Repositories list

• Sustainability-Shared-Code

  Public
  This repository houses scripts to access and format input data for CABBI's ecosystem models

  Python

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• FUN-PROSE

  Public archive
  Jupyter Notebook

  •1•0•0•0•Updated Sep 5, 2023Sep 5, 2023

• scRBA

  Public archive
  S. cerevisiae Resource Balance Analysis model

  GAMS

  •

  MIT License

  •2•0•0•0•Updated Jun 8, 2023Jun 8, 2023

• Landing-pad-model

  Public archive
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jun 6, 2023Jun 6, 2023

• Kmer-based-Subgenome-Mapping

  Public archive
  R

  •5•0•0•0•Updated Apr 18, 2023Apr 18, 2023

• PAPER_Howe_2023_switchgrass_MetaT

  Public archive
  Shell

  •

  MIT License

  •1•0•0•0•Updated Apr 11, 2023Apr 11, 2023

• CROPSR

  Public archive
  CROPSR is a python tool designed for genome-wide gRNA design and evaluation for CRISPR experiments, with special focus on complex genomes such as those found in energy-producing crops. CROPSR is a product of the DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI).

  machine-learninggenomicspython3+ 1crispr

  Python

  •

  Apache License 2.0

  •8•8•0•0•Updated Mar 16, 2023Mar 16, 2023

• k-sacce306

  Public archive
  K-FIT kinetic models for Saccharomyces cerevisiae CEN.PK and BY4741

  MATLAB

  •2•0•0•0•Updated Dec 22, 2022Dec 22, 2022

• iSace_GSM

  Public archive
  Repository of a genome-scale metabolic model for Saccharomyces cerevisiae

  Jupyter Notebook

  •1•0•0•0•Updated Nov 21, 2022Nov 21, 2022

• BECT-ABM

  Public archive
  An agent-based modeling tool supporting bioenergy and bio-product community communication regarding cellulosic bioeconomy development

  Python

  •4•1•0•0•Updated Jul 2, 2022Jul 2, 2022

• CORPSE-soil-jars

  Public archive
  R scripts and data for Ridgeway, J., Morrissey, E., Brzostek, E. Oct. 23, 2022. “Plant Litter Traits Control Microbial Decomposition and Drive Soil Carbon Stabilization.” Soil Biology and Biochemistry. DOI: 10.1016/j.soilbio.2022.108857.

  R

  •1•0•0•0•Updated Apr 21, 2022Apr 21, 2022

• ThioesteraseEnzymeSpecificity

  Public archive
  Jupyter Notebook

  •4•0•0•0•Updated Mar 27, 2022Mar 27, 2022

• KRED-data

  Public archive
  Photoinduced Chemomimetic Biocatalysis for Enantioselective Intermolecular Radical Conjugated Addition

  1•0•0•0•Updated Mar 6, 2022Mar 6, 2022

• lipo11557_growth

  Public archive
  Multi-omics analysis for Deewan et. al. (2022), "Systems analysis of Lipomyces starkeyi uncovered new gene targets for metabolic engineering"

  PostScript

  •1•0•0•0•Updated Mar 4, 2022Mar 4, 2022

• Metabolic-Modeling---Yield-Analysis-of-PhaG

  Public archive
  Repository containing scripts and analysis for Qiang et al., "Metabolic engineering strategies to produce medium-chain oleochemicals via acyl-ACP:CoA transacylase activity"

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 24, 2022Feb 24, 2022

• scer_ure2

  Public archive
  Multi-omics analysis for Liu et. al. (2021) "Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach.", AMB

  2•0•0•0•Updated Jan 13, 2022Jan 13, 2022

• rt88_growth

  Public archive
  Multi-omics analysis for Jagtap et. al. (2021), "Integrating transcriptomic and metabolomic analysis of the oleaginous yeast Rhodosporidium toruloides IFO0880 during growth under different carbon sources", AMB

  PostScript

  •1•0•0•0•Updated Jan 13, 2022Jan 13, 2022

• uncFBA

  Public archive
  Jupyter Notebook

  •1•0•0•0•Updated Nov 2, 2021Nov 2, 2021

• C4_dynamic_model

  Public archive
  MATLAB

  •

  Apache License 2.0

  •1•0•0•0•Updated Oct 13, 2021Oct 13, 2021

• FUN-BioCROP

  Public archive
  Bioenergy model of plant C spent on N acquistion and SOM cycling

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Oct 12, 2021Oct 12, 2021

• ECNet

  Public archive
  An evolutionary context-integrated deep learning framework for protein engineering

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •16•0•0•0•Updated Oct 1, 2021Oct 1, 2021

• NetID

  Public archive
  A global network optimization approach for untargeted LC-MS metabolomics data annotation and metabolite discovery

  HTML

  •

  GNU General Public License v3.0

  •25•0•0•0•Updated Sep 15, 2021Sep 15, 2021

• MetaFunPrimer_paper_info

  Public archive
  HTML

  •1•0•0•0•Updated Sep 7, 2021Sep 7, 2021

• TMTProC

  Public archive
  The TMTProC module is the group of Matlab scripts associated with our paper "TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level".

  MATLAB

  •3•0•0•0•Updated Jul 20, 2021Jul 20, 2021

• CoNSEPT

  Public archive
  Convolutional Neural Network-based Sequence-to-Expression Prediction Tool

  Python

  •

  MIT License

  •3•0•0•0•Updated Mar 14, 2021Mar 14, 2021

• Manuscript_tools

  Public archive
  C++

  •1•0•0•0•Updated Feb 27, 2021Feb 27, 2021

• iIsor_memote

  Public archive
  Repository for Issatchenkia orientalis SD108 genome-scale metabolic model iIsor

  Other

  •1•0•0•0•Updated Feb 5, 2021Feb 5, 2021

• biosteam_lca

  Public archive
  An agile life cycle assessment (LCA) platform that simultaneously characterize the economic and environmental impacts of biofuels and bioproducts under uncertainty.

  Python

  •

  Other

  •8•0•0•0•Updated Jan 22, 2021Jan 22, 2021

• LAMPS-miscanthus-microbiome

  Public archive
  Analysis files to accompany our sumbmitted paper characterizing the LAMPS Miscanthus Microbiome.

  MIT License

  •1•0•0•0•Updated Aug 27, 2020Aug 27, 2020

• Miscanthus-genome

  Public archive
  R

  •

  Other

  •1•0•0•0•Updated Jul 29, 2020Jul 29, 2020