If you liked it, you should have put a Seq on it
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- Job-Seq - getting a job industry as a bioinformatics/computational biologist - What is Biohub? - Lessons learned from my first year on the job
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If you liked it, you should have put a Seq on it
- 1. 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
- 2. Hello, I’m Olga. 2 I play cello I defended my Bioinformatics PhD in a Quinceañera dress I tried out for the Golden State Warriors Dance Team I studied in Math and Biological Engineering at MIT
- 3. Outline 1. Job-Seq a. My application-to-startdate timeline b. Writing a great CV and cover letter c. 2. What is CZ Biohub? (Biohub-Seq) 3. My first year on the job (Project-seq) a. A week in the life of an Olga b. Failed projects c. Successful projects
- 4. How to job-seq? *Names have been changed to protect the innocent
- 5. 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!
- 6. 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
- 7. 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?”
- 8. 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
- 9. 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
- 10. How to write a cover letter Salutation Me You Us together Timeline + Hope to hear from you soon Closing
- 11. 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
- 12. 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)
- 13. 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
- 14. What is CZ Biohub?
- 15. Slides from Amy Kistler
- 16. Background • Biohub incorporated as an independent non-profit MRO, in March, 2016 • 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 Agreements for 97,000 sf in Mission Bay and 5,000 at Stanford • $20 million gift from Reid Hoffman and Michelle Yee
- 18. Vision The Biohub will focus on understanding underlying mechanisms of disease and developing new technologies which will lead to actionable diagnostics and effective therapies.
- 20. CZ Biohub Leadership Steve Quake Co-President Jonathan Weissman Cell Atlas Project Leader Advisory Group Peter Kim ID Project Leader Jennifer Doudna Advisory Group Russ Altman Advisory Group Joe DeRisi Co-President Lucy Shapiro Chair, Stanford Biohub Committee Gajus Worthington Chief Operating Officer
- 22. 47 Chan Zuckerberg Biohub Investigators Competition Administered by Lubert Stryer, Stanford Category Percent Clinical 14% Computational 9% Engineering 27% Assistant Prof. 47% Biomedical 50%
- 23. CZ Biohub Investigator Program
- 24. Platforms
- 25. Chan Zuckerberg Biohub Platforms Imaging Engineering Rafael Gómez-Sjöberg Genome engineering Andy May Genomics Norma Neff Data Sciences Jim Karkanias Shalin Mehta
- 26. My first year on the job (Project-seq)
- 27. A slice of my schedule in February WFH = work from home Actually get work done Actually get work done Actually get work done Meetings Meetings
- 28. Project-Seq - How to choose a good project? - “Failed” projects (unclear outcome) - Dobby the free and open source package - Batch effect correction - Cupcakes + Coding - Successful projects (clear outcome) - Tabula Muris paper
- 29. “Failed” project - Dobby the free and open source package for Illumina sample sheets - Wet lab techs were manually filtering excel sheets - Needed to do this 1000s of times - Wrote a command line tool to automate this - Protocols & feature request changed daily!
- 30. “Failed Project” - Comparison of single-cell RNA-seq (scRNA-Seq) batch effects (fx) algorithms - Students from summer course all did the same scRNA-seq experiment, batch effects ensued - Perfect data for comparing batch fx algorithms! - But, students were new to programming - Entire labs work on batch fx correction
- 31. “Failed project” - Cupcakes + Coding - Audience: wet lab scientists - Weekly 1.5 hour sessions - Initially taught software carpentry curriculum, later became “office hours” - People “leveled up” enough that they were able to pick up a programming course or book on their own
- 32. Tabula Muris: single cell RNA-seq of mouse tissues - Collaboration with ~15 different tissue expert labs at Stanford and UCSF - Taught them how to use R/Seurat for analyses and Git/GitHub for code
- 33. Open science through GitHub Pull Requests! https://github.com/czbiohub/tabula-muris
- 34. Reflection on failed vs successful projects Teaching Collaboration High Low Importance of project i.e. how invested are the people you’re working with, in completing the project? What is the division of labor? What do the other people know that you don’t know? Tabula Muris paper Cupcakes + Coding Batch Effect Correction Dobby/Sample sheets Less obvious successful outcome Obvious successful outcome
- 35. Acknowledgements: The Data Science Team Jim Karkanias Paola Castro Sarah Kefayati Olga Botvinnik David Dynerman Joshua Batson James Webber Zhou Shi Questions? Angela Pisco Jay Kasberger Aaron McGeever AnithaPriya Krishnan
- 36. Supplementary
- 37. Dissertation formatting is really annoying Defended: May 12 Start date: May 29 https://github.com/olgabot/dissertation