1 / 49

Integration of BioInformatics tools at NUS

Integration of BioInformatics tools at NUS. GenBank Growth Chart. Bases. Year. Use of Computers in Molecular Biology. Powerful tools for organise the data itself. Exponential growth. A new release is made every two months. Data Analysis. Retrieval. Homology Search.

taylormatthew
Download Presentation

Integration of BioInformatics tools at NUS

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Integration of BioInformatics tools at NUS

  2. GenBank Growth Chart Bases Year

  3. Use of Computers in Molecular Biology • Powerful tools for organise the data itself. • Exponential growth. • A new release is made every two months. • Data Analysis. • Retrieval. • Homology Search. • Modelling purposes - Drug Design • Data Integration • Data Visualisation

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

  5. BioPortal

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

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

  8. 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.

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

  10. Graphical Representation of BioPortal Functionality

  11. 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?"

  12. 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

  13. Formats supported

  14. Results for Signal Scan

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

  16. Special features • Temp 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 distant users to use the same program simultaneously. • Remote retrieval and analysis:This interface allows you to access your program from anywhere in the world.

  17. 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.

  18. BioKleisli or BioKris

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

  20. 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

  21. BioWebWatch or Bio-Eyes

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

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

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

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

  26. Cyberspace is a big place New Query Useless Hits Search GoodHits!

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

  28. Creating a Query • Enter search string • Choose source • Preview search • Create Channel

  29. Gathering Information

  30. Working with Information

  31. Distributed Processing for scalable performance

  32. BioJake

  33. BioJAKE • BioJAKE is a graphical program allowing for the onscreen creation, manipulation and visualization of metabolic pathways. • Pathways are represented as a series of molecules (images) linked together by a series of reactions (lines). • Each molecule is defined through it’s image, name, type and states.

More Related