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| # MTPHandler - Tool for Microtiter Plate Data Handling | ||
| # MTPHandler | ||
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| [](https://fairchemistry.github.io/MTPHandler/) | ||
| [](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml) | ||
| [](https://badge.fury.io/py/mtphandler) | ||
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| ## ℹ️ Overview | ||
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| `mtphandler` is a tool for managing and processing data from microtiter plates. It allows to directly read in the output files of various photometers, enabling low friction data processing. The tool facilitates a workflow for reading in raw data, assigning molecules with their respective concentration and and unit to wells. Furthermore, wells for creating a standard curve can be automatically detected and applied to different calibration models, which can be used to calculate the concentration of unknown samples. Finally, the plate data can be transformed into time-course concentration data in the EnzymeML format for subsequent analysis of the concentration data. | ||
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| ``` mermaid | ||
| graph LR | ||
| AP[🧪 Plate Reader] --> A[📄 Output File]; | ||
| style AP fill:transparent,stroke:#000,stroke-width:2px; | ||
| A -->|read| B{MTPHandler} | ||
| style B stroke-width:4px | ||
| subgraph in Jupyter Notebook | ||
| subgraph with MTPHandler | ||
| B --> B1[Enrich Data with Metadata] | ||
| B1 --> B2[Blank Data] | ||
| B2 --> B3[Create and Apply Calibration Models] | ||
| B3 --> B | ||
| style B1 stroke-dasharray: 5, 5 | ||
| style B2 stroke-dasharray: 5, 5 | ||
| style B3 stroke-dasharray: 5, 5 | ||
| end | ||
| B -->|convert| G[📄 EnzymeML time-course Data] | ||
| G <-.-> H[📊 Data Science and Insights] | ||
| style H stroke-dasharray: 5, 5,fill:transparent | ||
| end | ||
| G -->|export| I[📄 EnzymeML File] | ||
| ``` | ||
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| ## 🛤 What is MTPHandler? | ||
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| 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 | ||
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| Key Features of MTPHandler: | ||
| - **🚀 Parser Functions** | ||
| Features a custom parser for various plate readers, enabling low-fricton data processing. | ||
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| - __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. | ||
| - **🌟 Enrich measured data with metadata** | ||
| Assigns molecules with their respective concentration and unit to wells, capturing the experimental context of each well. | ||
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| ## ⚡️ Quick Start | ||
| - **⚙️ Adaptive Data Processing** | ||
| Automatically adapts and blanks measurement data based on initial conditions set for each well. Treats wells without protein as calibration data and wells with protein as reaction data. | ||
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| Get started with CaliPytion by cloning this repository: | ||
| - **🌐 FAIR Data** | ||
| Maps well data to the standardized EnzymeML format, yielding time-course data with metadata for further analysis. | ||
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| ```Bash | ||
| git clone https://github.com/FAIRChemistry/MTPHandler/ | ||
| ## 🔬 Supported Plate Readers | ||
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| ``` | ||
| The following table lists the currently supported plate readers output files: | ||
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| Or install from PyPi: | ||
| | Manufacturer | Model | File Format | | ||
| |--------------------|------------------------------|-------------| | ||
| | Agilent | BioTek Epoch 2 | `xlsx` | | ||
| | Molecular Devices | SpectraMax 190 | `txt` | | ||
| | Tekan | Magellan (processing software)| `xlsx` | | ||
| | Tekan | Spark | `xlsx` | | ||
| | Thermo Scientific | Multiskan SkyHigh | `xlsx` | | ||
| | Thermo Scientific | Multiskan Spectrum 1500 | `txt` | | ||
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| ```Bash | ||
| ``` | ||
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| ## 🔖 Example Code | ||
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| coming soon | ||
| ## 📦 Installation | ||
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| ## ⚖️ License | ||
| Install `MTPHandler` via pip: | ||
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| Copyright (c) 2023 FAIR Chemistry | ||
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| 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: | ||
| ```bash | ||
| pip install MTPHandler # 🚧 not released yet | ||
| ``` | ||
| or from source: | ||
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| The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. | ||
| ```bash | ||
| pip install git+https://github.com/FAIRChemistry/MTPHandler.git | ||
| ``` | ||
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| 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. | ||
| Please refer to the [documentation](https://fairchemistry.github.io/MTPHandler/) for more information on how to use the package. |