If I wasn’t such a mess Olga Botvinnik R Ladies Philly + DataPhilly 2019-04-16 Twitter, GitHub: @olgabot

Hello, I’m Olga. 2 I play cello I defended my Bioinformatics PhD in a Quinceañera dress I’m a member of a hip-hop dance company I breakdance (bgirl) I studied in Math and Biological Engineering at MIT

Olga Botvinnik Data Sciences Chan Zuckerberg Biohub

Background • The CZ Biohub is an independent non-profit 501(c)3 MRO • Grant Agreement signed: $600 million over 10 years. • Master Collaboration Agreement (MCA) signed among the Biohub, Stanford, UC San Francisco, and UC Berkeley. • Space Use Agreement for 97,000 sf in Mission Bay

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Vision The Biohub will focus on understanding underlying mechanisms of disease and developing new technologies which will lead to actionable diagnostics and effective therapies.

Chan Zuckerberg Biohub Steve Quake Co-President Jonathan Weissman Peter Kim Jennifer Doudna Russ Altman Joe DeRisi Co-President Gajus Worthington COO Lucy Shapiro Susan Marqusee Jeremy Reiter

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Investigator Program

47 Chan Zuckerberg Biohub Investigators Competition Administered by Lubert Stryer, Stanford Category Percent Clinical 14% Computational 9% Engineering 27% Assistant Prof. 47% Biomedical 50%

CZ Biohub Investigator Program

Chan Zuckerberg Biohub Platforms Imaging Engineering Rafael Gómez-Sjöberg Genomics Norma Neff Data Sciences Jim Karkanias Shalin Mehta

CZ Biohub Data Science Team Joshua Batson James Webber Angela Pisco Aaron McGeever David Dynerman Olga Botvinnik Saransh Kaul Jenny Folkesson Jack Hamm Lucy Li Jim Karkanas Lekha Karanam AnithaPriya Krishnan Phoenix Logan Samantha Hao Vedran Hadziosmanovic Sabera Talukder

In-toto imaging of early morphogenesis nuclei labelled fly embryo (Loic Royer) volumetric image dimension 532 x 1352 x 108, 2500 time points, 21 hour recording, 30 second intervals, 1TB Loic Royer

Internal Projects: Cell Atlas & Infectious Disease

Infectious Disease Initiative •Partner with local and global health groups •Training programs and expertise exchanges •Global IDSeq Portal • bNAb characterization • New vaccine strategies and technologies • Immunogen identification and design •NGS-based pathogen detection and identification •Novel diagnostics for microbial antibiotic resistance •Discovery of host-factor antiviral drug targets •Create large-scale replicon generation •Identification of host factors Emily Crawford Leslie Goo Andreas Puschnik Amy Kistler Cristina Tato Krista McCutcheon DETECT TREAT PREVENT RESPOND

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Cell Atlas Initiative Architecture •Endogenous protein tagging •In vivo localization of every protein •Defining the interactome of all proteins Theory • Rethinking the foundations of cell biology and providing quantitative, testable hypotheses Lineage •Microscopy based lineage measurement technologies in worm, fish and mouse •Nuclease bar coding approaches to genetic lineage tracing in xenografts Identity •Single cell transcriptome and proteome analysis in mouse and human •Tabula Muris Manu Leonetti Loic Royer Spyros Darmanis Greg Huber ARCHITECTURE LINEAGE IDENTITY THEORY

What makes Biohub unique to me? 20 Live streaming channel twitch.tv/BioinformaticsBeyonce Cupcakes & Coding Weekly programming demos or office hours

If you liked it, you should have put a Seq on it Olga Botvinnik, PhD Data Sciences Chan Zuckerberg Biohub March 2nd, 2018 UC Davis - Current Progress in Biotechnology Seminar

How to job-seq? *Names have been changed to protect the innocent

Application timeline: ~6 months from start to finish 2016 December Prepared CV 2017 January Applied to postdocs Postdoc interviews Started applying to industry February Kept applying to industry jobs March Phone interviews April Onsite interviews Received offers May Defended Started new job!

What kind of job do you want? - Type of organization - Academic postdocs - Startups - Established companies - Consider: company size - <20 - small, tight-knit, room to grow - 20-100 - In the middle of growing pains - 100-200 - established but small, you’ll still recognize everyone’s face - 200+ - large, won’t know everyone in the org - How much should you be paid? - Check location-based salaries on Glassdoor.com

Use your network to meet people to get jobs - Social media presence - Conferences - Ask for introductions to friends of friends who work at companies you’re interested in - Before you meet with them, do your homework. Know what the company does and where the industry is overall. Don’t ask “googleable” questions e.g. asking an Illumina employee. “How does this sequencing thing work?”

Have a great online presence - Have an (up to date) website - Blog is not necessary, but information is - Have recent publications or projects listed prominently - “Hugo” framework (https://gohugo.io/) has nice academic templates - GitHub pages with READMEs!! - It’s weird when you go to someone’s GitHub page and all they have is projects from a few years ago - Great READMEs tell me this person has great communication skills - Facebook, Twitter, etc should be accurate - Your most recent school/location - Profile pictures should look like you

How to write your CV - It’s okay to feel inadequate for a little bit - Then pause, take a deep breath and stop comparing yourself - Find someone’s CV with a nice template and copy it - Mine is a fork: github.com/olgabot/latex-moderncv - This template does combined CV + Cover Letter as one PDF - Academic vs Industry? - I used the same one - Add sections that showcase things you’re proud of - E.g. I added a “software” section to show software packages I wrote or contributed code changes to - Keep significant contributions only: I technically have contributed to SciPy through a docstring change but I didn’t feel it was sufficient

How to write a cover letter Salutation Me You Us together Timeline + Hope to hear from you soon Closing

Where I applied + stories from the interview trail Company Phone interview Onsite interview Received offer Early cancer detection startup Yes No No Bioinformatics consulting company Yes Yes No CRISPR startup Yes Yes No Chan Zuckerberg Initiative Yes Yes No Large tech company's venture into biology Yes Yes No Single cell startup Yes Yes Yes Chan Zuckerberg Biohub Yes Yes Yes Focused on small (<200 people) companies because I wanted to be part of the growth phase

My positives and red flags from onsite interviews - “Appreciation ping-pong” - Thoughtful management style - Focus on relationships, making sure the people are good to work with - Experience in the industry - Concrete growth plan for maintaining culture - Awesome projects - Open source-y - Not polite to waitstaff - C-level people were happy, my-level people weren’t - Difference between people there for <3 months vs 3+ months - “Management style? What do you mean?” - Interview outing is really an “outing” and not a regular thing - Interviewer tries to sound smarter than you Positives Red Flags (negatives)

Focus on things you can control vs things you can’t - You might get some hard hitting questions - E.g. an interviewer criticizes or attacks you - Remember, they were strangers to you a day ago! This is your first time meeting them and they’re trying to understand where you come from - When someone criticizes you for a past decision, you can say: “At the time, I was thinking about X” - In retrospect, I would have .. - Bring the conversation back to your accomplishments

Why am I such a mess?

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Maybe I’m not as much of a mess as I thought I was ...

What would you do if you weren’t such a mess?