scientific-writer 2.3.1__py3-none-any.whl

scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex

@@ -0,0 +1,199 @@
+% Block Diagram Template
+% For system architecture, data flow, and component diagrams
+%
+% Usage:
+%   1. Copy and customize this template
+%   2. Modify blocks and connections
+%   3. Compile with: pdflatex block_diagram_template.tex
+%   4. Include in paper with: \includegraphics{block_diagram.pdf}
+
+\documentclass[tikz, border=5mm]{standalone}
+\usepackage{tikz}
+
+% Load shared styles
+\input{tikz_styles.tex}
+
+\begin{document}
+
+% === Example 1: Data Acquisition System ===
+\begin{tikzpicture}[blockdiagram]
+
+% Components
+\node[component] (sensor) {Sensor};
+\node[component, right=of sensor] (adc) {ADC};
+\node[component, right=of adc] (micro) {Micro-\\controller};
+\node[component, above right=1cm and 1.5cm of micro] (wireless) {Wireless\\Module};
+\node[component, below right=1cm and 1.5cm of micro] (display) {Display};
+\node[component, right=3cm of micro] (server) {Server};
+
+% Connections with data flow
+\draw[dataflow] (sensor) -- node[above, font=\footnotesize] {analog} (adc);
+\draw[dataflow] (adc) -- node[above, font=\footnotesize] {digital} (micro);
+\draw[dataflow] (micro) -- node[above right, font=\footnotesize] {WiFi} (wireless);
+\draw[dataflow] (micro) -- node[below right, font=\footnotesize] {SPI} (display);
+\draw[dataflow] (wireless) -- node[above, font=\footnotesize] {TCP/IP} (server);
+
+% Optional: control signals
+\draw[control, <->] (server) to[bend left=20] node[above, font=\footnotesize] {control} (micro);
+
+\end{tikzpicture}
+
+\vspace{1cm}
+
+% === Example 2: Software Architecture (Three-Tier) ===
+\begin{tikzpicture}[blockdiagram]
+
+% Presentation Layer
+\node[subsystem] (web) {Web UI};
+\node[subsystem, right=of web] (mobile) {Mobile App};
+
+% Business Logic Layer
+\node[subsystem, below=2cm of web, xshift=1.5cm] (api) {API Server};
+\node[component, left=of api] (auth) {Auth\\Service};
+\node[component, right=of api] (worker) {Worker\\Queue};
+
+% Data Layer
+\node[component, below=2cm of auth] (db) {Database};
+\node[component, below=2cm of api] (cache) {Cache};
+\node[component, below=2cm of worker] (storage) {File\\Storage};
+
+% Connections
+\draw[dataflow, <->] (web) -- (api);
+\draw[dataflow, <->] (mobile) -- (api);
+\draw[dataflow, <->] (api) -- (auth);
+\draw[dataflow, <->] (api) -- (worker);
+\draw[dataflow, <->] (auth) -- (db);
+\draw[dataflow, <->] (api) -- (db);
+\draw[dataflow, <->] (api) -- (cache);
+\draw[dataflow, <->] (worker) -- (storage);
+
+% Layer labels
+\node[annotation, left=2.5cm of web] {Presentation\\Layer};
+\node[annotation, left=2.5cm of api] {Business\\Logic};
+\node[annotation, left=2.5cm of db] {Data\\Layer};
+
+\end{tikzpicture}
+
+\vspace{1cm}
+
+% === Example 3: Experimental Setup ===
+\begin{tikzpicture}[blockdiagram, node distance=2.5cm]
+
+% Equipment chain
+\node[component] (source) {Light\\Source};
+\node[component, right=of source] (filter) {Filter};
+\node[component, right=of filter] (sample) {Sample\\Chamber};
+\node[component, right=of sample] (detector) {Detector};
+\node[component, right=of detector] (amp) {Amplifier};
+\node[component, above right=0.5cm and 1cm of amp] (daq) {Data\\Acquisition};
+\node[component, below=1.5cm of sample] (temp) {Temperature\\Controller};
+
+% Signal flow
+\draw[dataflow] (source) -- node[above, font=\footnotesize] {light} (filter);
+\draw[dataflow] (filter) -- (sample);
+\draw[dataflow] (sample) -- (detector);
+\draw[dataflow] (detector) -- node[above, font=\footnotesize] {signal} (amp);
+\draw[dataflow] (amp) -- (daq);
+
+% Control
+\draw[control, <->] (temp) -- (sample);
+\draw[control] (daq.south) |- (temp.east);
+
+% Computer
+\node[subsystem, right=of daq] (computer) {Computer};
+\draw[dataflow, <->] (daq) -- (computer);
+
+\end{tikzpicture}
+
+\end{document}
+
+% === Customization Guide ===
+%
+% BLOCK TYPES (from tikz_styles.tex):
+%   component - Standard component (blue, medium size)
+%   subsystem - Larger system block (green, larger, bold)
+%   interface - Connection point (orange circle)
+%
+% ARROW TYPES:
+%   dataflow  - Data flow arrow (solid, blue)
+%   control   - Control signal (dashed, red)
+%   arrow     - Generic arrow (black)
+%
+% ARROW DIRECTIONS:
+%   -->  : Left to right
+%   <->  : Bidirectional
+%   |-   : Vertical then horizontal
+%   -|   : Horizontal then vertical
+%
+% POSITIONING:
+%   right=of node     - To the right
+%   below=of node     - Below
+%   above=of node     - Above
+%   right=2cm of node - Specific distance
+%   above right=1cm and 2cm of node - Diagonal
+%
+% LABELS ON ARROWS:
+%   \draw[dataflow] (a) -- node[above] {label} (b);
+%   \draw[dataflow] (a) -- node[below, font=\footnotesize] {label} (b);
+%   \draw[dataflow] (a) -- node[pos=0.3, above] {label} (b);
+%
+% CURVED CONNECTIONS:
+%   \draw[dataflow] (a) to[bend left=30] (b);
+%   \draw[dataflow] (a) to[bend right=30] (b);
+%   \draw[dataflow, out=45, in=135] (a) to (b);
+%
+% GROUPING COMPONENTS:
+% Use fit library to draw box around multiple components:
+%
+%   \node[background, fit=(comp1) (comp2) (comp3)] {};
+%   \node[above, font=\small] at (group.north) {Subsystem Name};
+%
+% Or manually draw a box:
+%
+%   \draw[thick, okabe-green, rounded corners] 
+%     (x1, y1) rectangle (x2, y2);
+%   \node at (x, y) {Group Label};
+%
+% LAYER/HIERARCHY VISUALIZATION:
+% Add horizontal lines and labels to show layers:
+%
+%   % Draw separators
+%   \draw[thick, gray, dashed] (-2, 0) -- (8, 0);
+%   \draw[thick, gray, dashed] (-2, -3) -- (8, -3);
+%   
+%   % Add layer labels
+%   \node[annotation, left] at (-2, 1) {Layer 1};
+%   \node[annotation, left] at (-2, -1.5) {Layer 2};
+%
+% SIGNAL TYPES:
+% Annotate data/signal types on connections:
+%   - Digital/Analog
+%   - Protocol (SPI, I2C, UART, Ethernet, etc.)
+%   - Data rate (Mbps, Hz)
+%   - Voltage levels
+%
+% TYPICAL USAGE IN PAPER:
+%
+% \begin{figure}[h]
+%   \centering
+%   \includegraphics[width=0.9\textwidth]{block_diagram.pdf}
+%   \caption{System architecture showing data flow from sensor through
+%            signal processing to display and wireless transmission.
+%            Solid arrows indicate data flow, dashed arrows show control signals.}
+%   \label{fig:architecture}
+% \end{figure}
+%
+% MULTI-PANEL DIAGRAMS:
+% Combine overview and detail views:
+%   - Panel A: High-level system overview
+%   - Panel B: Detailed view of one subsystem
+%
+% Add panel labels:
+%   \node[font=\large\bfseries] at (-3, 5) {A};
+%   \node[font=\large\bfseries] at (-3, -2) {B};
+%
+% RESOURCES:
+% - UML diagrams: https://www.uml-diagrams.org/
+% - System architecture patterns
+% - IEEE recommended practice for architectural description
+

scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex

@@ -0,0 +1,159 @@
+% Circuit Diagram Template using CircuitikZ
+% For electrical schematics, instrumentation diagrams, and signal processing
+%
+% Usage:
+%   1. Copy and customize this template
+%   2. Compile with: pdflatex circuit_template.tex
+%   3. Include in paper with: \includegraphics{circuit.pdf}
+
+\documentclass[tikz, border=5mm]{standalone}
+\usepackage{tikz}
+\usepackage{circuitikz}
+
+% Load shared colors (optional, for consistent styling)
+\input{tikz_styles.tex}
+
+\begin{document}
+
+% === Example 1: RC Filter Circuit ===
+\begin{circuitikz}[american, scale=1.2, transform shape]
+
+% Input
+\draw (0,0) node[left] {$V_{in}$}
+  to[short, o-] (0.5,0)
+  to[R, l=$R_1$, v^>=$V_R$] (3,0)
+  to[short, -o] (3.5,0) node[right] {$V_{out}$};
+
+% Capacitor to ground
+\draw (3,0) to[C, l=$C_1$, *-] (3,-2)
+  node[ground] {};
+
+% Component values annotation (optional)
+\node[below, font=\small] at (1.5,-2.5) {$R_1 = 1\,\mathrm{k}\Omega$, $C_1 = 10\,\mu\mathrm{F}$};
+
+\end{circuitikz}
+
+\vspace{1cm}
+
+% === Example 2: Voltage Divider ===
+\begin{circuitikz}[american, scale=1.2, transform shape]
+
+% Voltage source
+\draw (0,0) to[V, v=$V_s$, invert] (0,3);
+
+% Resistors
+\draw (0,3) to[short] (2,3)
+  to[R, l=$R_1$] (2,1.5)
+  to[short, -o] (3,1.5) node[right] {$V_{out}$}
+  (2,1.5) to[R, l=$R_2$] (2,0)
+  to[short] (0,0);
+
+% Ground
+\draw (0,0) node[ground] {};
+
+\end{circuitikz}
+
+\vspace{1cm}
+
+% === Example 3: Amplifier Circuit ===
+\begin{circuitikz}[american, scale=1.0, transform shape]
+
+% Input
+\draw (0,0) node[left] {$V_{in}$}
+  to[C, l=$C_{in}$, o-] (1.5,0);
+
+% Biasing resistor
+\draw (1.5,0) to[R, l=$R_b$, *-] (1.5,2)
+  to[short] (0,2) node[left] {$+V_{cc}$};
+
+% Transistor
+\node[npn] (npn) at (3,0) {};
+\draw (1.5,0) to[short] (npn.base);
+
+% Collector resistor
+\draw (npn.collector) to[R, l=$R_c$] (3,2.5)
+  to[short] (3,3) node[above] {$+V_{cc}$};
+
+% Emitter to ground
+\draw (npn.emitter) to[short] (3,-1.5) node[ground] {};
+
+% Output
+\draw (npn.collector) to[C, l=$C_{out}$, *-o] (5,0.75) node[right] {$V_{out}$};
+
+\end{circuitikz}
+
+\end{document}
+
+% === CircuitikZ Component Reference ===
+%
+% PASSIVE COMPONENTS:
+%   to[R, l=$R_1$] - Resistor with label
+%   to[C, l=$C_1$] - Capacitor
+%   to[L, l=$L_1$] - Inductor
+%   to[D, l=$D_1$] - Diode
+%   to[vR] - Variable resistor
+%   to[vC] - Variable capacitor
+%
+% SOURCES:
+%   to[V, v=$V_s$] - Voltage source
+%   to[I, i=$I_s$] - Current source
+%   to[sV] - Sinusoidal voltage source
+%   to[battery] - Battery
+%
+% SEMICONDUCTORS:
+%   node[npn] (name) {} - NPN transistor
+%   node[pnp] (name) {} - PNP transistor
+%   node[nmos] (name) {} - N-channel MOSFET
+%   node[pmos] (name) {} - P-channel MOSFET
+%   node[op amp] (name) {} - Operational amplifier
+%
+% CONNECTIONS:
+%   to[short] - Wire/short circuit
+%   to[short, o-] - Wire starting with open circle
+%   to[short, -o] - Wire ending with open circle
+%   to[short, *-] - Wire starting with filled dot
+%   to[short, -*] - Wire ending with filled dot
+%
+% OTHER:
+%   node[ground] {} - Ground symbol
+%   node[vcc] {} - VCC symbol
+%   to[meter, l=$V$] - Voltmeter
+%   to[ammeter] - Ammeter
+%
+% VOLTAGE/CURRENT ANNOTATIONS:
+%   v=$V_x$ - Voltage drop label
+%   v^>=$V_x$ - Voltage with arrow pointing up
+%   v_<=$V_x$ - Voltage with arrow pointing down
+%   i=$I_x$ - Current label
+%
+% CUSTOMIZATION:
+%
+% 1. Change style to european:
+%    \begin{circuitikz}[european]
+%
+% 2. Scale the circuit:
+%    \begin{circuitikz}[scale=1.5, transform shape]
+%
+% 3. Change colors (using okabe-ito palette):
+%    to[R, l=$R_1$, color=okabe-blue]
+%
+% 4. Rotate components:
+%    to[R, l=$R_1$, rotate=90]
+%
+% 5. Add node at specific coordinate:
+%    \draw (2,3) node[npn] {};
+%
+% TYPICAL USAGE IN PAPER:
+%
+% \begin{figure}[h]
+%   \centering
+%   \includegraphics[width=0.6\columnwidth]{circuit.pdf}
+%   \caption{Schematic diagram of the measurement circuit.
+%            $R_1 = 1\,\mathrm{k}\Omega$, $C_1 = 10\,\mu\mathrm{F}$.}
+%   \label{fig:circuit}
+% \end{figure}
+%
+% RESOURCES:
+% - CircuitikZ manual: https://ctan.org/pkg/circuitikz
+% - Component library: See CircuitikZ documentation Section 4
+

scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex

@@ -0,0 +1,161 @@
+% CONSORT-Style Flowchart Template
+% For methodology sections, participant flow diagrams, and study design
+%
+% Usage:
+%   1. Copy this template
+%   2. Modify node contents and participant numbers
+%   3. Add/remove nodes as needed
+%   4. Compile with: pdflatex flowchart_template.tex
+%   5. Include in paper with: \input{flowchart.tex} or \includegraphics{flowchart.pdf}
+
+\documentclass[tikz, border=5mm]{standalone}
+\usepackage{tikz}
+
+% Load shared styles
+\input{tikz_styles.tex}
+
+\begin{document}
+
+\begin{tikzpicture}[consort]
+
+% === Nodes ===
+% Modify these to match your study
+
+% Initial assessment
+\node[flowbox] (assessed) {
+  Assessed for eligibility\\
+  (n=500)
+};
+
+% Exclusions
+\node[flowbox, below=of assessed] (excluded) {
+  Excluded (n=150)
+};
+
+% Exclusion criteria (side annotation)
+\node[infobox, right=of excluded] (reasons) {
+  \textbf{Exclusion criteria:}\\
+  Age $<$ 18 years: n=80\\
+  Declined participation: n=50\\
+  Other reasons: n=20
+};
+
+% Randomization
+\node[flowbox, below=of excluded] (randomized) {
+  Randomized\\
+  (n=350)
+};
+
+% Treatment groups
+\node[groupbox, below left=2cm and 1.5cm of randomized] (treatment) {
+  \textbf{Treatment Group}\\
+  Allocated to intervention\\
+  (n=175)
+};
+
+\node[groupbox, below right=2cm and 1.5cm of randomized] (control) {
+  \textbf{Control Group}\\
+  Allocated to control\\
+  (n=175)
+};
+
+% Follow-up (treatment)
+\node[flowbox, below=of treatment] (followup-t) {
+  Completed follow-up\\
+  (n=168)
+};
+
+\node[infobox, right=of followup-t] (lost-t) {
+  Lost to follow-up: n=7\\
+  (withdrew: n=5, other: n=2)
+};
+
+% Follow-up (control)
+\node[flowbox, below=of control] (followup-c) {
+  Completed follow-up\\
+  (n=170)
+};
+
+\node[infobox, left=of followup-c] (lost-c) {
+  Lost to follow-up: n=5\\
+  (withdrew: n=3, other: n=2)
+};
+
+% Analysis
+\node[flowbox, below=2.5cm of randomized] (analyzed) {
+  Analyzed\\
+  (n=338)
+};
+
+% === Connections ===
+% Arrows showing flow
+
+% Main flow
+\draw[arrow] (assessed) -- (excluded);
+\draw[arrow] (excluded) -- (randomized);
+
+% Randomization to groups
+\draw[arrow] (randomized) -| (treatment);
+\draw[arrow] (randomized) -| (control);
+
+% Follow-up
+\draw[arrow] (treatment) -- (followup-t);
+\draw[arrow] (control) -- (followup-c);
+
+% To analysis
+\draw[arrow] (followup-t) |- (analyzed);
+\draw[arrow] (followup-c) |- (analyzed);
+
+% === Optional Elements ===
+
+% Add panel label if part of multi-panel figure
+% \node[font=\large\bfseries, above left=0.2cm of assessed] {A};
+
+% Add study phase labels
+% \node[annotation, left=2cm of assessed] {Enrollment};
+% \node[annotation, left=2cm of randomized] {Allocation};
+% \node[annotation, left=2cm of followup-t] {Follow-up};
+% \node[annotation, left=2cm of analyzed] {Analysis};
+
+\end{tikzpicture}
+
+\end{document}
+
+% === Customization Notes ===
+%
+% 1. Change participant numbers (n=X) to match your study
+%
+% 2. Add more exclusion criteria in the infobox:
+%    \node[infobox, right=of excluded] (reasons) {
+%      \textbf{Exclusion criteria:}\\
+%      Criterion 1: n=XX\\
+%      Criterion 2: n=YY\\
+%      Criterion 3: n=ZZ
+%    };
+%
+% 3. Add more treatment arms (for 3+ group studies):
+%    \node[groupbox, below=2cm of randomized] (group3) {
+%      \textbf{Group 3}\\
+%      Description\\
+%      (n=XX)
+%    };
+%    \draw[arrow] (randomized) -- (group3);
+%
+% 4. Add intervention details:
+%    \node[infobox, right=of treatment] (intervention) {
+%      Received intervention: n=XXX\\
+%      Did not receive: n=YY\\
+%      \quad Reason 1: n=Z
+%    };
+%
+% 5. Modify colors by changing node styles in tikz_styles.tex
+%
+% 6. To use in your paper:
+%    \begin{figure}[h]
+%      \centering
+%      \includegraphics[width=0.9\textwidth]{flowchart.pdf}
+%      \caption{Study participant flow diagram following CONSORT guidelines.
+%               Boxes show participant numbers (n) at each stage.}
+%      \label{fig:consort}
+%    \end{figure}
+

scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex

@@ -0,0 +1,162 @@
+% Biological Pathway Template
+% For signaling cascades, metabolic pathways, and molecular interactions
+%
+% Usage:
+%   1. Copy and customize this template
+%   2. Modify node positions and labels
+%   3. Compile with: pdflatex pathway_template.tex
+%   4. Include in paper with: \includegraphics{pathway.pdf}
+
+\documentclass[tikz, border=5mm]{standalone}
+\usepackage{tikz}
+
+% Load shared styles
+\input{tikz_styles.tex}
+
+\begin{document}
+
+\begin{tikzpicture}[pathway]
+
+% === Example: MAPK Signaling Pathway ===
+
+% Nodes (proteins, genes, etc.)
+\node[protein] (ligand) at (0, 6) {Growth\\Factor};
+\node[protein] (receptor) at (2, 6) {Receptor};
+\node[protein] (ras) at (4, 6) {RAS};
+\node[protein] (raf) at (6, 6) {RAF};
+\node[protein] (mek) at (8, 6) {MEK};
+\node[protein] (erk) at (10, 6) {ERK};
+
+% Transcription factor (different style)
+\node[protein, fill=okabe-purple!20] (tf) at (10, 4) {TF};
+
+% Gene (italics, green)
+\node[gene] (target) at (10, 2) {\textit{Target\\Gene}};
+
+% === Interactions ===
+
+% Activation arrows (main cascade)
+\draw[activation-arrow] (ligand) -- (receptor);
+\draw[activation-arrow] (receptor) -- node[above, font=\footnotesize] {activates} (ras);
+\draw[activation-arrow] (ras) -- (raf);
+\draw[activation-arrow] (raf) -- (mek);
+\draw[activation-arrow] (mek) -- (erk);
+\draw[activation-arrow] (erk) -- (tf);
+\draw[activation-arrow] (tf) -- node[right, font=\footnotesize] {transcription} (target);
+
+% === Optional: Add inhibitor ===
+% Uncomment to show an inhibitor
+
+% \node[protein, fill=okabe-vermillion!20] (inhibitor) at (5, 8) {Inhibitor};
+% \draw[inhibit-arrow] (inhibitor) -- (raf);
+
+% === Optional: Add feedback loop ===
+% Uncomment to show negative feedback
+
+% \draw[inhibit-arrow, bend right=45] (erk) to node[left, font=\footnotesize] {feedback} (ras);
+
+% === Optional: Add complex formation ===
+% Uncomment to show protein complex
+
+% \node[complex] (complex) at (7, 4) {RAF-MEK\\Complex};
+% \draw[arrow, dashed] (raf) -- (complex);
+% \draw[arrow, dashed] (mek) -- (complex);
+
+% === Optional: Add subcellular compartments ===
+% Uncomment to show membrane, cytoplasm, nucleus
+
+% % Membrane
+% \draw[thick, okabe-dblue] (-0.5, 5) -- (11, 5) node[right, font=\small] {Plasma Membrane};
+%
+% % Nuclear membrane
+% \draw[thick, okabe-green] (9.5, 3) rectangle (10.5, 1.5);
+% \node[font=\small, okabe-green] at (10, 1.2) {Nucleus};
+
+\end{tikzpicture}
+
+\vspace{1cm}
+
+% === Example 2: Simple Linear Pathway ===
+\begin{tikzpicture}[pathway, node distance=2.5cm]
+
+% Linear pathway with enzyme catalysis
+\node[metabolite] (s1) {Substrate\\A};
+\node[metabolite, right=of s1] (s2) {Product\\B};
+\node[metabolite, right=of s2] (s3) {Product\\C};
+
+% Enzymes (above)
+\node[enzyme, above=1cm of s1] (e1) {Enzyme 1};
+\node[enzyme, above=1cm of s2] (e2) {Enzyme 2};
+
+% Catalysis arrows
+\draw[arrow, dashed] (e1) -- (s1);
+\draw[activation-arrow] (s1) -- node[above, font=\footnotesize] {catalyzed} (s2);
+\draw[arrow, dashed] (e2) -- (s2);
+\draw[activation-arrow] (s2) -- (s3);
+
+\end{tikzpicture}
+
+\end{document}
+
+% === Customization Guide ===
+%
+% NODE TYPES (from tikz_styles.tex):
+%   protein  - Rounded rectangle, blue
+%   gene     - Rectangle, green, italic text
+%   metabolite - Circle, yellow
+%   enzyme   - Ellipse, dark blue
+%   complex  - Rounded rectangle, orange, thick border
+%
+% ARROW TYPES:
+%   activation-arrow - Solid arrow, activation
+%   inhibit-arrow    - Blunt end, inhibition (red)
+%   arrow, dashed    - Dashed arrow, indirect effect
+%
+% POSITIONING:
+%   \node[protein] (name) at (x, y) {Label};
+%   or
+%   \node[protein, right=2cm of other] (name) {Label};
+%   or
+%   \node[protein, below=of other] (name) {Label};
+%
+% COLORS (Okabe-Ito colorblind-safe):
+%   okabe-blue, okabe-orange, okabe-green, okabe-yellow
+%   okabe-dblue, okabe-vermillion, okabe-purple
+%
+% SUBCELLULAR COMPARTMENTS:
+% Draw rectangles or regions to show membrane, cytoplasm, nucleus:
+%
+%   % Nucleus boundary
+%   \node[rectangle, draw=okabe-green, thick, minimum width=3cm, 
+%         minimum height=2cm] at (10, 3) {};
+%   \node[font=\small] at (10, 1) {Nucleus};
+%
+%   % Membrane
+%   \draw[very thick, okabe-dblue] (0, 5) -- (12, 5);
+%   \node[right, font=\small] at (12, 5) {Membrane};
+%
+% PATHWAY CONVENTIONS:
+%   - Proteins: Regular font
+%   - Genes: Italic font (\textit{gene} or use gene style)
+%   - Phosphorylation: Add "P" in circle or use annotation
+%     \node[circle, draw, fill=white, inner sep=1pt, font=\tiny] at (x,y) {P};
+%   - Ubiquitination: "Ub" annotation
+%   - Degradation: Dashed arrow to a "trash" symbol or text
+%
+% TYPICAL USAGE IN PAPER:
+%
+% \begin{figure}[h]
+%   \centering
+%   \includegraphics[width=0.8\textwidth]{pathway.pdf}
+%   \caption{MAPK signaling pathway. Growth factor binding activates
+%            receptor, triggering cascade through RAS, RAF, MEK, ERK to
+%            transcription factor (TF) and target gene expression.
+%            Arrows indicate activation.}
+%   \label{fig:pathway}
+% \end{figure}
+%
+% RESOURCES:
+% - Systems Biology Graphical Notation (SBGN): https://sbgn.github.io/
+% - Pathway Commons: https://www.pathwaycommons.org/
+% - KEGG Pathways: https://www.genome.jp/kegg/pathway.html
+