@saibolla/ada 0.1.2

package/skills/scientific-visualization/references/color_palettes.md

@@ -0,0 +1,348 @@
+# Scientific Color Palettes and Guidelines
+
+## Overview
+
+Color choice in scientific visualization is critical for accessibility, clarity, and accurate data representation. This reference provides colorblind-friendly palettes and best practices for color usage.
+
+## Colorblind-Friendly Palettes
+
+### Okabe-Ito Palette (Recommended for Categories)
+
+The Okabe-Ito palette is specifically designed to be distinguishable by people with all forms of color blindness.
+
+```python
+# Okabe-Ito colors (RGB values)
+okabe_ito = {
+    'orange': '#E69F00',      # RGB: (230, 159, 0)
+    'sky_blue': '#56B4E9',    # RGB: (86, 180, 233)
+    'bluish_green': '#009E73', # RGB: (0, 158, 115)
+    'yellow': '#F0E442',      # RGB: (240, 228, 66)
+    'blue': '#0072B2',        # RGB: (0, 114, 178)
+    'vermillion': '#D55E00',  # RGB: (213, 94, 0)
+    'reddish_purple': '#CC79A7', # RGB: (204, 121, 167)
+    'black': '#000000'        # RGB: (0, 0, 0)
+}
+```
+
+**Usage in Matplotlib:**
+```python
+import matplotlib.pyplot as plt
+
+colors = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+          '#0072B2', '#D55E00', '#CC79A7', '#000000']
+plt.rcParams['axes.prop_cycle'] = plt.cycler(color=colors)
+```
+
+**Usage in Seaborn:**
+```python
+import seaborn as sns
+
+okabe_ito_palette = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+                      '#0072B2', '#D55E00', '#CC79A7']
+sns.set_palette(okabe_ito_palette)
+```
+
+**Usage in Plotly:**
+```python
+import plotly.graph_objects as go
+
+okabe_ito_plotly = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+                     '#0072B2', '#D55E00', '#CC79A7']
+fig = go.Figure()
+# Apply to discrete color scale
+```
+
+### Wong Palette (Alternative for Categories)
+
+Another excellent colorblind-friendly palette by Bang Wong (Nature Methods).
+
+```python
+wong_palette = {
+    'black': '#000000',
+    'orange': '#E69F00',
+    'sky_blue': '#56B4E9',
+    'green': '#009E73',
+    'yellow': '#F0E442',
+    'blue': '#0072B2',
+    'vermillion': '#D55E00',
+    'purple': '#CC79A7'
+}
+```
+
+### Paul Tol Palettes
+
+Paul Tol has designed multiple scientifically-optimized palettes for different use cases.
+
+**Bright Palette (up to 7 categories):**
+```python
+tol_bright = ['#4477AA', '#EE6677', '#228833', '#CCBB44',
+              '#66CCEE', '#AA3377', '#BBBBBB']
+```
+
+**Muted Palette (up to 9 categories):**
+```python
+tol_muted = ['#332288', '#88CCEE', '#44AA99', '#117733',
+             '#999933', '#DDCC77', '#CC6677', '#882255', '#AA4499']
+```
+
+**High Contrast (3 categories only):**
+```python
+tol_high_contrast = ['#004488', '#DDAA33', '#BB5566']
+```
+
+## Sequential Colormaps (Continuous Data)
+
+Sequential colormaps represent data from low to high values with a single hue.
+
+### Perceptually Uniform Colormaps
+
+These colormaps have uniform perceptual change across the color scale.
+
+**Viridis (default in Matplotlib):**
+- Colorblind-friendly
+- Prints well in grayscale
+- Perceptually uniform
+```python
+plt.imshow(data, cmap='viridis')
+```
+
+**Cividis:**
+- Optimized for colorblind viewers
+- Designed specifically for deuteranopia/protanopia
+```python
+plt.imshow(data, cmap='cividis')
+```
+
+**Plasma, Inferno, Magma:**
+- Perceptually uniform alternatives to viridis
+- Good for different aesthetic preferences
+```python
+plt.imshow(data, cmap='plasma')
+```
+
+### When to Use Sequential Maps
+- Heatmaps showing intensity
+- Geographic elevation data
+- Probability distributions
+- Any single-variable continuous data (low → high)
+
+## Diverging Colormaps (Negative to Positive)
+
+Diverging colormaps have a neutral middle color with two contrasting colors at extremes.
+
+### Colorblind-Safe Diverging Maps
+
+**RdYlBu (Red-Yellow-Blue):**
+```python
+plt.imshow(data, cmap='RdYlBu_r')  # _r reverses: blue (low) to red (high)
+```
+
+**PuOr (Purple-Orange):**
+- Excellent for colorblind viewers
+```python
+plt.imshow(data, cmap='PuOr')
+```
+
+**BrBG (Brown-Blue-Green):**
+- Good colorblind accessibility
+```python
+plt.imshow(data, cmap='BrBG')
+```
+
+### Avoid These Diverging Maps
+- **RdGn (Red-Green)**: Problematic for red-green colorblindness
+- **RdYlGn (Red-Yellow-Green)**: Same issue
+
+### When to Use Diverging Maps
+- Correlation matrices
+- Change/difference data (positive vs. negative)
+- Deviation from a central value
+- Temperature anomalies
+
+## Special Purpose Palettes
+
+### For Genomics/Bioinformatics
+
+**Sequence type identification:**
+```python
+# DNA/RNA bases
+nucleotide_colors = {
+    'A': '#00CC00',  # Green
+    'C': '#0000CC',  # Blue
+    'G': '#FFB300',  # Orange
+    'T': '#CC0000',  # Red
+    'U': '#CC0000'   # Red (RNA)
+}
+```
+
+**Gene expression:**
+- Use sequential colormaps (viridis, YlOrRd) for expression levels
+- Use diverging colormaps (RdBu) for log2 fold change
+
+### For Microscopy
+
+**Fluorescence channels:**
+```python
+# Traditional fluorophore colors (use with caution)
+fluorophore_colors = {
+    'DAPI': '#0000FF',      # Blue - DNA
+    'GFP': '#00FF00',       # Green (problematic for colorblind)
+    'RFP': '#FF0000',       # Red
+    'Cy5': '#FF00FF'        # Magenta
+}
+
+# Colorblind-friendly alternatives
+fluorophore_alt = {
+    'Channel1': '#0072B2',  # Blue
+    'Channel2': '#E69F00',  # Orange (instead of green)
+    'Channel3': '#D55E00',  # Vermillion
+    'Channel4': '#CC79A7'   # Magenta
+}
+```
+
+## Color Usage Best Practices
+
+### Categorical Data (Qualitative Color Schemes)
+
+**Do:**
+- Use distinct, saturated colors from Okabe-Ito or Wong palette
+- Limit to 7-8 categories max in one plot
+- Use consistent colors for same categories across figures
+- Add patterns/markers when colors alone might be insufficient
+
+**Don't:**
+- Use red/green combinations
+- Use rainbow (jet) colormap for categories
+- Use similar hues that are hard to distinguish
+
+### Continuous Data (Sequential/Diverging Schemes)
+
+**Do:**
+- Use perceptually uniform colormaps (viridis, plasma, cividis)
+- Choose diverging maps when data has meaningful center point
+- Include colorbar with labeled ticks
+- Test appearance in grayscale
+
+**Don't:**
+- Use rainbow (jet) colormap - not perceptually uniform
+- Use red-green diverging maps
+- Omit colorbar on heatmaps
+
+## Testing for Colorblind Accessibility
+
+### Online Simulators
+- **Coblis**: https://www.color-blindness.com/coblis-color-blindness-simulator/
+- **Color Oracle**: Free downloadable tool for Windows/Mac/Linux
+- **Sim Daltonism**: Mac application
+
+### Types of Color Vision Deficiency
+- **Deuteranopia** (~5% of males): Cannot distinguish green
+- **Protanopia** (~2% of males): Cannot distinguish red
+- **Tritanopia** (<1%): Cannot distinguish blue (rare)
+
+### Python Tools
+```python
+# Using colorspacious to simulate colorblind vision
+from colorspacious import cspace_convert
+
+def simulate_deuteranopia(image_rgb):
+    from colorspacious import cspace_convert
+    # Convert to colorblind simulation
+    # (Implementation would require colorspacious library)
+    pass
+```
+
+## Implementation Examples
+
+### Setting Global Matplotlib Style
+```python
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+
+# Set Okabe-Ito as default color cycle
+okabe_ito_colors = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+                     '#0072B2', '#D55E00', '#CC79A7']
+mpl.rcParams['axes.prop_cycle'] = mpl.cycler(color=okabe_ito_colors)
+
+# Set default colormap to viridis
+mpl.rcParams['image.cmap'] = 'viridis'
+```
+
+### Seaborn with Custom Palette
+```python
+import seaborn as sns
+
+# Set Paul Tol muted palette
+tol_muted = ['#332288', '#88CCEE', '#44AA99', '#117733',
+             '#999933', '#DDCC77', '#CC6677', '#882255', '#AA4499']
+sns.set_palette(tol_muted)
+
+# For heatmaps
+sns.heatmap(data, cmap='viridis', annot=True)
+```
+
+### Plotly with Discrete Colors
+```python
+import plotly.express as px
+
+# Use Okabe-Ito for categorical data
+okabe_ito_plotly = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+                     '#0072B2', '#D55E00', '#CC79A7']
+
+fig = px.scatter(df, x='x', y='y', color='category',
+                 color_discrete_sequence=okabe_ito_plotly)
+```
+
+## Grayscale Compatibility
+
+All figures should remain interpretable in grayscale. Test by converting to grayscale:
+
+```python
+# Convert figure to grayscale for testing
+fig.savefig('figure_gray.png', dpi=300, colormap='gray')
+```
+
+**Strategies for grayscale compatibility:**
+1. Use different line styles (solid, dashed, dotted)
+2. Use different marker shapes (circles, squares, triangles)
+3. Add hatching patterns to bars
+4. Ensure sufficient luminance contrast between colors
+
+## Color Spaces
+
+### RGB vs CMYK
+- **RGB** (Red, Green, Blue): For digital/screen display
+- **CMYK** (Cyan, Magenta, Yellow, Black): For print
+
+**Important:** Colors appear different in print vs. screen. When preparing for print:
+1. Convert to CMYK color space
+2. Check color appearance in CMYK preview
+3. Ensure sufficient contrast remains
+
+### Matplotlib Color Spaces
+```python
+# Save for print (CMYK)
+# Note: Direct CMYK support limited; use PDF and let publisher convert
+fig.savefig('figure.pdf', dpi=300)
+
+# For RGB (digital)
+fig.savefig('figure.png', dpi=300)
+```
+
+## Common Mistakes
+
+1. **Using jet/rainbow colormap**: Not perceptually uniform; avoid
+2. **Red-green combinations**: ~8% of males cannot distinguish
+3. **Too many colors**: More than 7-8 becomes difficult to distinguish
+4. **Inconsistent color meaning**: Same color should mean same thing across figures
+5. **Missing colorbar**: Always include for continuous data
+6. **Low contrast**: Ensure colors differ sufficiently
+7. **Relying solely on color**: Add texture, patterns, or markers
+
+## Resources
+
+- **ColorBrewer**: http://colorbrewer2.org/ - Choose palettes by colorblind-safe option
+- **Paul Tol's palettes**: https://personal.sron.nl/~pault/
+- **Okabe-Ito palette origin**: "Color Universal Design" (Okabe & Ito, 2008)
+- **Matplotlib colormaps**: https://matplotlib.org/stable/tutorials/colors/colormaps.html
+- **Seaborn palettes**: https://seaborn.pydata.org/tutorial/color_palettes.html

package/skills/scientific-visualization/references/journal_requirements.md

@@ -0,0 +1,320 @@
+# Journal-Specific Figure Requirements
+
+## Overview
+
+Different journals have specific technical requirements for figures. This reference compiles common requirements from major scientific publishers. **Always check the specific journal's author guidelines for the most current requirements.**
+
+## Nature Portfolio (Nature, Nature Methods, etc.)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: PDF, EPS, AI (preferred for graphs)
+  - Raster: TIFF, PNG (for images)
+  - Never: PowerPoint, Word, JPEG
+
+- **Resolution**:
+  - Line art: 1000-1200 DPI
+  - Combination (line art + images): 600 DPI
+  - Photographs/microscopy: 300 DPI minimum
+
+- **Color space**: RGB (Nature is digital-first)
+
+- **Dimensions**:
+  - Single column: 89 mm (3.5 inches)
+  - 1.5 column: 120 mm (4.7 inches)
+  - Double column: 183 mm (7.2 inches)
+  - Maximum height: 247 mm (9.7 inches)
+
+- **Fonts**:
+  - Arial or Helvetica (or similar sans-serif)
+  - Minimum 5-7 pt at final size
+  - Embed all fonts in PDF/EPS
+
+### Nature Specific Guidelines
+- Panel labels: a, b, c (lowercase, bold) in top-left corner
+- Scale bars required for microscopy images
+- Gel images: Include molecular weight markers
+- Cropping: Indicate with line breaks
+- Statistics: Mark significance; define symbols in legend
+- Source data: Required for all graphs
+
+### File Naming
+Format: `FirstAuthorLastName_FigureNumber.ext`
+Example: `Smith_Fig1.pdf`
+
+## Science (AAAS)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: EPS, PDF (preferred)
+  - Raster: TIFF
+  - Acceptable: AI, PSD (Photoshop)
+
+- **Resolution**:
+  - Line art: 1000 DPI minimum
+  - Photographs: 300 DPI minimum
+  - Combination: 600 DPI minimum
+
+- **Color space**: RGB
+
+- **Dimensions**:
+  - Single column: 5.5 cm (2.17 inches)
+  - 1.5 column: 12 cm (4.72 inches)
+  - Full width: 17.5 cm (6.89 inches)
+  - Maximum height: 23.3 cm (9.17 inches)
+
+- **Fonts**:
+  - Helvetica (or Arial)
+  - 6-8 pt minimum at final size
+  - Consistent across all figures
+
+### Science Specific Guidelines
+- Panel labels: (A), (B), (C) in parentheses
+- Minimal text within figures (details in caption)
+- High contrast for web and print
+- Error bars required; define in caption
+- Avoid excessive whitespace
+
+### File Naming
+Format: `Manuscript#_Fig#.ext`
+Example: `abn1234_Fig1.eps`
+
+## Cell Press (Cell, Neuron, Molecular Cell, etc.)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: PDF, EPS (preferred for graphs/diagrams)
+  - Raster: TIFF (for photographs)
+
+- **Resolution**:
+  - Line art: 1000 DPI
+  - Photographs: 300 DPI
+  - Combination: 600 DPI
+
+- **Color space**: RGB
+
+- **Dimensions**:
+  - Single column: 85 mm (3.35 inches)
+  - Double column: 178 mm (7.01 inches)
+  - Maximum height: 230 mm (9.06 inches)
+
+- **Fonts**:
+  - Arial or Helvetica only
+  - 8-12 pt for axis labels
+  - 6-8 pt for tick labels
+
+### Cell Press Specific Guidelines
+- Panel labels: (A), (B), (C) or A, B, C in top-left
+- Related panels should match in size
+- Scale bars mandatory for microscopy
+- Western blots: Include molecular weight markers
+- Arrows/arrowheads: 2 pt minimum width
+- Line widths: 1-2 pt for data
+
+## PLOS (Public Library of Science)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: EPS, PDF (preferred)
+  - Raster: TIFF, PNG
+  - TIFF with LZW compression acceptable
+
+- **Resolution**:
+  - Minimum 300 DPI at final size (all figure types)
+  - 600 DPI preferred for line art
+
+- **Color space**: RGB
+
+- **Dimensions**:
+  - Single column: 8.3 cm (3.27 inches)
+  - 1.5 column: 11.4 cm (4.49 inches)
+  - Double column: 17.3 cm (6.81 inches)
+  - Maximum height: 23.3 cm (9.17 inches)
+
+- **Fonts**:
+  - Sans-serif preferred (Arial, Helvetica)
+  - 8-12 pt for labels at final size
+
+### PLOS Specific Guidelines
+- Figures should be understandable without caption
+- Color required only if adding information
+- All figures convertible to grayscale
+- Panel labels optional but recommended
+- Open access: Figures must be CC-BY licensed
+- Source data files encouraged
+
+## ACS (American Chemical Society)
+
+### Technical Specifications
+- **File formats**:
+  - Preferred: TIFF, PDF, EPS
+  - Application files: AI, CDX (ChemDraw), CDL
+  - Acceptable: PNG (not for publication)
+
+- **Resolution**:
+  - Minimum 300 DPI at final size
+  - 600 DPI for line art and chemical structures
+  - 1200 DPI for detailed structures
+
+- **Color space**: RGB or CMYK (check specific journal)
+
+- **Dimensions**:
+  - Single column: 3.25 inches (8.25 cm)
+  - Double column: 7 inches (17.78 cm)
+
+- **Fonts**:
+  - Embedded fonts required
+  - Consistent sizing across figures
+
+### ACS Specific Guidelines
+- Chemical structures: Use ChemDraw or equivalent
+- Atom labels: 10-12 pt
+- Bond thickness: 2 pt
+- Panel labels: Lowercase bold (a, b, c)
+- High contrast required (many ACS journals grayscale print)
+
+## Elsevier Journals (varies by journal)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: EPS, PDF
+  - Raster: TIFF, JPEG (only for photographs)
+
+- **Resolution**:
+  - Line art: 1000 DPI minimum
+  - Photographs: 300 DPI minimum
+  - Combination: 600 DPI minimum
+
+- **Color space**: RGB (for online); CMYK (for print journals)
+
+- **Dimensions**: Vary by journal
+  - Common single column: 90 mm
+  - Common double column: 190 mm
+
+- **Fonts**:
+  - Preferred: Arial, Times, Symbol
+  - Minimum 6 pt at final size
+
+### Elsevier Specific Guidelines
+- Check individual journal guidelines (highly variable)
+- Some journals charge for color in print
+- Panel labels typically (A), (B), (C) or A, B, C
+- Graphical abstract often required (separate from figures)
+
+## IEEE (Engineering/Computer Science)
+
+### Technical Specifications
+- **File formats**:
+  - Vector: PDF, EPS (preferred)
+  - Raster: TIFF, PNG
+
+- **Resolution**:
+  - Photographs/graphics: 300 DPI minimum at final size
+  - Line art: 600 DPI minimum
+
+- **Color space**: RGB (online); CMYK (print)
+
+- **Dimensions**:
+  - Single column: 3.5 inches (8.9 cm)
+  - Double column: 7.16 inches (18.2 cm)
+
+- **Fonts**:
+  - Sans-serif preferred
+  - Minimum 8-10 pt at final size
+
+### IEEE Specific Guidelines
+- Figures should be readable in black and white
+- Color figures incur no charge (online publication)
+- Panel labels: (a), (b), (c) in lowercase
+- Captions below figures (not on separate page)
+- Use IEEE graphics checker tool before submission
+
+## BMC (BioMed Central) - Open Access
+
+### Technical Specifications
+- **File formats**:
+  - Any standard format accepted
+  - Preferred: TIFF, PDF, EPS, PNG
+
+- **Resolution**:
+  - Minimum 600 DPI for line art
+  - Minimum 300 DPI for photographs
+
+- **Color space**: RGB
+
+- **Dimensions**:
+  - Flexible, but consider readability
+  - Maximum width typically 140 mm
+
+- **Fonts**:
+  - Embedded and readable
+
+### BMC Specific Guidelines
+- Open access: CC-BY license required
+- Figure files uploaded separately
+- Panel labels as appropriate for field
+- Source data encouraged
+- Accessibility important (colorblind-friendly)
+
+## Common Requirements Across Journals
+
+### Universal Best Practices
+1. **Never use JPEG for graphs/plots**: Compression artifacts
+2. **Embed all fonts**: In PDF/EPS files
+3. **Layer structure**: Flatten images (merge layers in Photoshop)
+4. **RGB vs CMYK**: Most journals now RGB (digital-first)
+5. **High resolution**: Always better to start high, reduce if needed
+6. **Consistency**: Same style across all figures in manuscript
+7. **File size**: Balance quality with reasonable file sizes (typically <10 MB per figure)
+
+### Submitting Figures
+- **Initial submission**: Lower resolution often acceptable (for review)
+- **Revision/acceptance**: High-resolution required
+- **Separate files**: Each figure as separate file
+- **File naming**: Clear, systematic naming
+- **Supporting information**: May have different requirements
+
+## Quick Reference Table
+
+| Publisher | Single Column | Double Column | Min DPI (photos) | Min DPI (line art) | Preferred Format |
+|-----------|---------------|---------------|------------------|-------------------|------------------|
+| Nature | 89 mm | 183 mm | 300 | 1000 | EPS, PDF |
+| Science | 5.5 cm | 17.5 cm | 300 | 1000 | EPS, PDF |
+| Cell Press | 85 mm | 178 mm | 300 | 1000 | EPS, PDF |
+| PLOS | 8.3 cm | 17.3 cm | 300 | 600 | EPS, TIFF |
+| ACS | 3.25 in | 7 in | 300 | 600 | TIFF, EPS |
+
+## Checking Requirements
+
+### Before Submission Checklist
+1. Read journal's author guidelines (figure section)
+2. Check file format requirements
+3. Verify resolution requirements
+4. Confirm size specifications (width × height)
+5. Check font requirements
+6. Verify color space (RGB vs CMYK)
+7. Check panel labeling style
+8. Review supplementary materials requirements
+9. Confirm file naming conventions
+10. Check file size limits
+
+### Useful Tools
+- **ImageJ/Fiji**: Check/adjust DPI
+- **Adobe Acrobat**: Verify embedded fonts, check PDF properties
+- **GIMP**: Free alternative to Photoshop for raster editing
+- **Inkscape**: Free vector graphics editor
+
+## Resources
+
+- **Journal websites**: Always check "Author Guidelines" or "Instructions for Authors"
+- **Publisher resources**: Many provide templates and tools
+- **Format conversion**: Use reputable tools; check output quality
+- **Help desks**: Contact journal staff if unclear
+
+## Notes
+
+- Requirements change periodically - always verify current guidelines
+- Preprint servers (bioRxiv, arXiv) often have different requirements
+- Conference proceedings may have separate requirements
+- Some journals offer figure preparation services (often paid)
+- Supplementary figures may have relaxed requirements compared to main text figures