This is a great prompt because it pushes us to define the **functional core of the Autologos Toolkit** and how it will specifically operationalize the "airtight system" for the PI. It's essentially detailing the "how" behind the "what" of the research. Based on your prompt, here are specific roles and requirements for the Autologos Toolkit, designed to manage the entire research lifecycle efficiently, effectively, and in compliance with PMBOK/ISO principles for a single PI. This will form the heart of the revised Section 8.0. **Autologos Toolkit: Roles and Requirements for Research Lifecycle Management** **Overarching Goal:** To serve as the PI's primary operational support system, automating and assisting in all phases of the research lifecycle, from initial idea management to final deliverable production, while ensuring rigor, reproducibility, provenance, and compliance with project management standards. **I. Roles of the Autologos Toolkit (Conceptual Grouping of Application Functionalities):** 1. **Research Project & Workflow Manager (Orchestrator Role):** * **Function:** To assist the PI in planning, tracking, and executing research tasks aligned with the Master Plan and WBS. * **Key App(s) Involved (from image/concept):** "AI Workflow Orchestrator," potentially integrating with task management views derived from WBS/Master Plan. 2. **Knowledge Ingestion & Structuring Specialist (Librarian/Analyst Role):** * **Function:** To process, analyze, synthesize, and structure information from diverse sources (internal documents, external literature, PI notes) into the Autaxys Foundational Knowledge Base (AFKB). * **Key App(s) Involved:** "Text File Analyzer & Synthesizer," "Academic Reference Validator." 3. **Conceptual Development & Formalization Assistant (Research Associate Role):** * **Function:** To aid the PI in exploring conceptual relationships, developing formal models, generating hypotheses, and performing critical analysis of theoretical constructs. * **Key App(s) Involved:** "Autologos Iterative Process Engine" (for conceptual drafting), "Critical Analysis Toolkit," potentially specialized math/logic model assistants (future). 4. **Content Generation & Refinement Engine (Technical Writer/Editor Role):** * **Function:** To draft, refine, format, and iterate on all research outputs, including the Master Plan itself, research papers, reports, and AFKB entries. * **Key App(s) Involved:** "Autologos Iterative Process Engine." 5. **Quality Assurance & Methodological Rigor Monitor (QA/Reviewer Role):** * **Function:** To support the PI in maintaining high standards of research quality, methodological consistency, prompt engineering, and internal review. * **Key App(s) Involved:** "AI LLM Instruction Reviewer," "AI Peer Reviewer," "Critical Analysis Toolkit." 6. **Data & Artifact Management System (Archivist/System Admin Role):** * **Function:** To manage the storage, versioning, provenance, and export of all research data and artifacts. * **Key App(s) Involved:** This might be an underlying capability of the "AI Workflow Orchestrator" or a dedicated backend integrated with the AFKB technology. **II. Specific System Requirements for Lifecycle Management:** **A. Input & Idea Management (Initiation & Planning Phase - PMBOK):** 1. **`EVOLVE` Suggestion Capture:** * **REQ-A1.1:** System must allow PI to easily capture `EVOLVE` suggestions, research ideas, or ad-hoc notes. * **REQ-A1.2:** Each captured item must be timestamped and allow tagging with relevant Master Plan sections, WBS items, AFKB concepts, or projects. 2. **Literature Ingestion & Initial Processing (Project 6.1 Focus):** * **REQ-A2.1 (Text File Analyzer & Synthesizer):** System must ingest multiple text files (PDF, TXT, MD). * **REQ-A2.2 (Text File Analyzer & Synthesizer):** Extract key entities, phrases, themes, term frequencies, and generate a consolidated, machine-readable synthesis. * **REQ-A2.3 (Text File Analyzer & Synthesizer):** Provide an indexed overview with citation hints (e.g., APA-style parenthetical) to facilitate AFKB structuring. * **REQ-A2.4 (Academic Reference Validator):** For ingested references, simulate validation using mock search/browse tools, demonstrating API client initialization and identifying potential issues (e.g., broken DOIs, questionable sources based on PI-defined criteria). 3. **Master Plan & WBS Ingestion:** * **REQ-A3.1:** System must parse and internally represent the Master Plan and WBS structure, including dependencies. **B. Iterative Research & Development (Execution Phase - PMBOK):** 1. **AFKB Population & Management (Project 6.1 Focus):** * **REQ-B1.1:** Facilitate linking of processed literature (from REQ-A2) to AFKB concept nodes and relational edges, assisted by suggestions from the "Text File Analyzer & Synthesizer." * **REQ-B1.2:** Support PI in defining and refining AFKB concept nodes, their definitions, properties, and interrelations. * **REQ-B1.3:** Maintain provenance for all AFKB entries (PI-authored, external source, Autologos-generated summary/link). 2. **Conceptual Exploration & Formalization Support (Project 6.2, etc.):** * **REQ-B2.1 (Autologos Iterative Process Engine):** Accept PI prompts with context (from AFKB, Master Plan sections, specific WBS tasks) to iteratively draft conceptual elaborations, explore implications of principles (e.g., ontological closure on a given pattern), or outline formal arguments. * **REQ-B2.2 (Critical Analysis Toolkit):** Apply critical perspectives (adversarial critique, red-teaming, identifying blind spots) to PI-provided text (e.g., draft theories, URFE responses) or Autologos-generated drafts. * **REQ-B2.3:** Assist in exploring mappings between autaxic concepts and formal constructs (Sec 3.5.5) by generating potential representations or identifying relevant formalisms from the AFKB. 3. **Prompt & Instruction Engineering (Cross-cutting):** * **REQ-B3.1 (AI LLM Instruction Reviewer):** Analyze PI-drafted prompts/instructions for any Autologos app, providing feedback on clarity, effectiveness, and prompt engineering best practices to improve AI output quality and alignment. 4. **Workflow Orchestration & Task Management:** * **REQ-B4.1 (AI Workflow Orchestrator):** Allow PI to define multi-step research workflows (e.g., "Literature Review -> AFKB Synthesis -> Conceptual Draft -> Critical Analysis -> Refined Draft"). * **REQ-B4.2 (AI Workflow Orchestrator):** Manage the execution of these workflows, potentially triggering different Autologos apps or prompting PI for input/review at appropriate stages. * **REQ-B4.3 (AI Workflow Orchestrator):** Track progress against WBS items, update status based on workflow completion, and flag dependencies. **C. Output & Deliverable Generation (Execution & Closing Phases - PMBOK):** 1. **Drafting & Iteration (All documentation):** * **REQ-C1.1 (Autologos Iterative Process Engine):** Generate initial drafts of Master Plan sections, research papers, project reports, AFKB entries, PEAP records, etc., based on PI prompts, extensive AFKB context, and WBS requirements. * **REQ-C1.2 (Autologos Iterative Process Engine):** Iteratively refine these drafts based on PI feedback, critical analysis (from REQ-B2.2), and peer review simulations (from REQ-C2.1). 2. **Internal Quality Assurance:** * **REQ-C2.1 (AI Peer Reviewer):** Simulate a peer-review process for user-submitted text (draft papers, Master Plan sections), providing structured feedback and recommendations. * **REQ-C2.2:** Cross-reference claims in outputs against AFKB content for consistency and grounding in established project knowledge. 3. **Formatting & Export:** * **REQ-C3.1:** Format outputs according to specified templates or standards (e.g., Markdown for Master Plan, LaTeX for papers – with PI providing templates). * **REQ-C3.2:** Export documents in various standard formats (MD, PDF, potentially DOCX) for dissemination and archiving. 4. **Reference & Bibliography Management:** * **REQ-C4.1 (Academic Reference Validator / Text File Analyzer):** Ensure all cited external sources in outputs have corresponding entries in the AFKB bibliography. * **REQ-C4.2:** Assist in generating formatted bibliographies for publications. **D. Monitoring, Control, & Compliance (Monitoring & Controlling Phase - PMBOK):** 1. **Reproducibility & Provenance (ISO Quality Management):** * **REQ-D1.1:** All Autologos Toolkit interactions (PI prompts, app inputs/outputs, parameters used if any) relevant to the generation of a specific artifact or AFKB entry must be logged and associated with that artifact for reproducibility. * **REQ-D1.2:** Clear version control for all key documents (Master Plan, WBS, AFKB major states, core research papers, Autologos App Specifications). * **REQ-D1.3:** Strict adherence to knowledge provenance rules (PI vs. External vs. Synthetic) in all outputs and AFKB entries (REQ-B1.3). 2. **Compliance with ARM & Autologos Core Directives:** * **REQ-D2.1:** The "AI Workflow Orchestrator" and individual apps should operate in a manner consistent with the ARM (Section 7.0) and Autologos Core Directives (Appendix 14.6). * **REQ-D2.2 (AI LLM Instruction Reviewer):** Can be used by PI to check if a planned workflow or a complex instruction to an app aligns with these guiding principles. 3. **Change Management (Master Plan Evolution - Sec 12.0):** * **REQ-D3.1:** Facilitate tracking of `EVOLVE` suggestions and their integration into Master Plan revisions. * **REQ-D3.2:** Support PI in conducting periodic comprehensive reviews of the Master Plan by providing relevant data from WBS progress, AFKB insights, and PEAP evaluations. **E. File & Document Management (Cross-cutting, ISO Document Control):** 1. **Structured Storage:** * **REQ-E1.1:** Adhere to the defined `projects/AUTX/` directory structure for saving all generated and managed files. 2. **Naming Conventions & Versioning:** * **REQ-E2.1:** Consistently apply naming conventions and versioning (e.g., `_vX.Y`) to all key documents managed by the system. 3. **Cross-linking:** * **REQ-E3.1:** Maintain and update internal Markdown cross-links between segmented Master Plan files and other relevant documents within the project structure. 4. **Archiving Support:** * **REQ-E4.1:** Facilitate the preparation of document sets for archiving on external platforms (e.g., Zenodo) by ensuring files are in appropriate formats and metadata is available. **III. Non-Functional Requirements for the Toolkit:** * (As previously detailed: Usability, Performance, Reliability, Flexibility, Security, Interoperability). * **Modularity:** Individual apps within the toolkit should be developable, updatable, and usable somewhat independently, even if orchestrated. * **Extensibility:** The PI should be able to conceptualize and integrate new custom AI apps into the toolkit as research needs evolve. This detailed breakdown of roles and requirements for the Autologos Toolkit provides a solid foundation for the revised Section 8.0 of the Master Plan. It clarifies *how* AI will be leveraged at each stage, connecting specific app functionalities to the overall research process and compliance needs.