Changes between Version 42 and Version 43 of PhyloWS_workgroup

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2008/02/15 15:50:24 (16 years ago)
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rvos
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  • PhyloWS_workgroup

    v42 v43  
     1== PhyloWS BioHackathon Report == 
     2=== Brainstorm sessions (Monday) == 
     3* What's our scope for now? 
     4* Accumulate use cases 
     5* Accumulate requirements 
     6* Propose a simple API 
     7* Start reference implementations 
     8* Have another round of OTU discussions 
     9=== Formalizing scope, use cases, requirements (Tuesday) === 
     10* Identify inputs and outputs (white board) 
     11* For all I/O combinations, imagine a [https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS#Use_Cases use case], move to NESCent wiki 
     12* For each use case, classify [https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS#PhyloWS_Requirements scope] and requirements 
     13=== Scopes === 
     14* '''Phylogenetic tree database''', i.e. a persistence service based on BioSQL 
     15* '''Phylogenetic data conversion''', i.e. make sure that inputs and outputs of data work syntactically 
     16* '''Phylogenetic data analysis''', i.e. actual computations 
     17=== API design === 
     18''Assuming that syntax and semantics of the data can be solved, what would be the syntax and semantics of making the connections?'' 
     19=== API design principles === 
     20# Stateless REST, no accumulate-and-fire 
     21# Architecture modeled as resources on which CRUD operations are performed 
     22# Use common HTTP methods (GET, PUT, POST, DELETE) 
     23# Describe RESTful API in WSDL 2.0 
     24# Reuse prior art 
     25=== URL API === 
     26We started to design a URL API (pathinfo + query strings) on the NESCent Wiki 
     27=== Actual implementation === 
     28All displacement activities aside, we did some coding: 
     29* Started conversion and persistence services 
     30* Improve plumbing (format support, database support) 
     31=== Moving forward === 
     32* Expand/formalize API, following manifesto? Recommendations? 
     33* Implement services. 
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    148At present there is no standard web-service API for phylogenetic data that would allow integration of phylogenetic data and service providers into the programmable web. Hence, current approaches to integrate data and services into workflows are highly specific to the integration platform (CIPRES, Bioperl, Bio::Phylo, Kepler), and nearly unusable in other environments. This work group is formed to remedy this (to the extent that that's possible in a week). 
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