Software

DIAMOND

DIAMOND : an automatic pipeline for metabolic model comparison

Nicolas Beaume1, Maria Pires Pacheco 1 and Thomas Sauter 1

1 Life Science Research Unit, University of Luxembourg, Belvaux, L-4367, Luxembourg

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FASTCORE: Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Nikos Vlassis 1, Maria Pires Pacheco 2, and Thomas Sauter 2

1 Luxembourg Centre for Systems Biomedicine, University of Luxembourg
2 Life Sciences Research Unit, University of Luxembourg

PLoS Comput Biol. 2014 Jan;10(1):e1003424.

DOWNLOAD:

FASTCORE_1.0.zip 182,68 kB

FASTCORMICS: Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

Maria Pires Pacheco, Elisabeth John, Tony Kaoma, Merja Heinäniemi, Nathalie Nicot, Laurent Vallar, Jean-Luc Bueb, Lasse Sinkkonen and Thomas Sauter

BMC Genomics. 2015 Oct 19;16(1):809.

Example: Visualization of differentiation of monocytes into monocyte-derived macrophage (day4 - day11): Metabolic Model were built using the FASTCORMICS workflow and visualized with the shiny package (Rstudio). The spheres represent the different pathways in the models. Their size is proportional to the number of reactions in the pathway:

https://sautergroup.shinyapps.io/macro_visual

IDARE: Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network

Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M.

Nucleic Acids Res. 2014 Feb;42(3):1474-96.

LINK to IDARE webpage:

https://code.google.com/p/adipoflux/

Model: Identification of New IkappaBalpha Complexes by an Iterative Experimental and Mathematical Modeling Approach

Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms

PLoS Comput Biol. 2014 Mar 27;10(3):e1003528.

DOWNLOAD Final Model M3:

DyGloSA: Matlab-based tool for Dynamical Global parameter Sensitivity Analysis of ODE models of biological systems

Baumuratova T. 1;2; Dobre S. 3;4, Bastogne T. 3, Sauter T. 1

  • 1. Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, L-1511,
    Luxembourg.
  • 2. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, 4 Institutskaya st.,
    Pushchino, Moscow region, Russia.
  • 3. Centre de recherche en Automatique de Nancy (CRAN), INIRIA BIGS, Universit ´e de Lorraine,
    CNRS UMR 7039, Campus Science, BP 70239, 54506, Vandoeuvre-l`es-Nancy Cedex, France
  • 4. ISL, French-German Research Institute of Saint-Louis, 68300, Saint-Louis, France

PLoS One. 2013 Dec 18;8(12):e82973.

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MetaEaseMap: METAbolic DisEASE MAP

MetaEaseMap: METAbolic DisEASE MAP - a systematic mapping of the two relevant networks, metabolic disease gene network and metabolic disease network.
Thanh-Phuong NGUYEN1 , Laura CABERLOTTO2, 3 , S Jochen G. SCHNEIDER 4, 5 , and Thomas SAUTER 1
1 Systems Biology Group, Life Sciences Research Unit, University of Luxembourg
2 Aptuit Center for Drug Discovery and Development, Verona - Italy
3 The Microsoft Research, University of Trento Centre for Computational Systems Biology
4 Saarland University Medical Center, Dpt. of Internal Medicine II, Homburg , Germany
5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg

LINK to MetaEaseMap webpage: