Welcome to the Workflomics Documentation
========================================

Welcome to the official documentation for **Workflomics**—a platform designed to empower bioinformaticians in the generation and comparison of computational workflows for life science research.

Introduction
------------

**Workflomics** addresses the challenges faced by researchers dealing with large and complex datasets by facilitating the creation of optimal data analysis workflows. It integrates bioinformatics tools and metadata from the `ELIXIR Research Software Ecosystem <https://research-software-ecosystem.github.io/>`_ with technologies for automated workflow exploration and benchmarking. This supports the development of advanced workflows in any area of bioinformatics, with proteomics, metabolimics and mass spectrometry imaging used for demonstration, enhancing scientific quality, robustness, reproducibility, FAIRness (Findability, Accessibility, Interoperability, and Reusability), and maintainability of scientific workflows.

The platform is currently demonstrated on `workflomics.org <https://workflomics.org>`_ with mass spectrometry-based proteomics as a use case (domain), with metabolomics and mass spectrometry imaging coming soon. However, the **Workflomics** platform itself is domain-agnostic, aiming to support the wider life sciences community.

Contents
--------

.. toctree::
   :maxdepth: 2
   :caption: User Guide

   user-guide/web-interface

.. toctree::
   :maxdepth: 2
   :caption: Workflomics Benchmarker

   workflomics-benchmarker/benchmarker-overview
   workflomics-benchmarker/benchmarker-installation
   workflomics-benchmarker/benchmarker-usage

.. toctree::
   :maxdepth: 2
   :caption: Domain Expert Guide

   domain-expert-guide/adding-tools
   domain-expert-guide/domain-development

.. toctree::
   :maxdepth: 2
   :caption: Developer Guide

   developer-guide/installation
   developer-guide/standards
   developer-guide/pubmetric
   developer-guide/pubmetric_api

.. toctree::
   :maxdepth: 2
   :caption: Rational

   rational/annotating-tools
   rational/discussions
   

.. note::

   This project is under active development. Features and documentation are subject to change.

.. _contributors:

Contributors
************


The project was developed within the `"Great Bake Off" of Bioinformatics Workflows <https://research-software-directory.org/projects/bakeoff>`_ project by the project's core team:

* Vedran Kasalica (v.kasalica[at]esciencecenter.nl),
* Peter Kok,
* Rob Marissen,
* Magnus Palmblad,
* Anna-Lena Lamprecht


and the following contributors:

* Nauman Ahmed,
* Alma Nilsson,
* Felipe Morato,
* Sizheng Zhao