Overview of ProteoBench +++++++++++++++++++++++ .. toctree:: :maxdepth: 1 :hidden: :glob: About General information Modules Developer guide Contributing Changelog `ProteoBench `_ is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. ProteoBench provides a centralized web platform for developers and end-users to compare proteomics data analysis pipelines. This community-curated effort will allow for an easy and controlled comparison of tools developed or used by the participants to other state-of-the-art pipelines for specific applications. The goal is not to select a single best one-fits-all data analysis workflow, but to allow: 1. **end-users** to identify a good workflow to fulfill their specific needs 2. **developers** to identify the specific strengths and weaknesses in their workflows, guiding the development process 3. **the field** to easily position a newly published workflow within the context of the existing state-of-the-art Description =========== Participants (both end-users and developers) can download a set of input files (e.g., raw MS files, search databases, or spectral libraries) tailored to specific benchmark metrics. They can then analyze the data with any workflow, and upload the results in a homogenized format. A set of metrics will be retrieved or calculated from these results and can be visualized alongside all the other metrics calculated from the results of other participants (or of curated benchmark runs). Goals and non-goals =================== ProteoBench: 1. Allows for an easy and controlled comparison of existing data analysis workflows 2. Provides a frame of reference for newly developed workflows 3. Documents and implements benchmarks that each highlight strengths or weaknesses of data analysis workflow (steps) 4. Evolves continuously, according to the needs of the field 5. **DOES NOT** point to a single best one-fits-all data analysis workflow 6. **SHOULD NOT** be used as evidence for generalized statements about a workflow’s performance 7. **SHOULD NOT** be used by developers as single performance measure of their workflow Organization ============ The github repository for ProteoBench can be found `here `_. ProteoBench documentation is divided into two main parts: The different :doc:`modules/index` that exist, how they evolve and how to used them. The :doc:`developer-guide/index` provides information on the structure of the project and how to contribute. Contact us ========== email us `here `_. ---------- Contribution ============ People who contributed to ProteoBench (in alphabetical order) .. line-block:: **Robbin Bouwmeester** *VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium* *Department of Biomolecular Medicine, UGent, Ghent, Belgium* .. line-block:: **Nadezhda T. Doncheva** *Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Viktoria Dorfer** *Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria* .. line-block:: **Ralf Gabriels** *VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium* *Department of Biomolecular Medicine, UGent, Ghent, Belgium* .. line-block:: **Vedran Kasalica** *Netherlands eScience Center, Science Park 402, 1098 XH, Amsterdam, The Netherlands* .. line-block:: **Caroline Lennartsson** *Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Marie Locard-Paulet** *Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France* *Infrastructure nationale de protéomique, ProFI, FR 2048, Toulouse, France* .. line-block:: **Matthias Mattanovich** *Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Emmanuelle Mouton-Barbosa** *Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France* *Infrastructure nationale de protéomique, ProFI, FR 2048, Toulouse, France* .. line-block:: **Martin Rykær** *Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Julian Uszkoreit** *Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, Bochum, Germany* .. line-block:: **Tim Van Den Bossche** *Department of Biomolecular Medicine, Ghent University, Ghent, Belgium* *VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium* .. line-block:: **Bart Van Puyvelde** *ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Belgium* .. line-block:: **Veit Schwämmle** *Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark* .. line-block:: **Maximilian T. Strauss** *Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Henry Webel** *Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark* .. line-block:: **Witold E. Wolski** *Functional Genomics Center Zurich (FGCZ)−University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland* *Swiss Institute of Bioinformatics (SIB) Quartier Sorge−Batiment Amphipole, 1015 Lausanne, Switzerland*