.. emzed documentation master file, created by sphinx-quickstart on Tue Jan 24 18:40:08 2012. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. raw:: html

LCMS data analysis made easy

emzed is an open source toolbox for rapid and interactive development of LCMS data analysis workflows in Python and makes experimenting with new analysis strategies for LCMS data as easy as possible.


How to get started
Screenshots ----------- Click on images to enlarge. .. raw:: html
.. thumbnail:: screenshot_emzed_table_explorer.png :class: screenshot-left :width: 33% This is emzeds interactive table explorer .. thumbnail:: screenshot_emzed_spyder.png :class: screenshot-middle :width: 35.2% This is the spyder based development environment for emzed. .. thumbnail:: screenshot_emzed_pm_explorer.png :class: screenshot-right :width: 25% This is the sample inspectrom from emzed. .. raw:: html
Fundamental principles of emzed ------------------------------- 1. We choose **Python** which makes programming with ``emzed`` `as simple as possible `_ and approachable by LCMS experts without professional programming experience. 2. Analysis workflows consist of **Python** scripts composing function calls from the ``emzed`` library. Thus processing steps are explicitly written down as Python code which is crucial for `reproducible research `_. 3. In order to strengthen the trust in analysis results, ``emzed`` provides **interactive visualization** tools for intermediate and final results. An ``emzed`` workflow can deliver more insight into the achieved results than a bunch of numbers or static plots. 4. ``emzed.spyder`` is an `integrated development environment (IDE) `_ based on the `spyder IDE `_ tailored to support the overall development process. Development goals ----------------- * When we started developing LCSM analysis workflows in 2012, we realized that the existing software landscape can be divided into two groups. On the one hand there are fast and flexible frameworks, but in languages like C++, which can only be used efficiently by experienced programmers. On the other hand, there are applications with graphical user interfaces that are easy to use and learn, but difficult to adapt for special needs. **Our goal was to develop a toolbox that combines the positive aspects of both groups.** * The invention of programming environments such as **Matlab** and **R** leveraged the productivity of mathematicians and scientists from other fields. ``emzed`` attempts to introduce this concept for analyzing LCMS data. * Instead of reinventing the wheel we cherry pick algorithms from established libraries and frameworks such as `OpenMs `_. We provide a **consistent application programming interface (API)** and ``emzed`` based workflows avoid manual and error prone import and export steps. * We split ``emzed`` into a user interface agnostic core library (also called ``emzed``) which can be used on display less servers such as high performance computers, a library for the interactive inspection of LCMS data structures ``emzed.gui`` and the spyder based development environment ``emzed.spyder``. * ``emzed`` can be extended by community extensions, right now we offer an extension ``emzed.ext.mzmine2`` which wraps some algorithms from `MZmine2 `_. emzed in the press ------------------ Recent publications using ``emzed`` for data analysis: * Bidong D. Nguyen et al. **Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice**. Cell Host & Microbe (2020), https://doi.org/10.1016/j.chom.2020.04.013 * Hartl et al. **Untargeted metabolomics links glutathione to bacterial cell cycle progression**. Nature Metabolism (2020), https://doi.org/10.1038/s42255-019-0166-0 * Hartl et al. **Untargeted metabolomics links glutathione to bacterial cell cycle progression**, Nature Metabolism (2020), https://doi.org/10.1038/s42255-019-0166-0 * Hemmann et al. **Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites**. PNAS (2019), https://doi.org/10.1073/pnas.1911595116 For the full list of publications `continue to read here `_. Original publication: * Kiefer Patrick, Schmitt Uwe, Vorholt Julia. **eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows**, Bioinformatics, Volume 29, Issue 7, 1 April 2013, Pages 963–964, https://doi.org/10.1093/bioinformatics/btt080 Website Navigation ------------------ .. toctree:: :maxdepth: 1 get_started emzed_tutorial/index.rst faq license contact