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Cell Illustrator 相關文獻
    (5163 閱讀)   友善列印

Cell Illustrator是由GNI公司與東京大學共同開發的軟體工具,透過視覺化介面使生物醫學家直覺化地建立反應路徑, 如新陳代謝和基因調控路徑、訊息傳遞以及動態交互作用等。此軟體可和資料庫搭配,分析已知的目標基因作用機制,同時還可以更加有效地利用資料庫。使用者可以輸入自己的研究資料,並分析可能的基因網路、進行試驗,達到節省實驗成本及有效運用累積的實驗數據。本軟體有server-client架構,但每個client端需安裝軟體,目前沒有透過browser提供服務的機制。

Cell Illustrator 3.0 圖例

Graphic

Cell Illustrator Web Site

Link

Cell Illustrator 3.0 軟體文件

Tutorial (PDF, 1.4 MB) Download

User Guide (PDF, 2.3 MB) Download

Reference Manual (PDF, 1.1 MB) Download

Release Notes (PDF, 170 KB) Download

Brochure (PDF, 300 KB) Download

Gene Net Mode User Guide (PDF, 320KB KB) Download

Server Installation Manual (PDF, 56 KB) Download

Cell Illustrator 3.0 文獻

  1. Tasaki S, Nagasaki M, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S. Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data. Genome Informatics. 2006; 17(2): 226-238.[連結至NCBI原始文獻]
  2. Matsuno H, Li C, Miyano S. Petri Net based description for systematic understanding of biological pathways. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. 2006; 89-A: 3166-3174.[連結至原始文獻]
  3. Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 2006; 17(1): 46-61[連結至NCBI原始文獻] 
  4. Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics. 2006; 17(1): 112-23. [連結至原始文獻]
  5. Saito A, Nagasaki M, Doi A, Ueno K, Miyano S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid function Petri net with extension. Genome Informatics. 2006; 17(1): 100-11.[連結至NCBI原始文獻]
  6. Matsuno H, Inouye ST, Okitsu Y, Fujii Y, Miyano S. A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. Journal of bioinformatics and computational biology. 2006; 4(1): 139-53.[連結至NCBI原始文獻]
  7. Doi A, Nagasaki M, Matsuno H, Miyano S. Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 2006; 6(1-2): 0001.[連結至NCBI原始文獻]
  8. Nagasaki M, Doi A, Matsuno H, Miyano S. Computational modeling of biological processes with Petri Net-based architecture. Bioinformatics Technologies (Yi-Ping Phoebe Chen (Ed.)). Springer. 2005; 179-242.[連結至原始文獻 ]
  9. Nagasaki M, Doi A, Matsuno H, Miyano S. Petri Net Based Description and Modeling of Biological Pathways. Algebraic Biology 2005 - Computer Algebra in Biology, H. Anai and K. Horimoto, eds., Universal Academy Press, Inc., Tokyo. 2005; 19-31.
  10. Nagasaki M, Doi A, Matsuno H, Miyano S. Software for Pathway Modeling and Simulation – From Bench to Computer. Asia Pacific Biotech News, World Scientific Publishing Co., Singapore. 2005.
  11. Kato M, Nagasaki M, Doi A , Miyano S. Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data. Genome Informatics. 2005; 16(2): 22-31.(PubMed_16901086)[連結至NCBI原始文獻 ]
  12. Kitakaze H, Matsuno H, Ikeda N. Prediction of debacle points for robustness of biological pathways by using recurrent neural networks. Genome Informatics. 2005; 16(1): 192-202.(PubMed_16362922)[連結至NCBI原始文獻 ]
  13. Li C, Suzuki S, Ge Qi-Wei, Nakata M, Matsuno H, Miyano S. On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net, Proc. The 2005 Internatinal Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005; 348-53.
  14. Nagasaki M, Doi A, Matsuno H, Miyano S. A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Informatics. 2004; 15(1): 180-97.(PubMed_15712121)[連結至NCBI原始文獻 ]
  15. Nagasaki M. A Platform for Biopathway Modeling/Simulation and Recreating biopathway databases towards simulation. Ph.D Thesis, The University of Tokyo. 2004.
  16. Nagasaki M, Doi A, Matsuno H, Miyano S. Integrating biopathway databases for large-scale modeling and simulation. The Second Asia-Pacific Bioinformatics Conferences, Volume 29 of Conferences in Research and Practice in Information Technology, Australian Computer Society. 2004; 43-52.[連結至原始文獻 ]
  17. Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology. 2004; 4(3): 271-91.[連結至NCBI原始文獻 ]
  18. Matsui M, Fujita S, Suzuki S, Matsuno H, Miyano S. Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net. Journal of Integrative Bioinformatics. 2004; 0001.[連結至原始文獻 ]
  19. Fujita S, Matsui M, Matsuno H, Miyano S. Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. 2004; E87-A(11): 2919-28.[連結至原始文獻 ]
  20. Matsuno H, Murakami R, Yamane R, Yamasaki N, Fujita S, Yoshimori H, Miyano S. Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and a gene network modeling by Genomic Object Net. Pacific Symposium on Biocomputing. 2003: 152-63.[連結至NCBI原始文獻 ]
  21. Nagasaki M, Doi A, Matsuno H, Miyano S. Recreating biopathway databases towards simulation. In: Computational Methods in Systems Biology. Lecture Notes in Computer Science. 2003; 2602: 191-2.[連結至acm原始文獻 ]
  22. Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S. Biopathways Representation and Simulation on Hybrid Functional Petri Net. In Silico Biology. 2003; 3(3): 389-404.[連結至NCBI原始文獻 ]
  23. Nagasaki M, Doi A, Matsuno H, Miyano S. Genomic Object Net: a platform for modeling and simulating biopathways. Applied Bioinformatics. 2003; 2: 181-4.(PubMed_15130806)[連結至 NCBI原始文獻 ]
  24. Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S. Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension. Applied Bioinformatics. 2003; 2: 185-8.[連結至原始文獻 ]
  25. Doi A, Matsuno H, Matsui M, Hirata Y, Miyano S. Simulation of biological systems by hybrid Petri net with an enhancement. Proc. The International Conference on Fundamentals of Electronics, Communications and Computer Science 2002. 2002; S5: 13-8.[連結至原始文獻 ]
  26. Matsuno H, Doi A, Hirata Y, Miyano S. XML Documentation of Biopathways and Their Simulations in Genomic Object Net. Genome Informatics. 2001; 12: 54-62.[連結至NCBI原始文獻 ]
  27. Matsuno H, Doi A, Drath R, Miyano S. Genomic Object Net: Hybrid Petri net for describing biological systems. Currents in Computational Molecular Biology. 2001; 233-4.
  28. Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing 5. 2000; 341-52.[連結至NCBI原始文獻 ]
  29. Matsuno H, Doi A, Tanaka A, Aoshima H, Hirata Y, Miyano S. Genomic Object Net: basic architecture for representing and simulating biopathways.
  

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