Merge branch 'JWS-35' into JABAWS_Release_2_0

[jabaws.git] / IDEAS.txt

diff --git a/IDEAS.txt b/IDEAS.txt
index f9f65fd..ba3b9eb 100644 (file)
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,49 @@
 FUTURE TODO\r
 FUTURE TODO\r

-Registry for jalview WS - gives list of web services providers\r
+\r
+Pack the test cases and build file to run them in one of the distributives \r
+\r
+? Better native Mac support (and maybe abandon native windows support in \r
+favour of VM)\r
+\r
+Cluster stats: \r
+ -Remove hyperlinks from tasks which workdirs were removed \r
+ Way to do: Crawler is to update DB records if the directory is not found to prevent link \r
+generation for stats. \r
+ -graph generation \r
+ -user documentation (do not forget how to enable follow symlinks!)\r
+   \r
+Webpage for testing web services?\r
+\r
+Add interface for Jalview annotation \r
+\r
+Develop generic Interface to return Jalview annotation for easy to add new \r
+services (?) \r
+\r
+Philogeny Mrbayes + Philip\r
+ \r
+USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE\r
+- Receive user alignment \r
+- use hmmerbuild to turn it to profile\r
+- use hmmersearch to search the database \r
+\r
+#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE \r
+\r
+New data model for representing psiblast,blast,phmmer,jackhmmer results\r
+\r
+new parsers for the above programmes output (Stockholm MSA format?)\r
+\r
+Think hard on what to do with large output files? \r
+e.g. serve the hits table in full, but retrieve alignments on demand.\r
+What actually needs to be sent?   \r
+\r
+\r
+Add facility to distribute other results of the calculations like the trees and \r
+annotation file for probcons. \r
+\r
+(later) WRAP Amps\r
+\r
+(later) Implement utility to rerun died tasks from command line\r
+\r

 Registry for jalview WS - gives list of web services providers\r
  - checks the status of the web services\r
  - web service providers gives list of available WS\r
 Registry for jalview WS - gives list of web services providers\r
  - checks the status of the web services\r
  - web service providers gives list of available WS\r

@@ -26,7 +70,17 @@ FUTURE TASKS
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. \r
 JPRED REWRITING Wrap Jpred\r
 Wrap scanPS    \r
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. \r
 JPRED REWRITING Wrap Jpred\r
 Wrap scanPS    \r

-Look at SIFTS at EBI \r
+\r
+CBS soft: \r
+Transmembrane regions\r
+Phosphorilation sites\r
+Glycozilation sites\r
+Signal P\r
+\r
+They all have SOAP WS...\r
+ \r
+CDD domains\r
+PFAM domains\r

  \r
 JPRED IMPROVEMENTS\r
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration\r
  \r
 JPRED IMPROVEMENTS\r
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration\r