Applied Bioinformatics Course
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Welcome to ABC – the mirror site of Applied Bioinformatics Course!
(You may also visit ABC at Peking University if you are from universities in China)
As inspired by Walter Gilbert’s 1991 Nature article “We must hook our individual computers into the worldwide network that gives us access to daily changes in the database and also makes immediate our communications with each other”, this course is designed for wet-lab experimental graduate students in biology.
What we learn
We’ll learn, step by step, the ABCs of:
- How to find literature papers from PubMed efficiently
- How to search databases such as UniProt and RefSeq in an Advance mode
- How to align your DNA and protein sequences
- How to make a good Blast search to obtain your results with less false positive and false negative
- How to analyze your own DNA or protein sequences with various tools
- How to construct a phylogenetic tree for a set of sequences at your hand
- How to predict the three dimensional structure of your favorite protein
And lots more!
How we learn
We will run the course in a training room. Each student will have a PC connected into the Internet.
We start with introducing the international bioinformatics resources around the world, for example, NCBI and EBI. We then use the WebLab bioinformatics platform developed by CBI, to get familiar with dozens of bioinformatics tools through hands-on practice. We will do a lot of exercises for sequence alignment, database similarity search, motif finding, gene prediction, as well as phylogenetic tree construction and molecular modeling.
Finally, we will focus on several projects to solve real biological problems. You are encouraged to bring your own problems to discuss and, hopefully, to solve during the course!
You may read a brief introduction and the outline (in Chinese) of the course, or read the article Teaching the ABC of Bioinformatics (in English), or ABC Examples (in Chinese) for more details.
What you need before the course
- A desktop PC or laptop hooked to the Internet. You may also use iPad or mobile phone to browse most of the pages.
- A good background of biochemistry and molecular biology – you may try the Biotest_Cn (in Chinese) or BioTest_En (in English) to see how good at it you are.
- An ability to read the English text such as this page, and understand the meaning.
- At least three hours every week to have group discussions and to stick on the Internet to do exercises and homework assigments.
What you gain from the course
Don’t expect to become a bioinformatics expert at the end of the course, but you will believe what Alan Bleseby, one of the major developer of the EMBOSS package, indicated two decades ago:
Half day on the Web, saves you half month in the lab!
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