About

The scope of iPAVS ( Integrated System of Pathway Resources, Analysis and Visualization Tools) is three-fold.

Firstly, iPAVS provides a collection of highly-structured, manually drawn maps and curated pathway information from CIDMS-PD project (details here).

Main focus of CIDMS-PD project is curation of pathway information by experts and focuses on the following:
  • Molecular and interaction level context specific(tissue, organism, gender, perturbation, phenotype/disease, physiological) annotations (Evidence, citation to literature)
  • Annotation of pathways with their biological roles
  • Focuses on pathways with mechanistic details
  • Pathway Cross-talk and the annotations describing cross-talk context ( level of cross-talk, conditions for cross-talk etc)
Secondly, iPAVS serves as common point of access to biological pathway information including signaling, metabolic and gene regulatory networks collected from several public sources (listed at the end of this page) including databases, web sites and published pathway models.

Thirdly, it provides several easy to use but powerful tools to explore, search, analyze, visualize and compare the integrated pathway and associated information.


Acknowledgements

iPAVS is being developed by the Systems Biology Laboratory of Gwangju Institute of Science and Technology, Department of Life Sciences, Gwangju, South Korea. The project was supported by Korea MEST NRF grant (2010-0002159), GIST Systems Biology Infrastructure Establishment Grant (2010).

We are grateful to all the developers of the open-source and free software we use, without which our task would be impossible.
To mention few of the most used products: Apache Lucene ;Oracle Java / J2EE;MySQL;Carto.net (SVG resources);Glassfish;CellDesigner (free software)[1];Google Apps;Creately(free account);Atlassia JIRA;VmWare; JSBML[2](available under GPLv3 license);KEGGTranslator (binary jar available under LGPLv3 license)[3],BiNoM[4], PaxTools and several others.

We appreciate the dedicated efforts by data curators and institutions for making the curated information freely available to the community.


License
A commercial use of data /software/code provided  by iPAVS for non-academic use is not permitted unless exclusive licenses for commercial use are obtained by systems biology laboratory. Please contact support [at] cidms.org for licenses information.

Terms and conditions for usage of data, program / software and code:
  • The end user is authorized by the Systems Biology Laboratory (SBL) and by any Copy Right Holders(CRH) to use iPAVS program/software, code and data without any fee for academic and non-commercial purposes only. 
  • The SBL or CRH of iPAVS does not take any responsibility of any problems that arise directly or indirectly from using data, code, program/software from iPAVS.
  • The copyright for iPAVS remains with the SBL and its nominated CRH. Also data imported and stored in iPAVS from public databases is available under the license terms of each contributing database. The end user has to ensure that iPAVS or associated parts of it ( like data, code, documents etc.) are not used that conflicts with the license terms. 
  • We request you to show your support and encourage further development of useful and quality tools/utilities by citing our work. All forms of publications that use or rely on iPAVS data (e.g., web sites, research papers, databases, software, products, etc.) must cite iPAVS. You have to cite iPAVS main publication:
Title: IPAVS: Integrated Pathway Resources, Analysis and Visualization System
Author(s): Pradeep Kumar Sreenivasaiah, Shilpa Rani, Joseph Cayetano, Novino Arul, and Do Han Kim
Source: Nucleic Acids Research Published online: December 2, 2011  : gkr1208v1-gkr1208.
URL: http://nar.oxfordjournals.org/content/early/2011/12/02/nar.gkr1208.abstract
DOI: 10.1093/nar/gkr1208
  • All electronic or online applications must include hyperlinks from context that uses iPAVS data to the applicable IPAVS pathway pages.
  • You must notify iPAVS and describe how you are using our data.
  • All data is made available under the original license terms of the primary databases. We request users to also cite all primary sources to support their efforts.
View list of databases and pathways imported here

References:

  1. Funahashi, A., et al., CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE, 2008. 96(8): p. 1254-1265.
  2. Dräger, A., et al., JSBML: a flexible Java library for working with SBML. Bioinformatics, 2011. 27(15): p.     2167-8.
  3. Wrzodek, C., A. Dräger, and A. Zell, KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics, 2011. 27(16): p. 2314-5.
  4. Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics. 2008 Mar 15;24(6):876-7. Epub 2007 Nov 16
  5. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010;38:D204-D210.
  6. Frolkis A, Knox C, Lim E, Jewison T, Law V, Hau DD, Liu P, Gautam B, Ly S, Guo AC, et al. SMPDB: the Small Molecule Pathway Database. Nucleic Acids Res. 2010;38:D480-D487.
  7. Oda K, Kitano H. A comprehensive map of the toll-like receptor signaling network. Mol. Syst. Biol. 2006;2. 2006.0015.
  8. Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol. Syst. Biol. 2008;4:173.
  9. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, et al. The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 2010;28:935-942.
  10. Groenendyk J, Sreenivasaiah PK, Kim DH, Agellon LB, Michalak M. Biology of endoplasmic reticulum stress in the heart. Circ. Res. 2010;107:1185-1197.
  11. Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, et al. The systems biology graphical notation. Nat. Biotechnol. 2009;27:735-741.
  12. Kim SY, Volsky DJ. PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005;6:144.



Comments