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CDSB BioC2020 Birds of a Feather

CDSB BioC2020 Birds of a Feather

CDSB presentation at #BioC2020 https://bioc2020.bioconductor.org/ initially proposed at https://github.com/Bioconductor/BioC2020/issues/67

Leonardo Collado-Torres

July 29, 2020
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  1. CDSB community: efforts to strengthen
    the R/Bioconductor developer
    community in Mexico/LatAm
    results showcased by regutools
    @CDSBMexico
    @areyesq @josschavezf1 @BarjonCar
    @EmilianoSotel10 @fellgernon
    @RBioinformatica
    Slides: https://speakerdeck.com/lcolladotor

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  2. • 2017: conception at BioC2017
    • 2018: first workshop ^_^
    ○ Bioconductor instructors: Martin Morgan & Benilton
    Carvalho
    • 2019:
    ○ BioC2019 scholarship app assistance
    ○ Workshop using RStudio materials
    • 2020:
    ○ regutools Bioconductor package
    ○ Workshop with RStudio & Bioconductor
    https://comunidadbioinfo.github.io/
    Community of Bioinformatics Software Developers
    @fellgernon

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  3. Who knows about ?
    Sandrine Dudoit:
    She’s one of the @Bioconductor project founders!
    @cendrinou
    https://www.stat.berkeley.edu/users/sandrine/
    @lcgunam
    Fall 2007
    Slides: https://speakerdeck.com/lcolladotor
    @CDSBMexico

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  4. Education cycle
    ● Someone teaches in a local community
    ● Local members take initiative to learn more
    ● (ideally) local members teach other members of the local
    community
    Slides: https://speakerdeck.com/lcolladotor
    @CDSBMexico

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  5. http://www.wholebiome.com/team.html#james-bullard
    James Bullard
    January 2008
    1 week intensive course
    Slides: https://speakerdeck.com/lcolladotor
    @CDSBMexico

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  6. @AlexielMedyna
    http://liigh.unam.mx/profile/dra-alejandra-medina-rivera/
    Leonardo Collado Torres
    +
    Alejandra Medina Rivera
    BioC2008
    Developer’s day + 2
    conference days
    Supported by @lcgunam
    Slides: https://speakerdeck.com/lcolladotor
    @CDSBMexico

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  7. @fellgernon & Osam
    http://lcolladotor.github.io/courses/Courses/R/
    Fall 2008

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  8. Education cycle: issues
    ● Volunteer based
    ● Once local members leave, it’s hard to continue
    ● Funding can be challenging
    ● Language barriers

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  9. Data from the last 667 submitted to Bioconductor through Github
    (Made in 2018)
    Alejandro Reyes
    @areyesq
    http://alejandroreyes.org/
    BioC2017

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  10. http://congresos.nnb.unam.mx/
    Meetings, Courses, and Workshops

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  11. Interested → Users → Developers
    How can we enable this step in LA/Mexico?

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  12. We are not alone: support network
    ● Advice, ideas,
    ● teaching materials,
    ● community building activities,
    ● volunteer instructors,
    ● funding,
    ● visibility

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  13. We are not alone: (local) support network
    Experience organizing workshops, local payment infrastructure, legal body & bank
    accounts, classroom infrastructure for bioinformatics, official letters, reservations &
    support for guests, teaching assistants, direct access to identify local needs, ...
    @nnb_unam
    @RBioinformatica
    @ccg_unam
    @lcgunam

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  14. Comunidad de Desarrolladores de
    Software en Bioinformática
    ● Community as a (virtual) university department.
    ● Constructive discussion of novel ideas.
    ● Exchange of expertise and multidisciplinary collaborations.
    ● Remove barriers for beginners (mentoring)
    ● More access to specialized training for Latin American talent.
    https://comunidadbioinfo.github.io/
    Community of Bioinformatics Software Developers

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  15. Latin American R/Bioconductor
    Developers Workshop 2018
    ● Kick-starting event of the community.
    ● Teach participants the principles of reproducible data science
    through the development of R/Bioconductor packages.
    ● Turn bioinformatic software users into software developers.
    ● Continue with similar workshops in the future

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  16. Martin Morgan
    Bioconductor
    Benilton Carvalho
    Uni Campinas
    Selene Fernandez
    LANGEBIO
    Alicia Mastretta Yanes
    CONABIO
    María Teresa Ortíz
    CONABIO
    Ale Medina
    LIIGH
    Alejandro Ponce
    CONABIO
    Leo Collado
    LIBD/Johns Hopkins
    Heladia Salgado
    CCG
    Laura Gomez
    CCG
    Daniela Ledezma
    CCG
    Alejandro Reyes
    DFCI/Harvard
    YOU YOU YOU

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  17. @doctor_calvo
    @josschavezf1

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  18. @AnaBetty2304
    Co-founded
    @RLadies_Qro

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  19. Network
    ● Learn from others
    ● Meet potential instructors
    ● Ask for support
    ● Ensure newcomers are
    included
    ● ...

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  20. CDSB board until 2019

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  21. Sustainability or burn out?
    > I am proud and excited of what we have achieved with our one-week long CDSB workshops,
    but also with how we used the tools we’ve learnt from other communities in order to keep
    interacting and communicating throughout the rest of the year. Time will tell if our efforts
    created a ripple that grew into a wave or if we’ll end burning out. Sustainability is a
    challenge, but we are greatly motivated by the impact we’ve had and can only imagine a
    brighter future.
    bit.ly/cdsb2020post --> https://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico

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  22. Avoid repeating the past: bring in new
    volunteers!
    Joselyn Chavez @josschavezf1
    ● CDSB 2018 & 2019 alumni
    ● Joined CDSB board in 2019
    ● Founded R-Ladies Cuernavaca in 2019
    ● Will co-instruct the 2020 workshop

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  23. CDSB YouTube channel
    https://www.youtube.com/channel/UCHCdYfAXVzJIUkMoMSGiZMw

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  24. What we do
    ● Workshops
    ● Slack: as a virtual department
    ● Encourage members to apply to opportunities
    ● Help navigate application processes & overcome language barriers
    ● Train others: some might join our volunteer team
    ● Adapt ideas from others
    ● Promote work by our members & allies

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  25. What we would like to do (better)
    ● Reach out to more potential sponsors: maybe through BioC?
    ● Community calls & mini courses: had our first one in July 6th 2020 now on YouTube
    ● Balance between bio-focused workshops & R development: local interest vs our goals
    ● Promote more community contributions to our blog
    ● Job & career opportunities
    ● Reach beyond Mexico: hard to replicate our local support in Mexico
    ● Build capacity:
    ○ train more instructors & teaching assistants
    ○ bring in more volunteers
    ○ Paid Slack Workspace?
    ● Organize a BioC conference in a couple of years? (The wave in the R Consortium blog post)

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  26. https://comunidadbioinfo.github.io/post/cdsb2020-building-workflows-with-rstudio-and-scrnaseq-with-bioconductor/#.Xxxjhp5KguU
    Material from a
    rstudio::conf(2020) workshop
    +
    Material from the OSCA book
    Sponsors:

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  27. Help us increase our visibility! Thx ^^ bit.ly/bioc2020cdsb →
    https://twitter.com/CDSBMexico/status/1288139636477435906?s=20

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  28. What is regutools?

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  29. Regutools package project
    Motivation:
    ● Facilitate programmatic access to
    RegulonDB
    ● Easy integration with downstream
    BioC analysis tools
    ● Improve reproducibility

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  30. How it started?
    Undergraduate project
    Database
    Functions
    SQLite database

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  31. The role of CDSB as a catalyst of regutools
    What we had at this point
    ● Functions
    ● SQLite database
    Building regutools as a
    package
    ● Functions improvement
    ● Documentation
    ● Vignette
    ● Tests
    ● Integrated workflow

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  32. Regutools package project

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  33. Regutools integrates regulonDB with the Bioconductor environment by defining an
    S4 regulondb object. The database is distributed through AnnotationHub.
    Regutools package project

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  34. Regutools package project
    Retrieve and filter data

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  35. Regutools package project
    To ease integration with other Bioconductor packages, the convert_to_granges() function
    converts a regulondb_result object into a GRanges object whenever possible

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  36. What can you do with regutools?
    Extract and visualize regulatory networks

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  37. What can you do with regutools?
    Extract and visualize genomic elements
    Integration with Gviz

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  38. Regutools package project
    Future plans: Multi-organism version

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  39. https://doi.org/10.1093/bioinformatics/btaa575

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  40. Discussion
    @areyesq

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