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anl_projects

anme

bigg_sabio

A module to acquire reaction kinetics data from SABIO-RK for any BiGG model

biochemical-databases

The codes for collecting, aggregating, and exporting databases is provided.

biosimulations

A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

chemw

A rigorous software for determining the molecular weight of minerals, chemicals, and peptides

cobrakbase

KBase Interface for COBRApy

cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

codons

A Python module that translates DNA and RNA nucleotide sequences into the sequences of the encodes set of proteins.

commphitting

commscores

cv

dfbapy

A Dynamic Flux Balance Analysis package for computational biology

dgpredictor

hillfit

Fitting the Hill Equation to Experimental Data

karr_lab_projects

Research project6s in collaboration with the Karr lab of Mount Sinai School of Medicine

masc_thesis

metabolicmc_supplementary_git_v1

Code, examples, and publication details for the application of Molecular Communications to cellular metabolism

microbial_interactions

modelseeddatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

modelseedpy

Python package for building and analyzing models using ModelSEED

mutualinformationanalysismodule

nmrglue

A module for working with NMR data in Python

nutritional-database

A food database will be created that incorporates all of the known nutritional, carbon footprint, ethical, and preventative medicinal elements of foods for people to establish an accurate and easy perception of their dietary consumption as a powerful means of combatting global climate change, disease, and nutrition.

opentecr

openTECR database curation

organiclinks-v2

pdipy

A software that simulates photodynamic inactivation of a coccus bacterium

phreeqc

PHREEQC simulation code for RO desalination fluidics

projectnotebooks

Repository for Jupyter notebooks and associated data for various research projects of the ModelSEED team

protein_structure_hackathon

Hackathon repo for 11/28-11/30