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
DOI: 10.1093/nar/gkr1208

Share Bookmark

31 New Pathways released on 19-NOV-2011

posted Nov 18, 2011, 7:27 PM by Pradeep Kumar Sreenivasaiah   [ updated Nov 19, 2011, 1:54 AM ]

This months pathway release mainly contains pathway curated in context of Lysosomal storage disorder, metabolic and metabolic disease pathways, Cancer signaling , transcription regulatory pathways and drug-action pathways of NSAIDS, Renin-angiotensin system acting and Anti-diabetic drugs.

The following are the list of pathways released:

Lysosomal storage disorder pathways:

  • Gaucher_Disease_Pathway
  • Lactic_Acidemia_Metabolic_Disease_Pathway
  • Lactose_Intolerance_Metabolic_Disease_Pathway
  • Sialidosis_Metabolic_Pathway
  • The_Mucopolysaccharidoses_Lysosomal_Storage_Diseases_Pathway
    • Disease related to heparan Sulfate Degradation
      • Hunter syndrome (MPSII)
      • Hurler, Hurler-Scheie, Scheie syndrome (MPSI)
      • Sanfilippo syndrome A (MPSIIIA)
      • Sanfilippo syndrome C (MPSIIIC)
      • Sanfilippo syndrome B (MPSIIIB)
      • Sly syndrome (MPSVII)
      • Sanfilippo syndrome D (MPSIIID)
    • Disease related to Keratan Sulfate Degradation
      • Morquio syndrome A (MPSIVA)
      • Morquio syndrome B (MPSIVB)
      • Sanfilippo syndrome D (MPSIIID)
      • Tay-Sachs disease
      • Sandhoff disease
    • Dermatan Sulfate Degradation
      • Hunter syndrome A (MPSII)
      • Hurler, Hurler-Scheie, Scheie syndrome (MPSI)
      • Maroteaux-Lamy syndrome (MPSVI)
      • Tay-Sachs disease
      • Sandhoff disease
      • Sly syndrome (MPSVII)
  • Globoid_Cel_Leukodystrophy_or_Krabbe_disease_pathway

Drug-Action and Drug-metabolism pathways:
  • ACE_Inhibitors_Drug_Pathway
  • Anti-diabetic_Drug_Nateglinide_Pathway
  • Anti-diabetic_Drug_Repaglinide_Pathway
  • Candesartan_Drug_Pathway
  • Eplerenone_Drug_Pathway
  • Ketorolac_Drug_Pathway
  • Naproxen_Drug_Pathway
  • Piroxicam _Drug_Pathway
  • Renin-angiotension_system_acting_drug_pathway
  • Spironolactone_Drug_Pathway
  • Sulindac_Drug_Pathway
  • Suprofen_Drug_Pathway

Transcription regulatory pathways:

  • Assembly_of_General_Transcription_Factors_for_RNA_Polymerase_I_Pathway
  • Assembly_of_General_Transcription_Factors_for_RNA_Polymerase_II_Pathway
  • Assembly_of_General_Transcription_Factors_for_RNA_Polymerase_III_Pathway
  • DNA_damange_recognition_by_MMR_pathway
  • Calcitriol_VDR_RXR_mediated_transcriptional_regulation_pathway

Cancer signaling Pathway:
  • Bladder_cancer_signaling
  • Ovarian_cancer_signaling

Metabolism and metabolic-disease pathway:

  • Vitamin_D_metabolism_pathway
  • Pyrimidine_Metabolism_Disorder_Pathway
  • Porphyria_Variegat_Metabolic_Disease_Pathway

Signaling pathways:
  • Mechanisms_of_alcohol_induced_endoplasmic_reticulum_stress_and_organ_injuries_pathway
  • Relaxin_Signaling_Pathway
  • Renin-angiotension_system_pathway

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

19 New Pathways released on 28-OCT-2011

posted Oct 28, 2011, 7:28 PM by Pradeep Kumar Sreenivasaiah

Following pathways were released on 28-OCT-2011
We focused on curating Drug pathways (NSAIDS and Analgesics) and 1 Metabolic pathway

  • Androgen and Estrogen Metabolic Pathway
  • Benzocaine Local Anaesthetic Pathway
  • Bupivacaine Local Anaesthetic Pathway
  • Chloroprocaine Local Anaesthetic Pathway
  • Cocaine Local Anaesthetic Pathway
  • Dibucaine Local Anaesthetic Pathway
  • Diclofenac Drug Pathway
  • Diflunisal Drug Pathway
  • Ibuprofen Drug Pathway
  • Indomethacin Drug Pathway
  • Ketoprofen Drug Pathway
  • Levobupivacaine Local Anaesthetic Pathway
  • Mefenamic Acid Drug Pathway
  • Mepivacaine Local Anaesthetic Pathway
  • Nabumetone Drug Pathway
  • Oxybuprocaine Local Anaesthetic Pathway
  • Prilocaine Local Anaesthetic Pathway
  • Procaine Local Anaesthetic Pathway
  • Proparacaine Local Anaesthetic Pathway
  • Ropivacaine Local Anaesthetic Pathway

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)

11 New Pathways released on 08-OCT-2011

posted Oct 8, 2011, 3:48 AM by Pradeep Kumar Sreenivasaiah

Following pathways were released on 08-OCT-2011
We focused on curating metabolic pathways in disease and some drug ( NSAIDS and Analgesics) pathways

  • Methionine Adenosyltransferase Deficiency metabolic pathway
  • Malonic aciduria metabolic pathway
  • Saccharopinuria(Hyperlysinemia) II metabolic pathway
  • Tyrosinemia Type3 metabolic pathway
  • Prostaglandin Metabolic Pathway
  • Lidocaine Local Anaesthetic Pathway
  • ABCIXIMAB Drug Pathway
  • Oxaprozin Drug Pathway
  • Mefenamic Acid Drug Pathway
  • Von Gierke disease-metabolite pathway

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.

IPAVS updated!

posted Sep 20, 2011, 4:59 AM by Pradeep Kumar Sreenivasaiah   [ updated Sep 20, 2011, 5:12 AM ]

  • Data overlay can be animated (Animations can be customized with basic and advance animations settings )
  • Several bugs were fixed related to search, publications not displayed, reaction equations formats, analysis results display
  • Search module reimplemented -  more quicker search response time. The search results is displayed with subgrids ( ie. similar search results are grouped instead of showing them seperately)
  • Pathways in browser are now color coded depending on their assigned categories and biological roles
  • Several enhancements to user interface in analysis module (e.g Tabs are color coded - for better presentation)
  • Adding (~90) Biosymbols and symbol palette design is changed. now its easy to preview and choose symbols. ( see screen shots here: Use of symbols for mindmapping, UI )
  • Multiple files can be uploaded. The file upload can be done at any point of time into groups during analysis session. Even can upload a data from new file and merge data into a existing groups.
  • Several improvements in the way pathways are displayed (especially in multi-pathway group view).
  • Links fetches relevant information as well as marks the target content with visual cue. i.e. click on a link can open the target pathway and also mark the component on that pathway. e.g clicking on a reaction map-link will simultaneously open the details for the reaction; display the pathway in which reaction is modeled and also visually marks the reaction.
  • Valid BioPAX 3 files for all the pathway.
  • Will allow download of BioPAX,XGMML files in addition to existing formats.
  • Links to NCBI to show related publications and links to mining tools like iHOP from the publication tab
  • Users can now view the community contributions marked by tags on the pathway

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).

1-10 of 16