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haeussma committed Feb 6, 2024
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23 changes: 23 additions & 0 deletions .github/workflows/mkdocs.yml
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name: Deploy MkDocs

on:
push:
branches:
- docs

jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.x'

- name: Install dependencies
run: pip install mkdocs

- name: Build and deploy
run: mkdocs gh-deploy --force
12 changes: 12 additions & 0 deletions docs/about.md
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# What is MTPHandler

MTPHandler is a tool for managing and processing data from microtiter plates. Central to this tool is the `Plate` object, which provides comprehensive methods for manipulating chemical species within microtiter plates. This includes the addition and removal of species, assigning them to individual wells, and setting initial concentrations of reaction components.

Key Features of MTPHandler:

- __Parser functions__: Features a custom parser for different plate readers such as SpectraMax, Megellan, and MultiScan photometers, allowing for the mapping of raw TXT file data into the `Plate` data model. More photometers will be supported in the future.
- __Adaptive Data Processing__: Automatically adapts and blanks measurement data based on initial conditions set for each well.
- __Data Integration__: Incorporates additional data like pH and reaction temperature into the Plate object, which is not present in the photometer's TXT file.
- __Enhanced Object Definitions__: Utilizes Reactant and Protein objects, akin to those in EnzymeML Documents, complete with Systems Biology Ontology (SBO) annotations.
- __Versatile Experimental Applications__: Separately treats wells with and without protein species, facilitating both calibration (for creating standard curves) and reaction analysis.
- __EnzymeML Integration__: Maps well data to the EnzymeML data model using the specified conditions of the `Well` objects.
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20 changes: 20 additions & 0 deletions docs/index.md
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# MTPHandler

## ⚡️ Quick Start

To install MTPHandler, run the following command:

```bash
pip install git+https://github.com/pi/pa/po.git
```

```python
from MTPHandler import Plate
from MTPHandler.parsers import SpectraMaxParser

# Create a Plate object
plate = Plate.parse(SpectraMaxParser, "path/to/your/data.txt", ph=7.3)

# Visualize the plate
plate.visualize()
```
55 changes: 55 additions & 0 deletions mkdocs.yml
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site_name: MTPHandler
description: A simple tool to manage MTP data
theme:
name: 'material'
logo: 'images/MTPHandler_logo.png'

nav:
- Home: index.md
- About: about.md

markdown_extensions:
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- admonition
- attr_list
- codehilite:
guess_lang: true
use_pygments: true
- def_list
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user: squidfunk
repo: mkdocs-material
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custom_checkbox: true
clickable_checkbox: true
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toc_depth: 4
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