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Results: 1 to 20 of 96

1.

The Cell Collective: toward an open and collaborative approach to systems biology.

Helikar T, Kowal B, McClenathan S, Bruckner M, Rowley T, Madrahimov A, Wicks B, Shrestha M, Limbu K, Rogers JA.

BMC Syst Biol. 2012 Aug 7;6:96. doi: 10.1186/1752-0509-6-96.

PMID:
22871178
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

NEURONSESSIONS: a Web-based collaborative tool to create brain computational models.

Porto A, Rodríguez G, Dorado J, Pazos A.

Adv Exp Med Biol. 2010;680:635-42. doi: 10.1007/978-1-4419-5913-3_70.

PMID:
20865549
[PubMed - indexed for MEDLINE]
3.

A cell simulator platform: the cell collective.

Helikar T, Kowal B, Rogers JA.

Clin Pharmacol Ther. 2013 May;93(5):393-5. doi: 10.1038/clpt.2013.41. Epub 2013 Feb 20.

PMID:
23549147
[PubMed - indexed for MEDLINE]
4.

A data integration approach for cell cycle analysis oriented to model simulation in systems biology.

Alfieri R, Merelli I, Mosca E, Milanesi L.

BMC Syst Biol. 2007 Aug 1;1:35.

PMID:
17678529
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ADAM: analysis of discrete models of biological systems using computer algebra.

Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R.

BMC Bioinformatics. 2011 Jul 20;12:295. doi: 10.1186/1471-2105-12-295.

PMID:
21774817
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Modeling and simulation in signal transduction pathways: a systems biology approach.

Suresh Babu CV, Joo Song E, Yoo YS.

Biochimie. 2006 Mar-Apr;88(3-4):277-83. Epub 2005 Sep 22.

PMID:
16213652
[PubMed - indexed for MEDLINE]
7.

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

Sekiguchi T, Okamoto M.

J Bioinform Comput Biol. 2006 Jun;4(3):621-38.

PMID:
16960966
[PubMed - indexed for MEDLINE]
8.

Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Helikar T, Kowal B, Madrahimov A, Shrestha M, Pedersen J, Limbu K, Thapa I, Rowley T, Satalkar R, Kochi N, Konvalina J, Rogers JA.

PLoS One. 2012;7(10):e46417. doi: 10.1371/journal.pone.0046417. Epub 2012 Oct 17.

PMID:
23082121
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists.

Helikar T, Rogers JA.

BMC Syst Biol. 2009 Jun 6;3:58. doi: 10.1186/1752-0509-3-58.

PMID:
19500393
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Bringing Web 2.0 to bioinformatics.

Zhang Z, Cheung KH, Townsend JP.

Brief Bioinform. 2009 Jan;10(1):1-10. doi: 10.1093/bib/bbn041. Epub 2008 Oct 8.

PMID:
18842678
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

PathCase-SB: integrating data sources and providing tools for systems biology research.

Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Jadeja R, Dash RK, Lai N, Ozsoyoglu G, Ozsoyoglu ZM.

BMC Syst Biol. 2012 Jun 14;6(1):67. doi: 10.1186/1752-0509-6-67.

PMID:
22697505
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SYCAMORE--a systems biology computational analysis and modeling research environment.

Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U.

Bioinformatics. 2008 Jun 15;24(12):1463-4. doi: 10.1093/bioinformatics/btn207. Epub 2008 May 7.

PMID:
18463116
[PubMed - indexed for MEDLINE]
Free Article
13.

CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways.

Flórez LA, Lammers CR, Michna R, Stülke J.

Bioinformatics. 2010 Dec 1;26(23):2997-9. doi: 10.1093/bioinformatics/btq585. Epub 2010 Oct 14.

PMID:
20947526
[PubMed - indexed for MEDLINE]
Free Article
14.

Network analysis approach for biology.

Kwoh CK, Ng PY.

Cell Mol Life Sci. 2007 Jul;64(14):1739-51. Review.

PMID:
17415520
[PubMed - indexed for MEDLINE]
15.

E-photosynthesis: web-based platform for modeling of complex photosynthetic processes.

Safránek D, Cervený J, Klement M, Pospíšilová J, Brim L, Lazár D, Nedbal L.

Biosystems. 2011 Feb;103(2):115-24. doi: 10.1016/j.biosystems.2010.10.013. Epub 2010 Nov 10.

PMID:
21073914
[PubMed - indexed for MEDLINE]
16.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

Kell DB, Mendes P.

J Theor Biol. 2008 Jun 7;252(3):538-43. Epub 2007 Dec 3. Review.

PMID:
18054049
[PubMed - indexed for MEDLINE]
17.

Using views of Systems Biology Cloud: application for model building.

Ruebenacker O, Blinov M.

Theory Biosci. 2011 Mar;130(1):45-54. doi: 10.1007/s12064-010-0108-6. Epub 2010 Aug 21. Review.

PMID:
20730508
[PubMed - indexed for MEDLINE]
18.

BioPP: a tool for web-publication of biological networks.

Viswanathan GA, Nudelman G, Patil S, Sealfon SC.

BMC Bioinformatics. 2007 May 22;8:168.

PMID:
17519033
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

HPD: an online integrated human pathway database enabling systems biology studies.

Chowbina SR, Wu X, Zhang F, Li PM, Pandey R, Kasamsetty HN, Chen JY.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S5. doi: 10.1186/1471-2105-10-S11-S5.

PMID:
19811689
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

Alves R, Vilaprinyo E, Hernádez-Bermejo B, Sorribas A.

Biotechnol Genet Eng Rev. 2008;25:1-40. Review.

PMID:
21412348
[PubMed - indexed for MEDLINE]

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