Adapting an Activity: Making It Your Own How to use the Molecular
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1. 13 Enable Reports MW activity reports gather together all of the answers a student has typed in as well as any snapshots they have taken The report is a single cml file that the student can edit print or submit to our database To use a report in your activity simply add a create an activity report button by going to Insert gt Activity Controller gt Activity Button Where it says select an action choose create an activity report about this page in a new window This will create a button that students can press at the end of the activity to generate their report You can also create reports for multi page activities that gather the students responses across several cml pages More details Consult the User s Manual within the Molecular Workbench Creating a Report 14 Upload your page to a database You can upload any cml page you create to our database of user uploads It s a convenient way to share your model or activity any molecular workbench user can then access it To upload simply go to while not in editor mode Collaboration gt Upload current page To view uploads you just go to Collaboration gt View Uploads You can also get to them from MW Home Page gt User uploads Taking care of your model If you run the model and save the page the initial conditions inherited from the original copy will be replaced by the model s current state You may not want this In the case of Jmol the model can be replac2. Mini ees saadah omelo ceed sadias hs eiseanlas os shee Shake ahem sw itaae OK Cancel 8 Add a picture It is easy to delete pictures and insert your own On the menu bar choose Insert gt Picture gt From File Select the image you want to use and click OK Positioning pictures in any particular position is harder The BEST way to do it right now is to 1 Make sure the picture you want to use is in the same folder as the activity you are editing 2 Insert a textbox into the activity where you want the picture to be 3 Right click on the textbox and select Customize This Text Box 4 The editable textbox now shows up You must leave the existing HTML code as it is but you need to insert the name of your file as shown below lt html gt lt head gt lt head gt lt body gt lt img src PUT_YOUR_FILENAME_HERE gif gt lt body gt lt html gt and your picture should now show up inside the textbox If the entire picture does not show you may need to resize your picture if it is a very large file or resize the textbox Resize a picture An image within a text box can be resized by setting the width or height attribute of the IMG tag lt img src image gif width 50 gt Absolute size can be specified as well lt img src image gif width 200 gt 9 Add a free response question There are several different user input areas the smaller being a text field and the bigger being a text area
3. Adapting an Activity Making It Your Own How to use the Molecular Workbench MW authoring environment to modify an existing activity NOTE Versions of these pages are available both in the Blackboard tutorial and within MW itself in its Documentation section The advantage of reading it within MW is that you can follow links to the User s Manual Many Molecular Workbench activities can be easily altered by teachers and curriculum writers so that they better fit the needs of particular classes Some activities in our databases http molo concord org and http molit concord org however have been specially programmed to make them more effective These activities cannot be changed 1 Find an editable activity to modify and open it Either A Open the Molecular Workbench You will need to have downloaded the Molecular Workbench http mw concord org modeler index html Then go to the Molecular Workbench Home Page gt Library of Models Activity Center and select activity that interests you They are all editable here y Library of Models Activity Center Ne E Da Support A ef f es or B Go to the Molit database for the Molit project view http molit concord org database browse everything list Or the Molo database for the Molo project view http molo concord org database browse everything list and pick an activity marked editable You can also pull up a complete list of editable activities i
4. Suppose you want to ask students an additional question after the one at the bottom of the page Click to place the cursor where you want the question to appear then go to in the menu bar Insert gt User Input Text Area_ It is also possible to do this by right clicking and selecting through that menu In the dialog box that pops up you can type in your question and format it using HTML if you know how and specify the size of the answer box Once the question is there you can modify it by right clicking windows or Apple clicking on mac on it and selecting customize this text area You can modify other components in the same way More details Consult the User s Manual within the Molecular Workbench Adding a Text Area 10 Add a multiple choice question Put the cursor where you d like a multiple choice question and go to Insert gt Multiple Choice It is also possible to do this by right clicking and selecting through that menu More details Consult the User s Manual within the Molecular Workbench Adding a Multiple choice 11 Add Links In MW you can hyperlink to another cml page You can make it the other cml page open either in a new window or in the current window in which case you can come back by using the Back button on the toolbar You can also link to a web page which will launch a web browser To create a link simply 1 highlight some text 2 select the Hyperlink tool in the toolbar an
5. cross all pages of the activity e Use page titles set them by going to Edit gt Title e On each page include a link to a table of contents page or some reference to location in the activity such as page 3 of 5
6. d set the filename or URL Py uf Qaim 0 09A Insert hyperlink Hyperlinked text DNA Clear he DNA o When clicked _ Open the link in a new window Advanced ns Along Type URL or mailto dna cmll Or select from list Tis ain a http mw concord org modeler1 3 p http mw concord org modeler1 3 p Y htta Limia cancord orn imoadalarl 2 n u E53 pate OK List sources Recent URLs Bookmarks Cancel Note that links do not work while you are in editor mode More details Consult the User s Manual within the Molecular Workbench Hyperlinks 12 Enable the Snapshot button You can let students take a snapshot of a model a picture of it at a particular time by including a snapshot button Go to Insert gt Standard Controller for Model gt Button Next to select an action choose take a snapshot way at the bottom You can customize the text on the button and its color and border DE Customize buthon Select a model lt Molecular Model gt mut2 0 mmi fi Select an action Change size of model HH Show pair correlation function Ws Ck Text Show pair correlation function Ws Ws y Stop DNA transcription or translation Tool tip F Width Transcribe DNA to mRMA Transcribe step by step T Height Translate MREMA to protein a Translate step by step ki ia Take a snapshot More details Consult the User s Manual within the Molecular Workbench Snapshots
7. ed by the molecule s current view and perspective angles etc So you should be careful about this and know how to recover the initial conditions if you overwrite them accidentally You should go to the original page on the Web and use the remote model NOT the page to overwrite the one with changed initial conditions More Help Check out the amazingly detailed always up to date MW User s Manual by going to Help gt Online User s Manual You can t get there when you are in edit mode the menu item is not active under Help on the menu bar unless you are in view mode Multi page Activity Authoring Tips Advanced users may want to create elaborate many page activities like the ones we have created for our projects Molecular Logic and Molecular Literacy Here are a few tips on how to do this that aren t currently collected in one place in the user s Manual e Store all files used for an activity in one folder This allows you to automatically upload the whole thing by using Collaboration gt Upload Current Activity Folder e Use relative path just the file name and not the complete URL references when creating links between cml pages or using tags e Use a reasonable file naming scheme such as appending sequential numbers to the name of the file for each activity page This makes it much easier to link pages together and keep track of them e Use the multi page report button to gather together questions and snapshots a
8. lick Mac or right click Windows on the textbox and click the Remove This Text Box In some computers it may be easier to just place your cursor to the right of the textbox and press delete 7 Editing a textbox with HTML code You can erase the text in a textbox including all the HTML code You can make HTML in the textbox if you want or you can simply change the text and leave the HTML code when for example you like the font images etc Just avoid changing a lt tag gt There is a default font that will appear if you do not include HTML Set width Sah Draw border EJE Set height 230 Background color _ Transparent lt html lt head gt lt j head lt body gt font iden verdina siita d lt b gt Challenge 1 Make subarituti mutations elbs gi fonts lt font sizs J gt a Fonts lt i gt lt font face verdana size 4 gt 1 Run the model by clicking the run button abowe lt font gt lt img siea play gif gt lt font faces verdana sizea 4 gt AFLEI te see how the peptide chain above folds in water lt bre2 Click the lt b gt Take a snapshot lt bebutton above lt br gt 4 Click the reset button i lt font gt lt img sea reset gii gt lt font faces verdana sizea 4 gt 7100 cbras Choose a nucleotide to mike amp Substitution mutation Right click windows or apple click on the nucleotide imach 810 Choose Squot substitution mutation amp quot and then select anew nucleotide cbr C
9. n the databases by going to the bottom of the page and clicking View Only Editable Browsing Everything 5 The following are all of the activities from all categories and modules in alphabetical order gp yt The models are not sequentially numbered gaps in numbering do not indicate missing models but rather reflect the creation process 158 activities total Displaying activities 1 through 10 Activity List A Comparison of Liquid and Gas States Activation Energy advanced Active Filters demo e Air Filtration Amino Acids and Water 20 Alanine Model Aquatic Solutions and Our Cells Five day unit Atomic Layer Deposition Atomic Mass and Melting Point Atomic Structure Attractive Forces and Phase Change Atoms in Motion View Complete List View Only Editable View All Previous 10 Activities Next 10 Activities Editable activities will be marked at the top of their pages with an icon Sq it abs 2 Open launch an activity you want to change by clicking on the Launch Activity button see the arrow beneath the picture of the model An easy place to begin the activity A Comparison of liquid and Gas found in the Molo database http molo concord org database activities 201 html It is also in the library of models within Molecular Workbench 5 oh a a 4 i C Show wae cer tanks interactions Show aaircomelation functi
10. on Comi TAAN RA Shem wit dee Wants interactions Shaw uly carreata fuses 3 Save your own copy of the activity into a folder Make a new folder for the activity in an easy to find place and save the activity in it Click the Save button in the menu bar MW activities are made up of many files The text and layout of each page is stored in a cml file and each model is stored in a mml file More details Consult the User s Manual within the Molecular Workbench Saving a Page 009 Save Save As gasliquid cml LMS Dare Modified L basic light matter Sunday May 29 2005 9 52 PM 0 gt active filters1096584257000 copy Saturday October 2 2004 10 55 PM adapting_model Tuesday June 14 2005 5 46 PM eae a eg Pa A gt e File Format CML HA New Folder Cancel E Save 4 Switch to Editor mode BA Once you have saved the activity an Editor button 2 will appear on the left bottom of the menu bar see picture below when you are in view mode Fa to When you want to edit the activity click the editor button enable the Edit mode The red circle slash will no longer appear on the Edit button and a set of new editing controls will appear L itor oren Fed save SSS Cees Uy era rm prj Pig Pinal id a verdana W Ea B EEE eea 5 Edit the text MW s editor is a bit like Microsoft Word For example you can select some text and delete it then type in some ne
11. w text Easy You can even undo if you make a mistake Edit gt Undo or Command Z Also try out the text formatting options in the tool bar You can hold your mouse cursor over a tool button on the menu bar and a pop up textbox will tell you the purpose of that tool button More details Consult the User s Manual within the Molecular Workbench Editing Text Text can be entered either directly on the page or within a textbox If you can click on text and the cursor appears within that text you can edit it directly If no cursor appears within the text you are dealing with a textbox and must right click over the text to be able to customize the textbox Textboxes sometimes have lines around them but sometimes the lines are set to be invisible If a textbox has lines around it that are invisible the borders will only show in Editor mode not in View mode 6 Customize an Existing Text Box Let s say you want to keep the textbox but change the text within it You need to Right click Windows Apple click Mac on the textbox and the choice of customizing will come up Select Customize This Text Box Customize This Text Box above ae Remove This Text Box an Copy This Text Box If you want to write in the text box Right click Windows or command click Mac on the box Some find that it is important to click outside of the left or right margin when selecting a textbox If you want to remove the textbox just command c
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