sprime 0.1.0__tar.gz

sprime-0.1.0/.github/workflows/deploy-api-docs.yml

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+# Build pdoc API docs and deploy to GitHub Pages (single copy).
+# Updates on push to main or tag push (v*). No versioned paths.
+# Pages: https://mocomakers.github.io/sprime/
+
+name: Deploy API docs
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*"]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install package and pdoc3
+        run: |
+          python -m pip install -U pip
+          pip install -e .
+          pip install pdoc3
+
+      - name: Build API docs
+        run: pdoc --html --output-dir build sprime
+        # Output: build/sprime/ (not pdoc_html). pdoc_html is for local preview only.
+
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: build/sprime
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

sprime-0.1.0/.github/workflows/publish-pypi.yml

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+# Publish sprime to PyPI when a GitHub Release is published.
+# Uses Trusted Publishing (OIDC): no API token needed.
+# Setup: Add a pending publisher at https://pypi.org/manage/account/publishing/
+#   (owner/repo, workflow publish-pypi.yml, environment pypi).
+# See: https://docs.pypi.org/trusted-publishers/
+#      https://github.com/pypa/gh-action-pypi-publish
+
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi-publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sprime
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

sprime-0.1.0/.gitignore

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+__pycache__/
+docs/temp-docs-for-ai/
+venv/
+.pytest_cache/
+delta_s_prime_table.csv
+master_s_prime_table.csv
+.cursor/
+src/sprime/_version.py
+
+# Build and distribution
+dist/
+build/
+*.egg-info/
+*.egg
+
+# Coverage
+htmlcov/
+.coverage

sprime-0.1.0/.pre-commit-config.yaml

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+# Optional: run `pre-commit install` to rebuild and stage pdoc_html before each commit
+# when Python sources change. Requires: pip install -e ".[dev]"
+
+repos:
+  - repo: local
+    hooks:
+      - id: pdoc
+        name: Build pdoc HTML (pdoc_html) and stage for commit
+        entry: python scripts/build_docs_precommit.py
+        language: system
+        pass_filenames: false
+        files: \.py$

sprime-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 MoCo Maker Labs LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+

sprime-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sprime
+Version: 0.1.0
+Summary: A biomedical library for screening high-throughput screening data in preclinical drug studies
+Project-URL: Homepage, https://github.com/mocomakers/sprime
+Project-URL: Documentation, https://github.com/mocomakers/sprime#readme
+Project-URL: Repository, https://github.com/mocomakers/sprime
+Project-URL: Issues, https://github.com/mocomakers/sprime/issues
+Author-email: Matthew Zamora <matt@mocomakers.com>
+License: MIT
+License-File: LICENSE
+Keywords: biomedical,drug-screening,high-throughput-screening,preclinical
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.8
+Requires-Dist: numpy<3.0,>=1.20.0
+Requires-Dist: scipy>=1.7.0
+Provides-Extra: dev
+Requires-Dist: pdoc3; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# sprime
+
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Development Status](https://img.shields.io/badge/status-alpha-orange)](https://github.com/MoCoMakers/sprime)
+
+**sprime** (S' or S prime) is a Python library for analyzing quantitative high-throughput screening (qHTS) data in preclinical drug discovery studies. The library provides tools for processing dose-response curves, fitting Hill equations, and calculating S' values—a single metric that summarizes a drug's dose-response profile relative to a cell line and assay.
+
+## Overview
+
+sprime enables researchers to:
+
+- **Process qHTS data**: Load and analyze dose-response data from screening campaigns
+- **Fit Hill curves**: Automatically fit four-parameter logistic (4PL) models to dose-response data
+- **Calculate S' values**: Compute S' (S prime) metrics that combine potency and efficacy into a single score
+- **Compare cell lines**: Use delta S' (ΔS') to identify compounds with selective activity between reference and test cell lines
+- **Rank compounds**: Systematically prioritize drug candidates based on their dose-response profiles
+
+## About S' (S Prime)
+
+S' is a single value score that summarizes a drug's dose-response curve. The metric is calculated from Hill curve parameters using the formula:
+
+**S' = asinh((Upper - Lower) / EC50)**
+
+This is equivalent to:
+
+$$S' = \ln\left(\frac{\text{Upper} - \text{Lower}}{\text{EC50}} + \sqrt{\left(\frac{\text{Upper} - \text{Lower}}{\text{EC50}}\right)^2 + 1}\right)$$
+
+Where:
+- **Upper** = Upper asymptote of the dose-response curve
+- **Lower** = Lower asymptote of the dose-response curve  
+- **EC50** = Half-maximal effect concentration
+
+Higher S' values indicate stronger drug responses (higher efficacy and/or potency). See [Background and Concepts](docs/background_and_concepts.md#the-s-s-prime-metric) for detailed information.
+
+### Delta S' and Comparative Analysis
+
+**Delta S'** (ΔS') enables quantitative comparison of drug responses between different cell lines within a single assay:
+
+**ΔS' = S'(reference cell line) - S'(test cell line)**
+
+This metric allows researchers to:
+- Compare drug effects across cell lines
+- Rank compounds by selectivity
+- Prioritize drug candidates for further investigation
+
+For detailed information and examples, see [Delta S' for Comparative Analysis](docs/background_and_concepts.md#delta-s-for-comparative-analysis).
+
+This library implements **Generation 2** of the S' methodology, which evolved from the original S metric. See the [Citation](#citation) section below for references.
+
+## Installation
+
+### Requirements
+
+- Python 3.8 or higher
+- numpy >= 1.20.0, < 3.0
+- scipy >= 1.7.0
+
+### Install from PyPI
+
+```bash
+pip install sprime
+```
+
+### Install from Source
+
+For development or to get the latest version:
+
+```bash
+# Clone the repository
+git clone https://github.com/MoCoMakers/sprime.git
+cd sprime
+
+# Install in editable mode
+pip install -e .
+
+# Or install with development dependencies
+pip install -e ".[dev]"
+```
+
+### Development Setup
+
+To set up a development environment:
+
+```bash
+git clone https://github.com/MoCoMakers/sprime.git
+cd sprime
+python -m venv venv
+source venv/bin/activate   # Windows: venv\Scripts\activate
+pip install -e ".[dev]"
+pytest tests/
+pre-commit install        # optional: rebuild + stage pdoc_html on commit when .py changes
+```
+
+See **[Development guide](docs/development.md)** for full setup, pre-commit, API docs, and CI.
+
+## Quick Start
+
+The basic workflow in sprime is: **Load** raw data from CSV → **Process** (fit curves, calculate S') → **Analyze** (e.g. delta S' for comparative analysis).
+
+**Three ways to load data:**
+
+| Path | `values_as` | Your data | Required columns | What sprime does |
+|------|-------------|-----------|------------------|------------------|
+| **A — Raw (columns)** | `"columns"` | `DATA0`..`DATAN`, `CONC0`..`CONCN` (one column per value) | `Cell_Line`, `Compound_ID`, `Concentration_Units` | Fits Hill equation coefficients and stats → AC50, Upper, Lower, Hill Slope, r² → S' |
+| **A — Raw (list)** | `"list"` | `Responses`, `Concentrations` (comma-separated in one cell each) | `Cell_Line`, `Compound_ID`, `Concentration_Units` | Same as above |
+| **B — Pre-calculated** | N/A | `AC50`, `Upper`, `Lower` (optional: Hill Slope, r2, S', etc.) | `Cell_Line`, `Compound_ID` | Uses params as-is; always computes S' (warns if S' was provided) |
+
+Use **Path A (columns)** by default (`values_as="columns"`). Use **Path A (list)** with `sp.load(..., values_as="list")` when your data has `Responses` and `Concentrations` as comma-separated values. For list format, if the CSV is comma-delimited, quote those cells (e.g. `"4000,300,2"`). Any non-reserved columns in your CSV (e.g. MOA, assay_timescale) propagate forward by default into S' output and the master CSV export.
+
+### Path A — Raw data
+
+**Templates:** [template_raw.csv](https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/template_raw.csv) (columns), [template_raw_list.csv](https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/template_raw_list.csv) (list). See [Required headings](#required-headings) below.
+
+The **load** call changes with format; **process** does not. You must pass `values_as="columns"` (default) or `values_as="list"` — format is not auto-detected from headings.
+
+Run from the directory containing the demo CSVs (e.g. `docs/usage/`), or use paths like `docs/usage/demo_data_s_prime.csv`.
+
+**Option 1 — Columns** (DATA0..N, CONC0..N)
+
+```python
+from sprime import SPrime as sp
+
+# Download (columns), then save locally:
+# https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_s_prime.csv
+# https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_delta.csv
+# Demo files include both raw DATA/CONC and pre-calc params; refit from raw.
+
+raw_data, _ = sp.load("demo_data_s_prime.csv", values_as="columns")
+screening_data, _ = sp.process(raw_data, allow_overwrite_hill_coefficients=True)
+screening_data.export_to_csv("master_s_prime_table.csv")
+results = screening_data.to_dict_list()
+for profile in results:
+    print(f"{profile['compound_name']} vs {profile['cell_line']}: S' = {profile['s_prime']:.2f}")
+```
+
+**Option 2 — List** (Responses, Concentrations as comma-separated per cell)
+
+```python
+from sprime import SPrime as sp
+
+# Download (list), then save locally:
+# https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_raw_list.csv
+
+raw_data, _ = sp.load("demo_data_raw_list.csv", values_as="list")
+screening_data, _ = sp.process(raw_data)
+screening_data.export_to_csv("master_s_prime_table.csv")
+results = screening_data.to_dict_list()
+for profile in results:
+    print(f"{profile['compound_name']} vs {profile['cell_line']}: S' = {profile['s_prime']:.2f}")
+```
+
+### Path B — Pre-calculated
+
+**Sample file:** [demo_data_precalc.csv](https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_precalc.csv)  
+**Template:** [template_precalc.csv](https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/template_precalc.csv)
+
+```python
+from sprime import SPrime as sp
+
+# Download, then save locally:
+# https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_precalc.csv
+
+raw_data, _ = sp.load("demo_data_precalc.csv")
+screening_data, _ = sp.process(raw_data)
+screening_data.export_to_csv("master_s_prime_table.csv")
+results = screening_data.to_dict_list()
+for profile in results:
+    print(f"{profile['compound_name']} vs {profile['cell_line']}: S' = {profile['s_prime']:.2f}")
+```
+
+### Delta S' example
+
+Compare drug responses between reference and test cell lines (e.g. non-tumor vs tumor). Delta S' = S'(reference) − S'(test); more negative = more effective in test tissue.
+
+**Demo CSV (two cell lines):** [demo_data_delta.csv](https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_delta.csv)
+
+```python
+from sprime import SPrime as sp, ScreeningDataset
+
+# Download, then save locally:
+# https://raw.githubusercontent.com/MoCoMakers/sprime/refs/heads/main/docs/usage/demo_data_delta.csv
+
+raw_data, _ = sp.load("demo_data_delta.csv", values_as="columns")
+screening_data, _ = sp.process(raw_data, allow_overwrite_hill_coefficients=True)
+screening_data.export_to_csv("master_s_prime_table.csv")
+
+delta_results = screening_data.calculate_delta_s_prime(
+    reference_cell_lines=["ipnf05.5 mc"],   # e.g. non-tumor; list supports multiple
+    test_cell_lines=["ipNF96.11C"]          # e.g. tumor; list supports multiple
+)
+# Opt-in: add compound-level columns (1:1 in ref & test) to delta output and export:
+#   headings_one_to_one_in_ref_and_test=["assay_timescale"],  # etc.
+#   source_profile="test",   # "ref" or "test" — which profile to use for those values
+# Pass the same list to export_delta_s_prime_to_csv(..., headings_one_to_one_in_ref_and_test=[...])
+ScreeningDataset.export_delta_s_prime_to_csv(delta_results, "delta_s_prime_table.csv")
+
+for ref_cl, comparisons in delta_results.items():
+    for c in comparisons:
+        print(f"{c['compound_name']}: Delta S' = {c['delta_s_prime']:.2f}")
+```
+
+### Required headings
+
+- **All paths:** `Cell_Line`; and `Compound_ID`. (`NCGCID` is optional pass-through per compound.)
+- **Path A (raw):** **`Concentration_Units`** (required). Either **(columns)** `DATA0`..`DATA N`, `CONC0`..`CONC N` (same N), or **(list)** `Responses` and `Concentrations` (comma-separated values in one cell each). Use `values_as="columns"` (default) or `values_as="list"`. See [Supported concentration units](#supported-concentration-units) below.
+- **Path B (pre-calc):** `AC50` (or `ec50`), `Upper` (or `Infinity`), `Lower` (or `Zero`). Optional: `Hill_Slope`, `r2`, `S'`.
+
+Template files list the exact headers (required columns first); your CSV should match those. Column order in the file does not matter—matching is by header name only.
+
+### Supported concentration units
+
+For Path A (raw), `Concentration_Units` must be present. All values are converted to **microM** internally. Supported units (case-insensitive), smallest to largest: **fM** (`fm`, `femtom`); **pM** (`pm`, `picom`); **nM** (`nm`, `nanom`); **microM** (`µM`, `um`, `microm`, `micro`); **mM** (`mm`, `millim`); **M** (`m`, `mol`).
+
+### Next steps
+
+- **Format details:** [Basic Usage Guide](docs/usage/basic_usage_guide.md)
+- **Run all scenarios:** [Demo](docs/usage/demo.py)
+- **Individual profiles & pre-calculated parameters:** [Basic Usage Guide](docs/usage/basic_usage_guide.md) (*Processing Individual Profiles*, *Creating dose-response profiles from scratch*, *Working with Pre-calculated Hill Parameters*)
+
+## Key Features
+
+- **Automatic Curve Fitting**: Fits four-parameter logistic (Hill) curves to dose-response data
+- **Flexible Input**: Supports raw dose-response data or pre-calculated Hill parameters. When both exist, use `allow_overwrite_hill_coefficients=True` to refit from raw; overwrites are logged as warnings.
+- **CSV Loading**: Handles common screening data formats; rows are literal (empty = null, no forward-filling)
+- **Delta S' Analysis**: Compare drug responses across cell lines within a single assay
+- **CSV Export**: Built-in methods to export results and delta S' comparisons to CSV
+- **In-Memory Processing**: Process data directly from list of dictionaries without CSV files
+- **Metadata Support**: Extracts and preserves metadata (MOA, drug targets) from CSV files
+- **Type-Safe**: Uses Python dataclasses and type hints throughout
+- **Comprehensive Documentation**: Includes guides for users and detailed technical documentation
+
+## Documentation
+
+### Getting Started
+
+- **[API Reference](https://mocomakers.github.io/sprime/)** - API documentation (generated from docstrings)
+- **[Basic Usage Guide](docs/usage/basic_usage_guide.md)** - Comprehensive step-by-step guide to using sprime with your data, including advanced usage patterns and testing
+
+### Core Concepts
+
+- **[Background and Concepts](docs/background_and_concepts.md)** - Introduction to qHTS, assays, S' metric, and key terminology
+- **[Understanding 4PL Dose-Response Curves](docs/README_4PL_Dose_Response.md)** - Detailed explanation of the Hill equation model
+
+### Technical Documentation
+
+- **[Hill Curve Fitting Configuration](docs/usage/hill_curve_fitting_configuration.md)** - Technical details on curve fitting parameters and configuration options
+- **[Development guide](docs/development.md)** - Dev setup, tests, pre-commit, API docs, CI (for contributors)
+
+### Examples
+
+- **[Demo Script](docs/usage/demo.py)** - Consolidated demo: S' only (raw -> Hill -> S'), pre-calc only (bypass raw data), and Delta S' (raw -> Hill -> S' -> delta, export tables)
+
+## Requirements
+
+### Runtime Dependencies
+
+- **numpy** >= 1.20.0, < 3.0 - Numerical computing (compatible with numpy 1.x and 2.x)
+- **scipy** >= 1.7.0 - Scientific computing and curve fitting
+
+### Development Dependencies
+
+Development dependencies are optional and only needed if you plan to contribute to sprime or run the test suite:
+
+- **pytest** >= 7.0.0 - Testing framework for running the comprehensive test suite
+  - Used to execute unit tests, integration tests, and edge case tests
+  - Provides test discovery, fixtures, and assertion utilities
+  - Required for: `pytest tests/` commands
+
+- **pytest-cov** >= 4.0.0 - Coverage reporting plugin for pytest
+  - Generates code coverage reports to identify untested code
+  - Used with: `pytest --cov=src/sprime --cov-report=html`
+  - Helps ensure comprehensive test coverage during development
+
+- **pdoc3** - Generates API docs from docstrings into `pdoc_html/`
+- **pre-commit** - Optional; rebuilds `pdoc_html` before each commit when `.py` files change
+
+**Install development dependencies:**
+```bash
+pip install -e ".[dev]"
+```
+
+These dependencies are not required for normal usage of sprime - only for development and testing.
+
+## Testing
+
+sprime includes a comprehensive test suite. To run tests:
+
+```bash
+# Install development dependencies
+pip install -e ".[dev]"
+
+# Run all tests
+pytest tests/
+
+# Run with coverage
+pytest tests/ --cov=src/sprime --cov-report=html
+
+# Run specific test files
+pytest tests/test_sprime.py
+pytest tests/test_hill_fitting.py
+pytest tests/test_integration.py
+```
+
+See the [Basic Usage Guide](docs/usage/basic_usage_guide.md#running-the-test-suite) for more testing information.
+
+### API docs (pdoc_html)
+
+API docs live in `pdoc_html/` in the repo and are built from docstrings. The [API Reference](https://mocomakers.github.io/sprime/) on GitHub Pages is deployed from CI. Build locally: `python -m pdoc --html --output-dir pdoc_html --force sprime`. Optional: `pre-commit install` rebuilds and stages `pdoc_html` on commit when `.py` files change. See [Development guide](docs/development.md) for details.
+
+## Project Status
+
+This project is currently in **active development** (Alpha status). Features and API may change.
+
+### Current Version
+
+The package uses semantic versioning. Version is derived from **Git tags** (via [hatch-vcs](https://github.com/ofek/hatch-vcs)); `src/sprime/_version.py` is generated at build/install time and is not committed. Check the installed version:
+
+```python
+import sprime
+print(sprime.__version__)
+```
+
+**Tagging releases:** Create a Git tag (e.g. `v0.1.0`) and push it. The version used in built packages and on PyPI comes from that tag.
+
+```bash
+git tag v0.1.0
+git push origin v0.1.0
+```
+
+## Contributing
+
+Contributions are welcome! We appreciate your help in making sprime better.
+
+### How to Contribute
+
+1. **Fork the repository** on GitHub
+2. **Create a feature branch** (`git checkout -b feature/amazing-feature`)
+3. **Set up dev environment** — venv, `pip install -e ".[dev]"`, `pytest tests/`, optionally `pre-commit install`. See [Development guide](docs/development.md).
+4. **Make your changes** and add tests if applicable
+5. **Run the test suite** — `pytest tests/`
+6. **Commit your changes** (`git commit -m 'Add amazing feature'`). If you use pre-commit, the pdoc hook will rebuild and stage `pdoc_html` when you change `.py` files.
+7. **Push to the branch** (`git push origin feature/amazing-feature`)
+8. **Open a Pull Request**
+
+### Development Guidelines
+
+- Follow PEP 8 style guidelines
+- Add tests for new features
+- Update documentation as needed
+- Ensure all tests pass before submitting
+
+### Reporting Issues
+
+If you find a bug or have a feature request, please open an issue on GitHub:
+- [Issue Tracker](https://github.com/MoCoMakers/sprime/issues)
+
+### Questions
+
+For questions or support, please reach out via:
+- [MoCo Makers Contact](https://www.mocomakers.com/contact/)
+- Open a GitHub Discussion
+
+## Repository
+
+- **GitHub**: [https://github.com/MoCoMakers/sprime](https://github.com/MoCoMakers/sprime)
+- **Issues**: [https://github.com/MoCoMakers/sprime/issues](https://github.com/MoCoMakers/sprime/issues)
+
+## Citation
+
+If you use sprime in your research, please cite:
+
+### Generation 2 (S') Methodology
+
+New citations introducing Generation 2 (S') are forthcoming. Please check back for updated citation information.
+
+### Original S Metric
+
+This library implements **Generation 2** of the S' methodology, which evolved from the original S metric described in:
+
+> Zamora PO, Altay G, Santamaria U, Dwarshuis N, Donthi H, Moon CI, Bakalar D, Zamora M. Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency. *Cancers (Basel)*. 2023 Dec 12;15(24):5811. doi: [10.3390/cancers15245811](https://doi.org/10.3390/cancers15245811). PMID: 38136356; PMCID: PMC10742026.
+
+### Hill Curve Fitting Implementation
+
+The Hill curve fitting implementation in sprime is inspired by the four parameter logistic regression work by Giuseppe Cardillo:
+
+> Giuseppe Cardillo (2025). Four parameters logistic regression - There and back again (https://github.com/dnafinder/logistic4), GitHub. Retrieved December 24, 2025
+
+## Acknowledgments
+
+This library was developed by the **Computational Biology Working Group** at [DMV Petri Dish](https://compbio.dmvpetridish.com/) with support from the nonprofit [DMV Petri Dish](https://www.dmvpetridish.com/). 
+
+We're also part of the DIY tech/science community at [MoCo Makers](https://www.mocomakers.com/).
+
+## License
+
+This project is licensed under the **MIT License** - see the [LICENSE](LICENSE) file for details.
+
+Copyright (C) 2026 MoCo Maker Labs LLC
+
+## Support
+
+- **Documentation**: See the [docs](docs/) directory for comprehensive guides
+- **Issues**: Report bugs or request features on [GitHub Issues](https://github.com/MoCoMakers/sprime/issues)
+- **Contact**: Reach out via [MoCo Makers Contact](https://www.mocomakers.com/contact/)
+
+## Related Projects
+
+- [DMV Petri Dish Computational Biology](https://compbio.dmvpetridish.com/) - Computational biology research group
+- [MoCo Makers](https://www.mocomakers.com/) - DIY tech/science community