News and Notes


Release date of New pathways has been postponed

posted Dec 20, 2011, 8:39 PM by Pradeep Kumar Sreenivasaiah

Due to unavoidable circumstance we would be unable to release new pathways as planned on 20-DEC-2011. The new tentative release date is on 10-JAN-2012.

IPAVS published in Nucl. Acids. Res. database issue

posted Dec 12, 2011, 6:20 PM by Pradeep Kumar Sreenivasaiah   [ updated Dec 12, 2011, 6:58 PM ]

We are happy to share the news that the manuscript describing IPAVS is published in Nucl. Acids. Res. database issue (2011).

Title: IPAVS: Integrated Pathway Resources, Analysis and Visualization System
Author(s): Sreenivasaiah, Pradeep Kumar; Rani, Shilpa; Cayetano, Joseph; et al.
Source: Nucleic Acids Research Published online: December 2, 2011
URL: http://nar.oxfordjournals.org/content/early/2011/12/02/nar.gkr1208.abstract
DOI: 10.1093/nar/gkr1208

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IPAVS is the winner of Best SBGN outreach 2011 award

posted Nov 2, 2011, 6:59 PM by Pradeep Kumar Sreenivasaiah   [ updated Nov 2, 2011, 9:36 PM ]

IPAVS is the winner of Best SBGN outreach 2011 award

Scheduled maintainance on 22-OCT-2011

posted Oct 19, 2011, 11:42 PM by Pradeep Kumar Sreenivasaiah

NOTE: Due to scheduled maintenance at the GIST data centre, IPAVS will be shutdown on Saturday, 22-OCT-2011 between 7AM to 7PM (Standard Time +0900 UTC)

Improved download speed of IPAVS pathways!

posted Oct 3, 2011, 9:23 PM by Pradeep Kumar Sreenivasaiah   [ updated Oct 3, 2011, 9:33 PM ]

We are updating download module of IPAVS on 05-OCT-2011.
  • Downloads can be done at much faster speed.
  • Download what you see on the screen (WYSWYG). Just download fraction of the entire pathway ie specific zoomed regions.
  • Download can be with or without Overlay.
  • Can be exported as SVG, JPG or PNG graphics format. When exported as SVG, pathways retain their interactive features and can readily be viewed in a web browser without requiring IPAVS. It is also publishable on other websites (e.g., forums), which can then serve as a common place to exchange knowledge and ideas among collaborators.


Major software updates to IPAVS by 17-SEPT-2011

posted Sep 11, 2011, 4:41 PM by Pradeep Kumar Sreenivasaiah

IPAVS software modules will be updated with several improvements (majorly with search, visualization and user interface presentation) tentatively by 17-SEPT-2011.

  • Read more here
  • You can also try out some of the forthcoming features on our development/test server (here).

WYSWYG download

posted Aug 31, 2011, 7:48 PM by Pradeep Kumar Sreenivasaiah

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).

OldPosts

posted Aug 31, 2011, 7:45 PM by Pradeep Kumar Sreenivasaiah   [ updated Aug 31, 2011, 7:51 PM ]

  • 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

Next pathway release on 25 SEPT 2011

posted Aug 31, 2011, 7:45 PM by Pradeep Kumar Sreenivasaiah

Our focus for the next release will be disease pathways ( metabolic and signaling)

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