Systems Biology Research Group

Login: SBRG

Company: null

Location: La Jolla

email:

Blog: http://systemsbiology.ucsd.edu

Members

  1. Ali Ebrahim
  2. Ambros Gleixner
  3. Colton Lloyd
  4. Joshua Lerman
  5. Muyao
  6. Nathan Mih
  7. Nikolaus Sonnenschein
  8. Patrick Phaneuf
  9. Steve Federowicz
  10. Zachary A. King

Repositories

aledb_mut_scripts
Scripts to process mutations exported from ALE Analytics
bigg_models
The BiGG Models website server
bigg_models_data
The flat files for the BiGG Models website
Bootcamp
MASS Toolbox Bootcamp
bop27refseq
null
cobradb
COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.
cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
cobra-review
null
doi2bib
null
ecolime
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
ecoli_me_testing
Draft of the E. coli ME model to succeed iOL1650-ME
escher-maps
Extracted metabolic maps (OLD)
experiment_metadata
Collect metadata for sequencing experiments
gdparse
Python module for parsing Breseq's Genomic Diff (.gd) files.
GEMPro
null
iML1515_GP
GEM-PRO for the E. coli iML1515 metabolic model
MASS-Models
A collection of MASS Toolbox models
metastructure_model_whitepaper
A brief description of the data, workflow, and model to build this ecosystem
MetPath
MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
minspan
null
pcfba
Protein constrained FBA
Protein_ML
Machine learning workflows for analyzing high-throughput protein data
Recon3D
A 3-Dimensional View of Human Metabolism and Disease
RibosomeProfiling
Analysis pipeline for characterization of microorganisms
sbaas
null
solveme_pub
solveme public repository for the corresponding publication (citation: TBD)
solvemepy
solveME public repository
soplex_cython
Cython bindings to soplex 3.0
ssbio
A Python framework for structural systems biology
Strain_characterization_workflow
Code to characterize strains from multiple disparate data types
uFBA
unsteady-state Flux Balance Analysis (uFBA)
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.