Welcome to Workflomics's 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 with technologies for automated workflow exploration and benchmarking. This innovative approach supports the development of advanced workflows in bioinformatics, particularly within the proteomics domain, enhancing scientific quality, robustness, reproducibility, FAIRness (Findability, Accessibility, Interoperability, and Reusability), and maintainability.

The platform currently focuses on proteomics and plans to expand into other domains, such as metabolomics and genomics, to further support the 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