-
1
-
-
84886764465
-
-
Systems Biology Markup Language http://www.sbml.org
-
-
-
-
2
-
-
84886765907
-
-
SBMLR http://epbi-radivot.cwru.edu/SBMLR/
-
-
-
-
3
-
-
32544443964
-
Systems biology toolbox for MATLAB: A computational platform for research in systems biology
-
10.1093/bioinformatics/bti799 16317076
-
Schmidt H Jirstrand M Systems biology toolbox for MATLAB: A computational platform for research in systems biology Bioinformatics 2006 22 514-515 10.1093/bioinformatics/bti799 16317076
-
(2006)
Bioinformatics
, vol.22
, pp. 514-515
-
-
Schmidt, H.1
Jirstrand, M.2
-
4
-
-
84886765681
-
-
MathSBML http://sbml.org/software/mathsbml
-
-
-
-
5
-
-
84886764830
-
-
SBMLmerge Project http://sysbio.molgen.mpg.de/sbmlmerge/index.html
-
-
-
-
6
-
-
4544344218
-
Web-based kinetic modelling using JWS online
-
10.1093/bioinformatics/bth200 15072998
-
Olivier BG Snoep JL Web-based kinetic modelling using JWS online Bioinformatics 2004 20 2143-2144 10.1093/bioinformatics/bth200 15072998
-
(2004)
Bioinformatics
, vol.20
, pp. 2143-2144
-
-
Olivier, B.G.1
Snoep, J.L.2
-
7
-
-
33646203362
-
WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks
-
10.1093/bioinformatics/btl091 16543278
-
Lee D Yun C Cho A Hou BK Park S Lee SY WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks Bioinformatics 2006 22 1150-1151 10.1093/bioinformatics/btl091 16543278
-
(2006)
Bioinformatics
, vol.22
, pp. 1150-1151
-
-
Lee, D.1
Yun, C.2
Cho, A.3
Hou, B.K.4
Park, S.5
Lee, S.Y.6
-
8
-
-
33644877164
-
BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
1347454 16381960 10.1093/nar/gkj092
-
Le Novere N Bornstein B Broicher A Courtot M Donizelli M Dharuri H Li L Sauro H Schilstra M Shapiro B Snoep JL Hucka M BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucl Acids Res 2006 34 D689-691 1347454 16381960 10.1093/nar/gkj092
-
(2006)
Nucl Acids Res
, vol.34
-
-
Le Novere, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
10
-
-
4644293116
-
An introduction to biochemical modeling using JDesigner
-
Claremont, CA: Keck Graduate Institute
-
Sauro HM An introduction to biochemical modeling using JDesigner Claremont, CA: Keck Graduate Institute 2004
-
(2004)
-
-
Sauro, H.M.1
-
11
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
10.1016/S1478-5382(03)02370-9
-
Funahashi A Tanimura N Morohashi M Kitano H CellDesigner: A process diagram editor for gene-regulatory and biochemical networks BIOSILICO 2003 159-162 10.1016/S1478-5382(03)02370-9
-
(2003)
BIOSILICO
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
12
-
-
20144389891
-
Grid cellware: The first grid-enabled tool for modelling and simulating cellular processes
-
10.1093/bioinformatics/bti143 15546936
-
Dhar PK Meng TC Somani S Ye L Sakharkar K Krishnan A Ridwan ABM Wah SHK Chitre M Hao Z Grid cellware: The first grid-enabled tool for modelling and simulating cellular processes Bioinformatics 2005 21 1284-1287 10.1093/bioinformatics/bti143 15546936
-
(2005)
Bioinformatics
, vol.21
, pp. 1284-1287
-
-
Dhar, P.K.1
Meng, T.C.2
Somani, S.3
Ye, L.4
Sakharkar, K.5
Krishnan, A.6
Ridwan, A.B.M.7
Wah, S.H.K.8
Chitre, M.9
Hao, Z.10
-
13
-
-
0347506655
-
An overview of data models for the analysis of biochemical pathways
-
10.1093/bib/4.3.246 14582519
-
Deville Y Gilbert D Helden JV Wodak SJ An overview of data models for the analysis of biochemical pathways Briefings in Bioinformatics 2003 4 246-259 10.1093/bib/4.3.246 14582519
-
(2003)
Briefings in Bioinformatics
, vol.4
, pp. 246-259
-
-
Deville, Y.1
Gilbert, D.2
Helden, J.V.3
Wodak, S.J.4
-
14
-
-
34147142580
-
Modelling Codependence in Biological Systems
-
10.1049/iet-syb:20060002 17370426
-
Mandel JJ Palfreyman NM Dubitzky W Modelling Codependence in Biological Systems IET Systems Biology 2007 1 1 18-32 10.1049/iet-syb:20060002 17370426
-
(2007)
IET Systems Biology
, vol.1
, Issue.1
, pp. 18-32
-
-
Mandel, J.J.1
Palfreyman, N.M.2
Dubitzky, W.3
-
16
-
-
33747872720
-
Bistable Switching and Excitable Behaviour in the Activation of Src at Mitosis
-
10.1093/bioinformatics/btl201 16873466
-
Fuß H Dubitzky W Downes CS Kurth MJ Bistable Switching and Excitable Behaviour in the Activation of Src at Mitosis Bioinformatics 2006 22 14 e158-e164 10.1093/bioinformatics/btl201 16873466
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Fuß, H.1
Dubitzky, W.2
Downes, C.S.3
Kurth, M.J.4
-
17
-
-
0042665800
-
A kinetic model of the cyclin e/cdk2 developmental timer in xenopus laevis embryos
-
10.1016/S0301-4622(03)00060-7 12914904
-
Ciliberto A Petrus MJ Tyson JJ Sible JC A kinetic model of the cyclin e/ cdk2 developmental timer in xenopus laevis embryos Biophys Chem 2003 104 573-589 10.1016/S0301-4622(03)00060-7 12914904
-
(2003)
Biophys Chem
, vol.104
, pp. 573-589
-
-
Ciliberto, A.1
Petrus, M.J.2
Tyson, J.J.3
Sible, J.C.4
-
19
-
-
0141626866
-
E-cell 2: Multi-platform E-cell simulation system
-
10.1093/bioinformatics/btg221 15593410
-
Takahashi K Ishikawa N Sadamoto Y Sasamoto H Ohta S Shiozawa A Miyoshi F Naito Y Nakayama Y Tomita M E-cell 2: Multi-platform E-cell simulation system Bioinformatics 2003 19 1727-1729 10.1093/bioinformatics/btg221 15593410
-
(2003)
Bioinformatics
, vol.19
, pp. 1727-1729
-
-
Takahashi, K.1
Ishikawa, N.2
Sadamoto, Y.3
Sasamoto, H.4
Ohta, S.5
Shiozawa, A.6
Miyoshi, F.7
Naito, Y.8
Nakayama, Y.9
Tomita, M.10
-
22
-
-
84886757395
-
-
Java Compiler Compiler https://javacc.dev.java.net/
-
-
-
-
23
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
10.1016/0021-9991(76)90041-3
-
Gillespie D A general method for numerically simulating the stochastic time evolution of coupled chemical reactions J Comp Phys 1976 22 403-434 10.1016/0021-9991(76)90041-3
-
(1976)
J Comp Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.1
-
24
-
-
84886760280
-
-
JFreeChart http://www.jfree.org/jfreechart/
-
-
-
-
25
-
-
84886760302
-
-
Jeks http://www.eteks.com/jeks/
-
-
-
-
26
-
-
13844266102
-
Simulation tools for biochemical networks: Evaluation of performance and usability
-
10.1093/bioinformatics/bti018 15358616
-
Pettinen A Aho T Smolander O Manninen T Saarinen A Taattola K Yli-Harja O Linne M Simulation tools for biochemical networks: Evaluation of performance and usability Bioinformatics 2005 21 357-363 10.1093/ bioinformatics/bti018 15358616
-
(2005)
Bioinformatics
, vol.21
, pp. 357-363
-
-
Pettinen, A.1
Aho, T.2
Smolander, O.3
Manninen, T.4
Saarinen, A.5
Taattola, K.6
Yli-Harja, O.7
Linne, M.8
-
27
-
-
34147180141
-
Simulation study of differential equation model for protein kinase C signaling
-
Report 3 Institute of Signal Processing and Institute of Mathematics, Tampere, Finland
-
Manninen T Saarinen A and Linne ML Simulation study of differential equation model for protein kinase C signaling Report 3 Institute of Signal Processing and Institute of Mathematics, Tampere, Finland 2004
-
(2004)
-
-
Manninen, T.1
Saarinen, A.2
Linne, M.L.3
-
28
-
-
84886758977
-
-
Octave http://www.gnu.org/software/octave/
-
-
-
-
29
-
-
0003588772
-
Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations
-
Lawrence Livermore Laboratory, Livermore CAUCRL-ID-113855
-
Radhakrishnan K Hindmarsh AC Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations Lawrence Livermore Laboratory, Livermore 1993 CAUCRL-ID-113855
-
(1993)
-
-
Radhakrishnan, K.1
Hindmarsh, A.C.2
-
30
-
-
84886755053
-
-
SBML Validator http://sbml.org/validator/validate.php
-
-
-
-
31
-
-
84886756519
-
Narrator Project
-
Narrator Project http://www.narrator-tool.org
-
-
-
-
33
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
10.1038/nbt1111 16082367
-
Kitano H Funahasi A Matsuoka Y Oda Using process diagrams for the graphical representation of biological networks Nature Biotechnology 2005 23 961-966 10.1038/nbt1111 16082367
-
(2005)
Nature Biotechnology
, vol.23
, pp. 961-966
-
-
Kitano, H.1
Funahasi, A.2
Matsuoka, Y.3
Oda4
-
34
-
-
33845368513
-
COPASI - A COmplex PAthway Simulator
-
10.1093/bioinformatics/btl485 17032683
-
Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U COPASI - a COmplex PAthway Simulator Bioinformatics 2006 22 24 3067-3074 10.1093/bioinformatics/btl485 17032683
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
36
-
-
30044440098
-
Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
-
1345641 16267266 10.1091/mbc.E05-09-0824
-
Kohn KW Aladjem MI Weinstein JN Pommier Y Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology Mol Biol Cell 2006 17 1-13 1345641 16267266 10.1091/mbc.E05-09-0824
-
(2006)
Mol Biol Cell
, vol.17
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
37
-
-
34147189208
-
A Graphical Notation to describe the Logical Interactions of Biological Pathways
-
Moodie SL Sorokin A Groyanin I Ghazal P A Graphical Notation to describe the Logical Interactions of Biological Pathways Journal of Integrative Bioinformatics 2006 3 2 36 http://journal.imbio.de/index.php?paper_id=36
-
(2006)
Journal of Integrative Bioinformatics
, vol.3
, Issue.2
, pp. 36
-
-
Moodie, S.L.1
Sorokin, A.2
Groyanin, I.3
Ghazal, P.4
-
38
-
-
84886767100
-
-
CellML language http://www.cellml.org/tutorial/notation/
-
-
-
-
39
-
-
84886755249
-
-
Systems Biology Graphical Notation http://www.sbgn.org/
-
-
-
-
40
-
-
33747825750
-
A model diagram layout extension for SBML
-
10.1093/bioinformatics/btl195 16709586
-
Gauges R Rost U Sahle S Wegner K A model diagram layout extension for SBML Bioinformatics 2006 22 15 1879-1885 10.1093/bioinformatics/btl195 16709586
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1879-1885
-
-
Gauges, R.1
Rost, U.2
Sahle, S.3
Wegner, K.4
-
41
-
-
84886759856
-
-
Systems Biology Ontology http://www.ebi.ac.uk/sbo/
-
-
-
-
42
-
-
33745075591
-
Tools for kinetic modeling of biochemical networks
-
10.1038/nbt0606-667 16763599
-
Alves R Antunes F Salvador A Tools for kinetic modeling of biochemical networks Nature Biotechnology 2006 24 667-672 10.1038/nbt0606-667 16763599
-
(2006)
Nature Biotechnology
, vol.24
, pp. 667-672
-
-
Alves, R.1
Antunes, F.2
Salvador, A.3
-
43
-
-
23444446572
-
Closing the circle of osmoregulation
-
10.1038/nbt0805-941 16082361
-
D'haeseleer P Closing the circle of osmoregulation Nature Biotechnology 2005 23 941-942 10.1038/nbt0805-941 16082361
-
(2005)
Nature Biotechnology
, vol.23
, pp. 941-942
-
-
D'haeseleer, P.1
-
45
-
-
33745658975
-
Model-View-Controller
-
Sun Microsystems, Java BluePrints
-
Sun Microsystems, Java BluePrints Model-View-Controller 2002 http://java.sun.com/blueprints/patterns/MVC-detailed.html
-
(2002)
-
-
-
47
-
-
0003905225
-
Chaos and integrability in nonlinear dynamics: An introduction
-
Wiley New York
-
Tabor M Chaos and integrability in nonlinear dynamics: An introduction Wiley New York 1989
-
(1989)
-
-
Tabor, M.1
-
48
-
-
10644250404
-
Evolving a Lingua Franca and Associated Software Infrastructure for Computational Systems Biology: The Systems Biology Markup Language (SBML) Project
-
10.1049/sb:20045008 17052114
-
Hucka M Finney A Bornstein BJ Keating SM Shapiro BE Matthews J Kovitz BL Schilstra MJ Funahashi A Doyle JC Kitano H Evolving a Lingua Franca and Associated Software Infrastructure for Computational Systems Biology: The Systems Biology Markup Language (SBML) Project Systems Biology 2004 1 41-53 10.1049/sb:20045008 17052114
-
(2004)
Systems Biology
, vol.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.J.3
Keating, S.M.4
Shapiro, B.E.5
Matthews, J.6
Kovitz, B.L.7
Schilstra, M.J.8
Funahashi, A.9
Doyle, J.C.10
Kitano, H.11
-
49
-
-
0002203999
-
JARNAC: A system for interactive metabolic analysis
-
Stellenbosch, University Press Stellenbosch Hofmeyr J-HS, Rohwer JM, Snoep JL
-
Sauro HM JARNAC: A system for interactive metabolic analysis Animating the Cellular Map Stellenbosch, University Press Stellenbosch Hofmeyr J-HS, Rohwer JM, Snoep JL 2001 221-228
-
(2001)
Animating the Cellular Map
, pp. 221-228
-
-
Sauro, H.M.1
-
50
-
-
0347511691
-
Next generation simulation tools: The Systems BiologyWorkbench and BioSPICE integration
-
10.1089/153623103322637670 14683609
-
Sauro HM Hucka M Finney A Wellock C Bolouri H Doyle J Kitano H Next generation simulation tools: The Systems BiologyWorkbench and BioSPICE integration OMICS 2003 7 4 355-72 10.1089/153623103322637670 14683609
-
(2003)
OMICS
, vol.7
, Issue.4
, pp. 355-372
-
-
Sauro, H.M.1
Hucka, M.2
Finney, A.3
Wellock, C.4
Bolouri, H.5
Doyle, J.6
Kitano, H.7
-
51
-
-
3042595010
-
Cellware - A multi-algorithmic software for computational systems biology
-
10.1093/bioinformatics/bth067 14871872
-
Dhar P Meng TC Somani S Ye L Sairam A Chitre M Hao Z Sakharkar K Cellware - a multi-algorithmic software for computational systems biology Bioinformatics 2004 20 8 1319-1321 10.1093/bioinformatics/bth067 14871872
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1319-1321
-
-
Dhar, P.1
Meng, T.C.2
Somani, S.3
Ye, L.4
Sairam, A.5
Chitre, M.6
Hao, Z.7
Sakharkar, K.8
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