NOTE: 11-April-2014 - we have now launched IPAVS web-app and datawarehouse on a IBM blade cluster with high end resources. Users may see an improved performance. You can send enquiries /comments to admin (pradeep-a.t-cidms-d.o.t-org).
An Integrated Pathway Resources, Analysis and Visualization System
iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate,filter, browse, search, analyze, visualize and compare the integrated pathway resources.
iPAVS has implemented advanced functionalities to perform complex pathway analysis tasks and visualize the results. But, at the same time extensive efforts has been put to design the user interface simple and intuitive enough for biologists to use IPAVS functionalities with ease.
Main intention behind launching iPAVS is to
enable biologists to do systems biology and employ systems methodologies in their day to day research and produce testable hypothesis, without having to engage themselves in difficult, resource demanding and time consuming data integration and management tasks.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.
|iPAVS pathway data
Total number of pathways/Maps in iPAVS: Over 541 pathways with 27,100 Interactions
iPAVS curated pathways
At present 118 pathways/maps are loaded. See preview of forthcoming releases here.
Imported after partial curation
Total Imported pathways: 183
Automated data imports into iPAVS
- Panther: 165 human pathways
- RB pathways: 1 Map +16 sub-pathways
- SBI published Maps: 7 Maps
Total Imported pathways: 253
| iPAVS Visualization
- Easy to use efficient tools to explore and navigate large pathway diagrams
- Overlay pathways with custom colors,shapes and symbols
- Create visual cues -- 'mind mapping' on pathway
- Embed charts and heatmap of your data on the pathway
- Generate charts and heatmaps for your expression data
- Compare data and generate venn diagrams
- Uses SVG for visualization
- Notations:Mainly SBGN. But also other commonly used like KEGG
- Option to Visualize on single pathway as well as mmultiple pathways simultaneously.
- Animate overlay of multi-conditions/time-series data
- and more
| iPAVS Pathway Analysis
- Contextual Data Analysis: Filter and choose context specific pathway sets for analysis
- Visually compare your analysis results (allows simultaneous multiple comparisons) as: overlay on the multiple pathways, charts and heat maps
- Use enrichment algorithms such as Fishers' E test, Binomial Proportion test and PAGE for analyzing your data
- Get intuitive and easily comprehensible results.
- Save reports of your analysis along with pathway diagrams annotated with overlays like symbols, charts and heat maps.
- Export pathways/reports in publication ready formats.
- Instantly retrieve annotations from UniProt, Enzyme, GO, KEGG and other public databases..
- and more
| iPAVS data access and manipulation tools|
- "All in one screen Design": Allows access to every piece of information contextually and being on the same page.
- Make logical groups of data (observation columns and/or records) representing your experimental/analysis design
- Compare data using SET operations
- Use tool to manipulate your data and pathways used (Filter, Copy, Move, Delete records between groups)
- Generate reports like Venn diagrams for compared data
- Search using advance functions (Boolean, fuzzy search and range search)
- Get list of all signaling pathways that involves molecules from the input list.
- and more
| Curation theme of the month: Lysosomal storage disorder pathways (more>>) |
|Recent release of pathways was on: 19-NOV-2011
Next batch release date: (more>>)
|ER Stress Integrated Map
| ATF6 Pathway
| PERK Pathway
News and Notes
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- NEW! 11-April-2014 - IPAVS web-app and datawarehouse was launched on a IBM blade cluster with high end resources.
- 07-April-2014 Due to scheduled maintenance of GIST serer, IPAVS may function with only minimum modules. You may find that few modules may not function properly (e.g analysis module).
- Apologetic note : We noticed that server was malfunctioning since Feb 2 2013 - Feb 6 2013 and services may have been slow or failed. We have fixed the problem now.
- Apologetic note : Since few days we were facing problem with internet connection in the server room due to repair work. So IPAVS may have failed to function properly.We are sorry for any inconvenience caused. We have fixed the problem now.
- New! IPAVS published in NAR Database issue (details here)
- New! 31 New Pathways were released on 19-NOV-2011 (details here)
- New! IPAVS is the winner of Best SBGN outreach 2011 award
- Released 19 pathways on 28-OCT-2011 (details here)
- NOTE: Due to scheduled maintenance at the GIST data centre, IPAVS will be shutdown on Saturday, 22-OCT-2011 between 7AM and 7PM (Standard Time +0900 UTC)
- Released 11 pathways on 08-OCT-2011 (details here)
- IPAVS software updated with several improvements 20-SEPT-2011 (read more here).
- Released 9 new pathways on 01Sept2011 (details here)
- New! BioPAX files are now validated using BioPax Validator v2.0 (errors were fixed). Available from download page
- You can preview the pathways that is scheduled to be released in August and September 2011 here.
- New! IPAVS now allows download of the pathways along with the overlaid item and legend. The download can be entire pathway or zoomed in view of the pathway region (WYSWYG download).
- Released 24 new pathways on 14Aug2011.
- Fixed several bugs (visualization, search, fetching PUBMED details from NCBI using eutils) with New Release of IPAVS version 13Aug2011
- KEGG reactions now points to reactants and products on the pathway. Since KGML does not provide co-ordinates for the reaction line for easy exploration we point to molecules involved in the interaction.
- IPAVS now support comparison of analysis results, using tabular presentation of compared results. Also uses charts for graphical display.
- Same pathway can be cloned multiple times and multiple observations can be simultaneously overlaid on the pathways. Useful for visualization of time series / multiple conditions experimental data as tiled pathways. One observation (time point/condition) overlaid on one pathway and such several pathways tiled next to each other.
- Implemented Multi-pathways view to explore and visualize several pathways at a time(see slides).
- Heat maps can be created for the entire map or for molecules that are mapped onto a specific pathways
- Created BioSVG Symbol library consisting of >100 symbols/icons representing biomedical concepts ( few symbols have been incorporated into IPAVS as prototype already).
- Navigation features of the Map viewer were upgraded: can zoom in and out with mouse, use key board shortcuts to control the navigation. Pan the diagrams by click and dragging by mouse on the diagram.
- Added several pathway annotation features: 1) overlay different shapes with several colors, symbols, charts and heat maps over the pathway diagrams. Users can represent their thought/concepts with symbols over pathway while thinking about biological mechanisms. Visualize dispertate sets of experimental data simultaneously using various visual cues. Together this feature can help researchers as simple but powerful thinking aid, allow them to use it like a mind mapping tool.
- iPAVS updated its visualization:Users can visualize their data as dynamic Charts.
- Now iPAVS supports KEGG pathway maps and pathway information
IPAVS is the winner of Best SBGN Outreach 2011 award!
What People are Saying about this Website (click here)
Visitors between 15-Aug-2011 (made public) and 15-JAN-2012.