Integration of BioInformatics tools at NUS

1. Integration of BioInformatics tools at NUS Meena K Sakharkar Training Manager, BioInformatics Centre National University of Singapore

2. BioInformatics Tools at NUS • BioPortal • BioKris (formerly called BioKleisli) • BioWebWatch (Bio-Eyes) • BioJake • Other projects

3. BioPortal

4. BioPortal User friendly gateways to GCG and other software.

5. Prior Scenario Command line interface. • Basic OS knowledge. • User Interface(UI) for each program. • Platform dependent. Transient phase • Hyper text Menu Based Interface

6. 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.

7. Programs available • GCG • PHYLIP • CLUSTALW • GNUPLOT • SIGNALSCAN • LOCAL • ALIGN • TULLA

8. Graphical Representation of BioPortal Functionality

9. 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?"

10. 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

12. Formats supported

13. Results for Signal Scan

14. Special features Online Help • Speeds up your data entry and analysis. ConduitOutput can be piped to other programs for further analysis. Pileup Distances Growtree.

17. 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.

18. 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.

22. 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.

23. 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

24. BioKleisli or BioKris

25. Introduction • A BIC-KRDL collaboration • Open query system for broad-scale integration of heterogeneous distributed databanks • Flexible access for existing biological databanks

26. 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

27. 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".

28. 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

29. CPL-Kleisli Net Remote Servers pipe Driver Type Manager Module GSDB Comlpex GenBank Object NRC Process CPL Library GDB shared memory Primitive Optimizer Manager NCBI-BLAST Architecture

41. Blast Query against Protein DB

42. Blast Results

43. Analysis

44. BioWebWatch or Bio-Eyes

45. Problems • Too much Information? • Many sites to cover despite automatic notification. • Revisit your site of interest at least once a month.

46. BioWebWatch • Allows users to automate queries. • Channels. • Users • Keywords • Websites

47. Goals • Collecting, aggregating, managing and integrating information. • Integration with existing software tools. • Sharing information across the organisation. • Collaboration with other information servers.

48. What’s out there? • Electronic Journals • Web Pages • News Groups • Databases

49. Cyberspace is a big place New Query Useless Hits Search Good Hits!

50. An Information Butler Automated Query Search Useless Hits Results Good Hits! Automated Dispersal Information Management