Abstract
The move towards in silico experimentation has resulted in the use of computational models, in addition to traditional experimental models, to generate the raw data that is analysed and published as research findings. This change requires new methods to be introduced to facilitate independent validation of the underlying models and the reported results. The promotion of co-operative research has the potential to help to both validate results and explore wider problem areas. In this paper we leverage and extend two existing software frameworks to develop an infrastructure that has the potential to both promote the sharing of data between researchers pre-publication and enable access to the data for interested parties post-publication. The pre-publication sharing of data would enable larger problem spaces to be explored by distributed research groups; enabling access to the data post-publication would allow reviewers and the wider community to independently verify the published results which would, in the longer term, help to increase confidence in published results. The framework is used to perform reproducible and numerically validated individual-based computational experiments into the onset of colorectal cancer. Existing results are verified and new insights into the top-down versus bottom-up hypothesis of colorectal crypt invasion are given.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell, 4th edn. Garland Science, New York
Anderson AE, Ellis BJ, Weiss JA (2007) Verification, validation and sensitivity studies in computational biomechanics. Comput Methods Biomech Biomed Eng 10(3):171–184
Armbrust M, Fox A, Griffith R, Joseph AD, Katz R, Konwinski A, Lee G, Patterson D, Rabkin A, Stoica I, Zaharia M (2010) A view of cloud computing. Communications of the ACM 53:50–58
Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I (2009) Adaptable data management for systems biology investigations. BMC Bioinf 10(1):79
Brady JM, Gavaghan DJ, Simpson AC, Parada MM, Highnam RP (2003) e-DiaMoND: a grid-enabled federated database of annotated mammograms. In: Berman F, Fox GC, Hey AJG (eds) Grid computing: making the global infrastructure a reality. Wiley, Chichester, UK, pp 923–943
Brambilla M, Ceri S, Passamani M, Riccio A (2004) Managing asynchronous web services interactions. In: Proceedings of the IEEE international conference on web services (ICWS’04), pp 80–87
Buske P, Galle J, Barker N, Aust G, Clevers H, Loeffler M (2011) A comprehensive model of the spatio-temporal stem cell and tissue organisation in the intestinal crypt. PLoS Comput Biol 7(1):e1001045
Cary MP, Bader GD, Sander C (2005) Pathway information for systems biology. FEBS Lett 579(8):1815–1820
Crowder HP, Dembo RS, Mulvey JM (1978) Reporting computational experiments in mathematical programming. Math Program 15:316–329. doi:10.1007/BF01609036
Di Ventura B, Lemerle C, Michalodimitrakis K, Serrano L (2006) From in vivo to in silico biology and back. Nature 443(7111):527–533
Gorton I, Liu Y, Yin J (2010) Exploring architecture options for a federated, cloud-based system biology knowledgebase. In: 2010 IEEE second international conference on cloud computing technology and science (CloudCom), pp 218–225
Greenwood M, Goble C, Stevens R, Zhao J, Addis M, Marvin D, Moreau L, Oinn T (2003) Provenance of e-Science experiments—experience from bioinformatics. In: The UK OST e-Science second all hands meeting 2003 (AHM’03), pp 223–226
Grossman RL, White KP (2012) A vision for a biomedical cloud. J Intern Med 271(2):122–130
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U (2006) Copasi—a complex pathway simulator. Bioinformatics 22(24):3067–3074
Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, Arkin A, Bornstein B, Bray D, Cornish-Bowden A et al (2003) The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531
Ignizio JP (1971) On the establishment of standards for comparing algorithm performance. Interfaces 2(1):8–11
Ignizio JP (1973) Validating claims for algorithms proposed for publication. Oper Res 21(3):852–854
Izaguirre J, Chaturvedi R, Huang C, Cickovski T, Coffland J, Thomas G, Forgacs G, Alber M, Hentschel G, Newman S et al (2004) Compucell, a multi-model framework for simulation of morphogenesis. Bioinformatics 20(7):1129–1137
Jenkinson A, Albrecht M, Birney E, Blankenburg H, Down T, Finn R, Hermjakob H, Hubbard T, Jimenez R, Jones P, Kahari A, Kulesha E, Macias J, Reeves G, Prlic A (2008) Integrating biological data—the distributed annotation system. BMC Bioinf 9(Suppl 8):S3
Kitano H (2002) Computational systems biology. Nature 420(6912):206–210
Lansing C, Liu Y, Yin J, Corrigan A, Guillen Z, van Dam K, Gorton I (2011) Designing the cloud-based DOE systems biology knowledgebase. In: 2011 IEEE international symposium on parallel and distributed processing workshops and Phd forum (IPDPSW), pp 1062–1071
Loeffler M, Stein R, Wichmann H, Potten C, Kaur P, Chwalinski S (1986) Intestinal cell proliferation. i. a comprehensive model of steady-state proliferation in the crypt. Cell Prolif 19(6):627–645
Loutas N, Peristeras V, Bouras T, Kamateri E, Zeginis D, Tarabanis K (2010) Towards a reference architecture for semantically interoperable clouds. In: 2010 IEEE second international conference on cloud computing technology and science (CloudCom), pp 143–150
Meineke FA, Potten CS, Loeffler M (2001) Cell migration and organisation in the intestinal crypt using a lattice-free model. Cell Prolif 34:253–266
Osborne J, Walter A, Kershaw S, Mirams G, Fletcher A, Pathmanathan P, Gavaghan D, Jensen O, Maini P, Byrne H (2010) A hybrid approach to multi-scale modelling of cancer. Phil Trans R Soc A 368:5013–5028
Pathmanathan P, Bernabeu M, Bordas R, Cooper J, Garny A, Pitt-Francis J, Whiteley J, Gavaghan D (2010) A numerical guide to the solution of the bidomain equations of cardiac electrophysiology. Prog Biophys Mol Biol 102(2–3):136–155
Pitt-Francis J, Bernabeu M, Cooper J, Garny A, Momtahan L, Osborne J, Pathmanathan P, Rodriguez B, Whiteley J, Gavaghan D (2008) Chaste: using agile programming techniques to develop computational biology software. Phil Trans R Soc A 366:3111–3136
Pitt-Francis J, Pathmanathan P, Bernabeu M, Bordas R, Cooper J, Fletcher A, Mirams G, Murray P, Osborne J, Walter A, Chapman S, Garny A, van Leeuwen I, Maini P, Rodriguez B, Waters S, Whiteley J, Byrne H, Gavaghan D (2009) Chaste: a test-driven approach to software development for biological modelling. Comp Phys Comm 180(12):2452–2471
Radetzki U, Cremers A (2004) IRIS: a framework for mediator-based composition of service-oriented software. In: Proceedings of the IEEE international conference on web services, 2004 (ICWS‘04), pp 52–756
Sauro H, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H (2003) Next generation simulation tools: the systems biology workbench and biospice integration. Omics 7(4):355–372
Simpson AC, Power DJ, Russell D, Slaymaker MA, Bailey V, Tromans CE, Brady JM, Tarassenko L (2010) GIMI: the past, the present, the future. Phil Trans R Soc A Math Phys Eng Sci 368:3891–3905
Simpson AC, Slaymaker MA, Gavaghan DJ (2010b) On the secure sharing and aggregation of data to support systems biology research. In: Proceedings of the 7th international conference on data integration in the life sciences (DILS 2010). Springer Lecture Notes in Computer Science, vol 6254, pp 58–73
Slaymaker MA, Power DJ, Russell D, Simpson AC (2008a) On the facilitation of fine-grained access to distributed healthcare data. In: Jonker W, Petkovic M (eds) Proceedings of secure data management (SDM) 2008. Springer Lecture Notes in Computer Science, vol 5159, pp 169–184
Slaymaker MA, Power DJ, Russell D, Wilson G, Simpson AC (2008b) Accessing and aggregating legacy data sources for healthcare research, delivery and training. In: Wainwright RL, Haddad H (eds) Proceedings of the 2008 ACM symposium on applied computing (SAC), pp 1317–1324
Tromans CE, Brady JM, Power DJ, Slaymaker MA, Russell D, Simpson AC (2008) The application of a service-oriented infrastructure to support medical research in mammography. In: Proceedings of MICCAI-Grid 2008
Van Leeuwen I, Mirams G, Walter A, Fletcher A, Murray P, Osborne J, Varma S, Young S, Cooper J, Doyle B, Pitt-Francis J, Momtahan L, Pathmanathan P, Whiteley J, Chapman S, Gavaghan D, Jensen O, King J, Maini P, Waters S, Byrne H (2009) An integrative computational model for intestinal tissue renewal. Cell Prolif 42:617–636
Zdun U, Voelter M, Kircher M (2004) Pattern-based design of an asynchronous invocation framework for web services. Int J Web Serv Res 1
Acknowledgments
The authors acknowledge financial support from the BBSRC, through the OCISB project (BB/D020190/1). JMO is supported by Microsoft Research Cambridge and the EPSRC funded University of Oxford Doctoral Training Centres.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Slaymaker, M., Osborne, J., Simpson, A. et al. On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. Syst Synth Biol 6, 35–49 (2012). https://doi.org/10.1007/s11693-012-9095-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11693-012-9095-x