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Integration of BioInformatics tools at NUS
Meena K Sakharkar
Training Manager, BioInformatics Centre
National University of Singapore
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BioInformatics Tools at NUS
• BioPortal
• BioKris (formerly called BioKleisli)
• BioWebWatch (Bio-Eyes)
• BioJake
• Other projects
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BioPortalBioPortal
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BioPortal
User friendly gateways to
GCG and other software.
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Prior Scenario
Command line interface.
• Basic OS knowledge.
• User Interface(UI) for each program.
• Platform dependent.
Transient phase
• Hyper text Menu Based Interface
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Present Scenario
• User-Friendly web interface to Biosoftware.
• Platform Independent.
• Depends on Client - Server Technology.
• Common Gateway Interface (CGI) programs written in PERL and C.
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Programs available• GCG
• PHYLIP
• CLUSTALW
• GNUPLOT
• SIGNALSCAN
• LOCAL
• ALIGN
• TULLA
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Graphical Representation of BioPortal Functionality
User WWW Server BioPortalBio
SoftwareBio
Databases
ClientBrowser
(Netscape…)
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The web interface allows you to focus on
"How will I solve my sequence analysis problems?"
rather than on
"How do I use this software?"
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Special features
User Friendly Interface• The form based approach simplifies the task.
• It guides you through the whole program.
• No need to install and learn command line interface of all software.
Format Independent
Hyperlinks for Results
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Formats supported
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Results for Signal Scan
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Special features
Online Help • Speeds up your data entry and analysis.
ConduitOutput can be piped to other programs for further analysis.
Pileup Distances Growtree.
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Special features
• Tmp file usage:(a) Output of other programs is input for them.
(b) Programs which take a lot of time.
• Improved Operation Control:A fully customisable interface provides a flexible environment.
• Shared Access:This interface allows several distanct users to use the same program simultaneously.
• Remote retrieval and analysis:This interface allows you to access your program from anywhere in the world.
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Special features of JAVA ver.
Navigation Panel :
Java navigation allows to view the tree structure for the programs.
File handling Capability:
Local desk top file loading.
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Bioportal vs WWW2GCG
• File handling capability.
• Format independence.
• Work flow approach.
Bioportal vs SeqWeb
• Not all programs in GCG have been implemented.(about half) and not all options.
• Temp file usage feature is not there.
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Bioportal is a test bed software in:
Schering Plough (NJ)
Wistar Institute , Upenn
Wayne State University, Michigan, USA. (Prof. David Womble's Lab)
Boston University, Boston, USA. (Prof. Temple Smith's Lab).
The Signal Scan WWW Interface is in use at:
• NIH
• TIGEM, Italy
• Japan
Future Directions
Linking Bioportal to Kleisli
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BioKleisli orBioKleisli orBioKrisBioKris
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Introduction
A BIC-KRDL collaboration
Open query system for broad-scale integration of heterogeneous distributed databanks
Flexible access for existing biological databanks
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Features and Benefits
Features
Provides a query system that can integrate all types of biology databanks and analysis software
express high level views and transformations that go beyond flat tables
Flexible access = migrate + integrate + restructure
Benefits
More effective and easier access to world wide data for biologists
Enhances productivity and simplifies programming tasks
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BioKleisli ... Sequence Analysis ..
Functional Approach
• The computational analysis of the biological data was predominantly on an ad hoc basis - i.e. the application of a given piece of software on the biological data depended on the need of the moment.
• This functional approach often resulted in piecemeal computational analysis with large amount of intervening "dead-time".
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BioKris…Protocol Approach
• The present high-throughput availability of experimental biological data requires a more streamlined and integrated protocol approach
• BioKris starts with a sequence and builds a substantial custom data-warehouse of information from various sources e.g structure , sequence and medline databases
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Architecture
Remote Servers
GenBank
GSDB
GDB
NCBI-BLAST
Net
Process
Sybase
ASN.1
OPM
ACeDB
BLAST
Drivers
ProcessCPL
TypeModule
Optimizer
NRC
DriverManager
PrimitiveManager
ComlpexObjectLibrary
pipe
sharedmemory
CPL-Kleisli
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Blast Query against Protein DB
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Blast Results
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Analysis
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BioWebWatchBioWebWatchororBio-EyesBio-Eyes
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Problems
• Too much Information?
• Many sites to cover despite automatic notification.
• Revisit your site of interest at least once a month.
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BioWebWatch
• Allows users to automate queries.
• Channels.
• Users • Keywords• Websites
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Goals
• Collecting, aggregating, managing and integrating information.
• Integration with existing software tools.
• Sharing information across the organisation.
• Collaboration with other information servers.
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What’s out there?
• Electronic Journals
• Web Pages
• News Groups
• Databases
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Cyberspace is a big place
New Query
Search
Good Hits!
Useless Hits
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An Information Butler
Information ManagementInformation Management
Automated Query
Search
Results
Automated DispersalGood Hits!
Useless Hits
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Creating a Query
• Enter search string• Choose source• Preview search• Create Channel
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Gathering Information
News Services,Headlines Grabber,
…………
Query Broker
• Broadcast queriesto multiple searchengines
• Grab headlinesfrom multiplesources
BookmarkedWebSite A
BookmarkedWebSite B
BookmarkedWebSite C
• Dispatch agents(spiders) to targetweb sites
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Working with Information
Channel 1Title 1.1. .. summaryTitle 1.2 … summaryTitle 1.3 … summaryTitle 1.4 … summary
Channel 2
Title 2.1. .. summaryTitle 2.2 … summaryTitle 2.3 … summary
Channel 1’Title 1.1. .. summaryTitle 1.2 … summaryTitle 1.3 … summaryTitle 1.4 … summary
Channel 2’
Title 2.1. .. annotation summaryTitle 2.2 … summaryTitle 2.3 … summary
Delete / Filter
Comment / Annotate
Search / Rank
Channel 3
Title 1.2. .. summaryTitle 2.1 … summaryTitle 1.1 … summary
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Distributed Processing for scalable performance
Community Server : Collating Information from multiple WebWatch Server
WebWatchCommunity
WebWatch Server 1
WebWatch Server 2
WebWatch Server 3
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Enterprise wise Information Gathering
WebWatch Server• Query Broker• Community Server• Gateway to External Access
Internet
CorporateFirewall
Departments with WebWatch subServer,serving multiple internal departmental users. Some channels are shared outside of Department. Each WebWatch subServer uses WWServer as• Proxy for Internet (Gateway)• Community Server (Collaboration)
WebWatchUser
Community
WebWatchSuperServer
Updates• Software• Broker Scripts
Enterprise
EnterpriseWorkgroup
Server
InformationConsumers
within Enterprise
Remote Accessto WebWatch
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Other projects
• Molecular modelling
• Peptide based vaccine design
• Secondary structure prediction
• Crystallisation in conjunction with other NUS dept. and Stanford synchrotron centre.
• Genome analysis with specific reference to intron movements.
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Conclusion
• BIC has explored the ways to organise and query information and resources in a biologist friendly way.
• The protocol approach will be the new paradigm in bioinformatics on the Internet.
• Our aim is a step towards utilising the resources available to uncover a treasure trove.
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Computers in Peptide Vaccine Design
Prediction of T-cell epitopes
2. ANN (Brusic et al)
1. Statistics (Parker et al)
Computer Modeling of the predictions
CARA/SCEO
Biological Testing
(Lee .C & Subbiah 1991)