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Enrichment 1: your favorite genome

What is your favorite organism? Search for your favorite organism's genome online. What type of web resources are available for your organism? Try downloading your organism's genome. How big is it? What other files are included.

Enrichment 2: fasta and gff

We downloaded the yeast genome. This included .fasta files and .gff files (among other files). Learn more about .fasta files and .gff files. These are two examples of standardized file types. Standardized file types are very common in bioinformatics. They allow us to standardize information across different experiments, publications, and users. Learn more about other file formats on the UCSC Genome Browser Website Here.

Enrichment 3: standardized file formats

Standardized file formats are all around us. Try to notice some you encounter on a regular basis. Keep these in mind for next week's enrichment exercises.

Enrichment 4: finding text files in publications

Go through some papers in your field. Look at the supplemental datasets available. Are any of these datasets available as text files? What about excel files? Are any files very large? Try to download some of these files and play around with them using the terminal. You can also convert one page of an excel worksheet to a tab-delimited text file. Learn how to do this.

Enrichment 5: use the terminal

In the next few days, try to use the terminal for some operation for practice.

Enrichment 6: think about open source

Open Source is all around us, but it wasn't always the case. Try to think about things you take advantage of that are produced and then given away for free. What are the benefits or drawbacks of this approach compared to a consumer model?

Enrichment 7: Meet Linus Torvalds

Check out Linus Torvald's recent TED interview It's about 20 minutes. There is a link to the transcript if you prefer that.

assignments/enrichment1.txt ยท Last modified: 2017/08/22 06:14 by erin