Systematic Review (Up to 31 January 2025) on the Applications of Digital Organisms - mauriceling/mauriceling.github.io GitHub Wiki

Citation: Matarage, ML, Maiyappan, S, Sim, SSY, Ramesh, G, Low, L, Ling, MHT. 2025. Systematic Review (Up to 31 January 2025) on the Applications of Digital Organisms. Acta Scientific Microbiology 8(8): 14-26.

Link to [PDF].

Here is the permanent [PDF] and the dataset in my archive.

Digital organisms (DOs) are computer-based programs designed to replicate the behaviour of biological processes, such as replication and evolution. This makes DOs a useful tool to study evolutionary processes, especially ethically challenging areas such as antibiotics resistance. Currently, there is no systematic reviews to-date examining the range of applications and studies using DOs. Here, we aim to conduct a systematic review, using studies indexed in PubMed prior to 01 January 2025, on the range of applications and studies using DOs. A total of 147 papers were identified; of which, 80 were included after screening. These 80 studies were examined by focusing on five questions; namely, (a) What was the study about? (b) What tool(s) was / were used? (c) How DOs helped in the study? (d) What was / were discovered from the studies? (e) How were findings using DOs relevant to biology? Our findings show a wide range of applications of DOs in seven main areas; namely, (i) biomechanics and movement modelling, (ii) evolutionary and adaptation, (iii) molecular and cellular evolution, (iv) ecology and community dynamics, (v) computational and synthetic systems, (vi) biomedical and environmental applications, (vii) theoretical and cross-disciplinary studies; with 31 of the 80 studies (38%) uses Avida as experimental platform.