Song Research Group - Useful Links

Academic Societies 

• Americal Society for Microbiology (ASM); ASM Microbe
• Americal Institute of Chemical Engineers (AIChE)
• International Society for Microbial Ecology (ISME)  

Lectures

• 2020 Multiscale Microbial Dynamics Modeling Course (Dr. Song participated in as a lecturer)
   
  • Tutorial narratives on KBase (https://doi.org/10.25982/1722943) 
  • Post on KBase 
  • Lectures on YouTube 
  • EMSL Blog on the course 
  • The course on OSTI.GOV
• Courses taught by Dr. Song at UNL
  • Microbial Community Modeling through BSEN 892 (Special Topics) (Spring 2021) 
  • Data-Driven Modeling through BSEN 951 (Advanced Mathematical Modeling in Biological Engineering) (Spring 2020, Spring 2022):  
    • Brunton SL, Kutz JN. Data-driven science and engineering: Machine learning, dynamical systems, and control. Cambridge University Press; 2019 (online materials)
    • Kutz JN, Brunton SL, Brunton BW, Proctor JL. Dynamic mode decomposition: data-driven modeling of complex systems. Society for Industrial and Applied Mathematics; 2016 (online materials) 
    • Géron A. Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow, 2nd Edition, O'Reilly Media; 2020
    • Ford W. Numerical linear algebra with applications: Using MATLAB. Academic Press, 2014
    • Strang G. Linear algebra and learning from data. Wellesley-Cambridge Press; 2019
  • Guest lecture on Microbial Inactivation Models for Thermal Processes through FDST 403 (Quality Assurance of Foods; taught by Dr. Dongjin Park) (Spring 2021)
     
    • Mahdinia, Ehsan, Shaowei Liu, Ali Demirci, and Virendra M. Puri. "Microbial growth models." In Food Safety Engineering, pp. 357-398. Springer, Cham, 2020.
    • Akkermans, Simen, Cindy Smet, Vasilis Valdramidis, and Jan Van Impe. "Microbial Inactivation Models for Thermal Processes." In Food Safety Engineering, pp. 399-420. Springer, Cham, 2020.
• Bioinformatics and Computational Biology, and related courses at UNL

Databases

• Microbiomes
  • Earch Microbiome Project 
  • NIH Human Microbiome Project (Proctor et al., 2019)
  • gutMDisorder (Cheng et al., 2020)
  • 1,520 reference genomes from cultivated human gut bacteria (Zou et al., 2019)
  • MDB: Microbiome Database 
  • National Microbiome Data Collaborative (NMDC)
• Omics
  • National Center for Biotechnology Information (NCBI)
  • The Inflammatory Bowel Disease Multi'omics Database

Computational Libraries

• Optimization solvers
  • ILOG/CPLEX 
  • Gurobi 
  • GLPK (GNU Linear Programming Kit)

Biogeochemical Modeling

• CHNOSZ (Thermodynamic Calculations and Diagrams for Geochemistry)

Metabolic Network Modeling 

• Metabolic network reconstruction
  • KBase
    • KBase homepage 
    • KBase learn page
    • KBase documentation
    • KBase video tutorials 
  • ModelSEED
• COBRA (COnstraint-Based Reconstruction and Analysis)
  • COBRA matlab toolbox 
  • COBRApy (documentation for COBRApy)
• FBA tutorials
  • Orth et al. (2010) 
• Cybernetic modeling
  • Ramkrishna D and Song H-S, Cybernetic Modeling for Bioreaction Engineering, Cambridge Universtiy Press (2018)
  • Ramkrishna D and Song H-S, Dynamic models of metabolism: Review of the cybernetic approach, AIChE Journal (2012) 
  • Kompala DS, Ramkrishna D, Jansen NB, and Tsao GT, Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models, Biotechnol Bioeng (1986) 

Omics Data Processing 

• Gene normalization
  • Different types of normalization methods
     
  • Analyzing RNA-seq data with DESeq2
• Metabolic data analysis
  • Metabodiff: R package for metabolic differential analysis

Network Inference 

• CoNet (Co-occurrence Network Inference) 
  • CoNet Home 
  • CoNet in Cytoscape App Store

Visualization

• Network anlaysis and visualization 
  • NetworkX (Netwrok  Analysis in Python)
  • igraph
  • Gephi 
  • Cytoscape 
• Metabolic pathways 
  • Escher (under ModelSEED)
  • D3Flux
  • Roche Biochemical Pathways

Program Languages 

• Matlab
  • Live script 
  • Programming for Computations - MATLAB/Octave (a free e-book) 

Icons for presentation

• Icons8
• flaticon
• Noun Project
• Also read this article

Other Resources 

• Enroll Education: useful content for college graduates & job seekers who are looking for guidance on employment & post graduate opportunities in the data science industry)