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<title>Doc_Map_Agent - R&D Document Authoring Accelerator</title>
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<body>
<!-- Header -->
<header>
<div class="container header-container">
<div class="logo">
<img src="images/logo.png" alt="Doc_Map_Agent Logo" id="logo-placeholder">
<h1>Doc_Map_Agent</h1>
</div>
<div class="header-actions">
<div class="search-bar">
<input type="text" placeholder="Search documents...">
<button><i class="fas fa-search"></i></button>
</div>
<button class="settings-btn"><i class="fas fa-cog"></i></button>
</div>
</div>
</header>
<!-- Breadcrumb -->
<div class="breadcrumb">
<div class="container">
<ul id="breadcrumb-list">
<li><a href="#" onclick="navigateTo('home')">Home</a></li>
</ul>
</div>
</div>
<!-- Main Content -->
<main>
<div class="container">
<!-- Home Section -->
<div id="home" class="page-section">
<!-- Welcome Banner -->
<div class="card mb-3">
<div class="card-body">
<h2 class="text-center">Welcome to Doc_Map_Agent</h2>
<p class="text-center">A comprehensive R&D document authoring accelerator</p>
</div>
</div>
<!-- Main Navigation Cards -->
<div class="grid">
<!-- Document Catalog Card -->
<div class="dashboard-card">
<i class="fas fa-book"></i>
<h3>Document Catalog</h3>
<p>Browse and search all document types across R&D phases</p>
<a href="#" class="btn btn-primary mt-2" onclick="navigateTo('document-catalog')">Explore</a>
</div>
<!-- Process Visualization Card -->
<div class="dashboard-card">
<i class="fas fa-project-diagram"></i>
<h3>Process Visualization</h3>
<p>Visualize document workflows and dependencies</p>
<a href="#" class="btn btn-primary mt-2" onclick="navigateTo('process-visualization')">Explore</a>
</div>
<!-- Assessment Tools Card -->
<div class="dashboard-card">
<i class="fas fa-clipboard-check"></i>
<h3>Assessment Tools</h3>
<p>Evaluate document ecosystem and identify gaps</p>
<a href="#" class="btn btn-primary mt-2" onclick="navigateTo('assessment-tools')">Explore</a>
</div>
<!-- Document Blueprints Card -->
<div class="dashboard-card">
<i class="fas fa-file-alt"></i>
<h3>Document Blueprints</h3>
<p>Access templates and prompt libraries for document authoring</p>
<a href="#" class="btn btn-primary mt-2" onclick="navigateTo('document-blueprints')">Explore</a>
</div>
</div>
<!-- Recent Activity -->
<div class="card mt-3">
<div class="card-header">
Recent Activity
</div>
<div class="card-body">
<ul>
<li>04/05/2025 - Assessment completed for Client XYZ Pharma</li>
<li>04/02/2025 - Document blueprint updated: Clinical Study Report</li>
<li>03/28/2025 - New process flow created: IND Submission</li>
</ul>
</div>
</div>
</div>
<!-- Document Catalog Section -->
<div id="document-catalog" class="page-section" style="display: none;">
<h2 class="page-title">Document Catalog</h2>
<div class="two-column">
<!-- Filters Sidebar -->
<div class="sidebar">
<h3 class="sidebar-title">Filters</h3>
<div class="filter-group">
<h4>Phase</h4>
<div class="filter-options">
<div class="filter-option">
<label><input type="checkbox" name="phase" value="discovery"> Discovery</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="phase" value="preclinical"> Preclinical</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="phase" value="clinical"> Clinical</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="phase" value="regulatory"> Regulatory</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="phase" value="medical"> Medical Affairs</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="phase" value="postmarket"> Post-Marketing</label>
</div>
</div>
</div>
<div class="filter-group">
<h4>Document Type</h4>
<div class="filter-options">
<div class="filter-option">
<label><input type="checkbox" name="type" value="protocol"> Protocol</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="type" value="report"> Report</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="type" value="application"> Application</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="type" value="form"> Form</label>
</div>
<div class="filter-option">
<label><input type="checkbox" name="type" value="template"> Template</label>
</div>
</div>
</div>
<button class="btn btn-secondary btn-block">Clear All</button>
<button class="btn btn-primary btn-block mt-2">Apply Filters</button>
<button class="btn btn-primary btn-block mt-2" onclick="addNewDocumentType()">Add New Document</button>
</div>
<!-- Results Panel -->
<div class="results-panel">
<div class="results-header">
<h3>Results (125 documents)</h3>
<div class="sort-options">
<label>Sort by:
<select>
<option>Relevance</option>
<option>Name (A-Z)</option>
<option>Phase</option>
<option>Document Type</option>
</select>
</label>
</div>
</div>
<!-- Document Cards -->
<div class="document-card">
<h3>Clinical Study Protocol</h3>
<div class="document-card-meta">
<span><i class="fas fa-layer-group"></i> Clinical</span>
<span><i class="fas fa-user"></i> Clinical Operations</span>
</div>
<p>Defines the objectives, design, methodology, and statistical considerations for a clinical trial.</p>
<div class="document-card-actions">
<a href="#" class="btn btn-secondary" onclick="viewDocumentDetails('clinical-protocol')">View Details</a>
<a href="#" class="btn btn-primary" onclick="editDocument('clinical-protocol')">Edit</a>
</div>
</div>
<div class="document-card">
<h3>Investigator's Brochure</h3>
<div class="document-card-meta">
<span><i class="fas fa-layer-group"></i> Clinical</span>
<span><i class="fas fa-user"></i> Medical Writing</span>
</div>
<p>Compilation of clinical and non-clinical data on the investigational product relevant to study in human subjects.</p>
<div class="document-card-actions">
<a href="#" class="btn btn-secondary">View Details</a>
<a href="#" class="btn btn-primary">Edit</a>
</div>
</div>
<div class="document-card">
<h3>New Drug Application</h3>
<div class="document-card-meta">
<span><i class="fas fa-layer-group"></i> Regulatory</span>
<span><i class="fas fa-user"></i> Regulatory Affairs</span>
</div>
<p>Formal submission to FDA requesting approval to market a new drug in the United States.</p>
<div class="document-card-actions">
<a href="#" class="btn btn-secondary">View Details</a>
<a href="#" class="btn btn-primary">Edit</a>
</div>
</div>
<div class="document-card">
<h3>Target ID Report</h3>
<div class="document-card-meta">
<span><i class="fas fa-layer-group"></i> Discovery</span>
<span><i class="fas fa-user"></i> Research</span>
</div>
<p>Documents identifying and validating biological targets for potential therapeutic intervention.</p>
<div class="document-card-actions">
<a href="#" class="btn btn-secondary">View Details</a>
<a href="#" class="btn btn-primary">Edit</a>
</div>
</div>
<button class="btn btn-secondary btn-block mt-3">Load More Results</button>
</div>
</div>
</div>
<!-- Document Details Section -->
<div id="document-details" class="page-section" style="display: none;">
<h2 class="page-title">Clinical Study Protocol</h2>
<div class="two-column">
<!-- Document Summary -->
<div class="sidebar">
<div class="text-center mb-2">
<i class="fas fa-file-alt" style="font-size: 4rem; color: var(--secondary-color);"></i>
<p class="mt-1">Phase: Clinical</p>
</div>
<div class="sidebar-actions">
<button class="btn btn-secondary btn-block mb-1">View Template</button>
<button class="btn btn-secondary btn-block mb-1">View Prompts</button>
<button class="btn btn-primary btn-block">Export</button>
<button class="btn btn-danger btn-block mt-2" onclick="deleteDocumentType('clinical-protocol')">Delete Document</button>
</div>
</div>
<!-- Document Details -->
<div>
<div class="card mb-3">
<div class="card-header">Basic Information</div>
<div class="card-body">
<p><strong>Owner:</strong> Clinical Operations</p>
<p><strong>Purpose:</strong> Defines the objectives, design, methodology, and statistical considerations for a clinical trial.</p>
<p><strong>Format:</strong> PDF, DOCX</p>
<p><strong>Typical Length:</strong> 50-100 pages</p>
<p><strong>Update Frequency:</strong> As needed</p>
<p><strong>Retention:</strong> Life of product + 5 years</p>
<p><strong>Security Classification:</strong> Confidential</p>
</div>
</div>
<div class="card mb-3">
<div class="card-header">Document Dependencies</div>
<div class="card-body">
<h4>Predecessor Documents:</h4>
<ul>
<li>Investigational Product Profile <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'inv-product-profile', 'predecessor')" class="text-danger"><i class="fas fa-times"></i></a></li>
<li>Clinical Development Plan <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'clinical-dev-plan', 'predecessor')" class="text-danger"><i class="fas fa-times"></i></a></li>
</ul>
<button class="btn btn-secondary btn-sm" onclick="addDocumentDependency('clinical-protocol', 'predecessor')">+ Add Predecessor</button>
<h4 class="mt-2">Successor Documents:</h4>
<ul>
<li>Informed Consent Form <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'informed-consent', 'successor')" class="text-danger"><i class="fas fa-times"></i></a></li>
<li>Case Report Form <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'case-report-form', 'successor')" class="text-danger"><i class="fas fa-times"></i></a></li>
<li>Statistical Analysis Plan <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'stat-analysis-plan', 'successor')" class="text-danger"><i class="fas fa-times"></i></a></li>
<li>Clinical Study Report <a href="#" onclick="removeDocumentDependency('clinical-protocol', 'clinical-study-report', 'successor')" class="text-danger"><i class="fas fa-times"></i></a></li>
</ul>
<button class="btn btn-secondary btn-sm" onclick="addDocumentDependency('clinical-protocol', 'successor')">+ Add Successor</button>
<div class="mt-3">
<button class="btn btn-secondary" onclick="navigateTo('dependency-mapping')">View Dependency Map</button>
</div>
</div>
</div>
<div class="card">
<div class="card-header">Process Workflow</div>
<div class="card-body">
<ol>
<li>Protocol Synopsis Development</li>
<li>Full Protocol Drafting</li>
<li>Internal Review</li>
<li>Medical/Scientific Review</li>
<li>Statistical Review</li>
<li>Regulatory Review</li>
<li>Final Approval</li>
<li>Distribution</li>
</ol>
<button class="btn btn-secondary mt-2" onclick="navigateTo('process-visualization')">View Full Workflow</button>
</div>
</div>
</div>
</div>
</div>
<!-- Dependency Mapping Section -->
<div id="dependency-mapping" class="page-section" style="display: none;">
<h2 class="page-title">Document Dependency Mapping</h2>
<div class="card mb-3">
<div class="card-header">
<div class="d-flex justify-content-between align-items-center">
<div>
<label for="focus-document">Focus Document: </label>
<select id="focus-document" class="form-control-inline">
<option selected>Clinical Study Protocol</option>
<option>Investigator's Brochure</option>
<option>New Drug Application</option>
<option>Target ID Report</option>
</select>
</div>
<div>
<label>Dependency Depth: </label>
<label class="ml-2"><input type="radio" name="depth" value="direct"> Direct Only</label>
<label class="ml-2"><input type="radio" name="depth" value="level1" checked> 1 Level</label>
<label class="ml-2"><input type="radio" name="depth" value="level2"> 2 Levels</label>
<label class="ml-2"><input type="radio" name="depth" value="all"> All Levels</label>
</div>
<div>
<label>View Mode: </label>
<label class="ml-2"><input type="radio" name="view-mode" value="hierarchical"> Hierarchical</label>
<label class="ml-2"><input type="radio" name="view-mode" value="network" checked> Network</label>
<label class="ml-2"><input type="radio" name="view-mode" value="matrix"> Matrix</label>
</div>
</div>
</div>
</div>
<div class="visualization-container" id="dependency-network">
<!-- D3.js visualization will be rendered here -->
</div>
<div class="card mt-3">
<div class="card-header">Dependency Analysis</div>
<div class="card-body">
<h4>Critical Dependencies:</h4>
<ul>
<li>Investigational Product Profile → Clinical Study Protocol</li>
<li>Clinical Study Protocol → Informed Consent Form</li>
<li>Clinical Study Protocol → Case Report Form</li>
</ul>
<h4 class="mt-2">Impact Analysis:</h4>
<p>Changes to Clinical Study Protocol will impact 4 downstream documents and potentially delay study start by 2-4 weeks.</p>
<h4 class="mt-2">Recommendations:</h4>
<ul>
<li>Prioritize Protocol finalization to unblock dependent docs</li>
<li>Consider parallel development of Statistical Analysis Plan</li>
<li>Establish version control process for Protocol amendments</li>
</ul>
</div>
</div>
</div>
<!-- Process Visualization Section -->
<div id="process-visualization" class="page-section" style="display: none;">
<h2 class="page-title">Process Visualization</h2>
<div class="card mb-3">
<div class="card-header">
<div class="d-flex justify-content-between align-items-center">
<div>
<label for="process-select">Process: </label>
<select id="process-select" class="form-control-inline">
<option selected>Clinical Trial</option>
<option>IND Submission</option>
<option>NDA Submission</option>
<option>Protocol Development</option>
</select>
</div>
<div>
<label>Display Options: </label>
<label class="ml-2"><input type="checkbox" checked> Documents</label>
<label class="ml-2"><input type="checkbox" checked> Stakeholders</label>
<label class="ml-2"><input type="checkbox" checked> Timelines</label>
<label class="ml-2"><input type="checkbox"> Dependencies</label>
</div>
</div>
</div>
</div>
<div class="visualization-container" id="process-flow">
<!-- D3.js visualization will be rendered here -->
</div>
<div class="card mt-3">
<div class="card-header">Process Details</div>
<div class="card-body">
<p><strong>Selected Process:</strong> Clinical Trial Execution</p>
<p><strong>Duration:</strong> Typically 1-5 years</p>
<h4 class="mt-2">Key Milestones:</h4>
<ul>
<li>First Patient First Visit</li>
<li>Last Patient First Visit</li>
<li>Last Patient Last Visit</li>
<li>Database Lock</li>
</ul>
<h4 class="mt-2">Critical Documents:</h4>
<ul>
<li>Clinical Trial Protocol <a href="#" onclick="viewDocumentDetails('clinical-protocol')">View</a></li>
<li>Informed Consent Form <a href="#">View</a></li>
<li>Case Report Form <a href="#">View</a></li>
<li>Clinical Study Report <a href="#">View</a></li>
</ul>
</div>
</div>
</div>
<!-- Process Simulation Section -->
<div id="process-simulation" class="page-section" style="display: none;">
<h2 class="page-title">Process Simulation & Bottleneck Analysis</h2>
<div class="two-column">
<!-- Simulation Settings -->
<div class="sidebar">
<h3 class="sidebar-title">Simulation Settings</h3>
<div class="form-group">
<label for="sim-process-select">Process:</label>
<select id="sim-process-select" class="form-control">
<option selected>Clinical Trial</option>
<option>IND Submission</option>
<option>NDA Submission</option>
<option>Protocol Development</option>
</select>
</div>
<h4 class="mt-2">Resource Allocation:</h4>
<div class="form-group">
<label>Medical Writing:</label>
<select class="form-control">
<option>1</option>
<option>2</option>
<option selected>3</option>
<option>4</option>
<option>5</option>
</select>
</div>
<div class="form-group">
<label>Regulatory:</label>
<select class="form-control">
<option>1</option>
<option selected>2</option>
<option>3</option>
<option>4</option>
<option>5</option>
</select>
</div>
<div class="form-group">
<label>Clinical Ops:</label>
<select class="form-control">
<option>1</option>
<option>2</option>
<option>3</option>
<option selected>4</option>
<option>5</option>
</select>
</div>
<div class="form-group">
<label>Statistics:</label>
<select class="form-control">
<option>1</option>
<option selected>2</option>
<option>3</option>
<option>4</option>
<option>5</option>
</select>
</div>
<h4 class="mt-2">Timeline Constraints:</h4>
<div class="form-group">
<label>Start Date:</label>
<input type="date" class="form-control" value="2025-04-15">
</div>
<div class="form-group">
<label>End Date:</label>
<input type="date" class="form-control" value="2025-10-15">
</div>
<button class="btn btn-primary btn-block mt-2" onclick="runSimulation()">Run Simulation</button>
</div>
<!-- Simulation Results -->
<div>
<div class="visualization-container mb-3" id="simulation-timeline">
<!-- D3.js visualization will be rendered here -->
</div>
<div class="card">
<div class="card-header">Simulation Results</div>
<div class="card-body">
<p><strong>Estimated Timeline:</strong> 187 days (04/15/2025 - 10/19/2025)</p>
<p><strong>Status:</strong> <span style="color: var(--danger-color);">4 days behind target end date</span></p>
<h4 class="mt-2">Identified Bottlenecks:</h4>
<ul>
<li><strong>Protocol Review (15 days)</strong> - Regulatory resources constrained</li>
<li><strong>CRF Development (21 days)</strong> - Data Management resources needed</li>
<li><strong>Statistical Analysis (18 days)</strong> - Statistics team overallocated</li>
</ul>
<h4 class="mt-2">Recommendations:</h4>
<ul>
<li>Increase Regulatory resources from 2 to 3 (saves 5 days)</li>
<li>Start CRF development in parallel with Protocol finalization</li>
<li>Consider outsourcing part of statistical analysis</li>
</ul>
<div class="mt-2">
<button class="btn btn-secondary">Export Results</button>
<button class="btn btn-secondary">Save Scenario</button>
<button class="btn btn-secondary">Compare Scenarios</button>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Assessment Tools Section -->
<div id="assessment-tools" class="page-section" style="display: none;">
<h2 class="page-title">Document Ecosystem Assessment</h2>
<div class="two-column">
<!-- Assessment Configuration -->
<div class="sidebar">
<h3 class="sidebar-title">Assessment Type</h3>
<div class="form-group">
<label><input type="radio" name="assessment-type" value="quick"> Quick Scan</label>
</div>
<div class="form-group">
<label><input type="radio" name="assessment-type" value="comprehensive" checked> Comprehensive</label>
</div>
<div class="form-group">
<label><input type="radio" name="assessment-type" value="compliance"> Compliance Focus</label>
</div>
<h4 class="mt-3">Scope:</h4>
<div class="form-group">
<label><input type="checkbox" checked> Discovery</label>
</div>
<div class="form-group">
<label><input type="checkbox" checked> Preclinical</label>
</div>
<div class="form-group">
<label><input type="checkbox" checked> Clinical</label>
</div>
<div class="form-group">
<label><input type="checkbox" checked> Regulatory</label>
</div>
<div class="form-group">
<label><input type="checkbox" checked> Medical Affairs</label>
</div>
<div class="form-group">
<label><input type="checkbox" checked> Post-Marketing</label>
</div>
<button class="btn btn-secondary btn-block mt-2">Save Settings</button>
</div>
<!-- Client Information -->
<div>
<div class="card mb-3">
<div class="card-header">Client Information</div>
<div class="card-body">
<div class="form-group">
<label for="client-name">Client Name:</label>
<input type="text" id="client-name" class="form-control">
</div>
<div class="form-group">
<label for="industry">Industry:</label>
<select id="industry" class="form-control">
<option selected>Pharmaceutical</option>
<option>Biotechnology</option>
<option>Medical Device</option>
<option>CRO</option>
</select>
</div>
<div class="form-group">
<label for="project">Project:</label>
<input type="text" id="project" class="form-control">
</div>
<div class="form-group">
<label for="assessment-date">Assessment Date:</label>
<input type="date" id="assessment-date" class="form-control" value="2025-04-06">
</div>
<div class="form-group">
<label for="assessor">Assessor:</label>
<input type="text" id="assessor" class="form-control">
</div>
<button class="btn btn-primary btn-block">Start New Assessment</button>
</div>
</div>
<div class="card">
<div class="card-header">Assessment Tools</div>
<div class="card-body">
<div class="grid">
<div class="card p-3">
<h4>Gap Analysis</h4>
<p>Identify missing or outdated documents in the client's ecosystem.</p>
<button class="btn btn-secondary mt-2">Start</button>
</div>
<div class="card p-3">
<h4>Compliance Check</h4>
<p>Verify regulatory compliance of document ecosystem.</p>
<button class="btn btn-secondary mt-2">Start</button>
</div>
<div class="card p-3">
<h4>Maturity Model</h4>
<p>Assess process maturity and identify improvement areas.</p>
<button class="btn btn-secondary mt-2">Start</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Document Blueprints Section -->
<div id="document-blueprints" class="page-section" style="display: none;">
<h2 class="page-title">Document Blueprint: Clinical Study Protocol</h2>
<div class="two-column">
<!-- Blueprint Actions -->
<div class="sidebar">
<h3 class="sidebar-title">Blueprint Actions</h3>
<button class="btn btn-primary btn-block mb-2">Edit Blueprint</button>
<button class="btn btn-secondary btn-block mb-2">Export Template</button>
<button class="btn btn-secondary btn-block mb-2">View Prompts</button>
<button class="btn btn-secondary btn-block">Clone Blueprint</button>
</div>
<!-- Blueprint Content -->
<div>
<div class="card mb-3">
<div class="card-header">Section Structure</div>
<div class="card-body">
<ol>
<li>Protocol Title Page</li>
<li>Synopsis</li>
<li>Table of Contents</li>
<li>List of Abbreviations</li>
<li>Protocol Introduction</li>
<li>Study Objectives</li>
<li><a href="#" onclick="showSectionDetails('study-design')">Study Design</a></li>
<li>Subject Selection</li>
<li>Study Treatments</li>
<li>Study Procedures</li>
<li>Adverse Events</li>
<li>Statistical Methods</li>
<li>Data Management</li>
<li>Ethics and Regulations</li>
<li>References</li>
<li>Appendices</li>
</ol>
</div>
</div>
<div class="card" id="section-details">
<div class="card-header">Section Details: 7. Study Design</div>
<div class="card-body">
<p><strong>Purpose:</strong> Describes the overall design of the study, including study type, randomization, blinding, and duration.</p>
<h4 class="mt-3">Content Guidelines:</h4>
<ul>
<li>Clearly state study design type (e.g., parallel, crossover)</li>
<li>Describe randomization and blinding procedures</li>
<li>Define study periods and visit schedule</li>
<li>Include study schematic diagram</li>
<li>Specify duration of subject participation</li>
</ul>
<h4 class="mt-3">Prompt Library:</h4>
<ul>
<li><a href="#">Generate study design description based on parameters</a></li>
<li><a href="#">Create study schematic diagram from design elements</a></li>
<li><a href="#">Generate visit schedule based on procedures and timepoints</a></li>
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