General Onboarding Tasks

This is an overview/example of onboarding tasks for new members of the lab. This may be lab managers, PhD students or new undergrad RAs. Some of it is administrative, other is for lab content. This is a living document and may change – check with Avram or your advisor to see what the most current onboarding timeline looks like.

Last updated: Aug 2025

Technical onboarding

  • Join Holmes slack and possibly CAHBIR slack
  • Download box drive and request to be added to lab box (or, if you’re an undergrad, ask your advisor for what folders to be added to)
  • Broadly overview our lab wiki https://holmeslab.github.io/holmeslab/
  • Get card access for CAHBIR building – email cahbir-support#rutgers.edu and ask for access, cc lab manager & Avram (and mention your role in the lab, e.g., RA, PhD student, etc.)
  • Request Amarel account (linked to your netID) by filling out this form: https://oarc.rutgers.edu/amarel-cluster-access-request/
    • PI name = Avram Holmes
    • Campus = Piscataway
    • Department = Center for Advanced Human Brain Imaging Research
  • Request access to our lab partition on Amarel “/projects/f_ah1491_1” and “/scratch/f_ah1491_1” by emailing help@oarc.rutgers.edu and CC’ing Avram and lab manager
    • Copy Avram, Carrisa, and Kaley on any emails to OARC
  • Set up VPN if not on Rutgers wifi – VPN Setup Tutorial
  • Do CITI certificates – information here CITI Courses for Rutgers
    • Send CITI certifications to lab manager
  • Get access to NDA and other open source data
    • If you’re an undergrad – ask your advisor which open source data you should be added to. Then ask lab manager to add you to those.
    • If you’re a full-time RA, PhD student or Postdoc, ask lab manager to add you to all the open-source data agreements.
  • Add relevant lab calendars to your google calendar (see here)
  • Sign up for relevant listservs / Email lists (see here)
  • Set up a reference/citation/paper manager if you don’t have one already. Free (or covered by RU) options = EndNote, Zotero. Other = Paperpile. All will have browser extensions.

Lab Training

  • If full-time: Set up a meeting with each of the graduate students and postdocs in the lab to hear about their research!
  • Go through Amarel Computing section on lab wiki in detail
  • Go through Lab Policies section on lab wiki in detail
  • Set up time for L1 training for fMRI scanner (See CAHBIR MRI Suite section under Running Experiments in lab wiki & sign up here)
  • See lab wiki Resources section for materials on coding, grant writing, etc.; decide what’s relevant for you
  • Go through initial literature review papers recommended below
    • Note from Carrisa: recommend reading each paper 1-3 times and taking notes, including questions to talk with me about. If a particular concept/method is either confusing or otherwise interesting to you, I recommend going to the reference(s) cited in the paper you’re reading, and add that paper to your TBR list as well. These “secondary” reads can be less extensive of course (e.g., maybe just reading abstract or results), or fully read through with notes etc. as well - totally tailored to you given your level of interest, gaps in understanding you may have, etc.

Literature review

  • The TCP data collection paper (which we’re collecting ‘part 2’ of right now) just got published:
    • The Transdiagnostic Connectome Project: an open dataset for studying brain-behavior relationships in psychiatry. Scientific Data, 12(1), 923. https://doi.org/10.1038/s41597-025-04895-z
  • These 2 papers are good examples of the basic connection between ‘functional connectivity’ and various clinical/developmental factors which people analyze in the lab.
    • Orchard ER Protective role of parenthood on age-related brain function in mid- to late-life. [pdf]
    • Qu Y, Distinct brain network features predict internalizing and externalizing traits in children, adolescents, and adults. [pdf]
  • This paper combines a bunch of different methods used in the lab.
    • The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis.
    • Similar to Carrisa’s current work, and much of Avram’s interest. Looking at individuals with Psychosis, network and network reconfigurations and states using various methods.

Big papers in the field:

  • Cocuzza, C. V., Chopra, S., Segal, A., Labache, L., Chin, R., Joss, K., & Holmes, A. J. (2025). Brain network dynamics reflect psychiatric illness status and transdiagnostic symptom profiles across health and disease. In bioRxiv (p. 2025.05.23.655864). https://doi.org/10.1101/2025.05.23.655864
  • Chopra, S., Cocuzza, C. V., Lawhead, C., Ricard, J. A., Labache, L., Patrick, L. M., Kumar, P., Rubenstein, A., Moses, J., Chen, L., Blankenbaker, C., Gillis, B., Germine, L. T., Harpaz-Rotem, I., Yeo, B. T. T., Baker, J. T., & Holmes, A. J. (2025). The Transdiagnostic Connectome Project: an open dataset for studying brain-behavior relationships in psychiatry. Scientific Data, 12(1), 923. https://doi.org/10.1038/s41597-025-04895-z
  • Reinen, J. M., Chén, O. Y., Hutchison, R. M., Yeo, B. T. T., Anderson, K. M., Sabuncu, M. R., Öngür, D., Roffman, J. L., Smoller, J. W., Baker, J. T., & Holmes, A. J. (2018). The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis. Nature Communications, 9(1), 1157. https://doi.org/10.1038/s41467-018-03462-y
  • Bassett, D. S., & Sporns, O. (2017). Network neuroscience. Nature Neuroscience, 20(3), 353–364. https://doi.org/10.1038/nn.4502 Betzel, R. F., & Bassett, D. S. (2017). Generative models for network neuroscience: prospects and promise. Journal of the Royal Society, Interface / the Royal Society, 14(136). https://doi.org/10.1098/rsif.2017.0623
  • Laumann, T. O., Snyder, A. Z., & Gratton, C. (2024). Challenges in the measurement and interpretation of dynamic functional connectivity. Imaging Neuroscience, 2, 1–19. https://doi.org/10.1162/imag_a_00366 Lurie, D. J., Kessler, D., Bassett, D. S., Betzel, R. F., Breakspear, M., Kheilholz, S., Kucyi, A., Liégeois, R., Lindquist, M. A., McIntosh, A. R., Poldrack, R. A., Shine, J. M., Thompson, W. H., Bielczyk, N. Z., Douw, L., Kraft, D., Miller, R. L., Muthuraman, M., Pasquini, L., … Calhoun, V. D. (2020). Questions and controversies in the study of time-varying functional connectivity in resting fMRI. Network Neuroscience (Cambridge, Mass.), 4(1), 30–69. https://doi.org/10.1162/netn_a_00116
  • Buckholtz, J. W., & Meyer-Lindenberg, A. (2012). Psychopathology and the human connectome: toward a transdiagnostic model of risk for mental illness. Neuron, 74(6), 990–1004. https://doi.org/10.1016/j.neuron.2012.06.002
  • Parkes, L., Satterthwaite, T. D., & Bassett, D. S. (2020). Towards precise resting-state fMRI biomarkers in psychiatry: synthesizing developments in transdiagnostic research, dimensional models of psychopathology, and normative neurodevelopment. Current Opinion in Neurobiology, 65, 120–128. https://doi.org/10.1016/j.conb.2020.10.016
  • Kotov, R., Krueger, R. F., Watson, D., Achenbach, T. M., Althoff, R. R., Bagby, R. M., Brown, T. A., Carpenter, W. T., Caspi, A., Clark, L. A., Eaton, N. R., Forbes, M. K., Forbush, K. T., Goldberg, D., Hasin, D., Hyman, S. E., Ivanova, M. Y., Lynam, D. R., Markon, K., … Zimmerman, M. (2017). The Hierarchical Taxonomy of Psychopathology (HiTOP): A dimensional alternative to traditional nosologies. Journal of Abnormal Psychology, 126(4), 454–477. https://doi.org/10.1037/abn0000258
  • Cole, M. W., Repovš, G., & Anticevic, A. (2014). The frontoparietal control system: a central role in mental health. The Neuroscientist: A Review Journal Bringing Neurobiology, Neurology and Psychiatry, 20(6), 652–664. https://doi.org/10.1177/1073858414525995
  • McTeague, L. M., Goodkind, M. S., & Etkin, A. (2016). Transdiagnostic impairment of cognitive control in mental illness. Journal of Psychiatric Research, 83, 37–46. https://doi.org/10.1016/j.jpsychires.2016.08.001
  • Podcast recommendation from Kaley: “A great intro to basic network neuroscience concepts is this podcast episode: The Brain as a Complex System (I’m not sure your level of familiarity, but if not familiar, this gives a great intro into what people mean when they say ’network’, ’node’, etc etc):”