by Biosustain

Tags: mathematical modeling , general modeling

Optlang is a Python package for solving mathematical optimization problems, i.e. maximizing or minimizing an objective function over a set of variables subject to a number of constraints. Optlang provides a common interface to a series of optimization tools, so different solver backends can be changed in a transparent way. Optlang’s object-oriented API takes advantage of the symbolic math library sympy to allow objective functions and constraints to be easily formulated from symbolic expressions of variables

by Zachary A. King

Tags: visualization

Escher is a web-based tool for building, viewing, and sharing visualizations of biological pathways. These ‘pathway maps’ are a great way to contextualize data about metabolism.

by Biosustain

Tags: Synthetic Biology , strain design , general modeling

Cameo is a high-level python library developed to aid the strain design process in metabolic engineering projects. The library provides a modular framework of simulation methods, strain design methods, access to models, that targets developers that want custom analysis workflows.

Computationally heavy methods have been parallelized and can be run on a clusters using the IPython parallelization framework (see example and documentation for more details). The default fallback is python’s multiprocessing library.

Furthermore, it exposes a high-level API to users that just want to compute promising strain designs.

by opencobra

Tags: metabolic model , metabolic reconstruction , standardization , unit-testing , cobra , sbml

Our goal in promoting this tool is to achieve two major shifts in the metabolic model building community:

1. Models should be version-controlled such that changes can be tracked and if necessary reverted. Ideally, they should be available through a public repository such as GitHub that will allow other researchers to inspect, share, and contribute to the model.
2. Models should, for the benefit of the community and for research gain, live up to certain standards and minimal functionality.

The memote tool therefore performs four subfunctions:

1. Create a skeleton git repository for the model.
2. Run the current model through a test suite that represents the community standard.
3. Generate an informative report which details the results of the test suite in a visually appealing manner.
4. (Re-)compute test statistics for an existing version controlled history of a metabolic model.

by the MICOM developers

Tags: microbiota , microbiome , community modeling

MICOM is a Python package for metabolic modeling of microbial communities and is developed in the Human Systems Biology Group at the INMEGEN, Mexico abd Institute for Systems Biology, Seattle, USA.

MICOM allows you to construct a community model from a list on input COBRA models and manages exchange fluxes between individuals and individuals with the environment. It explicitly accounts for different abundances of individuals in the community and the tradeoff between individual and community-wide biomass production. MICOM can incorporate incorporate data from 16S amplicon sequencing or metagenomic shotgun experiments.

by Sven Thiele, Philipp Schneider, Axel von Kamp, Pavlos Stephanos Bekiaris, Steffen Klamt

Tags: strain-design , visualization , general-modeling , cobra , metabolic-model , minimal-cut-sets , models

CNApy is a graphical integrated environment for metabolic network analysis. With CNApy, it is possible to load, edit and create metabolic models together with interactive network maps. Many standard and advanced COBRA techniques (including, e.g., Flux Balance Analysis, Flux Variability Analysis and Minimal Cut Sets) are supported and all main results of these techniques can be directly visualized in the network maps. Furthermore, CNApy also provides a GUI for all major functions of the StrainDesign package.

by Systems Biology Research Group, UCSD

Tags: ME-models

COBRA Toolbox for constructing and manipulating genome-scale models of metabolism and expression (ME-models).

by EPFL-LCSB

Tags: thermodynamics , thermodynamics-based flux analysis

Thermodynamics-based Flux Analysis, in Python.

Implements: Henry, Christopher S., Linda J. Broadbelt, and Vassily Hatzimanikatis. “Thermodynamics-based metabolic flux analysis.” Biophysical journal 92.5 (2007): 1792-1805. DOI: https://doi.org/10.1529/biophysj.106.093138

by Peter St. John

Tags: visualization

This package implements a d3.js based visualization tool for cobrapy models.

by Christian Diener and Osbaldo Resendis-Antonio

Tags: reconstruction

CORDA, short for Cost Optimization Reaction Dependency Assessment is a method for the reconstruction of metabolic networks from a given reference model (a database of all known reactions) and a confidence mapping for reactions developed by A. Schultz and A. Qutub. The package allows you to quickly reconstruct metabolic models for tissues, patients or specific experimental conditions from a set of transcription or proteome measurements and is developed in the Human Systems Biology Group at the INMEGEN, Mexico.

by Mike Mundy

Tags: ModelSEED , models , gapfilling , reconstruction

Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Mackinac is a Python package that combines ModelSEED’s ability to automatically reconstruct metabolic models with COBRApy’s advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.

by Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt

Tags: strain-design , visualization , cell-factories , minimal cut sets

StrainDesign, a comprehensive Python package that integrates the most popular deterministic metabolic design algorithms, including nested strain optimization methods such as RobustKnock, OptCouple and OptKnock, as well as the more general minimal cut sets approach. The optimization approaches are embedded in individual modules, which can also be combined for setting up more elaborate strain design problems. Advanced features, such as the efficient integration of GPR-rules, the consideration of gene and reaction additions and of regulatory interventions are available for all modules. The package uses state-of-the art preprocessing methods, supports CPLEX, Gurobi, GLPK and SCIP and provides a number of enhanced tools for analyzing computed intervention strategies, for example, 2D and 3D plots of user-selected metabolic fluxes and yields. Furthermore, a user-friendlyGUI-based interface for the StrainDesign package has been implemented in the metabolic modeling software CNApy.

by Andre Schultz

Tags: visualization

SAMMI is an interactive tool for the visualization of constraint-based models. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps.

by Systems Biology Research Group

Tags: algorithms , flux analysis

This project calculates the minimal spanning vectors of the null space.

by Helena Mendes-Soares

Tags: microbiota , microbiome , web app , community modeling

MMinte (pronounced /‘minti/) is a set of widgets that allows you to explore the pairwise interactions (positive or negative) that occur in a microbial community. From an association network and 16S rDNA sequence data, MMinte identifies corresponding genomes, reconstructs metabolic models, estimates growth under specific metabolic conditions, analyzes pairwise interactions, assigns interaction types to network links, and generates the corresponding network of interactions. You can run the MMinte widgets as an integrated pipeline or run each widget independently.

Tags: strain design , cell factories , web app

DD-DeCaF is a Horizon 2020 project (grant agreement No 686070) bringing together leading academic partners from five European universities with five innovative European companies to address the challenge of building a comprehensive design tool. DD-DeCaF aims to develop cutting edge methods in order to use large scale data to design cell factories and communities for biotechnological applications. The project is built as a number of micro-services which can be used separately and via the web-based user-interface.

Tags: dynamic flux-balance analysis , dfba

The dfba project provides an object-oriented software package for dynamic flux-balance analysis (DFBA) simulations using implementations of the direct method or Algorithm 1 described in the paper Harwood et al., 2016. The main algorithms for solving embedded LP problems are written in C++ and use the GLPK (GNU Linear Programming (LP) Kit) and SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) CVODE or IDA. Extension modules to cobrapy are provided for easy generation and simulation of DFBA models.