Systems biology

merlin

  • Posted on: 6 November 2019
  • By: Daniel Faria

merlin is a simple, graphical and user-oriented solution for the reconstruction of genome-scale metabolic models. It will guide you along the model reconstruction, providing several tools that help to improve and curate the model throughout the whole process.

If you use this resource, please acknowledge: BioData.pt – Infraestrutura Portuguesa de Dados Biológicos refª 22231/01/SAICT/2016, funded by Portugal 2020.

CoBAMP

  • Posted on: 6 November 2019
  • By: Daniel Faria

CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models.

If you use this resource, please acknowledge: BioData.pt – Infraestrutura Portuguesa de Dados Biológicos refª 22231/01/SAICT/2016, funded by Portugal 2020.

OptFlux

  • Posted on: 6 November 2019
  • By: Daniel Faria

OptFlux is an open-source and modular software to support in silico metabolic engineering tasks aimed at being the reference computational application in the field.

A major new release of OptFlux is now available, with several important improvements and new features.

If you use this resource, please acknowledge: BioData.pt – Infraestrutura Portuguesa de Dados Biológicos refª 22231/01/SAICT/2016, funded by Portugal 2020.