SINGulator

Recent computational methodologies, such as agent-based modelling, may help in the search for explanatory insight into the collective behaviour of molecules and bring forward the discussion of intrinsic noise while simulating biological events.

SINGulator is a novel application that aims to model the diffusional motion of individual biomolecules and intermolecular interactions in continuous three-dimensional cellular environments with agent-based reaction-diffusion algorithms. In particular, emphasis is put on the simulation of enzymatic reactions at experimentally measured concentrations.

 
S2P

S2P is an open source application for fast and easy processing of 2D-gel and MALDI-based mass spectrometry protein data. It allows users to:

  • Import data from Progenesis SameSpots and save it as comma-separated values (CSV) files.
  • Import, process and save Mascot identifications reports.
  • Create MALDI plate designs and export them as PDF or CSV files.
  • Bind Mascot identifications to spots data.
  • Visualize and explore spots data in different ways.
 
Antimicrobial Combination Network

There is a growing interest in the use of antimicrobial synergistic combinations as a strategy to increase the antimicrobial spectrum, potentiate the efficacy, prevent the emergence of resistance, fight the increased resistance of MDR strains, and reduce toxicity and other side effects.

This tool presents the first ever network reconstruction of AMP-drug combinations, and details results obtained for the treatment of infections caused by the bacterium Pseudomonas aeruginosa, one of the most studied pathogenic microorganisms. This reconstruction led to the development of an integrated curation pipeline that combines text mining, manual curation and graph analysis methods and techniques.

The aim is to provide a global view of the available interaction data and thus help design new antimicrobial studies. As such, reconstruction is on-going, coping with new experimental results for P. aeruginosa and will be shortly extended to other meaningful microbial pathogens.

 
BiMS

BiMS (biclustering for mass spectrometry data) is a Java application designed to allow the application of biclustering algorithms to mass spectrometry datasets.

Users can load their MS datasets and apply different clustering and biclustering algorithms (current version includes Bimax and BiBit). In adition, users can load raw datasets (in mzML or mzXML formats) and preprocess them using MALDIquant package and MassSpecWavelet.

 
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