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<title>ProcessDSL + FlowCell-10 Proposal</title> |
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<h1>ProcessDSL + FlowCell-10 Proposal</h1> |
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<div class="highlight"> |
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<p><strong>This proposal outlines a pilot initiative to integrate the "genome as program" concept and cellular process flowcharting into the Virtual Cell project.</strong> The goal is to formalize biological processes as executable, interpretable programs that can be learned, simulated, and manipulated by AI.</p> |
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</div> |
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<h2>1. ProcessDSL Specification</h2> |
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<p><strong>ProcessDSL</strong> is a domain-specific language for representing cellular processes. It compiles human-readable flowcharts into machine-executable forms such as stochastic rule systems, Petri nets, or hybrid ODE/event simulators.</p> |
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<h3>Key features:</h3> |
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<ul> |
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<li>Reactions as rules with explicit guards and rate constants.</li> |
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<li>Conditional logic (IF/ELSE) for regulation.</li> |
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<li>Iterative loops (WHILE) for cyclic processes.</li> |
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<li>Event triggers for environmental or signaling changes.</li> |
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<li>Support for compartments (nucleus, cytosol, organelles).</li> |
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</ul> |
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<h2>2. FlowCell-10 Pilot Dataset</h2> |
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<p><strong>FlowCell-10</strong> is a curated set of ten well-characterized yeast pathways, each represented as:</p> |
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<ul> |
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<li>A canonical flowchart</li> |
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<li>A ProcessDSL file</li> |
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<li>Reference simulation outputs from literature data</li> |
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</ul> |
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<h3>Example pathways:</h3> |
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<ol> |
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<li>Glycolysis</li> |
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<li>TOR nutrient sensing pathway</li> |
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<li>Heat shock response</li> |
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<li>Autophagy initiation</li> |
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<li>Unfolded protein response (UPR)</li> |
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<li>Cell cycle G1/S transition</li> |
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<li>Mitochondrial respiration control</li> |
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<li>Amino acid biosynthesis regulation</li> |
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<li>Gluconeogenesis</li> |
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<li>Alcoholic fermentation</li> |
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</ol> |
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<h2>3. Example ProcessDSL (Glycolysis)</h2> |
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<div class="code-block"> |
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process Glycolysis in Cytosol: |
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state: [Glucose, G6P, F6P, F16BP, G3P, DHAP, PEP, Pyruvate, ATP, ADP, NAD+, NADH] |
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rule Hexokinase: Glucose + ATP -> G6P + ADP [guard: ATP>θ1] |
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rule PFK: F6P + ATP -> F16BP + ADP [guard: ATP<θ2 & AMP>θ3] |
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rule Aldolase: F16BP -> G3P + DHAP |
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rule TPI: DHAP <-> G3P |
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rule PyruvateKinase: PEP + ADP -> Pyruvate + ATP [allosteric: F16BP activates] |
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event GlucosePulse(t=0..T): inflow rate r_in |
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</div> |
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<h2>4. Expanded Glycolysis Flowchart</h2> |
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<p>Below is an example from FlowCell-10 showing <strong>Glycolysis in Yeast</strong> with branch and loop structure:</p> |
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<div class="flowchart-container"> |
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<img src="YeastFlowchart1.drawio.png" alt="Glycolysis Pathway in Yeast" style="max-width: 100%; height: auto;"> |
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</div> |
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<h2>5. Deliverables</h2> |
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<ul> |
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<li>ProcessDSL specification and parser.</li> |
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<li>FlowCell-10 diagrams, DSL files, and simulation benchmarks.</li> |
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<li>Jupyter notebook demo: diagram → ProcessDSL → simulation → data comparison.</li> |
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<li>Documentation for extending the dataset.</li> |
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</ul> |
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<h2>6. Benefits to the Virtual Cell Project</h2> |
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<div class="benefit-box"> |
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<ul> |
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<li>Provides an interpretable, executable representation of cellular processes.</li> |
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<li>Bridges molecular prediction tools (e.g., AlphaFold 3) to systems-level dynamics.</li> |
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<li>Enables counterfactual simulations and intervention planning.</li> |
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<li>Creates training data for AI models to learn biological program induction.</li> |
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</ul> |
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</div> |
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<div class="highlight"> |
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<p><strong>This proposal demonstrates how computational biology and artificial intelligence can converge to create interpretable, executable models of biological systems.</strong></p> |
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</div> |
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