About

About KCPAVS

This project is being developed by the Systems Biology Laboratory of Gwangju Institute of Science and Technology, Department of Life Sciences, Gwangju, South Korea. KCPAVS is freely avaialble to the public as an efficient tool for biological research.

KCPAVS is an highly interactive user friendly interface to the KEGG pathways and global maps. This tool provide several useful features like comprehensive browsing, simple and expert search, advanced visualization and analysis capabilities that could be effectively used by researchers (bench biologist, bioinformatics, systems biologist and physicians) in their day do day research. KCPAVS uses Scalable Vector Graphics (SVG one of the widely accepted graphics for the web supported by all the browsers) and Ajax to deliver the pathway content on web. It integrates relevant data from several databases and makes the content accessible by user at ease. KCPAVS is meticulously designed follows 'All in one  screen' design (AIOS design) concept, where user is able to work with their own data, explore integrated information (KEGG Pathways, protein/gene/enzyme annotations, gene ontology etc), analyze, visualize and view reports (charts, overlay) all in one screen. The design minimizes number of mouse clicks / screen the users have to navigate to access information. Therefore keeping user focused on their domain issues rather getting distracted by complexities of tool handling and navigating the information pages. With the mind mapping functionality users can use the tool during brainstorming to annotate pathways with information and ideas. With the collaborate features, created annotations over a pathway can be exchanged with peers. To summaries, KCPAVS implements more useful functionalities for visualization, navigation, data management, data comparison and analytical tools than any existing publicly available web based tools.

IPAVS (Integrated database for high quality curated pathways)

iPAVS provide biologists access to expert-curated pathways from experimental data belonging to specific biological contexts related to cell types, tissues, organs and diseases. IPAVS currently integrates over 500 human pathways (consisting of 24 574 interactions) that include metabolic-, signaling- and disease-related pathways, drug–action pathways and several large process maps collated from other pathway resources. IPAVS web interface allows biologists to browse and search pathway resources and provides tools for data import, management, visualization and analysis to support the interpretation of biological data in light of cellular processes.

Project Funding

The project was supported by Korea MESTNRF grant (2010-0002159), GIST Systems Biology Infrastructure Establishment Grant (2010).




Our major focus are:

  1. Development of high throughput technologies for system-wide data generation
  2. Efforts towards computational modeling and system analysis of cardiac pathophysiology such as cardiac hypertrophy, heart failure, arrhythmia and endoplasmic reticulum stress response: 
    • Development of integrative (multi-level) computational analysis methods aiding in prediction of clinical phenotypes and in providing therapeutic targets
    • Development of network incorporating regulatory mechanisms involving gene, gene product, small molecules and miRNA
  3. Development of tools and databases for the above work, to aid analysis or to provide a base for 
  4. further methodology/algorithm development. See the links page for list of some of the databases and tools developed, or under development.

Acknowledgements

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;Google Apps;Creately;Atlassia JIRA;VmWare 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:
  1. The end user is authorized by the Systems Biology Laboratory (SBL) and by any Copy Right Holders(CRH) to use KCPAVS program/software, code and data without any fee for academic and non-commercial purposes only. 
  2. The SBL or CRH of KCPAVS  does not take any responsibility of any problems that arise directly or indirectly from using data, code, program/software from KCPAVS .
  3. The copyright for KCPAVS remains with the SBL and its nominated CRH. Also data imported and stored in KCPAVS from public databases is available under the license terms of each contributing database. The end user has to ensure that KCPAVS or associated parts of it ( like data, code, documents etc.) are not used that conflicts with the license terms. 
  4. We request you to show your support and encourage further development of useful and quality tools/utilities and provide it freely to the community by citing our tools and data in your publications resulting from work which used KCPAVS.You have to mention KCPAVS with appropriate citations including the URL.
  5. All data is made available under the original license terms of the primary database KEGG. We request users to also cite all primary source KEGG to support their efforts.
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