Practical Data Science andInformatics EducationSean Davis, MD, PhDCenter for Cancer ResearchNational Cancer InstituteCI4CC, October 1, 2018 @seandavis12

Slides: http://bit.ly/sd-ci4cc-2018

http://bit.ly/sd-ci4cc-2018

- Information Transfer- ++Audience Sharing++- Panel Discussion- Sharing: http://bit.ly/CI4CC-DSE- Networking and Collaboration--KISS

principle

http://bit.ly/CI4CC-DSE

Learning objectives

- Name several practical venues to teaching Data Science (DS)

- Identify practical strategies to enhance DS education- Know that building a data mature organization involves

education and community-building- Appreciate the value of trainers in DS education- Recognize the importance of community efforts and

collaboration in DS education

ApproachIllustrative examples of formats

for Data Science education

Example Approach

Software Carpentry Two-day interactive teaching

Statistical Methods for Functional Genomics

Two week intensive course

Bioconductor Workshops Short, topical workshops

NIH Hackathons Hackathons

Software Carpentry is a volunteer project dedicated to teaching basic computing

skills to researchers.

Software Carpentry highlights

- Uses limited, highly-focused, community-developed curricula

- Requires that trainers be trained!- Value to organization:

- Visible and recognizable to leadership- Addresses need- Cheap and easy- Builds community of practice and identifies trainers

- Formal, utilizes best practices

CSHL course highlights

- Maintain identity as a statistics course, not bioinformatics- Longer course, allows creativity and flexibility- Isolate students from daily work environment- Do not underestimate value of “cost” of the course- Application process--force students AND instructors to

evaluate course objectives- Learning environment is ideal- No “project” involved--choose students who are in position

to apply knowledge

CSHL Daily schedule8-9am Breakfast

9-12noon “Interactive lectures”

12-1pm Lunch

1-4pm Afternoon lab

4-5pm Research Talk

5-7pm Dinner and free time

7-8:00pm Research Talk (continued)

8-11pm Open lab

https://seandavi.github.io/ITR/

https://seandavi.github.io/ITR/

Bioconductor Workshop highlights

- More than 50% of the 3-day annual Bioconductor conference

- Multiple 1-2 hour hands-on, topical practicums in analysis methods, taught by the developers

- Workshops delivered via cloud infrastructure- All materials developed collaboratively with continuous

integration testing (everything works)- Utilize standard template- Modern collaboration (github) and publishing (gitbook)

Bioconductor workshop syllabus template

https://github.com/Bioconductor/BioC2018/tree/c2bd6d8e6330d0ceff8d23d59e111bbc68c66564

Bioconductor workshop syllabus template

https://github.com/Bioconductor/BioC2018/tree/c2bd6d8e6330d0ceff8d23d59e111bbc68c66564

Results- 6 weeks- 15 workshops- 17 contributors- 388 pages- 125 participants over two

days-

https://biohackathons.github.io/ NIH Hackathons

(with notation of other formats and organizations)

https://biohackathons.github.io/

Hackathon highlights

- Best for participants with well-formed domain expertise and technical knowledge

- Goal- and outcome-oriented- Self-directed- Like Software Carpentry, can be very attractive to

leadership- Can require significant up-front planning and logistics

NIH Hackathon schedule

- Day -60: develop projects and project leads- Day -30: begin to develop teams- Day 0.5: Introductions, team organization, infrastructure

(github, cloud instances), roles- Day 1: morning hacking, report out at lunch, afternoon

hacking, report out in evening- Day 2: morning hacking, afternoon writing and publishing- Day 2: close with presentations- Day 3+: continue hacking, publication process

Tips

- Adult education is about building confidence- Adult education is about building community- Adult education is about utility- Do not underestimate the power of food- Focus on active learning using formative evaluation

(questions), faded examples, independent work- Allow lots of time for students to interact with the

instructor(s) one-on-one

Tips

- For many students, simply having dedicated time to focus on learning is valuable

- Value the trainers with training, recognition, and community

- Recognize that every educational opportunity is part of a community-building effort

- Adopt and encourage educational and community best-practices.

- We are not doing this in isolation!

Longer-term

- Mentors and mentoring (build a list)- Online forums (force students to ask a question)- Communication tools (Slack, email lists)- Organizational issues (but do not let this be a barrier)- Partnering- Funding

Oft-forgotten

- Licensing- Contributions and attribution- Code of conduct- Privacy and ethics- Disabilities and accessibility (physical and electronic)

Just do it!

Google Doc: http://bit.ly/CI4CC-DSE

http://bit.ly/CI4CC-DSE

Acknowledgments- Software Carpentry: Greg Wilson (SWC), Lisa Federer (NIH), Francis Collins

(NIH), Ben Busby (NIH)- Bioconductor Workshops: Levi Waldron (CUNY), Marcel Ramos (CUNY),

Martin Morgan (Roswell Park), Lori Shepherd (Roswell Park)- CSHL: Harmen Bussemaker (Columbia), Tuuli Lappalainen (NY Genome

Center), Olivier Elemento (Cornell), David Stewary (CSHL), Alicia Franco (CSHL), Tomas Rube (Columbia)

- NIH Hackathons: Ben Busby (NIH), MANY participants

seandavi@gmail.comhttps://seandavi.github.io@seandavis12

mailto:seandavi@gmail.comhttps://seandavi.github.io