Changes between Version 6 and Version 7 of DDBJ-KEGG-PDBj/Draft

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2009/06/29 16:31:06 (12 years ago)
Author:
akinjo
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  • DDBJ-KEGG-PDBj/Draft

    v6 v7  
    2121== Outcome == 
    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. 
    23 First, 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).   
     23First, 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, suggesting any web services should stick to the standard formats if any. 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), however, this would increase the burden of the client-side programming. 
    2424Finally, 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). 
     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). In summary, the implementation of the DDBJ-KEGG-PDBj workflow allowed us to realize the usefulness as well as limitations of the web services in its current status, and to identify the potential room for further improvements. 
     26The activity of this satellite group is recorded at http://hackathon2.dbcls.jp/wiki/DDBJ-KEGG-PDBj .