The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Boolean network simulations for life scientists
Open accessAbstract
Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as they are eminently suited at mapping biological observations and hypotheses into a mathematical formalism. The conceptual underpinnings of Boolean modeling are very accessible even without a background in quantitative sciences, yet it allows life scientists to describe and explore a wide range of surprisingly complex phenomena. In this paper we provide a clear overview of the concepts used in Boolean simulations, present a software library that can perform these simulations based on simple text inputs and give three case studies. The large scale simulations in these case studies demonstrate the Boolean paradigms and their applicability as well as the advanced features and complex use cases that our software package allows. Our software is distributed via a liberal Open Source license and is freely accessible from http://booleannet.googlecode.com.
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Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 892
Logic-Based Models for the Analysis of Cell Signaling Networks
Morris, M. K., Saez-Rodriguez, J., Sorger, P. K., & Lauffenburger, D. A. (2010) · Biochemistry · doi:10.1021/bi902202q · Cited by 332
The Cell Collective: Toward an open and collaborative approach to systems biology
Helikar, T., Kowal, B., McClenathan, S., Bruckner, M., Rowley, T., Madrahimov, A., Wicks, B., Shrestha, M., Limbu, K., & Rogers, J. A. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-96 · Cited by 254
Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways
van Wageningen, S., Kemmeren, P., Lijnzaad, P., Margaritis, T., Benschop, J. J., de Castro, I. J., van Leenen, D., Groot Koerkamp, M. J. A., Ko, C. W., Miles, A. J., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.021 · Cited by 133
Palma, A., Jarrah, A. S., Tieri, P., Cesareni, G., & Castiglione, F. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01659 · Cited by 122
Metadata
- Authors
- Albert, I., Thakar, J., Li, S., Zhang, R., & Albert, R.
- Venue
- Source Code for Biology and Medicine
- Published
- 2008-11-14
- Volume
- 3
- Issue
- 1
- Pages
- 16-16
- ISSN
- 1751-0473 (ISSN-L)
- OpenAlex
- W2103723044
- Cited by
- 301
- References
- 34
- FWCI
- 5.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
