IDEAS.txt

FUTURE TODO

Pack the test cases and build file to run them in one of the distributives 

? Better native Mac support (and maybe abandon native windows support in 
favour of VM)

Cluster stats: 
 -Remove hyperlinks from tasks which workdirs were removed 
 Way to do: Crawler is to update DB records if the directory is not found to prevent link 
generation for stats. 
 -graph generation 
 -user documentation (do not forget how to enable follow symlinks!)
   
Webpage for testing web services?

Add interface for Jalview annotation 

Develop generic Interface to return Jalview annotation for easy to add new 
services (?) 

Philogeny Mrbayes + Philip
 
USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE
- Receive user alignment 
- use hmmerbuild to turn it to profile
- use hmmersearch to search the database 

#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE 

New data model for representing psiblast,blast,phmmer,jackhmmer results

new parsers for the above programmes output (Stockholm MSA format?)

Think hard on what to do with large output files? 
e.g. serve the hits table in full, but retrieve alignments on demand.
What actually needs to be sent?   


Add facility to distribute other results of the calculations like the trees and 
annotation file for probcons. 

(later) WRAP Amps

(later) Implement utility to rerun died tasks from command line

Registry for jalview WS - gives list of web services providers
 - checks the status of the web services
 - web service providers gives list of available WS
 - synchronises with other registries
 - UI for adding new WS from third party provider
 - Jalview should include component for adding new Web service and WS registry  
 
 With Jim: 
Integration with Jalview
Jalview 
 - should use local engine to run tasks locally
 - keep sufficient information about the task to be able to re-run it on the same 
 or different service provider (task persistence)
 - Provide for configuration for choosing which registries/ws providers to use
 - be able to bypass firewalls and proxies to access WS
 
 
NOTES
1) Keep in mind that jobs could be submitted from behind the firewalls and proxies make sure to support this
2) Make sure it will be possible to distinguish between communication errors,  execution errors  
and possibly misconfiguration errors

FUTURE TASKS 
Prepare HMM profile for the user alignment and call jnet - instead of jpred. 
JPRED REWRITING Wrap Jpred
Wrap scanPS    

CBS soft: 
Transmembrane regions
Phosphorilation sites
Glycozilation sites
Signal P

They all have SOAP WS...
 
CDD domains
PFAM domains
 
JPRED IMPROVEMENTS
1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration
if large number of sequences is already generated, second approach is to search PFAM to see if the sequence is from the family
and if it is so, then use the family)
2) Use blast -m 7 option - generate xml output its 8 times more compact
3) Paralellize PSI blast
4) Improve unmask alignments routine 
 
/homes/ws-dev1/NOBACK/jpred3_submit_concise
/homes/ws-dev1/servers/JalviewWS/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/TestJWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/JalviewWS-back/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise


JAXB - cannot serialize Maps and instance variables in Enums!
Best replacement for Maps is a custom object for key->value pair and a HashSet for storing the pairs.
JaxB cannot serialize instances of generic classes(?)