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.
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posted Dec 12, 2011, 6:20 PM by Pradeep Kumar Sreenivasaiah
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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.abstractDOI: 10.1093/nar/gkr1208
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posted Nov 18, 2011, 7:27 PM by Pradeep Kumar Sreenivasaiah
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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
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posted Nov 2, 2011, 6:59 PM by Pradeep Kumar Sreenivasaiah
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updated Nov 2, 2011, 9:36 PM
]
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
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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) |
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
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posted Oct 3, 2011, 9:23 PM by Pradeep Kumar Sreenivasaiah
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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.
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posted Sep 20, 2011, 4:59 AM by Pradeep Kumar Sreenivasaiah
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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
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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).
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