SBRG/GDGA_Shortcourse SBRG/GDGA_Shortcourse

  • Stars
    star
    10
  • Rank 1,798,065 (Top 36 %)
  • Language
    Jupyter Notebook
  • License
    MIT License
  • Created almost 3 years ago
  • Updated almost 3 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
SBRG/GDGA_Shortcourse
github

SBRG

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Files for the Genome Design/Genome Analytics Short-course organized by the SBRG

More Repositories

1

ssbio

A Python framework for structural systems biology
Python
103
star
2

bigg_models

The BiGG Models website server
Python
75
star
3

cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Python
33
star
4

precise-db

A high-fidelity E. coli RNA-seq compendium
Jupyter Notebook
31
star
5

Recon3D

A 3-Dimensional View of Human Metabolism and Disease
MATLAB
25
star
6

MASSpy

Python
23
star
7

Protein_ML

Machine learning workflows for analyzing high-throughput protein data
23
star
8

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.
Python
20
star
9

lifelike

Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
Python
20
star
10

pymodulon

Python package for analyzing and visualizing iModulons
Python
11
star
11

GEMPro

Jupyter Notebook
6
star
12

iML1515_GP

GEM-PRO for the E. coli iML1515 metabolic model
Scheme
4
star
13

minspan

Python
4
star
14

ecolime

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
Python
4
star
15

solvemepy

solveME public repository
Python
3
star
16

MetPath

MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
MATLAB
3
star
17

precise1k

Jupyter Notebook
3
star
18

pcfba

Protein constrained FBA
3
star
19

ChIPdb

A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.
HTML
3
star
20

modulome_ppu

iModulon structure of Pseudomonas putida KT2440
HTML
3
star
21

Kinetome_profiling

R
2
star
22

precise2

HTML
2
star
23

sbaas

GAP
2
star
24

modulome_saci

iModulon structure of Sulfolobus acidocaldarius DSM 639
Jupyter Notebook
2
star
25

RibosomeProfiling

Analysis pipeline for characterization of microorganisms
Python
2
star
26

oxidizeme

OxidizeME model and notebooks
Python
2
star
27

ecoli_me_testing

Draft of the E. coli ME model to succeed iOL1650-ME
1
star
28

bop27refseq

HTML
1
star
29

bigg_models_data

The flat files for the BiGG Models website
Python
1
star
30

modulytics

Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
1
star
31

Strain_characterization_workflow

Code to characterize strains from multiple disparate data types
Jupyter Notebook
1
star
32

Bootcamp

MASS Toolbox Bootcamp
Objective-C
1
star
33

uFBA

unsteady-state Flux Balance Analysis (uFBA)
MATLAB
1
star
34

RiboRid_Design

Design oligos for RiboRid protocol
Python
1
star
35

escher-maps

Extracted metabolic maps from simpheny/bigg1
Python
1
star
36

IM-ML

Jupyter Notebook
1
star
37

MASS-Models

A collection of MASS Toolbox models
Mathematica
1
star
38

noncoding_alleleome

Jupyter Notebook
1
star
39

PromoterModeling

Sequence-based ML models of gene regulation
Jupyter Notebook
1
star
40

escher-fba

JavaScript
1
star
41

soplex_cython

Cython bindings to soplex 3.1.1
Python
1
star
42

dynamicme

Dynamic ME simulations (separate module)
Python
1
star