Difference between revisions of "CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed"

|  Hello everyone. Welcome to this tutorial on''' Build and Modify Process Diagram''' in''' CellDesigner'''.

|  In this tutorial, we will learn to: use '''Macros''' , move '''Components''' on the '''draw area''' , connect a '''reaction line''' around a '''species''',

|  align and extend a reaction line , add a '''Product''' and a '''Reactant'''.

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

|  To follow this tutorial, learners should be familiar with: undergraduate''' Biochemistry,''' '''CellDesigner '''interface.

|If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website.

|  Let us begin.

|  Now, we’ll use '''CellDesigner''' to create this '''process diagram'''.

|  Now type: '''./runCellDesigner4.3''' and press '''Enter'''.

|  CellDesigner window is now open on your terminal.

|  Open a new file by pressing''' CTRL+N''' and name it '''Build and Modify Process Diagram'''.

|  On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the '''draw area'''.

|  For that, click on the '''Edit''' menu and then click on ''''Select All'.'''

|Alternately, you may press '''Ctrl + A '''keys.

|  Now, click anywhere on the highlighted components and drag them to the desired location.

|  Let's proceed.

|  Again, on the draw area, right click on the''' Generic Protein S1.'''

|  However, if you want to reflect the change to all '''components''' of the '''species''', click ‘'''Yes'''’. Here, I will click''' ‘No’'''.

|  Observe the''' Generic Protein S1 '''is now a simple molecule named '''2-keto-isovalerate.'''

|  Right-click in the center of the''' end-point ''' '''Generic protein'''-'''S1 ''' which is a '''product'''.

|  Click in the center of the ''''end-point species''' i.e.''' Valine '''and drag and drop at the desired location.

|  Repeat the same with '''Aminotransferase'''.

|  Keep the default width and height and click on '''OK''' button.

|  In the main menu, click on the icon for '''State Transition'''.

|Then, on the draw area, hover the '''mouse''' on ‘'''start-point'''' '''Species, Protein 1'''.

|  In the same manner, hover the '''mouse''' on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.

|  If we hover the mouse on either of the 2 '''process nodes''', a plus sign appears.

|  Click anywhere on the '''draw area''' to uncheck the highlighted components.

|  From here on, we will proceed with the '''Process diagram'''.

|  Let us come back to the '''Build and Modify Process Diagram''' window.

|  Let’s add a '''Reactant '''and a '''Product''' to the existing reaction.

|  Click on the highlighted '''process node.'''

|From the toolbar, use the icons: '''State Transition''' , '''Simple Molecule''',  '''Generic Protein''' and '''Catalysis'''.

|  Let us summarize. In this tutorial, we have learnt: to use '''Macros''',

|move '''Components''' on the '''draw area''' , connect a reaction line around a species,

|  align and extend a reaction line, add a '''Product''' and a '''Reactant'''.

|  For the assignment: Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''.  

Explore the '''Macros''' for '''GTP/GD'''.

Find out how to create a ’Curve’ reaction line.

|  About the '''Spoken Tutorial''' project-  

|Watch the video at the following link. It summarizes the Spoken Tutorial project.

| If you do not have a good bandwidth, please download and watch it.

|  The''' Spoken Tutorial Project '''team: conducts- workshops using Spoken tutorials

| and gives certificates for those who pass an online test.

|  '''Spoken Tutorial''' project is a part of '''Talk to a Teacher project.''' It is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the given link.

|  This is '''Bella Tony '''from''' IIT Bombay,''' signing off.