Comparative analyses of simulation tools in biochemical networks

2015-05-15
Tuncer, Gökçe
Purutçuoğlu Gazi, Vilda
Biyokimyasal Ağlar için Simülasyon Araçlarının Karşılaştırmalı Değerlendirilmesi GökçeTuncer, Vilda Purutçuoğlu Özet Son zamanlarda araştırmacılar tarafından biyokimyasal ağların dinamiklerini gözlemlemek için geliştirilen birçok simülasyon aracı bulunmaktadır. Bu araçlar temel olarak stokastik ve deterministik simülasyonlar için tasarlanmıştır ve bazıları da deterministik modellemeler altında model parametrelerinin çıkarımını destekler. Bu nedenle biyokimyasal sistemler için simülasyon yazılımları olarak bilinirler. Bu araçlar uygulamada aynı amacı amaçlasa da kendi avantajları ve dezavantajları vardır. Bu vesileyle, bu çalışmada, kullanıcıların amaçlarına en uygun simülasyon araçlarını seçmelerine yardımcı olmak için, ilk olarak Cellware, COPASI, Dizzy, Dynetica, E-CELL, GENESIS, Jarnac / JDesigner, Systems Biology Toolbox ve Virtual Cells yazılımları ve ardından bunları seçtiğimiz özelliklere göre karşılaştırın. Karşılaştırma kriterleri için temayı, kullanım kolaylığını, desteklenen platformları, yazılımın dilini, simülasyondaki kapasiteyi, çıkarımı, görselleştirmeyi ve Sistem Biyolojisi İşaretleme Dilini tanımlıyoruz. Son olarak, seçim için makul temel özelliklerini dikkate alarak akademik ve akademik olmayan kullanıcılar için bazı araçlar öneriyoruz.

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Citation Formats
G. Tuncer and V. Purutçuoğlu Gazi, “Comparative analyses of simulation tools in biochemical networks,” presented at the 28th International Conference of Jangjeon MathematicalSociety, (15 - 19 Mayıs 2015), 2015, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/82303.