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
Computational Libraries
- Optimization solvers
- ILOG/CPLEX
- Gurobi
- GLPK (GNU Linear Programming Kit)
Biogeochemical Modeling
Metabolic Network Modeling
- Metabolic network reconstruction
- COBRA (COnstraint-Based Reconstruction and Analysis)
- FBA tutorials
-
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
- Metabolic data analysis
Network Inference
- CoNet (Co-occurrence Network Inference)
Visualization
- Metabolic 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)