Neurospora crassa Pathway-Genome Knowledgebase

What is being modeled?
Genome scale model of metabolism
Description & purpose of resource

This is a Biocyc genome-scale model of Neurospora crassa, with on-going curation including metabolism, regulation, and genome, adopted from the original work by Dreyfuss, Zucker, et al. (https://doi.org/10.1371/journal.pcbi.1003126).

Spatial scales
molecular
cellular
Temporal scales
10-6 - 10-3 s
10-3 - 1 s
1 - 103 s
hours
days
This resource is currently
mature and useful in ongoing research
Has this resource been validated?
Yes
How has the resource been validated?

This knowledgebase has previously been extensively curated with experimental data, and additional curation is on-going.  

Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)
Yes
Which resources?

The a genome scale flux-balance model is linked to the database.  

Key publications (e.g. describing or using resource)
Collaborators
Bill Cannon
PI contact information
jeremy.zucker@pnnl.gov
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Control of Intracellular Molecular Networks Using Algebraic Methods

Submitted by reinhard.laube… on

Many problems in biology and medicine have a control component. Often, the goal might be to modify intracellular networks, such as gene regulatory networks or signaling networks, in order for cells to achieve a certain phenotype, what happens in cancer. If the network is represented by a mathematical model for which mathematical control approaches are available, such as systems of ordinary differential equations, then this problem might be solved systematically.

Simulation of Platelets Suspension Flowing Through a Stenosis Model Using a Dissipative Particle Dynamics Approach

Submitted by jawaadsheriff on

Stresses on blood cellular constituents induced by blood flow can be represented by a continuum approach down to the μm level; however, the molecular mechanisms of thrombosis and platelet activation and aggregation are on the order of nm. The coupling of the disparate length and time scales between molecular and macroscopic transport phenomena represents a major computational challenge.

Viscous flow simulation in a stenosis model using discrete particle dynamics: a comparison between DPD and CFD

Submitted by jawaadsheriff on

Flow and stresses induced by blood flow acting on the blood cellular constituents can be represented to a certain extent by a continuum mechanics approach down to the order of the μm level. However, the molecular effects of, e.g., adhesion/aggregation bonds of blood clotting can be on the order of nm. The coupling of the disparate length and timescales between such molecular levels and macroscopic transport represents a major computational challenge.

Center for Reproducible Biomedical Modeling

The Center for Reproducible Biomedical Modeling is  an NIBIB/NIGMS/NSF funded center to encourage the publication of reproducible models. Studies indicate that the bulk of published peer-reviewed computational models in physiology and systems biology cannot be reproduced from the description in the published pape. Even if the code used in the study is made available it can be dififcult to reproduce the reported findngs.

The dynamics of canalyzing Boolean networks

Submitted by reinhard.laube… on

Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by regulatory rules driving the dynamics that have certain so-called canalizing properties. In this paper, we investigate the dynamics of a random Boolean network with such properties using analytical methods and simulations.

GranSim

What is being modeled?
Tuberculosis (TB) granuloma formation and function in the lung
Description & purpose of resource

GranSim, the Agent-based model (ABM) describing tuberculosis (TB) granuloma formation and function in the lung, was developed based on four basic concepts: an environment (section of the lung parenchyma), agents (immune cells), ABM rules that govern the agents and their interactions, and the time-step (Δt) used to update events. The attached documentation illustrates the details of how each of these features have been implemented in the form of a pseudocode. The model was first published in 2004 but has been continually updated to include the latest biological information and technological advances.

Collaborators
Denise Kirschner
PI contact information
kirschne@umich.edu
Keywords
agent based modeling
tuberculosis
granuloma
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3D GranSim

What is being modeled?
Tuberculosis (TB) granuloma formation and function in the lung
Description & purpose of resource

GranSim is a hybrid agent-based computational model (ABM) that describes the formation and function of a granuloma during Mycobacterium tuberculosis infection in the lung. Although granulomas are 3D entities, due to the high computational costs associated to simulate a 3D version, GranSim has been developed and curated since 2004 only in 2D. [2-4, 6-10] This website and the recent manuscript [hyperlink here] illustrate our first attempt to simulate a 3D TB granuloma in the lung.

Collaborators
Denise Kirschner
PI contact information
kirschne@umich.edu
Keywords
tuberculosis
granuloma
Lung model
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Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology

Submitted by kirschne on

Immune responses to pathogens are complex and not well understood in many diseases, and this is especially true for infections by persistent pathogens. One mechanism that allows for long‐term control of infection while also preventing an over‐zealous inflammatory response from causing extensive tissue damage is for the immune system to balance pro‐ and anti‐inflammatory cells and signals. This balance is dynamic and the immune system responds to cues from both host and pathogen, maintaining a steady state across multiple scales through continuous feedback.