“Learning Bioinformatics”

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The Story

“Learning Bioinformatics”
by Esther Landhuis
The Scientist, July 1, 2016

The pitch


Here’s a pitch for the Careers section of The Scientist.

Bench to Bioinformatics
Transitioning from ‘wet lab’ to computers doesn’t always require formal training.

As a microbiology major fresh out of college, Jennifer Fouquier hit the ground running working in biotech. “I had timers on my hip and at my desk,” she recalls. “Thinking about all the experiments I had going really kept me on my feet.” After several years, though, the long days of pipetting, dissecting and cell sorting left the young researcher exhausted and discontent. “Sometimes I’d start experiments at 2am and go for 17 hours. It was really hard work,” Fouquier says. “I really wanted to be more involved with the data analysis and see how everything turned out. It became frustrating because I didn’t get to see the end results of the work.”

That yearning led Fouquier to pursue a master’s degree in biomedical informatics, which helped her land her current job as a bioinformatics programmer at Scripps Research Institute in La Jolla, California. Several others in her circles have made a similar journey from “wet lab” to bioinformatics, albeit with varied routes that did not involve formal training.

Katie Fisch, a computational biologist at the University of California, San Diego, took a DIY approach. As a population genetics PhD with no prior training in computer programming, Fisch applied for a two-year grant and spent the first year of her postdoc teaching herself Python and R through online CS courses.

Tim Putman transitioned from “wet lab” biology into bioinformatics through a users group (multi-disciplinary discussion-based get-togethers) at Oregon State University, where he had been researching bacterial pathogens as a PhD student. Putman learned to code through workshops and seminars put on by the users group and is now a postdoc at Scripps Research Institute, working to create an open central database for microbial genetic data.
I met Fouquier, Fisch and Putman last month on a trip to San Diego to attend a rare disease conference. All three shared practical tips that would be helpful to TS readers considering a similar career shift from wet lab into bioinformatics.

The story would include US/worldwide statistics on the growth of the bioinformatics field in recent decades, e.g. number of undergraduate courses, graduate training programs, jobs and such. And depending on length/scope it could include more detail on user groups such as the Oregon State group that was instrumental in Putman’s transition to bioinformatics — e.g. how to start these groups, how they help life science researchers get training and make connections in the computational realm.

About me:

I transitioned from science (PhD immunology) to journalism about a decade ago by way of the UC Santa Cruz science writing program. Since then I’ve been a staff reporter for Alzheimer Research Forum and have written for Science, Scientific American, Science News for Students and other outlets since going freelance in 2014. More info and clips at http://www.estherlandhuis.com.

I got your contact info from TS freelance contributors [redacted], who also live in the SF Bay Area and did the UC Santa Cruz program.

Could you please let me know if you’re interested in this Careers story, and what your rates are?

Thanks for your consideration,

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