News for what is in the next release:
Our development/test server can be accessed here if you wish to test some of the upcoming features mentioned. NOTE the server runs on a PC so the response time may not be as good as production server (IBM cluster) running IPAVS.
- Bugs will be fixed
- Some of the imported pathways will be corrected for errors and updated with latest annotations.
- Corrections to vitamin B6 pathway by Panther database (fixed and available!)
- Corrections to Glycosaminoglcan degradation pathway in Kegg. Glycan structure is now displayed and hyperlinks are fixed (fixed and available!)
- GABA_Transaminase_Deficiency_Metabolite_pathway was not displayed in multi-pathway view (fixed and available!)
- Correction to SIF files (currently not properly exported) (fixed and available!).
- When large maps are overlaid and tried to download as JPG/PNG -- the response time is too large or even chashes browser some time. We will fix this problem by reimplementing the way we do the conversion from sVG to JPG/PNG (fixed and available!)
- Report generation of the analysis results, analysis comparison results and export in PDF and XML format. Several reports can be generated : ( under testing )
- Analysis summary reports: Includes summary and information about top enriched pathways and their scores for the given data
- Detailed report for an Enriched pathway: Information about enriched pathways can be exported as reports which can include details about the molecules from the user data that matched the pathway molecules. List of interactions in which these matching molecules participates.
- Analysis comparison report: Analyze using different pathway analysis algorithm and then compare the top enriched or overrepresented pathways among them and export it as a report.
- Improvements in Pathway analysis module ( beta-version already available!):
- Able to save analysis results as reports and is available as long as the session is avaialble
- The reports can be accessed and loaded at any time during the session
- Make comparisons with the previously saved analysis reports
- Produce analysis charts for the compared reports
- Able to import pathway data from tree into groups for analysis
- Animate the data overlay and analysis (already available!)
- Isomers overlay was not marked on reference map. This was recently fixed. Black circle is displayed on the reference map when isomers are overlaid on he main map
- New SVG symbols were added to SVG overlay palette (recently updated and available!).
- Dynamic filtering functionality will be implemented. The content of the table/grid can be filtered using text(keywords) or the numerical values (work under progress).
Several enhancements to IPAVS is currently under development
( wish list)
Data curation and update of pathway information
- Diseases due to alteration in metabolic and signaling pathways (work under progress - see here)
- Support microarrary probes
identifiers from illumina and Affymetrics
- Integrating pathways from Reactome and Nature NCI database
- Support several other organism by orthology mapping
- Normalize pathway data between databases at level of entity(molecules) and events (interactions/reactions)
- Allow user to upload their own pathways and use it in the analysis and annotation along with other pathway in IPAVS.
- Switching to more efficient data upload and processing algorithms for faster user experience
- Providing APIs for other applications to interact with IPAVS
- Communication with other external systems for analysis and data
- Integration with text mining features
- creation of dynamic network diagrams
- Charts (boxplot, scatter plot)
- Animate the overlay for multiple condition / time series data (beta version already available)
- Visualization of clustering using heat maps and other Charts
- Implementation of GAGE algorithm of gene set enrichment analysis
- Implementation of pathway topology analysis (DEGRAPH and SPIA)
- Implementation of basic clustering algorithms
Project Management Capability
- Generate print quality comprehensive reports ( pdf, rtf formats) for analysis (work under progress)
Knowledge networking capabilities
- User account and login for advance usage of system
- Workflow monitoring
- Allowing users to annotate pathways and its components over the web (work under progress)
- Able to export annotated pathways as interactive maps.
- Tagging pathway components and enhancements with social interaction and networking features (work under progress)