MIEP
  • Menu
  • Go
  • About
  • Team
  • Immunology
  • Models
  • Tools
  • Projects
  • Data
  • Education
  • Home Tools

Tools


  • ENISI Suite

    ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI can simulate in silico experiments from signaling pathways to tissue level events. ENISI’s architecture integrates multiple modeling technologies. During the development of ENISI, 3 versions were released; ENISE HPC, ENISI Visual, ENISI MSM.


  • COPASI

    COPASI enables researchers to construct biochemical models that help them understand how a system works. Model parameters can be adjusted as necessary to reproduce experimental results.


  • CellDesigner

    CellDesigner is a process diagram editor for gene-regulatory and biochemical networks based on standardized technologies and with wide transportability to other SBML-compliant applications. CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi.


  • Labkey

    LabKey is a web-based platform designed for translational research teams. The NIMML uses a customized version of LabKey as its internal electronic notebook and laboratory management information (LIMS) system for real time data-acquisition, data analysis, collaboration, and for publication of raw and processed data


  • Galaxy

    Galaxy captures information that allows users to repeat and understand a complete computational analysis. Galaxy also facilitates sharing and publishing analysis. Galaxy’s public service web site makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist.


  • CellPublisher

    CellPublisher is a free and open source program to make highly interactive representations of biochemical processes. CellPublisher complements CellDesigner by facilitating the understanding of complex diagrams and by providing the possibility to share any CellDesigner diagram online with collaborators and get their feedback. NIMML makes use of CellPublisher to disseminate the models developed to the scientific community in a user friendly way.

  • Contact
  • Education
  • News & Events
  • Publications

© 2000 - 2025 NIMML Institute


  • Clinical
    • Clinical Development (Phase I-IV)
  • Pig Models
    • Neonatal pig model
    • Inflammatory bowel disease
    • Novel Pig Model of H. pylori
  • Media & Press Kit
    • Mission, Vision, Values
    • History
    • Quick Facts
    • Strategic Initiatives
  • ENISI Helicobacter Pylori Model
    • Sensitivity Analysis
    • Cell Movement Modeling
  • CDiff Computational Model Archive
    • Mucosal Immune Responses
    • PPAR γ and miRNA
  • EAEC Computational Model
    • Mucosal Immune Responses
    • T Cell Response
    • Epithelial Cell Responses
  • Macrophage Computational Model Archive
    • April 2012
    • Jan 2012
    • Oct 2011
  • COPASI Helicobacter Pylori Computational Model Archive
    • May 2012
    • April 2012
    • Jan 2012
    • Sep 2011
  • CD4+ T Cell Model Archive
    • Feb 2014
    • October 2012
    • August 2012
    • April 2012
    • Jan 2012
    • Sep 2011
    • June 2011
    • March 2011
  • Immunology
    • Helicobacter pylori
    • CD4+ T cell differentiation
    • Human Studies
    • Enteroaggregative E. coli
  • Animal Models
    • Type 2 Diabetes
    • Clostridium dificile infection
    • Influenza
    • Inflammatory bowel disease
    • Helicobacter pylori
    • Pig Models
    • Murine Models
  • Infectious Diseases
    • Helicobacter pylori
    • Clostridium difficile
    • Enteroaggregative E. coli
  • Immune Mediated Diseases
    • Novel IBD Interventions
  • Nutritional Immunology
    • Novel IBD Interventions
    • Phytochemicals
    • Dietary Lipids
    • Prebiotics and Probiotics
  • Drug Development
    • Host-targeted Therapeutics
    • Translational Medicine
  • Data
    • Modeling NLRX1 response to H.pylori
    • Modeling Clostridium difficile Immune Response
    • EAEC Zinc Deficiency
    • IL-21 in the Gastric Mucosa
    • Novel Pig Model
    • CD4+ T Cells
    • Modeling H. pylori Immune Response
    • Clostridium difficile
    • Enteroaggregative Escherichia coli
    • ENISI V0.9 in silico experiments
  • Computational Models
    • Inflammatory bowel disease
    • CD4+ T Cell Model
    • Host Responses to H. pylori
    • Host Responses to EAEC
    • Host Responses to C. difficile
    • Macrophages
  • Tools
    • CMS
    • CellDesigner
    • ENISI Suite
    • COPASI Suite
    • Galaxy
    • LabKey
    • RedCap
    • Intranet
    • CellPublisher
  • Projects
    • Alternate Preclinical Models Of Enteric Infection
    • Modeling Infectious Disease Kinetics (MIDK-cWMD)
  • Immunoinformatics
    • Computational Modeling
    • High Performance Computing
    • Transcriptomics
  • NIMML POLICIES
    • FCOI