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Biological computation and computational biology: survey, challenges, and discussion

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Abstract

Biological computation involves the design and development of computational techniques inspired by natural biota. On the other hand, computational biology involves the development and application of computational techniques to study biological systems. We present a comprehensive review showcasing how biology and computer science can guide and benefit each other, resulting in improved understanding of biological processes and at the same time advances in the design of algorithms. Unfortunately, integration between biology and computer science is often challenging, especially due to the cultural idiosyncrasies of these two communities. In this study, we aim at highlighting how nature has inspired the development of various algorithms and techniques in computer science, and how computational techniques and mathematical modeling have helped to better understand various fields in biology. We identified existing gaps between biological computation and computational biology and advocate for bridging this gap between “wet” and “dry” research.

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Notes

  1. https://www.asimovinstitute.org/blog/.

  2. https://www.asimovinstitute.org/author/fjodorvanveen/.

  3. A jumping library is a set of pairs mate-pair reads derived from long fragments of DNA. A mate-pair read is a pair of sequence reads from a single fragment of DNA (often the distance between the reads is approximately known).

  4. An allele is a variant form of a given gene. Individuals who are heterozygous for a certain gene carry two different alleles.

  5. Mechanisms of breakpoint origination remain a mystery, but the idea of genes playing the role of “solid” regions can be explained by the fact that their functionality, if lost, may result in the death of the cell, and thus a cell whose genomes have such “broken” genes would most likely not procreate.

  6. Most of the figures and some of the materials presented in this section are taken from Bayzid (2016).

  7. https://hadoop.apache.org/.

  8. https://storm.apache.org/.

  9. https://samza.apache.org/.

  10. https://spark.apache.org/.

  11. https://flink.apache.org/.

  12. https://blast.ncbi.nlm.nih.gov/Blast.cgi.

  13. https://beast.community/.

  14. https://www.megasoftware.net/.

  15. https://cme.h-its.org/exelixis/software.html/.

  16. https://wolbachia.biology.virginia.edu/WuLab/Software.html.

  17. https://www.biomolecular-modeling.com/Ascalaph/.

  18. https://www.dnastar.com/.

  19. https://www2.decipher.codes/.

  20. https://meme-suite.org/.

  21. https://kappalanguage.org/.

  22. https://cellsignaling.lanl.gov/bionetgen/.

  23. https://www.biospice.org/.

  24. https://www.insilico-biotechnology.com/discovery_en.html.

  25. https://www.biorxiv.org/.

  26. https://arxiv.org.

  27. https://ncatlab.org/nlab/show/HomePage.

  28. https://oeis.org/..

  29. https://git-scm.com/.

  30. https://fossil-scm.org/.

  31. https://veracity-scm.com/.

  32. https://www.mercurial-scm.org/.

  33. https://www.monotone.ca/.

  34. https://bioperl.org/.

  35. https://biopython.org/.

  36. https://www.open-bio.org/wiki/BOSC.

  37. https://www.open-bio.org/.

  38. https://bioconda.github.io/.

  39. https://snakemake.readthedocs.io.

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Acknowledgements

This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 702527. Authors would also like to thank Professor Stephen Smale, Fields Medal awardee, who mentored the workshop organized by the first author, Dr. Zaineb Chelly Dagdia, at the \(5^{th}\) Heidelberg Laureate Forum. The outcome of an analysis that has been done during this workshop presents the current research manuscript. Additional thanks to all organizers of the \(5^{th}\) Heidelberg Laureate Forum, to the Heidelberg Institute for Theoretical Studies, Mathematisches Forschungszentrum Oberwolfach and Schloss Dagstuhl - Leibniz Center for Informatics, and to the Heidelberg Laureate Forum Foundation’s Scientific Committee.

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  1. Université Paris-Saclay, UVSQ, DAVID, Versailles, France

    Zaineb Chelly Dagdia

  2. LARODEC, ISG, Université de Tunis, Tunis, Tunisia

    Zaineb Chelly Dagdia

  3. Department of Mathematics and Computational Biology Institute, The George Washington University, Washington, USA

    Pavel Avdeyev

  4. Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka , Bangladesh

    Md. Shamsuzzoha Bayzid

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  1. Zaineb Chelly Dagdia
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Correspondence to Zaineb Chelly Dagdia.

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The discussion in this paper about the challenges and importance of filling the gaps between the biological computation and computational biology communities represents the outcome of an analysis that has been done in the 5th Heidelberg Laureate Forum; specifically during a workshop https://scilogs.spektrum.de/hlf/experience-learn-share-heidelberg-laureate-forum/ organized by Dr. Zaineb Chelly Dagdia and mentored by Professor Stephen Smale (Fields Medal awardee). After the workshop, a collaboration was formed between Dr. Zaineb Chelly Dagdia who works on biological computation and two participants and contributors to the workshop, Pavel Avdeyev and Dr. Md. Shamsuzzoha Bayzid, who work on different areas in computational biology.

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Chelly Dagdia, Z., Avdeyev, P. & Bayzid, M.S. Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 54, 4169–4235 (2021). https://doi.org/10.1007/s10462-020-09951-1

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