What is BioInformatics? Intro Tutorial- Cytoscape GenePattern io (1/2)
Channel: Elliott
Date: 2019-01-17

Interested in a bioinformatics, computational biology, bioengineering, or machine learning career? This introduction tutorial shows how to prepare for these fields with a reading list in biology, physics, statistics, and computer science. The next video will cover how to combine cytoscape, genepattern, and io software together to do scientific research.

*What is Jupyter? What is io?*
Jupyter is a new operating system has become the most popular tool in data science. io is a new versions of jupyter that is perfect for beginners wanting learn how to code, because it’s easy to install and gives you all the tools you need. io also lets you program on any device! This is because io is a website that runs on google cloud compute engine. I also show how you can build fast jupyter applications using io online.

*Books*
Cartoon Guide to Chemistry: Gonick and Criddle
Cartoon Guide to Physics: Gonick and Huffman
Cartoon Guide to Genetics: Larry Gonick and Mark Wheelis
Doing Bayesian Data Analysis: John Kruschke
Deep Learning: Goodfellow, Bengio, Courville
Information Theory, Inference and Learning Algorithms: David MacKay
Machine Learning- A Probabilistic Perspective: Kevin Murphy
CRISPR/Cas9 in Genome Editing and Beyond: Wang, La Russa, Qi
Statistical Methods in Molecular Evolution: Rasmus Nielsen
Molecular Biology of the Cell: Bruce Alberts, et al
Chemistry- A Molecular Approach: Nivaldo Tro
University Physics with Modern Physics:  Young and Freedman
Consistent Quantum Theory: Robert Griffiths
Mathematical Foundations of Quantum Mechanics: John Von Neumann

*Tutorial Topics*

Introduction- 0:0
Here we explain what bioinformatics is. BioInformatics is were biology computer science, and statistics meet. BioEngineering Professor Russ Altman, notes that these fields are combined together to create software. 
You learn how biology can be used to solve computer science problems. For instance, how open source software can be analyzed using phylogenetic algorithms.
We also introduce io which lets you do computer programming in any language on any device. I do most of my programming on an ipad! You can also use io to build websites. 

Birth of Machine Learning and Statistical Physics- 3:10
We start by learning how chemistry and data science are connected through an interesting algorithm called entropy. Entropy is was invented by physicist Gibbs and later invented by Claude Shannon. Shannon invented this in something called information theory. Von Neumann told Shannon about the connection between these, which is why both are called entropy.

Physics in Machine Learning and Evolutionary Biology- 6:40
We learn how the statistical algorithms invented in physics are used today in the cutting edge of biology and machine learning. A great example of this is the Ising model which uses variational inference. We also cover what books to read learn about neural network and bayesian statistics. It also introduces the programming language R.

How to Learn Biology- 9:30
I show where to begin in genetics and then what book to read when you want a deeper molecular biology approach. I introduce a great research paper on CRISPR CAS9 technology, but then also mention that there are other technologies, for instance high throughput sequencing methods like microfluidics in abate lab.

How to Learn Programming- 11:00
I recommend the best websites and youtube channels for learning programming. The websites codecademy, w3 schools, and google cloud's quickstart tutorials are awesome for learning to code. Also Socratica's youtube channel is great for python.

Cytoscape and io Online- 13:05
Learn to take any  graphical network you create in cytoscape and then publish it as a website using io Online. I build a website that anyone can go to to check out the bioinformatics reading list. In the next video I'm going to combine io, Cytoscape, and GenePattern to show examples of scientific research in bioinformatics.