GENESIS – The GENEric SImulation System for Modelling State Transitions

Article, Software Paper English OPEN
Gillman, Matthew S.;
  • Publisher: Ubiquity Press
  • Journal: volume 5,issue 1eissn: 2049-9647
  • Related identifiers: doi: 10.5334/jors.179, pmc: PMC5627703
  • Subject: Simulation and Modelling, Open Software, Health Informatics, Computer Software | simulation, modelling, disease progression, state transitions, state machine, probabilities, Perl, C++, random number generation, Markov chain, Markov process | C++ | simulation | disease progression | random number generation | modelling | state transitions | Article | Markov chain | simulation; modelling; disease progression; state transitions; state machine; probabilities; Perl; C++; random number generation; Markov chain; Markov process | state machine | Perl | probabilities | Markov process

This software implements a discrete time Markov chain model, used to model transitions between states when the transition probabilities are known a priori. It is highly configurable; the user supplies two text files, a “state transition table” and a “config file”, to th... View more
  • References (10)

    1. Yang, P C, Zhang, S X, Sun, P P, Cai, Y L, Lin, Y and Zou, Y H 2017 “Development of Markov models for Art. 24, p.  6 of 6 economics evaluation of strategies on hepatitis B vaccination and population-based antiviral treatment in China.” Zhonghua Liu Xing Bing Xue Za Zhi, 38(7): 845-851.

    2. Wang, Y, Sun, M, Bao, H and White, A 2013 “T3_MM: a Markov model effectively classifies bacterial type III secretion signals.” PLoS One, 8(3). DOI: https://doi. org/10.1371/journal.pone.0058173

    3. Torchala, M, Moal, I, Chaleil, R, Agius, R and Bates, P 2013 “A Markov-chain model description of binding funnels to enhance the ranking of docked solutions.” Proteins, 81(12): 2143-9. DOI: https://doi. org/10.1002/prot.24369

    4. Chor, B and Steel, M 2015 “Do tree split probabilities determine the branch lengths?” J Theor Biol., 374: 54-9. DOI:

    5. Surveillance Research Program “CISNET Model Registry” 15th May 2017. [Online]. Available: https://

    6. Spedicato, G A, Kang, T S, Yalamanchi, S B, Thoralf, M, Yadav, D, Castillo, N C and Jain, V “markovchain: Easy Handling Discrete Time Markov Chains” 16 August 2017. [Online]. Available: https:// [Accessed 25 August 2017].

    7. Nicholson, W “DTMCPack: Suite of functions related to discrete-time discrete-state Markov Chains” 28 May 2013. [Online]. Available: https:// [Accessed 25 August 2017].

    8. Landy, R, Windridge, P, Gillman, M S and Sasieni, P D “What cervical screening is appropriate for women who have been vaccinated against highrisk HPV? A simulation study.” Submitted for peer review.

    9. Ramírez-Cervantes, K L 2017 Costs and benefits of implementing an organized colorectal cancer screening program in México (MSc dissertation) London: Queen Mary University of London.

    10. “State Design Pattern” [Online]. Available: patterns/state [Accessed 22nd March 2017].

  • Related Research Results (2)
  • Metrics
    views in OpenAIRE
    views in local repository
    downloads in local repository

    The information is available from the following content providers:

    FromNumber Of ViewsNumber Of Downloads
    King's Research Portal - IRUS-UK 0 1
Share - Bookmark