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Study cases for the Diplôme Universitaire en Bioinformatique Intégrative (DU-Bii)

Table of contents

Introduction

This repository contains a description of the study cases used for the different courses of the Diplôme Universitaire en Bioinformatique Intégrative (DU-Bii) organised by the Université Paris-Diderot and the Institut Français de Bioinformatique (IFB).

This includes:

  • a description of the study cases;
  • links to the reference publications and data sources;
  • scripts enabling to download the data from its original sources;
  • optionally, some small demo datasets derived from the raw data, in order to facilitate its use for the different courses of the diploma (Python, Unix, statistics with R, ...).

Beware: this repository should by no means not contain any massive data like the raw read files or mass spectrometry profiles.

Study case descriptions

Escherichia coli

Arabidopsis thaliana

  • Strehmel et al. (2017).

    • Data types: Metabolomics and proteomics
    • Reference: Strehmel N, Hoehenwarter W, Mönchgesang S, Majovsky P, Krüger S, Scheel D, Lee J. Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates. Front Plant Sci. 2017 Jul 21;8:1292. doi: 10.3389/fpls.2017.01292. eCollection 2017. PubMed PMID: 28785276; PubMed Central PMCID: PMC5520323.
    • Article: https://www.frontiersin.org/articles/10.3389/fpls.2017.01292/full
  • Liang et al. (2016).

Homo sapiens

Mus musculus

Resources to get study cases

Biostudies

Web: https://www.ebi.ac.uk/biostudies/

The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI.

Sci. data special issue on multi-omics data

Reference : Conesa, A., Beck, S. Making multi-omics data accessible to researchers. Sci Data 6, 251 (2019). https://doi.org/10.1038/s41597-019-0258-4. https://www.nature.com/articles/s41597-019-0258-4

Some, papers:

ProteomeXchange datasets

Vizcaíno, J., Deutsch, E., Wang, R. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32, 223–226 (2014). - https://doi.org/10.1038/nbt.2839 - Datasets: http://proteomecentral.proteomexchange.org/cgi/GetDataset

Access

Local installation

For contributors (members of the team)

git clone [email protected]:DU-Bii/study-cases.git

For non-members of the team

git clone https://github.com/DU-Bii/study-cases.git

Credits

License

This content is released under the Creative Commons Attribution-ShareAlike 4.0 (CC BY-SA 4.0) license. See the bundled LICENSE file for details.

Ce contenu est mis à disposition selon les termes de la licence Creative Commons Attribution - Partage dans les Mêmes Conditions 4.0 International (CC BY-SA 4.0). Consultez le fichier LICENSE pour plus de détails.

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