Organic farming with special reference to vermiculture
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
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
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
25. Chan Zuckerberg Biohub Platforms
Imaging
Engineering
Rafael Gómez-Sjöberg
Genome engineering
Andy May
Genomics
Norma Neff
Data Sciences
Jim Karkanias Shalin Mehta
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