Upgrade to Pro — share decks privately, control downloads, hide ads and more …

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

More Decks by Leonardo Collado-Torres

Other Decks in Science


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

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

  8. Education cycle: issues • Volunteer based • Once local members

    leave, it’s hard to continue • Funding can be challenging • Language barriers
  9. Data from the last 667 submitted to Bioconductor through Github

    (Made in 2018) Alejandro Reyes @areyesq http://alejandroreyes.org/ BioC2017
  10. http://congresos.nnb.unam.mx/ Meetings, Courses, and Workshops

  11. Interested → Users → Developers How can we enable this

    step in LA/Mexico?
  12. We are not alone: support network • Advice, ideas, •

    teaching materials, • community building activities, • volunteer instructors, • funding, • visibility
  13. None
  14. 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
  15. None
  16. 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
  17. 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
  18. 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
  19. None
  20. @doctor_calvo @josschavezf1

  21. @AnaBetty2304 Co-founded @RLadies_Qro

  22. Network • Learn from others • Meet potential instructors •

    Ask for support • Ensure newcomers are included • ...
  23. CDSB board until 2019

  24. 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
  25. 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
  26. CDSB YouTube channel https://www.youtube.com/channel/UCHCdYfAXVzJIUkMoMSGiZMw

  27. 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
  28. 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)
  29. @CDSBMexico

  30. 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:
  31. Help us increase our visibility! Thx ^^ bit.ly/bioc2020cdsb → https://twitter.com/CDSBMexico/status/1288139636477435906?s=20

  32. None
  33. What is regutools?

  34. Regutools package project Motivation: • Facilitate programmatic access to RegulonDB

    • Easy integration with downstream BioC analysis tools • Improve reproducibility
  35. How it started? Undergraduate project Database Functions SQLite database

  36. 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
  37. Regutools package project

  38. Regutools integrates regulonDB with the Bioconductor environment by defining an

    S4 regulondb object. The database is distributed through AnnotationHub. Regutools package project
  39. Regutools package project Retrieve and filter data

  40. 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
  41. What can you do with regutools? Extract and visualize regulatory

  42. What can you do with regutools? Extract and visualize genomic

    elements Integration with Gviz
  43. Regutools package project Future plans: Multi-organism version

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

  45. Discussion @areyesq