The start of a new phase for me

Today I have accepted a new role at the Lieber Institute for Brain Development (LIBD) as an Investigator. Since LIBD is affiliated with Johns Hopkins University (JHU), LIBD will support me on becoming a JHU faculty member 1. This change means that I’ll now be leading a team at LIBD, which is why I’m actively working on a new website 2 called R/Bioconductor-powered Team Data Science. On that website I’m implementing the ideas I recently proposed on another type of data science group which involve Data Science guidance sessions based on my three year experience as a teaching assistant for the MPH capstone at JHBSPH.

I also plan to make publicly available as much material as we can. This will include a series of bootcamps that I’m going to start running today for my team members and guests. It will also include our team journal/software club presentations as well as the LIBD rstats club presentations. The material that I’ll be using was made by many collaborators and friends at JHU, Harvard, WEHI, RStudio and the rstats community in general. I’m really thankful that so many people have shared their educational materials in ways that can be re-used and for making it easier for all of us to learn from them. Thank you!

Beyond the 20% education and data science guidance efforts, my team will be working with our LIBD peers, JHU collaborators, and external allies on interesting research projects such as the teamSpatial 3 that developed #spatialLIBD, #recount3, and many other upcoming projects in the realms of RNA-seq, R/Bioconductor, and genomics. We will be developing methods and software, analyzing data, and aim to build a stronger bridge between LIBD and JHU.

I’m really thankful to everyone who has been a part of my journey: mentors, colleagues, allies, sponsors, and many friends. I want to highlight my mentors Jeff Leek and Andrew Jaffe without whom I wouldn’t be where I am right now. They’ve always been my fiercest advocates and have looked out for me all these years. It’s now my turn to try have a positive influence in others, though they set a very high bar! I have a lot to learn and work to do, but I’m looking forward to it. At LIBD, JHU and elsewhere I have many people I can ask for support, which I’m grateful for.

Finally, after reading Jeff Leek’s How to be a modern scientist book in preparation for the first bootcamp today, I’ve updated my Twitter username to match my GitHub one. That is, I’ve gone from fellgernon to lcolladotor. See you around on Twitter and elsewhere!

P.S. If you find this type of team and the work that we do appealing, let me know and we’ll evaluate what options are available =)

Acknowledgments

This blog post was made possible thanks to:

R/Bioconductor-powered Team Data Science was made possible thanks to bookdown and a GitHub Actions workflow that depends on Bioconductor’s docker image, which in turn depends on the Rocker Project.

References

[1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.10. 2019. URL: https://CRAN.R-project.org/package=knitcitations.

[2] G. Csárdi, R. core, H. Wickham, W. Chang, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://CRAN.R-project.org/package=sessioninfo.

[3] A. Oleś, M. Morgan, and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.17.0. 2020. URL: https://github.com/Bioconductor/BiocStyle.

[4] Y. Xie. bookdown: Authoring Books and Technical Documents with R Markdown. ISBN 978-1138700109. Boca Raton, Florida: Chapman and Hall/CRC, 2016. URL: https://github.com/rstudio/bookdown.

[5] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown.

Reproducibility

## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 4.0.2 (2020-06-22)
##  os       macOS Catalina 10.15.6      
##  system   x86_64, darwin17.0          
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2020-09-21                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package       * version date       lib source                            
##  assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.0.0)                    
##  bibtex          0.4.2.2 2020-01-02 [1] CRAN (R 4.0.0)                    
##  BiocManager     1.30.10 2019-11-16 [1] CRAN (R 4.0.0)                    
##  BiocStyle     * 2.17.0  2020-05-14 [1] Bioconductor                      
##  blogdown        0.20    2020-06-23 [1] CRAN (R 4.0.2)                    
##  bookdown        0.20    2020-06-23 [1] CRAN (R 4.0.2)                    
##  cli             2.0.2   2020-02-28 [1] CRAN (R 4.0.0)                    
##  colorout      * 1.2-2   2020-05-18 [1] Github (jalvesaq/colorout@726d681)
##  crayon          1.3.4   2017-09-16 [1] CRAN (R 4.0.0)                    
##  digest          0.6.25  2020-02-23 [1] CRAN (R 4.0.0)                    
##  evaluate        0.14    2019-05-28 [1] CRAN (R 4.0.0)                    
##  fansi           0.4.1   2020-01-08 [1] CRAN (R 4.0.0)                    
##  generics        0.0.2   2018-11-29 [1] CRAN (R 4.0.0)                    
##  glue            1.4.2   2020-08-27 [1] CRAN (R 4.0.2)                    
##  htmltools       0.5.0   2020-06-16 [1] CRAN (R 4.0.2)                    
##  httr            1.4.2   2020-07-20 [1] CRAN (R 4.0.2)                    
##  jsonlite        1.7.1   2020-09-07 [1] CRAN (R 4.0.2)                    
##  knitcitations * 1.0.10  2019-09-15 [1] CRAN (R 4.0.0)                    
##  knitr           1.29    2020-06-23 [1] CRAN (R 4.0.2)                    
##  lubridate       1.7.9   2020-06-08 [1] CRAN (R 4.0.2)                    
##  magrittr        1.5     2014-11-22 [1] CRAN (R 4.0.0)                    
##  plyr            1.8.6   2020-03-03 [1] CRAN (R 4.0.0)                    
##  R6              2.4.1   2019-11-12 [1] CRAN (R 4.0.0)                    
##  Rcpp            1.0.5   2020-07-06 [1] CRAN (R 4.0.2)                    
##  RefManageR      1.2.12  2019-04-03 [1] CRAN (R 4.0.0)                    
##  rlang           0.4.7   2020-07-09 [1] CRAN (R 4.0.2)                    
##  rmarkdown       2.3     2020-06-18 [1] CRAN (R 4.0.2)                    
##  sessioninfo   * 1.1.1   2018-11-05 [1] CRAN (R 4.0.0)                    
##  stringi         1.5.3   2020-09-09 [1] CRAN (R 4.0.2)                    
##  stringr         1.4.0   2019-02-10 [1] CRAN (R 4.0.0)                    
##  withr           2.2.0   2020-04-20 [1] CRAN (R 4.0.0)                    
##  xfun            0.17    2020-09-09 [1] CRAN (R 4.0.2)                    
##  xml2            1.3.2   2020-04-23 [1] CRAN (R 4.0.0)                    
##  yaml            2.2.1   2020-02-01 [1] CRAN (R 4.0.0)                    
## 
## [1] /Library/Frameworks/R.framework/Versions/4.0branch/Resources/library

  1. The rules are Department and School specific at JHU, which is something that I have yet to explore in detail.↩︎

  2. It’s technically a book made using bookdown.↩︎

  3. Keri Martinowich, Kristen Maynard, Stephanie Hicks, and their team members.↩︎

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