WWW & Internet Technologies for Biomedical Applications Aman Shakya, PhD Assistant Professor Dept. of Electronics and Computer Engineering IOE, Pulchowk Campus

Outline Internet and the Web Bio-Medical Web Applications Bio-Medical Online Resources Bio-Medical Mobile Apps Social Web applications Information sharing with Open Data

Internet and the Web What is the Net? Internet Web WWW Online Cyber Net Cloud Facebook ? Google ? Apps ?

4 What’s the Internet: What’s the Internet: : “nuts and bolts” view Millions of connected computing devices: hosts, end- systems ◦ pc’s workstations, servers ◦ PDA’s phones, toasters running network apps communication links ◦ fiber, copper, radio, satellite routers: forward packets (chunks) of data thru network Internet: “network of networks” local ISP company network regional ISP router workstation server mobile

5 A closer look at network structure: network edge: applications and hosts network core: ◦ routers ◦ network of networks access networks, physical media ◦ communication links

6 The Network Core Mesh of interconnected routers How is data transferred through net? ◦ packet-switching: data sent thru net in discrete “chunks”

7 The network edge: end systems (hosts): ◦ run application programs ◦ e.g., WWW, ◦ at “edge of network” client/server model ◦ client host requests, receives service from server ◦ e.g., WWW client (browser)/ server; client/server peer-peer model: ◦ host interaction symmetric ◦ e.g.: teleconferencing, torrent, napster

8 Internet protocol stack application: supporting network applications ◦ FTP, SMTP, HTTP transport: host-host data transfer ◦ TCP, UDP network: routing of data packets from source to destination ◦ IP, routing protocols link: data transfer between neighboring network elements ◦ PPP, ethernet physical: bits “on the wire” application transport network link physical

 runs on the Internet  An Internet application (an application layer software) The Web 9

WWW (Web)… is A large-scale, on-line repository of information that users can search using interactive application program called a browser Interactive program that permits a user to view multimedia information as a Web document, including hyperlinks to other Web documents 10

World Wide Web (WWW) An Application that runs on the Internet A Global network of web documents ◦ Web Documents (HTML) ◦ Located by URLs ◦ Hyperlinks Inventor of the Web ◦ Sir Tim Berners-Lee (1990) (but Internet dates back to 1960’s) 11

12/24/2011IT Conf. 2011, SOCIT Innovations12 A Snapshot of the WWW (just 20 yrs old!)

What happens when you click a Link ? You get a Web page … simple That simple ?? Lets watch a Movie ! Warriors of the Net

Bio-Medical Web Applications Web Technologies ◦ For Bio-Medical Applications Online Resources Online Software and Services

Biomedical Search Engine

Bio-Medical Web Technologies WIRM (Web Interfacing Repository Manager) ◦ Application server for developing web information systems ◦ Interfaces for visualizing, integrating and analyzing heterogeneous multimedia data WIRM in action ◦ MyPACS: A medical image management system for radiologists. MyPACS ◦ Brain Mapper: An experiment management system for neuroscience research laboratories. Brain Mapper ◦ Ontolog: A navigation interface for hierarchical structured vocabularies. Ontolog ◦ Digital Anatomist Repository: An image archiving system for medical schools. Digital Anatomist Repository ◦ Fathom: tools for facilitating natural language processing of clinical reports. Fathom

Free CMMS (Computerized Maintenance Management System )

Healthcare EAM (Enterprise Asset Management)

Online Bio-Medical Resources Library collections Databases Catalogs Taxonomies Search engines Online services

Mobiles and Tablet devices

Nepali App

What is Web 2.0? Web 2.0 involves User Participation A Social Web User-generated contents Harness Collective Intelligence Rich Internet applications (RIA) ◦ Rich user experience Web services, Mash-ups  RSS, Google maps, multimedia embedding, etc

Blogs

Wiki Wikis

Social Networking

Social Media – multimedia sharing

Social Bookmarking

Tagging - folksonomy Tag Cloud

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Information Sharing ◦ Information publishing ◦ Understandable meaning ◦ Information dissemination Shared information ◦ Better utilization  Increased value Shared information put together ◦ Valuable knowledge 56

Open Data on the Web 57 Open Data Anyone is free to use, reuse, and redistribute Linked Open Data (LOD) Publishing and interlinking structured data on the WWW

Linked Open Data Rating - Available on the web (whatever format), but with an open licence - Available as machine-readable structured data (e.g. excel instead of image scan of a table) - Non-proprietary format (e.g. CSV instead of excel) - All the above plus, Use open standards from W3C (RDF) to identify things - All the above, plus: Link your data to other people’s data (Berners-Lee, 2010) ★ ★★ ★★★ ★★★★ ★★★★★ 58

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60 APPS SHOWCASE

Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch.

Thank You! Enjoy your work Enjoy the Web !