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Phase II — Exploration

Phase II looks to introduce students to the various subfields in computational biology. Each course is designed around a track that can be followed for Phase III and Phase IV. This is the smallest phase and will have courses that lightly touch on the history, purpose, motivation, and current state-of-the art in each Area.


Computational Biology is a rapidly growing field with many subfields/specializations cropping up all the time due to the advancement of experimental technology as well as the availability & diversity of open source biological data that can be leveraged for in silico work. We have broken down computational biology in a way that we hope can lead learners to their interests, but understand that this is not all encompassing of computational biology as a field. It’s also important to note that there’s a good chance some people working in computational biology are very good at multiple areas we have here which is awesome! We by no means want learners to syphon themselves into a single category, but rather provide a framework for what may pique their interests. We believe that over time learners will probably find they needs some combination of area profiency for their interests and hope that they continue to reference each section as they grow. Here we hope to expose learners to the basics of each major category so they can continue to follow their interests. With that, this will be the final section that we recommend completing from start to finish. All other sections you can complete only which areas interest you.

Modelling Biological Systems
To get started, check out this wikipedia page about modeling biological systems. This gives a general overview of what kind of biological modeling is done as well as, some of the software available for creating biological systems models.

The National Center for Multiscale Modeling of Biological Systems (MMBioS) develops tools to advance and facilitate cutting-edge research at the interface between high performance computing and the life sciences. Take a look at the Research that they do to understand how biological modeling looks across different scales.

Uri Alon: Into the Unknown
Uri Alon is one of the best in Systems Biology research and in this talk he is shedding some wisdom needed before you really start your journey. No matter what you do, keep going and know where you came from! Follow your interests and look back at your progress!


Cell and Systems Modeling

Cellular Modeling
This wiki page goes into detail specifically about what cellular modeling is, why we do it, and what software is used. We recommend reading it thoroughly and look at all the related projects, especially the MMBioS Project.

Systems Biology Overview
This YouTube video will help you understand the basics as to why we do systems biology modeling!

Build a complete Cellular Model using PyBioNetGen and BioNetGen. This will introduce you to a easy-to-use programing langauge BNGL and it’s Python CLI tool!

Computational Structural Biology

Computational Omic Analysis (Bioinformatics)

Bioimage Informatics

Environmental & Ecological Informatics