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baciq

BACIQ is the python-compatible program associated with our paper "Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-Statistics with Peptide Quantification Concordance". Please refer to the Readme.docx for further instructions.

bect-abm

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

bioindustrial-park

BioSTEAM's Premier Repository for Biorefinery Models and Results

biosteam

The Biorefinery Simulation and Techno-Economic Analysis Modules; Chemical Process Simulation Under Uncertainty

biosteam_lca

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

c4_dynamic_model

consept

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

corpse-soil-jars

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.

cropsr

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).

cropwatr

Implementation of FAO 56 (similar to CropWat, but with expanded features) in R

ecnet

An evolutionary context-integrated deep learning framework for protein engineering

esm-r-script

Script created for ESM calculations on large datasets

fun-biocrop

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

fun-prose

iisor_memote

Repository for Issatchenkia orientalis SD108 genome-scale metabolic model iIsor

isace_gsm

Repository of a genome-scale metabolic model for Saccharomyces cerevisiae

k-sacce306

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

kmer-based-subgenome-mapping

kred-data

Photoinduced Chemomimetic Biocatalysis for Enantioselective Intermolecular Radical Conjugated Addition

lamps-miscanthus-microbiome

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

landing-pad-model

lipo11557_growth

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

manuscript_tools

metabolic-modeling---yield-analysis-of-phag

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

metafunprimer_paper_info

miscanthus-genome

netid

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

paper_howe_2023_switchgrass_metat

pave

ra-abm

This is the code to implement the FBRK method for the paper "Reward-based Participant Management for Crowd-Sourcing Rainfall Monitoring: An Agent-Based Model Simulation"