Difference between revisions of "CellDesigner/C2/Create-and-Edit-Components/English-timed"

|  In this tutorial, we will learn to: open an already saved ''''.xml'''' file in the '''draw''' area,

| change the following in a '''compartment''': shape, size, color and thickness of the border,

| create multiple files in''' CellDesigner''', change identity of a '''Species'''.

|  We will also learn how to '''cut, copy''' and '''paste''' a '''Species''', about Start-point and End-point of a '''Species''',

|how to activate and change color of a''' Species''', change properties of a ''' Reaction''' , how to close a''' File'''.

|  Here I am using '''Ubuntu Linux OS version 14.04''', '''CellDesigner version 4.3''', '''Java version 1.7'''.

| If not, for relevant''' CellDesigner tutorials''', please visit our website''' www.spoken-tutorial.org'''.

|''' CellDesigner '''window now opens on your screen.

|  Our file '''Create_and_Edit.xml '''is now open in the '''draw''' area.

|  Select the compartment. Go to the '''Component''' in the ''' main menu ''' bar.

| On the '''draw''' area, we now have an oval compartment.

| For a thinner boundary line, change the '''Membrane Thickness''' from '''12''' to '''8''' or below.

|  To change the color, go to''' Color''' panel.

| In the''' Color''' panel is a color wheel, with a pointer like handle.

|  After all the modifications are done, click on '''Apply''', and then on ''''Ok''''.

| We will keep the default width and height and click on '''Ok''' button.

|  Now, click on the icon for ''''Generic protein'''' from the toolbar. Click on the '''draw''' area.

|  Now right-click on the''' Generic protein Pectin'''

|and click on the option '''Change Identity'''.

|Let's say''' Fructose''' and click on '''Apply''' button.

|  Observe that our''' Protein Pectin''' is now converted to a simple molecule named''' Fructose'''.

|I will use the same '''Fructose''' that is already present on the '''draw''' area.  

|  To '''paste''' the '''species''', go back to the ''''Edit'''' menu, scroll down and click on '''Paste'''.

|The''' Species Fructose''' reappears on the '''draw area'''.

|  To make a copy of the '''Species''', go to ''' Edit''' on the main menu bar.

|Notice here that the shortcut key for '''Copy''' is''' Ctrl+C'''.  Click on '''Copy'''. Click on the '''draw''' area.

|This time, let us press''' Ctrl + V''' to '''paste'''.

|  We now have a copy of '''Fructose''' on the '''draw''' area.

|  To '''undo''' any action, press''' Ctrl+Z''' and to '''redo''' any action, press''' Ctrl+Y'''.  

|  Let us drag and move the''' Fructose molecules''' aside on the '''draw area'''.

|  Next we will learn,  what are '''start-point''' and '''end-point''' '''species''' and how to activate a '''species'''?

|So, click on ''' Protein 2''' and press '''A''' on the keyboard.

|  Let me '''undo''' this change by pressing''' Ctrl + Z''' keys.

|  Notice that the activated '''species''' is wrapped by a dashed line.

|Observe the color changes in the ''' species.'''  

|Now, select '''Change Identity''' option.

|  Select the required reaction from the drop-down menu in the '''Type''' box, say''' Transcription''', Click on ''''Ok''''.

|  Observe that the''' reaction''' has changed on the '''draw''' area.

|We do not see the name that we gave on the '''reaction arrow''' in the draw area.

| A dialog box '''Confirmation''' appears on the screen asking if we wish to '''save''' the changes.

|open an already saved '''.xml''' file in the draw area,

|change shape, size, color and thickness of the border of the ''' Compartment''',

| create multiple files in''' CellDesigner''' and change identity,

| and, '''Cut, Copy''' and '''Paste''' a '''Species'''.

|  We also learnt: about Start-point and End-point of a '''Species''',

| how to activate a''' Species''', change color of a''' Species''', change properties of a ''' Reaction''' and close a''' File'''.

|  For your assignment: create a''' complex''' and place a''' Species''' inside the''' Complex'''.

|About the '''spoken tutorial''' project.

| The video at this link summarizes the Spoken Tutorial project. Please download and watch it.

|  The Spoken Tutorial Project  conducts workshops and gives certificates on passing an on-line test. For more details, please write to us.

|  Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available on this link.

|  This is Bella Tony from''' IIT Bombay''', signing off. Thank you for joining.