Bioinformatics For Programmers

Question

[John]

I will be flying from the East Coast, USA to the West Coast this week and will have some spare time during the flight to read, write, etc.

I am interested in learning more about Bioinformatics from a programmers point of view since I am a programmer and not a biologist.

Can anyone recommend a free video lecture that introduces Bioinformatics from a programmers point of view? Every video I find is designed for Biologists who are unfamiliar with programming.

Thank you!

Answer 1

[Will]

One of the talks at PyCon this year showed sequence alignment from a programmer's point of view (you can see the video here). He showed how he used Bloom Filters to do contig assembly. The talk was very good and his Bioinformatics paper was enlightening. Although I don't know of any single video that shows all parts of bioinformatics from a programmer's point of view

I'm sure after a few hours there will be a nice collection from the community though.

Answer 2

[Alastair Kerr]

I recommend learning some basic biology on the subject areas that may interest you. Knowing that will help refine your code much better than anything else I can think of. Browse you tube for some inspiration and get some appropriate material from your local library or google for documents in suitable subject areas.

For example if you are working with microscopy or proteomics data get some inspiration from the Inner life of a cell or if working on next gen sequence data search youtube for illumina, 454, solid and ion torrent platforms.

Examples of good biology text books to get from your library

• Cell biology: Cell Biology
• Genetics: Genes X

Answer 3

[User 1933]

Playing with database and then trying to understand the content and basic stuff of how data are driven and collected in that database, and what does each parameter mean would be a good approach to get feeling as biologist.

For instance, Microarray data (GEO) and how they work, or in enzymes say BRENDA database for instance, what each parameter represent and how they measure.