no_toc}
+
+The most frequently used consumables (probes, drugs, viruses, etc.).
+
+#### Hardware device statistics
+{: .no_toc}
+
+The most frequently used Hardware devices (data acquisition devices, cameras, surgical equipment, etc.).
+
+## Navigation Tips
+
+- Click any item name to view its detail page
+- Hover over items to see quick action options
+- Use the search bar (top right) to find specific entries
+- Use the left sidebar navigation for full list views
+- Filter data by project using the project dropdown

docs/webinterface/user-profile.md

@@ -8,8 +8,85 @@ nav_order: 5
 # User profile
 {: .no_toc}
 
-The user profile page shows:
+## Overview
 
-- __Personal details__: View and edit your information
-- __Groups__: Overview of your group memberships
-- __Projects__: List of your projects and their permissions
+The user profile page is your personal hub in BrainSTEM, displaying your account information, affiliations, and access permissions. You can access your profile by clicking on your username in the top-right corner of any page and selecting **Profile**.
+
+## Personal Details
+
+View and edit your personal information to keep your profile up to date and help collaborators identify you within BrainSTEM.
+
+| Field | Description |
+|-------|-------------|
+| **Name** | Your full name displayed throughout BrainSTEM |
+| **Email** | Primary contact email and login identifier |
+| **ORCID** | Link to your ORCID profile |
+| **Google Scholar** | Link to your google Scholar profile |
+| **Website** | Link to your website |
+| **Profile Picture** | Avatar displayed next to your contributions | 
+
+### How to Edit Your Profile
+{: .no_toc}
+
+1. Click on your username in the top-right corner
+2. Select **Profile** from the dropdown menu
+3. Click the **Edit** button next to the section you want to modify
+4. Make your changes and click **Save**
+5. Verify any email changes by clicking the confirmation link sent to your new address
+
+{: .note }
+> Updating your profile information helps collaborators find and recognize you when working on shared projects. A complete profile with ORCID linking also ensures proper attribution for your contributions.
+
+## Group Memberships
+
+This section displays all groups you belong to, helping you understand your organizational affiliations and permissions.
+
+| Information Displayed | Purpose |
+|----------------------|---------|
+| **Group Name** | The laboratory or organizational group you're part of |
+| **Membership Roles** | Your role within the group (Manager, Owner) |
+
+{: .note }
+> The Group memberships list is a private list, but other users can see your group memberships from the list of groups.
+
+### Understanding Your Group Membership Roles
+{: .no_toc}
+
+- **Member**: Can view and edit group data based on assigned permissions
+- **Manager**: Can manage members and their permissions
+- **Owner**: Full control over group and members
+
+{: .important }
+> If you need different permissions within a group, contact the group owner or manager. You can find their contact information by clicking on the group name.
+
+{: .note }
+> The Project memberships list is a private list, and other users cannot see your project memberships, besides any shared projects.
+
+## Project Permissions
+
+View all projects you have access to and understand your permissions for each project.
+
+| Column | Description |
+|--------|------------|
+| **Project Name** | Name of the research project |
+| **Membership Roles** | Any additional permissions (Create, Manager, Owner) |
+
+### Project Membership Roles Explained
+{: .no_toc}
+
+| Permission | What You Can Do |
+|------------|-----------------|
+| **Member** | Browse project data, sessions, and subjects |
+| **Create** | View and modify existing entries, add new data |
+| **Manager** | Manage project memberships |
+| **Owner** | Full control of the project |
+
+## Account Settings
+
+Additional account management options available from your profile:
+
+- **Two-Factor Authentication**: Enable 2FA for enhanced account security
+- **API Tokens**: Generate personal access tokens for programmatic access
+
+{: .warning }
+> Keep your email address up to date to ensure you receive important notifications about data changes, permission updates, and system announcements.