Changes between Version 5 and Version 6 of DDBJ-KEGG-PDBj/Draft

Show
Ignore:
Timestamp:
2009/06/29 16:24:12 (12 years ago)
Author:
akinjo
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • DDBJ-KEGG-PDBj/Draft

    v5 v6  
    2222We were able to implement the above workflow within the three days of BioHackathon. The following is a list of what we have noticed during the development. 
    2323First, we had to do a significant amount of coding in spite of the wealth of web services. Most of the codes were dedicated to converting file formats between different steps. Although some of such conversions may be automated by providing new web services, we suspect that non-trivial amount of coding for format conversions is inevitable if we try to tackle new problems. It was also noted that the non-standard output format of BLAST search in PDBj's sequence navigator caused some trouble. Second, it can take a significant amount of time to finish a whole analysis. This is for the most part due to the amount of BLAST searches required for constructing a phylogenetic profile. In retrospect, this problem might have been solved if our client program was made multi-threaded (assuming the web servers can handle hundreds of requests at the same time).   
    24 By actually solving biologically oriented problems, we can identify some typical use cases which might be useful for further development of web services. 
    25 e.g. 1. Given a set of gene names, return a phylogenetic profile. 
    26 e.g. 2. Given a set of blast hits, group them according to their species. 
     24Finally, by actually solving biologically oriented problems, we could identify some typical use cases which might be useful for further development of web services 
     25(e.g., Given a set of gene names, return a phylogenetic profile; Given a set of blast hits, group them according to their species).