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ttime: an R Package for Translating the Timing of Brain Development Across Mammalian Species

Neuroinformatics volume 8, pages 201–205 (2010)Cite this article

Abstract

Understanding relationships between the sequence and timing of brain developmental events across a given set of mammalian species can provide information about both neural development and evolution. Yet neurodevelopmental event timing data available from the published literature are incomplete, particularly for humans. Experimental documentation of unknown event timings requires considerable effort that can be expensive, time consuming, and for humans, often impossible. Application of suitable statistical models for translating neurodevelopmental event timings across mammalian species is essential. The present study implements an established statistical model and related functions as an open-source R package (ttime, translating time). The model incorporated into ttime allows predictions of unknown neurodevelopmental timings and explorations of phylogenetic relationships. The open-source package will enable transparency and reproducibility while minimizing redundancy. Sustainability and widespread dissemination will be guaranteed by the active CRAN (Comprehensive R Archive Network) community. The package updates the web-service (Clancy et al. 2007b) www.translatingtime.net by permitting predictions based on curated event timing databases which may include species not yet incorporated in the current model. The R package can be integrated into complex workflows that use the event predictions in their analyses. The package ttime is publicly available and can be downloaded from http://cran.r-project.org/web/packages/ttime/index.html.

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Acknowledgements

Supported by NSF DBI-0849684 to RN, NSF DBI-0849627 to BC, NSF DBI-0848612 to BLF, and NIH Grant Number P20 RR-16460 from the IDeA Networks of Biomedical Research Excellence (INBRE) Program of the National Center for Research Resources to RN and BC.

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Affiliations

  1. Division of Biomedical Informatics, University of Arkansas for Medical Sciences, COPH/UAMS, Room 3234, 4301W Markham, Slot 781, Little Rock, AR, 72205-7199, USA

    Radhakrishnan Nagarajan

  2. Department of Psychology, Cornell University, Ithaca, NY, USA

    Richard B. Darlington & Barbara L. Finlay

  3. Department of Biology, University of Central Arkansas, ConWay, AR, USA

    Barbara Clancy

Authors
  1. Radhakrishnan Nagarajan
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  2. Richard B. Darlington
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  3. Barbara L. Finlay
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  4. Barbara Clancy
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Correspondence to Radhakrishnan Nagarajan.

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Nagarajan, R., Darlington, R.B., Finlay, B.L. et al. ttime: an R Package for Translating the Timing of Brain Development Across Mammalian Species. Neuroinform 8, 201–205 (2010). https://doi.org/10.1007/s12021-010-9081-y

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  • DOI: https://doi.org/10.1007/s12021-010-9081-y

Keywords

  • Open-source
  • R package
  • Cross-species modeling
  • Cross-species comparisons
  • Neurodevelopment