(note this onboarding is also applicable to high school students and any other lab interns below the PhD/MS level; HB = Dr. Holly Bik, Lab PI)
Gaining hands-on reserach training is an important part of of the undergraduate experience, and the Bik Lab welcomes applications from any student who is interested in our reserach areas (read our lab website before applying). We partiuculary welcome students from underrepresented backgrounds (women, underrepreented minorities, LBGTQ, first-generation college students, etc.)
Our lab has a limited number spaces for undergraduate students. We accept students on a rolling basis throughout the academic year (Sept-June) as well as over the summer (July/August). Students who are accepted to work in the Bik Lab will receive either hourly pay or course credit (or both; please discuss in person with HB)
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Our lab aims to equip students with an interdisciplinary skill set, particularly emphasizing computational skill dvelopment alongside traditional molecular lab tasks. Command line training is difficult and requires perserverence. Complete these tutorials to get started:
- Indtroduction to the Command Line (Unix Shell)
- QIIME2 introductory tutorial - "Moving pictures of the human microbiome" (16S rRNA amplicon dataset that takes you through data processing, OTU picking, and ecological diversity analyses)
- Our lab-specific QIIME tutorial (for 18S eukaryotic data, which is similar but some steps are slightly different, such as the databases you're using to assign taxonomy to DNA sequences):
- (Remember: Googling your error messages is the secret to bioinformatics!
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Students are also expected to read the scientific literature, and think conceptually about why we are carrying out different lab protocols and data analysis. If you are waiting for assistance or find yourself with extra time, we expect you to always be reading the literaure! Here are some review papers and references related to the work we do in the lab:
- Creer et al. (2016) The ecologists field guide to sequenced-based identification of biodiversity Methods in Ecology and Evolution
- Bik et al. (2012) Sequencing our way to understanding global eukaryotic biodiversity, Trends in Ecology and Evolution
- The above review papers are just a starting point - for every reserach area mentioned in these papers you should be looking at the cited references (big list of journal articles referred to by author/number and listed at the end of the paper). Review papers only summarize what others have found; the real work is published in the primary literature (original hypothesis-driven reserach studies).
- Use Google Scholar to look up papers (paste in the title) and search for other papers within the same reserach field (use a combination of relevant keywords like: metagenomics, DNA sequencing, nematodes, marine sediments, etc.)
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Based on your literature reading and experiences in the lab, propose an idea that you'd like me to give you $1,000 to test. If you can convince us, we will spend the money! Aim for questions/hypotheses that are thought-provoking and will dramatically increase our understanding of basic biological processes.
- Try to propose at least one new idea every week that you work in the lab.
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Scenario: The Bik lab has ground to a halt becaue of an issue with one of our critical protocols. Suggest some reasons why you think this has happened, and explain it to us. (Possible protocols: DNA extraction, PCR amplification, Sanger Sequencing, Illumina Sequencing)
These thought exercises are designed to help you learn the scientific method and think deeply about scientific problems. You need to acquire broad scientific knowledge, and learn how to apply this knowledge to solve probelms in the lab. Science is about experimenting and failing until you (hopefully, eventually) succeed and gain insight on an important biological phenomenon.