SYCAMORE - a systems biology computational analysis and modeling research environment

被引:24
|
作者
Weidemann, Andreas [1 ]
Richter, Stefan [2 ]
Stein, Matthias [2 ]
Sahle, Sven [1 ]
Gauges, Ralph [1 ]
Gabdoulline, Razif [2 ]
Surovtsova, Irina [1 ]
Semmelrock, Nils [2 ]
Besson, Bruno [2 ]
Rojas, Isabel
Wade, Rebecca [2 ]
Kummer, Ursula [1 ]
机构
[1] Heidelberg Univ, BIOQUANT, COS, Inst Zool,Dept Modeling Biol Proc, D-69120 Heidelberg, Germany
[2] EML Res, Mol & Cellular Modeling Grp, D-69118 Heidelberg, Germany
关键词
D O I
10.1093/bioinformatics/btn207
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.
引用
收藏
页码:1463 / 1464
页数:2
相关论文
共 50 条
  • [1] Approaches to complexity reduction in a systems biology research environment (sycamore)
    Surovtsova, Irina
    Sahle, Sven
    Pahle, Jargen
    Kummer, Ursula
    PROCEEDINGS OF THE 2006 WINTER SIMULATION CONFERENCE, VOLS 1-5, 2006, : 1683 - +
  • [2] Computational Modeling, Formal Analysis, and Tools for Systems Biology
    Bartocci, Ezio
    Lio, Pietro
    PLOS COMPUTATIONAL BIOLOGY, 2016, 12 (01)
  • [3] From systems to biology: A computational analysis of the research articles on systems biology from 1992 to 2013
    Zou, Yawen
    Laubichler, Manfred D.
    PLOS ONE, 2018, 13 (07):
  • [4] Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
    Schmidt, H
    Jirstrand, M
    BIOINFORMATICS, 2006, 22 (04) : 514 - 515
  • [5] Systems Biology in Immunology: A Computational Modeling Perspective
    Germain, Ronald N.
    Meier-Schellersheim, Martin
    Nita-Lazar, Aleksandra
    Fraser, Iain D. C.
    ANNUAL REVIEW OF IMMUNOLOGY, VOL 29, 2011, 29 : 527 - 585
  • [6] Hybrid computational modeling methods for systems biology
    Cruz, Daniel A.
    Kemp, Melissa L.
    PROGRESS IN BIOMEDICAL ENGINEERING, 2022, 4 (01):
  • [7] ENZYME KINETICS AND COMPUTATIONAL MODELING FOR SYSTEMS BIOLOGY
    Mendes, Pedro
    Messiha, Hanan
    Malys, Naglis
    Hoops, Stefan
    METHODS IN ENZYMOLOGY: COMPUTER METHODS, PART B, 2009, 467 : 583 - 599
  • [8] Computational systems biology and in silico modeling of the human microbiome
    Borenstein, Elhanan
    BRIEFINGS IN BIOINFORMATICS, 2012, 13 (06) : 769 - 780
  • [9] Computational Systems Biology in Cancer: Modeling Methods and Applications
    Materi, Wayne
    Wishart, David S.
    GENE REGULATION AND SYSTEMS BIOLOGY, 2007, 1 : 91 - 110
  • [10] Computational systems biology for omics data analysis
    Chen, Luonan
    JOURNAL OF MOLECULAR CELL BIOLOGY, 2019, 11 (08) : 631 - 632