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Programming for Scientists: Enhancing Research Skills

Learn why scientists need to know how to program and discover the benefits of integrating programming skills into scientific research. Develop expertise in managing data, building experiments, finding funding, communicating results, and more.

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Programming for Scientists: Enhancing Research Skills

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Presentation Transcript

  1. Why?

  2. Why are you learning this? “I’m [studying to be] a scientist, not a programmer. Why do I need to know how to program?”

  3. To do good science ... • Know your field, and your data • Be creative, with interesting ideas • Manage a research group • Communicate your results • Find funding • Understand politics • Do public speaking • Build experiments • Know others that can help with the above

  4. Scientists are generalists Don’t need to know everything about everything. Do need to know a bit about most things. And a lot about a few things.

  5. “Know your data” Bioinformatics works with large data sets. How do you learn about 100 GB of sequence data? Must use computers to help out.

  6. Applications “Restaurant meals” • web-based BLAST, FASTA, HMMER • PubMed, Entrez, Google • Ensembl, WormBase

  7. Components “Canned meals” • command-line BLAST, FASTA, HMMER • unix utilities, from grep to Emboss • web-services like EUtilities • Excel

  8. Toolkits “Ingredients” • programming languages - Perl, Python, C, C++, Java, Visual Basic, PHP • software libraries - BioPerl, Biopython, and BioJava • databases - MySQL, Postgres, Oracle

  9. These Levels Mix Add spices to a restaurant meal Combine fresh and canned ingredients • Write a program to do the same Entrez search every week and list the new hits. • Do a BLAST search against sequences which have your new “QUIBBET” motif • Merge results from different searches • Import data into Excel for plotting

  10. “Build Experiments” Bioinformatics is an experimental science, where the experiments are done on computers. In a wet lab, you can buy a machine for some experiments (like sequencing) Or you can use several machines (stirrer, centrifuge, glassware) and piece them together. Or make your own hardware.

  11. New hardware New hardware might be some tape and glue. Or you might have a lab technician. Or a department technician. Or hire outside help (like me)

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