Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models

IEEE Journal of Biomedical and Health Informatics

Volumn 18, Issue 3, 2014, Pages 824-831

  Sakkalis, Vangelis ^a   Sfakianakis, Stelios ^a   Tzamali, Eleftheria ^a   Marias, Kostas ^a   Stamatakos, Georgios ^b   Misichroni, Fay ^b   Ouzounoglou, Eleftherios ^b   Kolokotroni, Eleni ^b   Dionysiou, Dimitra ^b   Johnson, David ^c   McKeever, Steve ^d   Graf, Norbert ^e  

^a INSTITUTE OF COMPUTER SCIENCE   (Greece)

^b INSTITUTE OF COMMUNICATION AND COMPUTER SYSTEMS   (Greece)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d UPPSALA UNIVERSITY   (Sweden)

^e SAARLAND UNIVERSITY   (Germany)

Author keywords

Cancer systems biology; clinical translation; computational oncology; personalized medicine; Scientific workflows

Indexed keywords

CLINICAL RESEARCH; ONCOLOGY; PATIENT TREATMENT; PERSONALIZED MEDICINE;

CANCER SIMULATIONS; CLINICAL TRANSLATION; COMPUTATIONAL ONCOLOGIES; EUROPEAN COMMISSION; GRAPHICAL WORKFLOW; SCIENTIFIC WORKFLOWS; SYSTEMS BIOLOGY; VIRTUAL PHYSIOLOGICAL HUMAN;

DISEASES;

BIOLOGICAL MODEL; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; HUMAN; INTERNET; NEOPLASM; PERSONALIZED MEDICINE; PROCEDURES; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

COMPUTER SIMULATION; HUMANS; INDIVIDUALIZED MEDICINE; INTERNET; MODELS, BIOLOGICAL; NEOPLASMS; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 84900549090     PISSN: 21682194     EISSN: None     Source Type: Journal    
DOI: 10.1109/JBHI.2013.2297167     Document Type: Article

References (39)

1. G. Stamatakos, "In silico oncology part I: Clinically oriented cancer multilevel modeling based on discrete event simulation," in Multiscale Cancer Modeling, T. Deisboeck and G. Stamatakos, Eds. Boca Raton, FL, USA: CRC Press, 2011, pp. 407-436.
2. T. S. Deisboeck, Z. Wang, P. Macklin, and V. Cristini, "Multiscale cancer modeling," Annu. Rev. Biomed. Eng. , vol. 13, no. 1, pp. 127-155, Aug. 2011.
3. A. Roniotis, V. Sakkalis, I. Karatzanis,M. E. Zervakis, and K. Marias, "Indepth analysis and evaluation of diffusive glioma models," IEEE Trans. Inf. Technol. Biomed. , vol. 16, no. 3, pp. 299-307, May 2012.
4. V. Sakkalis, A. Roniotis, C. Farmaki, I. Karatzanis, and K. Marias, "Evaluation framework for the multilevel macroscopic models of solid tumor growth in the glioma case," in Proc. IEEE 32nd Eng. Med. Biol. Soc. Conf. , Buenos Aires, Argentina, 2010, pp. 6809-6812.
5. A. Roniotis, G. C. Manikis, V. Sakkalis,M. E. Zervakis, I. Karatzanis, and K. Marias, "High grade glioma diffusive modeling using statistical tissue information and diffusion tensors extracted from atlases," IEEE Trans. Inf. Technol. Biomed. , vol. 16, no. 2, pp. 255-263, Mar. 2011.
6. P. P. Delsanto, C. A. Condat, N. Pugno, A. S. Gliozzi, and M. Griffa, "A multilevel approach to cancer growth modeling," J. Theor. Biol. , vol. 250, no. 1, pp. 16-24, Jan. 2007.
7. L. B. Edelman, J. A. Eddy, and N. D. Price, "In silico models of cancer," Wiley Interdiscip. Rev. Syst. Biol. Med. , vol. 2, no. 4, pp. 438-459, Jul. /Aug. 2010.
8. K. A. Rejniak and A. R. Anderson, "Hybrid models of tumor growth," Wiley Interdiscip. Rev. Syst. Biol. Med. , vol. 3, no. 1, pp. 115-125, Jan. /Feb. 2010.
9. T. Alarcn, T. Alarćon, H. M. Byrne, and P. K. Maini, "Towards wholeorgan modelling of tumour growth," Prog. Biophys. Mol. Biol. , vol. 85, no. 2-3, pp. 451-472, Jun. /Jul. 2004. (Pubitemid 38629922)
10. Z. Wang, C. M. Birch, J. Sagotsky, and T. S. Deisboeck, "Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model," Bioinformatics, vol. 25, no. 18, pp. 2389-2396, Sep. 2009.
11. A. Roniotis, K. Marias, V. Sakkalis, G. Stamatakos, and M. Zervakis, "Comparing finite elements and finite differences for developing diffusive models of glioma growth," in Proc. IEEE 32nd Eng. Med. Biol. Soc. Conf. , Buenos Aires, Argentina, 2010, pp. 6797-6800.
12. V. Sakkalis, S. Sfakianakis, K. Marias, G. Stamatakos, F. Misichroni, D. Dionysiou, S. McKeever, D. Johnson, T. S. Deisboeck, and N. Graf, "The TUMORproject: integrating cancer model repositories for supporting predictive oncology," presented at the Abstract Booklet VPH 2012 Integrative Approaches Comput. Biomed. , London, U. K. , 2012.
13. BioSharing Standards. (2009). [Online]. Available: http://www. biosharing. org/standards.
14. COMBINE-The Computational Biology Network. [Online]. Available: http://mbine. org/
15. D. Johnson, S. McKeever, G. Stamatakos, D. Dionysiou, N. Graf, V. Sakkalis,K. Marias, Z. Wang, and T. S. Deisboeck, "Dealingwith diversity in computational cancer modeling," Cancer Inf. , vol. 12, pp. 115-124, 2013.
16. C. M. Lloyd, M. D. Halstead, and P. F. Nielsen, "CellML: Its future, present and past," Prog. Biophys. Mol. Biol. , vol. 85, no. 2-3, pp. 433-450, Jun. /Jul. 2004. (Pubitemid 38629921)
17. M. Hucka, F. Bergmann, S. Hoops, S. M. Keating, S. Sahle, and D. J. Wilkinson, "The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1," Nature Precedings, 2010, doi:10. 1038/npre. 2010. 4123. 1.
18. N. L. Nov́ere, A. Finney, M. Hucka, U. S. Bhalla, F. Campagne, J. Collado-Vides, E. J. Crampin, M. Halstead, E. Klipp, P. Mendes, P. Nielsen, H. Sauro H, B. Shapiro, J. L. Snoep, H. D. Spence, and B. L. Wanner, "Minimum information requested in the annotation of biochemical models (MIRIAM)," Nat. Biotech. , vol. 23, no. 12, pp. 1509-1515, Dec. 2005. (Pubitemid 41752928)
19. S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer, "COPASI-A complex pathway simulator," Bioinformatics, vol. 22, no. 24, pp. 3067-3074, Dec. 2006.
20. A. C. Ahn, M. Tewari, C. Poon, and R. S. Phillips, "The limits of reductionism in medicine: Could systems biology offer an alternative" PLoS Med. , vol. 3, no. 6, p. e208, May 2006.
21. A. Belloum, E. Deelman, and Z. Zhao, "Scientific Workflows," Scientific Programming, vol. 14, no. 3, p. 171, 2006. (Pubitemid 46474554)
22. S. Sfakianakis, V. Sakkalis, K. Marias, G. Stamatakos, S. McKeever, T. S. Deisboeck, and N. Graf, "An architecture for integrating cancer model repositories," in Proc. IEEE 34th Eng. Med. Biol. Soc. Conf. , San Diego, CA, USA, 2012, pp. 6628-6631.
23. M. G. Vander Heiden, "Understanding theWarburg effect: The metabolic requirements of cell proliferation," Science, vol. 324, no. 5940, pp. 1029-1033, May 2009.
24. R. A. Gatenby and R. J. Gillies, "Why do cancers have high aerobic glycolysis" Nat. Rev. Cancer, vol. 4, no. 11, pp. 891-899, Nov. 2004. (Pubitemid 39472955)
25. C. Athale, Y. Mansury, and T. S. Deisboeck, "Simulating the impact of a molecular 'decision-process' on cellular phenotype and multicellular patterns in brain tumors," J. Theor. Biol. , vol. 233, no. 4, pp. 469-481, Apr. 2005. (Pubitemid 40320594)
26. T. Shlomi, T. Benyamini, T. Benyamini, E. Gottlieb, R. Sharan, and E. Ruppin, "Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect," PLoS Comput. Biol. , vol. 7, no. 3, p. e1002018, Mar. 2011.
27. N. C. Duarte, S. A. Becker, N. Jamshidi, I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, and B. O. Palsson, "Global reconstruction of the human metabolic network based on genomic and bibliomic data," Proc. Nat. Acad. Sci. USA, vol. 104, pp. 1777-1782, Feb. 6, 2007. (Pubitemid 46239855)
28. A. Wolf, S. Agnihotri, and A. Guha, "Targeting metabolic remodeling in glioblastoma multiforme," Oncotarget, vol. 1, no. 7, pp. 552-562, Nov. 2010.
29. C. Colin, N. Baeza, C. Bartoli, F. Fina, N. Eudes, I. Nanni, P. M. Martin, L. Ouafik, and D. Figarella-Branger, "Identification of genes differentially expressed in glioblastoma versus pilocytic astrocytoma using suppression subtractive hybridization," Oncogene, vol. 25, no. 19, pp. 2818-2826, May 2006.
30. E. Tzamali, V. Sakkalis, and K. Marias, "The effects of near optimal growth solutions in genome-scale human cancer metabolic model," in Proc. IEEE Int. Conf. BioInformatics BioEng. , Larnaca, Cyprus, 2012, pp. 626-631.
31. G. S. Stamatakos, E. Kolokotroni, D. Dionysiou, C. Veith, Y. J. Kim, A. Franz, K. Marias, J. Sabczynski, R. Bohle, and N. Graf, "In silico oncology: Exploiting clinical studies to clinically adapt and validate multiscale oncosimulators," in Proc. IEEE 35th Annu. Int. Conf. Eng. Med. Biol. Soc. , Osaka, Japan, Jul. 3-7, 2013, pp. 5545-5549.
32. G . S. Stamatakos, E. A. Kolokotroni, D. D. Dionysiou, E. Ch. Georgiadi, and C. Desmedt, "An advanced discrete state-discrete event multiscale simulation model of the response of a solid tumor to chemotherapy: Mimicking a clinical study," J. Theor. Biol. , vol. 266, no. 1, pp. 124-139, Sep. 2010.
33. C. Farmaki, K. Marias, V. Sakkalis, and N. Graf, "Spatially adaptive active contours: a semi-automatic tumor segmentation framework," Int. J. Comput. Assist. Radiol. Surg. , vol. 5, no. 4, pp. 369-384, 2010.
34. E. Skounakis, C. Farmaki, V. Sakkalis, A. Roniotis, K. Banitsas, N. Graf, and K. Marias, "DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images," Open Med. Informatics J. , vol. 4, pp. 105-115, 2010.
35. T. Oinn, M. Addis, J. Ferris, D. Marvin, T. Carver, M. R. Pocock, and A. Wipat, "Taverna: a tool for the composition and enactment of bioinformatics workflows," Bioinformatics, vol. 20, no. 17, pp. 3045-3054, Jun. 2004. (Pubitemid 39619196)
36. C. A. Goble and D. C. De Roure, "my Experiment: social networking for workflow-using e-scientists," in Proc. 2nd Workshop Workflows Support Large-Scale Sci. , Monterey, CA, USA, 2007, pp. 1-2. (Pubitemid 47291445)
37. J. Goecks, A. Nekrutenko, J. Taylor, and The Galaxy Team, "Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences," Genome Biol. , vol. 11, no. 8, p. R86, 2010.
38. M. Abouelhoda, M. Ghanem, and S. Alaa, "Meta-workflows: Patternbased interoperability between Galaxy and Taverna," in Proc. 1st Int. Workshop Workflow Approaches New Data-Centric Sci. , 2010.
39. S. Sfakianakis, V. Sakkalis, K. Marias, G. Stamatakos, S. McKeever, T. Deisboeck, and N. Graf, "An architecture for integrating cancer model repositories," in Proc. IEEE 34th Annu. Int. Conf. Eng. Med. Biol. Soc. , San Diego, CA, USA, Aug. 28-Sep. 1, 2012, pp. 6628-6631.