Facebook MySpace. Build virtual communities in a bottom-u

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Toward an OpenSocial Life Science Gateway

• Wenjun Wu, Michael E. Papka, Rick Stevens

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Web 2.0 Gadget and Social networking

• Gadget
• Mini web application
• AJAX
• Social Networking
• Facebook MySpace
• Build virtual communities in a bottom-up manner
• Leverage science gateway portals
• Rich user interface
• Collaboration social networking

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OpenSocial

• A standardized framework for building social
  applications
• Provides Specification for both gadget and
  social-networking
• Gadget JavaScript API gadgets.
• OpenSocial JavaScript API opensocial.
• ltPeople, Relationship, Activity, Persistencegt
• Enabling web developers to write gadgets with
  social capability that can run in any OpenSocial
  compliant container
• iGoogle, Orkut,MySpace, Hi5
• Apache Shindig
• Open Source OpenSocial container

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OpenSocial Gadget vs Portlet
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Open Life Science Gatway Services

• A TeraGrid Science Gateway Project
• Integrates a group of bio-informatics
  applications and data collections into a portal
• Alignment - Blast and ClustalW
• Protein domain InterProScan
• Protein Structure Prediction
• Job History browsing
• RPC API
• Web-Services
• JSON-RPC
• OLSGW Portlets

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Open Life Science Gateway Framework
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Open Life Science Gateway Framework

• Generic RPC Services
• both a generic SOAP-RPC service and JSON-service,
  unmarshall RPC requests from clients, and create
  the job objects along with job execution scripts
• Application Service
• responsible for parsing an application XML
  description, generating service stubs and
  formatting application specific web-pages and
  portlet codes.
• Job Factory
• builds a job execution script and constructs a
  job object in the persistence job storage

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Application Service ( for clustalw )
ltparameter iscommand"1" ishidden"1"
type"String"gt ltnamegtclustalwlt/namegt
ltattributesgt ltformatgt ltlanguagegtperllt/language
gt ltcodegt"clustalw"lt/codegt lt/formatgt
lt/attributesgt lt/parametergt ltparameter
ismandatory"1" issimple"1" type"Sequence"gt
ltnamegtinfilelt/namegt ltattributesgt ltprecond
gt ltlanguagegtperllt/languagegt ltcodegtactions
ne "-profile" and actions ne "-sequences"lt/codegt
lt/precondgt ltpromptgtSequences File (or
Alignment File for Bootstrap and Tree actions)
(-infile)lt/promptgt ltformatgt ltlanguagegtperllt/lan
guagegt ltcodegt " -infilevalue"lt/codegt ltlangu
agegtseqlablt/languagegt ltcodegt "
-infilevalue"lt/codegt lt/formatgt lt/seqfmtgt
lt/attributesgt lt/parametergt
Serialized Command-Line Objects
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Generic RPC Services ( for clustalw )
function runClustalW() var params new
Object() params.javaClass 'java.util.Hashtabl
e' params.map params.map'actions'
'-align' params.map'quicktree' 'fast'
params.map'outfile' 'OUTPUT' var seqinput
document.getElementById("seqinput")
params.map'infile' seqinput.value //
Hashtable params result jsonrpc.JobService.r
unJob(callback, "clustalw", params)  
Generic RPC Service String JobID runJob (String
application, HashmapltString, Stringgt params)
JavaScript code segment for running clustalw jobs
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Building OpenSocial gadgets for OLSGW

• URL gadgets
• IFrame
• Wrap any Html pages in OLSGW
• Session Cookie
• HTML gadgets
• Gadget XML
• HTML markups
• JavaScript codes.

lt?xml version"1.0" encoding"UTF-8"?gt ltModulegt ltM
odulePrefs title"Run ClustalW" scrolling"true"
width"1000" height"600"gt ltRequire
feature"views"/gt ltRequire feature"dynamic-height
"/gt lt/ModulePrefsgt ltContent type"url"
view"canvas" href"http//cbc.lac.uic.edu8080/jo
bsubportlets/gadget/clustalw.html"gtlt/Contentgt lt/Mo
dulegt
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HTML gadgets

• Advantage utilize the rich features of
  OpenSocial JavaScript API
• JSON-RPC service to run bio-applications
• gadgets.io.makeRequest
• Allows the gadget JavaScript to communicate with
  remote services through a proxy in the gadgets
  OpenSocial container

var params paramsgadgets.io.RequestParameter
s.AUTHORIZATION gadgets.io.AuthorizationType.OA
UTH paramsgadgets.io.RequestParameters.CONTENT_T
YPE gadgets.io.ContentType.TEXT paramsgadgets
.io.RequestParameters.METHOD
gadgets.io.MethodType.POST var rpcdata
rpcreq.data paramsgadgets.io.RequestParameters
.POST_DATA gadgets.io.encodeValues(rpcdata) gad
gets.io.makeRequest(this.serverURL, response,
params)
JavaScript code for sending a makeRequest to
invoke JSON-RCP Service
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Gadgets Authorization

• OAuth
• An open authorization delegation mechanism
• Three Steps
• The consumer obtains an unauthorized request
  token.
• The user authorizes the request token.
• The consumer exchanges the request token for an
  access token.
• OAuth Entities in OLSGW
• OAuth Consumer makeRequest proxy in an
  OpenSocial container
• OAuth Provider the JSON-RPC service provider
• OAUTH servlets and filter

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OAuth Implementation for JSON-RPC
Request Token Servlet
Authorization Servlet
Access Token Servlet
OAuth Security Filter
JSON-RPC Service Provider
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Message flow in OAuth steps
HTTP Request Callback URL
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Open Life Science Gateway Bio-gadgets (rendered
in iGoogle)
Blast gadget run on both iGoogle and orkut
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Open Life Science Gateway gadgets
Job History gadget
ClustalW gadget
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Questions Answers

• Demo on Tuesday
• 1200PM Argonne Booth
• 130PM Indiana Booth