Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Netbooks contains a catalog of 19 case studies in regulatory genomics using the Network Zoo tools.

Code availability

Netbooks can be accessed through and the individual Jupyter notebooks are available at


  1. Tiwari, K. et al. Mol. Syst. Biol. 17, e9982 (2021).

    Article  Google Scholar 

  2. Kluyver, T. et al. In Positioning and Power in Academic Publishing: Players, Agents and Agendas (eds Loizides, F. and Scmidt, B.) 87–90 (IOS Press, 2016);

  3. Torre, D., Lachmann, A. & Ma’ayan, A. BioJupies: automated generation of interactive notebooks for RNA-Seq data analysis in the cloud. Cell Syst. 7, 556–561.e553 (2018).

    Article  CAS  Google Scholar 

  4. Naldi, A. et al. Front. Physiol. 9, 680 (2018).

    Article  Google Scholar 

  5. Ragan-Kelley, B. & Willing, C. in Proc. 17th Python in Science Conf. (Akici, F. et al., eds) 113–120 (2018).

  6. Clarke, D. J. B. et al. Patterns (N Y) 2, 100213 (2021).

    Article  Google Scholar 

  7. Reich, M. et al. Cell Syst. 5, 149–151.e141 (2017).

    Article  CAS  Google Scholar 

  8. Heil, B. J. et al. Nat. Methods 18, 1132–1135 (2021).

    Article  CAS  Google Scholar 

  9. Lopes-Ramos, C. M. et al. Cancer Res. 81, 5401–5412 (2021).

    Article  CAS  Google Scholar 

  10. Weighill, D. et al. Preprint at arXiv (2021).

Download references


M.L.K. and R.T.P. are supported by grants from the Norwegian Research Council (313932) and the Norwegian Cancer Society (214871). M.L.K. is also supported by the Norwegian Research Council, Helse Sør-Øst and University of Oslo through the Centre for Molecular Medicine Norway (187615). K.G. is supported by a grant from the US National Heart, Lung, and Blood Institute, National Institutes of Health, K25HL133599. J.P. is supported by US National Heart, Lung, and Blood Institute grant K25HL140186. C.M.L.-R., R.B., D.W., M.B.G. and J.Q. are supported by a grant from the National Cancer Institute, National Institutes of Health, R35CA220523; J.Q. and M.B.G. are also supported by U24CA231846; J.Q. is supported by additional grants from the US National Institutes of Health, 2P50CA127003, 5R01CA205406 and 5R01HL135142. C.M.L.-R. is also supported by a grant from the American Lung Association, LCD-821824 and by the National Heart, Lung, and Blood Institute, 5T32HL007427-41. M.F. is supported by a Marie Sklodowska-Curie grant (PATTERNS 845083). M.A. is supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant no. 01ZX1912C).

Author information

Authors and Affiliations



M.B.G. and J.Q conceived the project. D.W., C.M.L.-R, R.B., R.T.P., K.P., M.S., M.F., D.S., K.G., M.A., M.L.K. and J.P. contributed use cases for the collection of notebooks. All authors edited and approved the final manuscript.

Corresponding author

Correspondence to John Quackenbush.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Laurence Calzone and Michael Reich for their contribution to the peer review of this work.

Supplementary Information

Supplementary Information

Supplementary Note 1 and Table 1

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ben Guebila, M., Weighill, D., Lopes-Ramos, C.M. et al. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods 19, 511–513 (2022).

Download citation

  • Published:

  • Issue Date:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing