We currently use Joomela 3 for the package webpage and if you are registered you can login to the admin backend here: http://thegrantlab.org/bio3d/administrator/index.php

Adding Content:

First you need to create your content (step 1), mark it as published and publicly accessible (step 2) and then add a link to it from somewhere sensible (step 3).

Step 1: Creating new content

Click: Content > Article Manager > Add New Article.

Chose the an appropriate article Category (see below). For example, Vignettes, Static content or News.

Step 2: Marking as published and accessible

NB: To make your article visible, you need to put it on Published status and Public Access with the options in the sidebar section

Step 3: Add a menu item (to your article)

To have your new content be discoverable from the top menu you need to add a link to it (e.g. the main menu bar or home page)

1. Navigate to Menus --> Main Menu --> Add New Menu Item
2. Enter the name of the menu item
3. Select Menu item type (e.g. Articles --> Single articles)
4. Select the article you want to link to

Typically you will want your item to be nested under an existing menu item (i.e. as part of the drop-down list). For example a new vignette would be listed under the Tutorials menu item.

Find the Parent Item label and click on the drop-down menu to select the parent menu for the new menu item we're creating.

Article categories

Categories for articles allow you to group your content better. We have a Vignettes category and … [Fill in details of what we should do with it!!]

To add a new category: Content > Category Manager > Add New Category.

Components

Using components to add a particular type of new content (e.g. a vignette, news feed, etc.)

If you want to create a page with news feed for example, you need to go to: Components > Newsfeeds > Feeds and than click the big green NEW button.

Phoca download

1. Components --> Phoca Download --> Files
2. Click on New
3. Enter Title, and choose Category,
4. select Filename, and upload the file if necessary
5. Save and close

Vignettes

(see below)

How to find out the available template content positions?

See overview here.

To find out what are the names of any Joomla template positions and where they are situated on the front end. First, go to Extensions > Template Manager.

Then click on the Options button in the top menu. Here, switch the Preview Module Positions to Enabled and click on the Save green button in the top left part of the page.

Finally, go to the front of your website, and add the index.php?tp=1 option at the end of your URL. It should look like this http://yoursite.com/index.php?tp=1. You will see an annotated output with position labels.

Speeding up the website

To Do Urgently! http://www.siteground.com/tutorials/joomla/joomla-speed.htm

Quick Notes

To upload a new vignette:

1. Upload the markdown (.md) file along with associated figures using scp to bio3d/vignettes/newvignette
2. At the Joomla! site, navigate to Content --> Article --> Add new article
3. Enter the name of the article (e.g. New vignette), choose category Vignettes, and click Save and close
4. Navigate to Components --> Markdown Manage
5. Click on the New button
6. Enter the relative path to the vignette files (e.g. vignettes/newvignette/)
7. Enter the name of the .md file (e.g. newvignette.md)
8. Select the article ID you created in step 3.
9. Click Save
10. Click UPDATE ARTICLE, and voila !
11. Click Close

To update a vignette:

1. Upload the markdown (.md) file along with associated figures using scp to bio3d/vignettes/Bio3D_pca
2. At the Joomla! site, navigate to Components --> Markdown Manage
3. Check the vignette you want to edit, and click Edit
4. Click UPDATE ARTICLE, and voila !
5. Click Close

To add a news item:

1. Content --> Article --> Add new article
2. Select category News
3. Enter title and content
4. Click Save and close

To edit an existing static page:

1. Content --> Article
2. Select the article to edit
3. Edit the article
4. Click Save and close