PRACTICAL 2: PRACTICAL USES OF INTERNET SERVICES

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1 PRACTICAL 2: PRACTICAL USES OF INTERNET SERVICES AIMS: 1. to develop skills in using multiple Web search engines 2. to explore and use several Internet services that could be of value in bioinformatics. Assessment Value: 5% Though it is expected that ALL exercises are attempted, not all are assessable. The assessable exercise/s are to be shown to or submitted to the designated tutor by the end of the practical class. The marked exercise will be returned the following week. Assessable exercises are marked with n* (where n is the number of marks allocated) Exercise 1: Search Engines 1. Read through the search engine recommend list, found at 2. (15minutes) Search engines are different and produce different results. Select one of the following topics and search for information about it using each of the search engines listed. Copy and paste the search query into each of the search engines query box. On the first pass of the search query for each of the search engines record the following: how many results were listed? Was the information in the right knowledge domain? Discuss the results. Topic: 1. Fairy tales that are in DVD format, and are for sale 2. Sansui amplifiers 3. fishing in Africa 4. dna Search engines: Google Alta Vista Excite Northern Lights PubMed * (30 minutes) Form teams of no more than 3, and participate in the Bio-informatics Web Treasure Hunt. For this treasure hunt you need to find the answers to a number of questions, record how you did it, and how many clicks it took to find the correct answer. The team needs to document its trail, then this to your designated Micro tutor by the end of the class. The needs to contain: the question and number, the answer, the path you followed to get the answer (that is the audit trail), how many clicks it took to get the correct answer, the team members names, and of course the Prac class number. The team with the least number of clicks wins (prize yet to be determined).

2 Exercise 2: FTP, gopher, Newsgroups Students should work individually for the following exercises. 1. 1* FTP. Replicate, then complete the following table for four ftp sites that would be useful for retrieving biomedical information. (use both the Web and an FTP program such as WS-FTP to view the content of the sites). Show your work to your IT tutor by the end of the class. FTP Address and organisation ftp://ftp.ebi.ac.uk/ European Bioinformatics Institute Bio Catalog Web enabled yes Login process automatic Useful for / comments 2. 1* FTP upload (if unavailable, the Newsgroup exercise becomes assessable) Create a simple text document listing the names (no ID numbers) of the members of your Treasure Hunt group, and your tutors/demonstrators names). Save the file according to the file name given to you by the IT tutor (eg Wednesday-01.txt). Upload the file to the ftp server (the address of the server will be given to you during the class). This is to be completed by the end of the class. 3. Newsgroups / UseNet Replicate, then complete the following table for four newsgroups that would be useful for retrieving biomedical information. (Some of the newsgroups can be read on the Web, others use only) NEWSGROUP Address and organisation Web enabled only Registration process Useful for / comments 4. 1* Threaded discussion groups Access the BMS2062 Discussion Group (the location of the discussion group will be given to you in class, and is on the unit web site). Add a message that lists your two favourite search engines for retrieving biomedical information, and a short statement as to why they are your favourites? Exercise 3: Conferencing Microsoft NetMeeting needs to be installed on the computer for the following exercise. If it isn t not, do the exercise in your own time many of the open access computers have NetMeeting installed. For this exercise we will be using several of the very basic features of MS NetMeeting. More advanced features include voice and video conferencing. 1. (30 minutes) Check to see if NetMeeting is installed. Check the Start>Program, if not there then you will need to install it (The software is probably on the computer, just no one has used it yet). Click on My Computer> Program Files> Open Files> NetMeeting> double click conf.exe Follow the installation wizard (don t worry about the audio settings) a. Select New Call and type in one of the IP address given to you. b. Play around with the each of the following features: Share program. Chat. Whiteboard. Transfer files

3 2. As a class discuss potential uses of these in the biomedical field (this could be posted on the Disucssion Area). Extra exercise: Other services / tools 1. Replicate, then complete the following table for three vrml sites that are related to biomedical science. (If short of time and results, they are a bit hard to find, students can work in groups and do one each, then share information) VRML Address and organisation MathMol (Mathematics and molecules) NewYork University Useful for / comments (requires Cosmo Player) FEEDBACK: Feel free to Kathy; the lecturer in charge of the IT pracs, (Kathy.lynch@sims.monash.edu.au) any comments regarding the prac exercises, in particular the level of diffic ulty, appropriateness, interest value, enjoyment value, or anything else to do with the prac exercises. Please use the subject line: bms feedback Some useful links: List of freeware /shareware biomedical software sites. (University of Florida) Biomedical information services (Spring Hill College, Alabama) The Genome database (The Hospital for Sick Children, Toronto Canada) addresses: IT tutor: Micro tutor: Lecturer in charge: kathy.lynch@sims.monash.edu.au A FLOPPY DISK IS REQUIRED FOR NEXT WEEK S PRAC SESSION

4 PRACTICAL 3: WEBPAGES DESIGN AND USE AIMS: 1. to develop skill and understanding of the basics of good web page design 2. to develop skill in constructing web pages using a web authoring tool 3. to construct a simple suite of Web pages for use by the general public. The pages are to consist of at least text, images, hyperlinks and navigation between the pages. Assessment Value: 5% Though it is expected that ALL exercises are attempted, not all are assessable. The assessable exercise/s are to be shown to or submitted to the designated tutor by the end of the practical class. The exercises will be assessed according to good web design practices. The marked exercise will be returned the following week. Assessable exercises are marked with n* (where n is the number of marks) The topics to be chosen will be from one of the following (allocated by the demonstrators): 1. Cystic fibrosis 2. Haemophilia 3. Marfan syndrome 4. Retinoblastoma 5. Prader-Willi syndrome 6. Huntington's disease 7. Kleinfelter's syndrome 8. Hurler's disease 9. Tays-Sach syndrome 10. Von Willebrand's disease 11. Muscular dystrophy 12. Burkitt's lymphoma 13. Lowe's syndrome 14. Kaposi's sarcoma Exercise 1: Web page design Using the given topic from the above list, and Word or pen and paper 1. Construct a table of contents that is an overview of what you are going to present 2. Sketch the navigation structure (flowchart) 3. Sketch the screen layout, determine the language/graphic style, colour scheme Exercise 2: Web page construction 4* You will be using FrontPage to construct the Web pages. If it is not loaded, you will have to use Netscape Composer. 1. Create a workspace for your files (U: drive, C: drive or A: drive). Frequently SAVE your work 2. Search the Web for content primarily urls, text, images, and animations etc Save and organise content into sections (as per table of contents). 3. Construct the first page (save it as index.html) for the Web site, include the following a. Heading b. Overview or introduction 4. Using your screen layout, place any other text, or images (picture) onto the page. 5. Manipulate the page until it is right. This could include the use of dot points, numbered lists, tables, colour. 6. Make a copy of the index.html page, and call it page2.html (or something more appropriate) 7. Place the relevant text into the page. This may be done in a number of ways, the most common are by typing or copy and paste. 8. Make a copy of the page2.html page, and call it page3.html (or something more appropriate) 9. Finish adding content to all pages 10. Navigation can be done in a number of ways the simplest is by using a hyperlink from a textual phrase, word or image to the destination page (file or url). a. create a link to index.html (the home page) from all subordinate (or child) pages, b. create a hyperlink to all the subordinate pages from the index.html page c. create a least one hyperlink to a file on the Web which is not part of you suite of pages 11. Add a FrontPage Theme to your suite of pages. 12. If time allows, do some of the extra exercises list at the end of the prac notes.

5 Exercise 3: The finishing touches 1* Add the following to all your pages; 1. image text tags 2. metadata, 3. title tag, 4. feedback mechanism, 5. copyright and ownership information, 6. date created and updated. Exercise 4: Publishing Publish the Web pages onto the Monash University silas server (or other Web space), and the url to your IT tutor. If this can not be done, place all the files for your web pages on to a labelled (day, name and ID) floppy disk, and submit it to the IT tutor at the end of the prac class. Exercise 5: Accessibility If the Web pages are actually on a Web server, run it through Bobby ( What were the results? Extra exercises: 1. Using FrontPage replace your textual navigation system with a graphical navigation system. 2. Using FrontPage or another ImageMap program, create an image map for a section of your pages (could be an add-on to the navigation, or something new). 3. Create your own (biomedical) animation. Collect at least four.gif images. They need to be the same pixel size, and don t make them too large (350x250 is fine). Insert this into your Web page. (Shareware software: MS Animator, found at and is 1MB) FEEDBACK: Feel free to Kathy; the lecturer in charge of the IT pracs, (Kathy.lynch@sims.monash.edu.au) any comments regarding the prac exercises, in particular the level of difficulty, appropriateness, interest value, enjoyment value, or anything else to do with the prac exercises. Please use the subje ct line: bms2062 feedback addresses: IT tutor: Micro tutor: Lecturer in charge: kathy.lynch@sims.monash.edu.au A FLOPPY DISK IS REQUIRED FOR NEXT WEEK S PRAC SESSION

6 PRACTICAL 4: Using PowerPoint AIMS: 1. to develop skill in the basics of good design for support materials for oral presentations 2. to develop skill in constructing a presentation using MS PowerPoint, consisting of at least text, images, sound, transitions and navigation between the slides. Assessment Value: 5% Though it is expected that ALL exercises are attempted, not all are assessable. The assessable exercise/s are to be shown to or submitted to the designated tutor by the end of the practical class. The exercises will be assessed according to good design practices, and content. The marked exercise will be returned the following week. Assessable exercises are marked with n* (where n is the number of marks allocated) Exercise 1: Presentation design The presentation is to be designed for use in a lecture theatre using a data projector and a Windows laptop. (10 minutes) For this practical, you will use the content gathered for the previous practical 1. Design your presentation screen layout (sketch) and navigation (use a flowchart) 2. Explore the existing pre-set presentation templates in PowerP oint (Format>Apply Design templates). 3. Select one that best suits your design. Remember you are in charge of the content, the presentation needs to run smoothly, and bells and whistles are not always appropriate. Exercise 2: Slide presentation construction 4* 1. Starting with the title slide, type the required text. Frequently SAVE your work. 2. Insert the next slide, selecting the most appropriate format, add content. (You could copy and paste the text from another source). 3. Change the slide template to suit your needs by editing the Master Slide layout. 4. Add a few more slides (content and images). 5. Explore the functions of Group/Ungroup, Bring to Back/Forward, and the various viewing options. 6. Navigation through the presentation is often by consecutive slide number, change this by incorporating each of the following methods; a. Add a hyperlink from a textual phrase, word or image to the destination page (file or url). Insert> Hyperlink> Place in this document> and select the slide number (or url, or file) b. Add an action button to a slide (or url or file). Select SlideShow>Action buttons> select a bottom and an event (slide number, url or file) 7. Incorporate the following in the finished slide presentation a. staggered bullet points b. sound to every action button c. transition between slides d. animation to the heading on the title page e. on a slide that has both text and an image, add animation to the image f. add slide numbers, and date to all pages but the title page (You may choose to submit exercise 4 instead of exercise 2) Exercise 3: The paperwork 1* Many presentations require a paper handout, and notes pages for the presenter. 1. Add a footer, header and page numbers for the printed handout 2. Print off one A4 page of the presentation that contains 3 slides and lines to write notes, to a page. 3. Print off one A4 page of the presentation that contains 6 slides to a page. 4. Print off one A4 page of the presentation that contains the presenter s notes.

7 Exercise 4: Creating your own design 1* bonus Presentation design should reflect the content of the presentation, MS PowerPoint doesn t have many (if any) biomedical themes available, so you need to create your own. 1. Start a new Blank Presentation 2. Set up your own design a. Explore Format> all options except for Apply Design Template. b. Using the Master slide view, Set background and any images to appear on every page 3. Import the content from your previous presentation. Insert>Slides from Files> Select All> Close Extra exercises: 1. If you did an animation last week, insert it into this presentation (Animations only work in PowerPoint 2000 and above) 2. Add a commercially created animation (get one off the Web) 3. Add music that plays continually throughout the presentation (only use when set on automatic and unattended) 4. Convert the presentation into HTML format. View it through a Web browser 5. Constructing a slide presentation from a Word document. a. When importing using the Outline function in Word, text needs to be formatted using Styles. View the existing style by clicking (in Word) View>Outline b. In Word, modify the styles to suit your needs. You need to use styles, Heading 1 signifies the commencement of a new slide. Don t worry about formatting for table s, bullets, or images as these formats are not imported. Save then close the file. c. In PowerPoint, click on Insert> Slides from Outline> and select the file. View the results. d. Slide length is critical text off the slide is very unprofessional. You may need to go back into Word and adjust the amount of text under any one Heading 1, then re-import the outline. FEEDBACK: Feel free to Kathy; the lecture in charge of the IT pracs, (Kathy.lynch@sims.monash.edu.au) any comments regarding the prac exercises, in particular the level of difficulty, appropriateness, interest value, enjoyment value, or anything else to do with the prac exercises. Please use the subject line: bms feedback addresses: IT tutor: Micro tutor: Lecturer in charge: kathy.lynch@sims.monash.edu.au Good luck with your next suite of web pages and slide presentations. Remember, the layout of the content, the fonts, colours and media, and the transitions between content are important. If your get them wrong, it doesn t matter how good your content is, no-one will be interested in the slides. Kathy