From fly behavior toward open science and RDM, a career path.

Dr. Julien Colomb

Research data management

Colomb and Gerlach (2019)

An Open Science enthusiast

  • Fundamental neurobiology research in fruit fly

  • scholarly communication (open peer review, executable article, contributor roles)

  • Open science communities and training (OSMOOC, turing way, OLS)

  • Open FAIR hardware

  • Research data management (outreach and tools)

Career path, timeline

Code 
library('rorcid')
library(data.table)
library(dplyr)
library(vistime)
library(tidyr)

meorcid = "0000-0002-3127-5520"

me_act=orcid_activities(meorcid)

act_table = rbindlist(me_act[[1]]$educations$`affiliation-group`$summaries, fill=TRUE)
act_table_w = rbindlist(me_act[[1]]$employments$`affiliation-group`$summaries, fill=TRUE)



act_table_w$`employment-summary.end-date.year.value` = replace_na(act_table_w$`employment-summary.end-date.year.value`, "2026")

act_table_w2 = act_table_w |> 
  mutate(
    across(where(is.character), ~replace_na(.x, "01"))
  ) |>
  transmute (
  event =paste0(`employment-summary.role-title`, ", \n",`employment-summary.organization.name`),
  start = paste (`employment-summary.start-date.year.value`,`employment-summary.start-date.month.value`,`employment-summary.start-date.day.value`, sep="-"),
  end = paste (`employment-summary.end-date.year.value`,`employment-summary.end-date.month.value`,`employment-summary.end-date.day.value`, sep="-")
  )
act_table2 = act_table |>
  replace_na (list(rep("01", ncol(act_table_w))) )|>
  transmute (
  event = paste0(`education-summary.role-title`, ", \n",`education-summary.organization.name`),
  start = paste (`education-summary.start-date.year.value`,`education-summary.start-date.month.value`,`education-summary.start-date.day.value`, sep="-"),
  end = paste (`education-summary.end-date.year.value`,`education-summary.end-date.month.value`,`education-summary.end-date.day.value`, sep="-")
)

timeline =rbind (act_table_w2,act_table2) |> arrange(start)
timeline$group = c(rep("Research",3),rep("Animal behavior and data analysis",4), rep ("Project management, RDM",3))



timeline |> vistime(show_labels=FALSE, col.event = "event",
col.tooltip="event")

Research

  • Neurogenetics in Drosophila

  • learning and memory

  • Brains as output-input systems

Mendoza et al. (2014)

Interest in open science

  • Paris: One standard excel sheet for the whole lab.
  • Berlin: open data on figshare, code reads the data directly there.
  • Berlin: open science and OSS with Prof. Bjoern Brembs:
    • open source analysis software
    • live figure

https://f1000research.com/articles/3-176/v2

Figure 3b: Flies with PKCi expression in motorneurons, are impaired in self-learning.
Colomb and Brembs (2016)

Scholarly communication

open peer review

Tennant et al. (2017)

Contributor roles

Evolution and Adoption of Contributor Role Ontologies and Taxonomies,, Mohammad Hosseini1, Julien Colomb2, Alex O. Holcombe3, Barbara Kern4, Nicole A. Vasilevsky5, Kristi L. Holmes^1,6

In press, follow up of:

Vasilevsky et al. (2020)

Open science communities

@community2020 Community and Scriberia (2020)

GIN-tonic: folder structure template

Colomb et al. (2021)

References

my career in open science.

Colomb, Julien, Thorsten Arendt, Keisuke Sehara, and The Gin-Tonic team. 2021. “Towards a Standardized Research Folder Structure.” Generation Research. https://doi.org/10.25815/WCY6-M233.
Colomb, Julien, and Björn Brembs. 2016. “PKC in Motorneurons Underlies Self-Learning, a Form of Motor Learning inDrosophila.” PeerJ 4 (April): e1971. https://doi.org/10.7717/peerj.1971.
Colomb, Julien, and Roman Gerlach. 2019. “Why Research Data Management: Four Videos,” March. https://doi.org/10.5281/ZENODO.2602634.
Community, The Turing Way, and Scriberia. 2020. “Illustrations from the Turing Way Book Dashes,” February. https://doi.org/10.5281/ZENODO.3678226.
Mendoza, Ezequiel, Julien Colomb, Jürgen Rybak, Hans-Joachim Pflüger, Troy Zars, Constance Scharff, and Björn Brembs. 2014. “Drosophila FoxP Mutants Are Deficient in Operant Self-Learning.” Edited by Hiromu Tanimoto. PLoS ONE 9 (6): e100648. https://doi.org/10.1371/journal.pone.0100648.
Tennant, Jonathan P., Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, et al. 2017. “A Multi-Disciplinary Perspective on Emergent and Future Innovations in Peer Review.” F1000Research 6 (November): 1151. https://doi.org/10.12688/f1000research.12037.2.
Vasilevsky, Nicole A., Mohammad Hosseini, Samantha Teplitzky, Violeta Ilik, Ehsan Mohammadi, Juliane Schneider, Barbara Kern, et al. 2020. “Is Authorship Sufficient for Today’s Collaborative Research? A Call for Contributor Roles.” Accountability in Research 28 (1): 23–43. https://doi.org/10.1080/08989621.2020.1779591.