EcoliWiki - User contributions [en]

Help:Database table

2009-07-08T20:30:22Z

Clements:

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

== Fields ==
[[Image:Database_Quickview.jpg|right]]

; Link/URL
: A link to the online database. Can be typed either as just a URL, or as a wiki link:
:: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
:: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
::: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
: Short description of database. This can also be a link to a page at the database.

; Who
: Institution, lab, PI, ... supporting or hosting the database. Can be a link.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T20:14:19Z

Clements:

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

[[Image:Database_Quickview.jpg|right]]
== Fields ==

; Link/URL
: A link to the online database. Can be typed either as just a URL, or as a wiki link:
:: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
:: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
::: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
: Short description of database. This can also be a link to a page at the database.

; Who
: Institution, lab, PI, ... supporting or hosting the database. Can be a link.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T20:12:36Z

Clements: /* Fields */

[[Image:Database_Quickview.jpg|right]]
==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

== Fields ==

; Link/URL
: A link to the online database. Can be typed either as just a URL, or as a wiki link:
:: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
:: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
::: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
: Short description of database. This can also be a link to a page at the database.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T20:12:02Z

Clements:

[[Image:Database_Quickview.jpg|right]]
==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

== Fields ==

; Link/URL
: A link to the online database. Can be typed either a just a URL, or as a wiki link:
:: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
:: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
::: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
: Short description of database. This can also be a link to a page at the database.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T20:09:12Z

Clements: /* Fields */

[[Image:Database_Quickview.jpg|right]]
==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

== Fields ==

; Link/URL
* A link to the online database. Can be typed either a just a URL, or as a wiki link:
*: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
*: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
*:: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
* Short description of database. This can also be a link to a page at the database.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T20:06:16Z

Clements:

[[Image:Database_Quickview.jpg|right]]
==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

== Fields ==

; Link/URL
* A link to the online database. Can be typed either a just a URL, or as a wiki link:
*: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
*: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
*:: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

; What
Short description of database.

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T19:59:22Z

Clements: /* Fields */

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

[[Image:Database_Quickview.jpg|left]]
<BR>

<br clear='all'>

== Fields ==

; Link/URL

* A link to the online database. Can be typed either a just a URL, or as a wiki link:
*: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
*: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
*:: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T19:59:04Z

Clements: /* Fields */

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

[[Image:Database_Quickview.jpg|left]]
<BR>

<br clear='all'>

== Fields ==

; Link/URL

* A link to the online database. Can be typed either a just a URL, or as a wiki link:
*: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
*: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
**: This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T19:56:16Z

Clements: /* About */

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below. See [[:Category:Databases]] for a complete list.

[[Image:Database_Quickview.jpg|left]]
<BR>

<br clear='all'>

== Fields ==

; Link/URL

* A link to the online database. Can be typed either a just a URL, or as a wiki link:
*: <tt>http://2dbase.techfak.uni-bielefeld.de/</tt>
*: <tt><nowiki>[http://2dbase.techfak.uni-bielefeld.de/ 2DBase]</nowiki></tt>
** This will be shown as [http://2dbase.techfak.uni-bielefeld.de/ 2DBase]

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Database table

2009-07-08T19:44:55Z

Clements: /* About */

Help:Database table

2009-07-08T19:43:39Z

Clements: /* About */

==About==

The Database Quickview provides an overview of an online [[:Category:Databases|database]] of interest to the EcoliWiki community. Users can add or edit information by editing the table. A picture of the table is below.

[[Image:Database_Quickview.jpg|left]]
<BR>

<br clear='all'>

{{TableHelpVertical}}

[[Category:Predefined table types in EcoliWiki]]
[[Category:Help|Database table]]

Help:Cellular levels

2009-07-08T18:45:27Z

Clements: /* Table fields */

[[Category:Help]]
== Introduction ==
[[Image:Cellular level table.jpg|thumb|a cellular level table|600px]]
One of our goals is to gather data from the literature about the steady-state levels of gene products in ''E. coli''. Each gene is associated with an expression page, and at the top of each expression page is an editable table where users can record information from the literature. Genes where a minimum level of information has been added to the table are listed in [[:Category:Expression level data]].

== Examples ==

* [[ftsL:Expression]] - Protein
* [[ftsQ:Expression]] - Enzyme activity
* [[mug:Expression]] - Protein

== Table fields ==
[[Image:Cellular level table fields.jpg|thumb|400px|Editing the table]]
=== Molecule ===
Molecule refers to what was measured. Options are:
* Protein
* Enzyme activity
* RNA
* other. If you select 'other', an extra text box will appear where you can enter the kind of molecule measured.

=== Organism or Strain ===

=== Cellular level ===

Some example values:
* 20-40
* ~35
* 200 +/- 45
* 440

This is paired with the Units column.

=== Units ===

Chose from the pulldown menu.

=== Medium ===

Example values:
* NZY (rich media, recipe described on page 7717)
* M63 minimal glycerol medium
* L broth
* LB

=== Other ===

=== Growth rate ===

Example values:
* mid-exponential phase

=== Assay used ===

Chose from the pulldown menu.

=== Notes ===

Anything else of importance.

=== Reference(s) ===
As with other EcoliWiki tables, putting a PubMed ID in the table will automatically be converted into a citation.

== Finding information about expression levels in the literature ==

== References ==
{{RefHelp}}
<references/>

Help:Cellular levels

2009-07-08T18:30:52Z

Clements: /* Introduction */

[[Category:Help]]
== Introduction ==
[[Image:Cellular level table.jpg|thumb|a cellular level table|600px]]
One of our goals is to gather data from the literature about the steady-state levels of gene products in ''E. coli''. Each gene is associated with an expression page, and at the top of each expression page is an editable table where users can record information from the literature. Genes where a minimum level of information has been added to the table are listed in [[:Category:Expression level data]].

== Examples ==

* [[ftsL:Expression]] - Protein
* [[ftsQ:Expression]] - Enzyme activity
* [[mug:Expression]] - Protein

== Table fields ==
[[Image:Cellular level table fields.jpg|thumb|400px|Editing the table]]
=== Molecule ===
Molecule refers to what was measured. Options are:
* Protein
* Enzyme activity
* RNA
* other. If you select 'other', an extra text box will appear where you can enter the kind of molecule measured.

=== Organism or Strain ===

=== Cellular level ===

=== Units ===

=== Medium ===

=== Other ===

=== Growth rate ===

=== Assay used ===

=== Notes ===

=== Reference(s) ===
As with other EcoliWiki tables, putting a PubMed ID in the table will automatically be converted into a citation.

== Finding information about expression levels in the literature ==

== References ==
{{RefHelp}}
<references/>

Help:Cellular levels

2009-07-08T18:16:32Z

Clements: /* Introduction */

[[Category:Help]]
== Introduction ==
[[Image:Cellular level table.jpg|thumb|a cellular level table|600px]]
One of our goals is to gather data from the literature about the steady-state levels of gene products in ''E. coli''. Each gene is associated with an expression page, and at the top of each expression page is an editable table where users can record information from the literature. Genes where a minimum level of information has been added to the table are listed in [[:Category:Expression level data]].

== Table fields ==
[[Image:Cellular level table fields.jpg|thumb|400px|Editing the table]]
=== Molecule ===
Molecule refers to what was measured. Options are:
* Protein
* Enzyme activity
* RNA
* other. If you select 'other', an extra text box will appear where you can enter the kind of molecule measured.

=== Organism or Strain ===

=== Cellular level ===

=== Units ===

=== Medium ===

=== Other ===

=== Growth rate ===

=== Assay used ===

=== Notes ===

=== Reference(s) ===
As with other EcoliWiki tables, putting a PubMed ID in the table will automatically be converted into a citation.

== Finding information about expression levels in the literature ==

== References ==
{{RefHelp}}
<references/>

Help:Accounts

2009-07-08T18:10:15Z

Clements: /* What is the My Watchlist link and how do I add topics to my watchlist? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''my watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''my contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2009-07-08T18:09:53Z

Clements: /* What is the User Contribution link? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''My Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''my contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2009-07-08T18:07:56Z

Clements: /* What is the My Watchlist link and how do I add topics to my watchlist? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''My Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''User Contribution''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2009-07-08T18:06:35Z

Clements: /* Can I customize EcoliWiki? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''My Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the '''my preferences''' link in the upper right hand corner of your browser. Under the watchlist tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''User Contribution''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2009-07-08T18:05:47Z

Clements: /* How do I change my password? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the my preferences link in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''My Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the '''my preferences''' link in the upper right hand corner of your browser. Under the watchlist tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''User Contribution''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2009-07-08T18:01:59Z

Clements: /* Can I invite new users to join EcoliWiki? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the my preferences link in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the my preferences link in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''My Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the '''my preferences''' link in the upper right hand corner of your browser. Under the watchlist tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''User Contribution''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

GMOD

2009-06-24T17:47:00Z

Clements: /* GMOD Tools */

[[Category:Databases]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://gmod.org/wiki/Main_Page Gmod.org/wiki]
|-
!align=left {{table heading style}} |What:
||
An open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more.
|-
!align=left {{table heading style}} |Who:
||
Community Based
|-
!align=left {{table heading style}} |Updates:
||
Daily
|-
!align=left {{table heading style}} |Upcoming events:
||
[http://gmod.org/wiki/Calendar GMOD Calendar]
|-
!align=left {{table heading style}} |Web Services:
||
None

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1682.H4a25986e7dca1&page=1682&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

[[Image:GMOD_home.jpg|right|Home Page|thumb|350px]]

[http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases.

== GMOD Tools ==

GMOD has a wide variety of tools for many different purposes:

{| cellpadding="10px"
| valign="top" |
'''Community Annotation'''
* [http://gmod.org/wiki/Apollo Apollo]
* Wiki [http://gmod.org/wiki/Table Editor Table Editor]

'''Comparative Genome Visualization'''
*[http://gmod.org/wiki/CMap CMap]
*[http://gmod.org/wiki/GBrowse_syn GBrowse_syn]
*[http://gmod.org/wiki/SynView SynView]
*[http://gmod.org/wiki/SynBrowse SynBrowse]
*[http://gmod.org/wiki/Sybil Sybil]

'''Database schema'''
*[http://gmod.org/wiki/Chado Chado]
Chado web front ends:
* [http://gmod.org/wiki/GMODWeb GMODWeb]
* [http://gmod.org/wiki/Tripal Tripal]

'''Database tools'''
*[http://gmod.org/wiki/Argos Argos]
*[http://gmod.org/wiki/BioMart BioMart]
*[http://gmod.org/wiki/Genome_grid Genome grid]
*[http://gmod.org/wiki/GMODTools GMODTools]
*[http://gmod.org/wiki/InterMine InterMine]
*[http://gmod.org/wiki/LuceGene LuceGene]
*[http://gmod.org/wiki/XORT XORT]
| valign="top" |
'''Gene Expression Visualization'''
*[http://gmod.org/wiki/Caryoscope Caryoscope]
*[http://gmod.org/wiki/GeneXplorer GeneXplorer]
*[http://gmod.org/wiki/Java_TreeView Java TreeView]

'''Genome Annotation'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/MAKER MAKER]

'''Genome Visualization & Editing'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/Flash_GViewer Flash GViewer]
*[http://gmod.org/wiki/GBrowse GBrowse]
*[http://gmod.org/wiki/GMODWeb GMODWeb]
*[http://gmod.org/wiki/JBrowse JBrowse]
*[http://gmod.org/wiki/Restriction_Graphic_Viewer Restriction Graphic Viewer]

'''Literature Tools'''
* [http://gmod.org/wiki/PubSearch PubSearch]
* [http://gmod.org/wiki/Textpresso Textpresso]
| valign="top" |
'''Molecular Pathway Visualization'''
* [http://gmod.org/wiki/Pathway_Tools Pathway Tools]

'''Ontology Visualization'''
* [http://gmod.org/wiki/GO_Graphic_Viewer Go Graphic Viewer]

'''Workflow Management'''
*[http://gmod.org/wiki/TIGR-Workflow_/_Ergatis Ergatis]

'''Middleware'''
*[http://gmod.org/wiki/Modware Modware]
*[http://gmod.org/wiki/Chado::AutoDBI Chado::AutoDBI]

'''Tool Integration'''
*[http://gmod.org/wiki/Galaxy Galaxy]

'''Sequence Alignment'''
*[http://gmod.org/wiki/BLAST_Graphic_Viewer |Blast Graphic]

'''Utilities'''
*[http://gmod.org/wiki/org.bdgp org.bdgp]

|}

GMOD

2009-06-24T17:45:16Z

Clements:

[[Category:Databases]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://gmod.org/wiki/Main_Page Gmod.org/wiki]
|-
!align=left {{table heading style}} |What:
||
An open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more.
|-
!align=left {{table heading style}} |Who:
||
Community Based
|-
!align=left {{table heading style}} |Updates:
||
Daily
|-
!align=left {{table heading style}} |Upcoming events:
||
[http://gmod.org/wiki/Calendar GMOD Calendar]
|-
!align=left {{table heading style}} |Web Services:
||
None

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1682.H4a25986e7dca1&page=1682&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

[[Image:GMOD_home.jpg|right|Home Page|thumb|350px]]

[http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases.

== GMOD Tools ==

GMOD has a wide variety of tools for many different purposes:

{|
| valign="top" |
'''Community Annotation'''
* [http://gmod.org/wiki/Apollo Apollo]
* Wiki [http://gmod.org/wiki/Table Editor Table Editor]

'''Comparative Genome Visualization'''
*[http://gmod.org/wiki/CMap CMap]
*[http://gmod.org/wiki/GBrowse_syn GBrowse_syn]
*[http://gmod.org/wiki/SynView SynView]
*[http://gmod.org/wiki/SynBrowse SynBrowse]
*[http://gmod.org/wiki/Sybil Sybil]

'''Database schema'''
*[http://gmod.org/wiki/Chado Chado]
Chado web front ends:
* [http://gmod.org/wiki/GMODWeb GMODWeb]
* [http://gmod.org/wiki/Tripal Tripal]

'''Database tools'''
*[http://gmod.org/wiki/Argos Argos]
*[http://gmod.org/wiki/BioMart BioMart]
*[http://gmod.org/wiki/Genome_grid Genome grid]
*[http://gmod.org/wiki/GMODTools GMODTools]
*[http://gmod.org/wiki/InterMine InterMine]
*[http://gmod.org/wiki/LuceGene LuceGene]
*[http://gmod.org/wiki/XORT XORT]
| valign="top" |
'''Gene Expression Visualization'''
*[http://gmod.org/wiki/Caryoscope Caryoscope]
*[http://gmod.org/wiki/GeneXplorer GeneXplorer]
*[http://gmod.org/wiki/Java_TreeView Java TreeView]

'''Genome Annotation'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/MAKER MAKER]

'''Genome Visualization & Editing'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/Flash_GViewer Flash GViewer]
*[http://gmod.org/wiki/GBrowse GBrowse]
*[http://gmod.org/wiki/GMODWeb GMODWeb]
*[http://gmod.org/wiki/JBrowse JBrowse]
*[http://gmod.org/wiki/Restriction_Graphic_Viewer Restriction Graphic Viewer]

'''Literature Tools'''
* [http://gmod.org/wiki/PubSearch PubSearch]
* [http://gmod.org/wiki/Textpresso Textpresso]
| valign="top" |
'''Molecular Pathway Visualization'''
* [http://gmod.org/wiki/Pathway_Tools Pathway Tools]

'''Ontology Visualization'''
* [http://gmod.org/wiki/GO_Graphic_Viewer Go Graphic Viewer]

'''Workflow Management'''
*[http://gmod.org/wiki/TIGR-Workflow_/_Ergatis Ergatis]

'''Middleware'''
*[http://gmod.org/wiki/Modware Modware]
*[http://gmod.org/wiki/Chado::AutoDBI Chado::AutoDBI]

'''Tool Integration'''
*[http://gmod.org/wiki/Galaxy Galaxy]

'''Sequence Alignment'''
*[http://gmod.org/wiki/BLAST_Graphic_Viewer |Blast Graphic]

'''Utilities'''
*[http://gmod.org/wiki/org.bdgp org.bdgp]

|}

GMOD

2009-06-24T17:42:17Z

Clements:

[[Category:Databases]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://gmod.org/wiki/Main_Page Gmod.org/wiki]
|-
!align=left {{table heading style}} |What:
||
An open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more.
|-
!align=left {{table heading style}} |Who:
||
Community Based
|-
!align=left {{table heading style}} |Updates:
||
Daily
|-
!align=left {{table heading style}} |Upcoming events:
||
[http://gmod.org/wiki/Calendar GMOD Calendar]
|-
!align=left {{table heading style}} |Web Services:
||
None

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1682.H4a25986e7dca1&page=1682&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

[[Image:GMOD_home.jpg|right|Home Page|thumb|350px]]

[http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases.

== GMOD Tools ==

GMOD has a wide variety of tools for many different purposes:

{|
| valign="top" |
'''Community Annotation'''
* [http://gmod.org/wiki/Apollo Apollo]
* Wiki [http://gmod.org/wiki/Table Editor Table Editor]

'''Comparative Genome Visualization'''
*[http://gmod.org/wiki/CMap CMap]
*[http://gmod.org/wiki/GBrowse_syn GBrowse_syn]
*[http://gmod.org/wiki/SynView SynView]
*[http://gmod.org/wiki/SynBrowse SynBrowse]
*[http://gmod.org/wiki/Sybil Sybil]

'''Database schema'''
*[http://gmod.org/wiki/Chado Chado]
Chado web front ends:
* [http://gmod.org/wiki/GMODWeb GMODWeb]
* [http://gmod.org/wiki/Tripal Tripal]

'''Database tools'''
*[http://gmod.org/wiki/Argos Argos]
*[http://gmod.org/wiki/BioMart BioMart]
*[http://gmod.org/wiki/Genome_grid Genome grid]
*[http://gmod.org/wiki/GMODTools GMODTools]
*[http://gmod.org/wiki/InterMine InterMine]
*[http://gmod.org/wiki/LuceGene LuceGene]
*[http://gmod.org/wiki/XORT XORT]
| valign="top" |
'''Gene Expression Visualization'''
*[http://gmod.org/wiki/Caryoscope Caryoscope]
*[http://gmod.org/wiki/GeneXplorer GeneXplorer]
*[http://gmod.org/wiki/Java_TreeView Java TreeView]

'''Genome Annotation'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/MAKER MAKER]

'''Genome Visualization & Editing'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/Flash_GViewer Flash GViewer]
*[http://gmod.org/wiki/GBrowse GBrowse]
*[http://gmod.org/wiki/GMODWeb GMODWeb]
*[http://gmod.org/wiki/JBrowse JBrowse]
*[http://gmod.org/wiki/Restriction Graphic Viewer Restriction Graphic Viewer]

'''Literature Tools'''
* [http://gmod.org/wiki/PubSearch PubSearch]
* [http://gmod.org/wiki/Textpresso Textpresso]
| valign="top" |
'''Molecular Pathway Visualization'''
* [http://gmod.org/wiki/Pathway_Tools Pathway Tools]

'''Ontology Visualization'''
* [http://gmod.org/wiki/GO_Graphic_Viewer|Go Graphic Viewer GO_Graphic_Viewer|Go Graphic Viewer]

'''Workflow Management'''
*[http://gmod.org/wiki/TIGR-Workflow_/_Ergatis Ergatis]

'''Middleware'''
*[http://gmod.org/wiki/Modware Modware]
*[http://gmod.org/wiki/Chado::AutoDBI Chado::AutoDBI]

'''Tool Integration'''
*[http://gmod.org/wiki/Galaxy Galaxy]

'''Sequence Alignment'''
*[http://gmod.org/wiki/BLAST_Graphic_Viewer|Blast Graphic BLAST_Graphic_Viewer|Blast Graphic]

'''Utilities'''
*[http://gmod.org/wiki/org.bdgp org.bdgp]

|}

GMOD

2009-06-24T17:41:30Z

Clements:

[[Category:Databases]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://gmod.org/wiki/Main_Page Gmod.org/wiki]
|-
!align=left {{table heading style}} |What:
||
An open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more.
|-
!align=left {{table heading style}} |Who:
||
Community Based
|-
!align=left {{table heading style}} |Updates:
||
Daily
|-
!align=left {{table heading style}} |Upcoming events:
||
[http://gmod.org/wiki/Calendar GMOD Calendar]
|-
!align=left {{table heading style}} |Web Services:
||
None

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1682.H4a25986e7dca1&page=1682&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

[[Image:GMOD_home.jpg|left|Home Page|thumb|250px]]

[http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases.

== GMOD Tools ==

GMOD has a wide variety of tools for many different purposes:

{|
| valign="top" |
'''Community Annotation'''
* [http://gmod.org/wiki/Apollo Apollo]
* Wiki [http://gmod.org/wiki/Table Editor Table Editor]

'''Comparative Genome Visualization'''
*[http://gmod.org/wiki/CMap CMap]
*[http://gmod.org/wiki/GBrowse_syn GBrowse_syn]
*[http://gmod.org/wiki/SynView SynView]
*[http://gmod.org/wiki/SynBrowse SynBrowse]
*[http://gmod.org/wiki/Sybil Sybil]

'''Database schema'''
*[http://gmod.org/wiki/Chado Chado]
Chado web front ends:
* [http://gmod.org/wiki/GMODWeb GMODWeb]
* [http://gmod.org/wiki/Tripal Tripal]

'''Database tools'''
*[http://gmod.org/wiki/Argos Argos]
*[http://gmod.org/wiki/BioMart BioMart]
*[http://gmod.org/wiki/Genome_grid Genome grid]
*[http://gmod.org/wiki/GMODTools GMODTools]
*[http://gmod.org/wiki/InterMine InterMine]
*[http://gmod.org/wiki/LuceGene LuceGene]
*[http://gmod.org/wiki/XORT XORT]
| valign="top" |
'''Gene Expression Visualization'''
*[http://gmod.org/wiki/Caryoscope Caryoscope]
*[http://gmod.org/wiki/GeneXplorer GeneXplorer]
*[http://gmod.org/wiki/Java_TreeView Java TreeView]

'''Genome Annotation'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/MAKER MAKER]

'''Genome Visualization & Editing'''
*[http://gmod.org/wiki/Apollo Apollo]
*[http://gmod.org/wiki/Flash_GViewer Flash GViewer]
*[http://gmod.org/wiki/GBrowse GBrowse]
*[http://gmod.org/wiki/GMODWeb GMODWeb]
*[http://gmod.org/wiki/JBrowse JBrowse]
*[http://gmod.org/wiki/Restriction Graphic Viewer Restriction Graphic Viewer]

'''Literature Tools'''
* [http://gmod.org/wiki/PubSearch PubSearch]
* [http://gmod.org/wiki/Textpresso Textpresso]
| valign="top" |
'''Molecular Pathway Visualization'''
* [http://gmod.org/wiki/Pathway_Tools Pathway Tools]

'''Ontology Visualization'''
* [http://gmod.org/wiki/GO_Graphic_Viewer|Go Graphic Viewer GO_Graphic_Viewer|Go Graphic Viewer]

'''Workflow Management'''
*[http://gmod.org/wiki/TIGR-Workflow_/_Ergatis Ergatis]

'''Middleware'''
*[http://gmod.org/wiki/Modware Modware]
*[http://gmod.org/wiki/Chado::AutoDBI Chado::AutoDBI]

'''Tool Integration'''
*[http://gmod.org/wiki/Galaxy Galaxy]

'''Sequence Alignment'''
*[http://gmod.org/wiki/BLAST_Graphic_Viewer|Blast Graphic BLAST_Graphic_Viewer|Blast Graphic]

'''Utilities'''
*[http://gmod.org/wiki/org.bdgp org.bdgp]

|}

GMOD

2009-06-24T17:16:14Z

Clements: Stripped out all unpopulated sections.

GMOD

2009-06-24T17:11:18Z

Clements: Table edited by Clements via TableEdit

GMOD

2009-06-24T17:09:43Z

Clements: /* About {{PAGENAME}} */

GMOD

2009-06-24T17:04:53Z

Clements: Table edited by Clements via TableEdit

GMOD

2009-06-24T17:01:36Z

Clements:

Help:Jmol in EcoliWiki

2009-04-23T20:04:36Z

Clements:

Jmol is a Java-based molecular visualization tool. Extensive documentation can be found on the [http://jmol.org Jmol website]. This page describes how you can embed images and set scenes inside EcoliWiki using [http://wiki.jmol.org:81/index.php/MediaWiki Jmol's MediaWiki extension].

Working with Jmol in EcoliWiki is a bit of an advanced topic, so it may be useful to familiarize yourself with MediaWiki markup conventions. Start with the [[Help:Editing|Editing help page]] and see [[:Category:Help]] for more advanced topics.

== Embedding Jmol by transclusion ==
{{Image:1JHE.pdb}} The markup for Jmol can be verbose, and putting Jmol scripts directly in pages can make them hard to edit. So we suggest making a page for your Jmol viewer and including it in the desired page by [[Help:Editing:Intermediate|transclusion]]. A convenient way to do this is to use the Image page created by uploading a .pdb coordinate file. For example, the page at [[:Image:1JHE.pdb]] was created when the JHE.pdb file was uploaded to the wiki. The page was then edited to add the Jmol viewer. To put it in this page, we used <nowiki>{{Image:1JHE.pdb}}</nowiki>, where the curly brackets tell Mediawiki to copy the content of the Image page. Similar approaches can be used to transclude an image from any other page in the wiki, in case you want different default behavior.

== Making the viewer ==
You can build a viewer from scratch, or you can start by using <nowiki>{{subst:Jmol_template}}</nowiki> and saving to incorporate a template viewer. You'll still have to edit it, but this will put the viewer in a box on the right that allows text to wrap around it, add the Help link, set the background to white, and so on.
===The viewer block===
The viewer settings reside inside flanking jmol and jmolApplet tags. For example:
<pre>
<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents >1JHE.pdb</uploadedFileContents>
<script>
wireframe off; trace off;
rotate on;
spacefill on;
color chain;
</script>
</jmolApplet>
</jmol></pre>

The '''script''' tags are used in several contexts in the Jmol extension. Here, they tell the applet the default script to run when the applet loads.
===Setting the pdb file===
Put the name of the pdb file between
<uploadedFileContents >pdb file name</uploadedFileContents>
Note that this is just the filename, without Image: or Media; prefixes. Alternatively, you can create a wiki page with the the coordinates and use
<wikiPageContents>page of the wiki containing the molecular data</wikiPageContents>
or use
<inlineContents>contents of the molecular file</inlineContents>
to put the coordinates right in the viewer.

== Making external links to control the viewer ==
As with the viewers, we suggest making link scripts on a separate wiki page and including them by transclusion. A convenient way to arrange these is to put some documentation for Jmol links in the talk page for an uploaded pdb file, and make the scripts as subpages. For example,
* The structure above is at [:Image:1JHE.pdb]]
* Discussion of the structure file is at [[Image_talk:1JHE.pdb]]
* Subpages of the talk page can be used for scripts that save specific views.

Example: [[Image_talk:1JHE.pdb/catalytic_site]] contains a Jmol link script, which is incorporated to make this link {{Image_talk:1JHE.pdb/catalytic_site}}using <nowiki>{{Image_talk:1JHE.pdb/catalytic_site}}</nowiki>

=== Known bugs ===
* the transclusion does not work if the markup is included in the wiki markup for a list or indented text
* start the next word after the transclusion immediately after - don't leave a space.

=== More examples ===
* [[:Image:1LMB.pdb]], [[Image_talk:1LMB.pdb]], and [[lambda_repressor/N-domain]]

== Jmol scripting ==
Here, we'll just cover a few commonly used commands. See below for links to more extensive documentation and tutorials.
<protect>

{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
|-
!|Command!!Notes!!Examples
|-
|
select [atom-expression]
|
You need to select things to work on them selectively. Atom expressions include:
* numbers for residues
* :chain_id for chains (subunits)
* backbone
* sidechains
|
* select 1-10; selects residues 1-10 in all chains
* select *:A; selects all atoms in chain A
* select 84:A, 156:B; selects two residues, one in chain A and one in chain B.
|-
|
spacefill (on/off/only)
(synonym: cpk)
|
Shows atoms as VdW sized spheres
|

|-
|
wireframe (on/off/only)
|
shows the bonds between atoms.
|

|-
|
cartoon (on/off/only)
|
shows helices and sheets in cartoon form.
|

|-
|
* zoom (atom-expression) %zoom
* zoomto (atom-expression) %zoom
|
centers on atom-expression and zooms there to the specified percentage of the 100% default. The zoom factor can range from 5 to 20,000, where larger numbers are zoomed in.
|
zoomto (84:A) 500;

|-
|
color [drawn-object] [RGB-color]
|
if drawn-object is ommitted, color uses whatever is selected. Colors can be:
* color names:
**white, blue, red, cyan, etc.
**special names
*** monomer - gives a rainbow from N to C
*** cpk
*** amino - by aa type for proteins
*** shapely - by base type for nucleic acids
*** structure - helices and sheets
*** chain - subunits
* hex values: [xRRGGBB] (brackets needed)
* RGB triples: [255,0,255]
|

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.150401.D49e185e8b9d29&page=150401&pagename={{FULLPAGENAMEE}}&type=0&template= edit table] || ||
|}
</protect>

== See also ==
* [http://wiki.jmol.org:81/index.php/Scripting Scripting] on the Jmol wiki.
* [http://jmol.sourceforge.net/jscolors/ Colors]
* [http://chemapps.stolaf.edu/jmol/docs/?ver=11.8 scripting commands]

== References ==
{{RefHelp}}
<references/>

EcoliWiki:TableEdit Sandbox

2008-09-26T22:42:35Z

Clements: /* Templated table example */ Added Template prefix.

<protect>This Sandbox page is a place where users can play with the table editor. Additional documentation is at [[Special:TableEdit]]
* Unregistered users can:
** Open the example tables and use the editor. However, any changes will not be saved to the page
* Registered users can:
** Save changes
** Make new tables in the play area
== Freeform table example ==
This table allows editing. It was created using the markup:
<nowiki><newTableEdit>
Heading 1
Heading 2
Heading 3</newTableEdit></nowiki>
You can change the heading text, background color, or alignment, add columns, add data, or rotate the table
<protect>

{|class = 'sortable' {{Prettytable}} id='213180'
|- bgcolor = yellow
!Heading 1!!Heading 2!!Heading 3
|-
|
data 1
|
data 2
|
data 3
|-
|
data 4
|
data 5
|
data 6
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=63ce1649aab8b3180235b0af7618f667.0.C46ac07827444c&page=0&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
</protect>

== Templated table example ==

In this table the headings are set from a template using the markup <nowiki><newTableEdit>Template:GO_table_product</newTableEdit></nowiki> where [[Template: GO_table_product| GO_table_product]] is a template for the table type. It illustrates how you can customize the editing interface with pulldown menus, queries to other databases, and simple calculations. For example GO terms have the form "GO:ddddddd" where ddddddd is a seven digit number. Try typing GO:0000123 in the GO id field and then click update. Try putting a PMID in the references cell.
<protect>

{|class = 'sortable' {{Prettytable}} id='213211'
|- {{table_heading_style}}
!Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=63ce1649aab8b3180235b0af7618f667.105298.M46ac0834b09fd&page=105298&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>
</protect>

== Play area for registered users==
Table nesting is possible, but if you just use <nowiki><newTableEdit/></nowiki> on the inside, any edits of the outer table destroy the inner table. Updates to the inner table are not recorded as changes to the outer table.
<protect>

{|class = 'sortable' {{Prettytable}} id='214444'
|- bgcolor = pink
!Outside table Heading 1!!Outside table Heading 2
|-
|
This is in the outer table
|
This is in the outer table
|-
|
this is in the outer table
|
<protect>
[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=63ce1649aab8b3180235b0af7618f667.105298.Q46aca0b3a977b&page=105298&pagename={{FULLPAGENAMEE}}&type=0 Create Table Here]
</protect>
|-
|
more in the outer table
|
edit the outer table
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=63ce1649aab8b3180235b0af7618f667.105298.P46ac9e72a1a9f&page=105298&pagename={{FULLPAGENAMEE}} edit table] ||
|}
</protect>

<protect>

{|class = 'sortable' {{Prettytable}} id='242205'
|-
!Gene Product!!Qualifier!!GO ID!!Go term name!!Aspect!!Reference!!Annotator!!Date
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.105298.U4855f7cb1b81b&page=105298&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}
</protect>

<protect>

{|class = 'sortable' {{Prettytable}} id='242206'
|- {{table_heading_style}}
!Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.105298.K4855f81255456&page=105298&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

MediaWiki:Common.css

2008-05-15T21:02:54Z

Clements: Added wikitable class.

/** CSS placed here will be applied to all skins */

/* Adding wikitable from wikipedia. This is roughly, and possibly exactly, equivalent to the prettytable template. */

/* wikitable class for skinning normal tables */
table.wikitable {
margin: 1em 1em 1em 0;
background: #f9f9f9;
border: 1px #aaa solid;
border-collapse: collapse;
}

table.wikitable th, table.wikitable td {
border: 1px #aaa solid;
padding: 0.2em;
}

table.wikitable th {
background: #f2f2f2;
text-align: center;
}

table.wikitable caption {
margin-left: inherit;
margin-right: inherit;
font-weight: bold;
}

table.wikitable code {
background-color: transparent;
}

Help:Editing:Basics

2008-05-15T20:58:52Z

Clements: /* What if I don't like the Page Name after I've saved it? */

[[Category:Help]]
[[Category:Editing Help]]
==Be bold!==
Remember,
*Content is more important than formatting. The wiki system allows more experienced proofreaders to clean up your entries if they don't have perfect formatting. Go ahead and put something in the wiki, and then [[Help:Asking for help|ask for help]] if you want someone to clean up the formatting or discuss the content with you. As you gain experience you can help others with their pages.
*You can try out different editing techniques in the [[Sandbox]].
*You can't mess up anything so badly that we can't go back to the previous version. EcoliWiki saves old versions of every page.
*Use the [[Help:Discussion Pages|discussion pages]] or the [http://ecoliwiki.org/phpbb2 bbs] if you're not sure about something.
*Editing is a collaborative effort that should strive for a neutral point of view ([[NPOV]]). We want links to your strong opinions, but these should be placed outside the main EcoliWiki site, where others can't edit them. See [[Help:Trackbacks]].

==Editing Existing Pages==
To edit a page, click either the edit tab on top of the display, or one of the edit links for a specific subsection. This will bring up an editing form.
==Starting New Pages==
There are different ways of creating new pages in EcoliWiki.

===Using the Page Generator===
The EcoliWiki team has created preformatted templates for different types of pages in the wiki, such as Gene Pages, Literature Pages, and Strain Pages. If you want to create a new page that corresponds to one of these types of pages, use the [[http://ecoliwiki.net/dev/index.php/Page_Generator Page_Generator]]. The Page Generator will create a new page that is already formatted with all the boxes ready to fill in.

===Following a Red Link===
Often, you will be reading a page that someone else created that has both Blue and Red text links. Links in red text are to pages that don't exist yet; whoever put in the link thought a page was needed, but didn't get around to creating one. If you click on such a link, you'll get an edit page for that page.

===Create new page from search results===
Before creating a new page, it is useful to see if a similar page already exists. If you search for a page and nothing comes up, EcoliWiki will offer you a chance to create a new page.

===What if I don't like the Page Name after I've saved it?===
Moving a page will rename it and create a redirect to the new name. If you can't move the page, [[Help:Asking for help|ask for help]] from one of our administrators. If you want to have a different Page name link to an existing page, you need to make a redirect. This is done by making a page with the desired nickname, containing ''only'' the following:

#REDIRECT <nowiki>[[link in internal link style]]</nowiki>
Where "link in internal link style" is how you would link to the target page with a normal wiki link.

For example: The page for the Protein Data Bank contains information about that database, on a page named [[Protein Data Bank (PDB)]]. We would like to create another page called [[Protein Data Bank]] that redirects the user to [[Protein Data Bank (PDB)]]. We create a new page with the page name Protein Data Bank, and then add the content
#REDIRECT <nowiki>[[Protein Data Bank (PDB)]]</nowiki>
In this case, the redirect page already exists.

Redirects are useful for cases where there are different ways of referring to the same thing. EcoliWiki uses redirects to make finding what you want easier.

==Working in Edit Mode==
[[Image:Edit_buttons.jpg|thumb|framed|right|Edit buttons at bottom of a page in Edit mode]]
Adding or editing is just like any other web form. Click or drag to select an insertion point, and just type away. Just remember '''don't use the TAB key''' to space your text. That will take you out of the editing box.

Note that you can preview your changes before saving them. This is useful, since things don't always come out as expected, but you should also be sure to save at regular intervals. If you don't, your changes could be lost if your session times out, or if someone else starts editing the page while you're working on it. The show changes button shows you what parts of the page you've changed. The Summary box allows you to put in a short description of why you edited the page. This is optional, but it can be useful for when you, or others, come back and edit the page again. For example, if you delete a material that you think is inappropriate for a page, you might want to explain that to keep others from adding it back without thinking about it. Others may disagree with you and add it back anyway, but in that case, you should work out a neutral consensus text with the other editors. Each page in the wiki has a [[Help:Discussion Pages|discussion page]] which is a good place to work things out.

Here's a common unintended effect:
If your text winds up in a box like this, it's because you started it on a line beginning with one or more blank spaces. So don't try to indent your paragraphs!

This is all you need to know to start editing. If you're just adding text or fixing typos, you can just go ahead and skip the rest of this tutorial.

===Adding Links===
One of the most important aspects of making a page useful are the links to other pages. These can be links to other pages in EcoliWiki or links to pages on other websites
====Internal Links====
To insert a link to another page in EcoliWiki, put the name of the page inside a pair of brackets.
:<nowiki>[[What's new?]]</nowiki>
creates
:[[What's new?]]
Note that this is case-sensitive. [[What's New?]], [[what's New?]], and [[what's new?]] all give red links, indicating no pages with those names. However, if you want different capitalizations to all lead to the same page you can create those pages and have them contain only a [[#What if I don't like the Page Name after I've saved it?|REDIRECT]] statement that points to the original page.
=====Piped Links=====
Often, it is useful to have link to a page using different text than the page name. For example, at the top of this page, there is a sentence that starts with:
<blockquote>Use the [[Help:Discussion Pages|discussion pages]] or...</blockquote>
This actually links to [[Help:Discussion Pages]], not [[discussion pages]]. The link as made using a pipe character (|) between the PageName and the text for the link:
:<nowiki>[[Help:Discussion Pages|discussion pages]]</nowiki>
=====Linking to a Subsection=====
To link to a subsection in the middle of the page, use the # sign after the PageName, followed by a subsection name. For example:
:<nowiki>[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]</nowiki>
gives
:[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]
which links to a subsection on this Help page. Of course, this can be used in a piped link too, as in [[Help:Editing:Basics#Italics, Bold, and Bold Italics|how to make italics]].

=====Linking to Category Indices=====
Pages can be placed into categories, and the index pages for different categories are very useful for finding content. The PageName for a Category index is Category:CategoryName, but making a link as
:<nowiki>[[Category:Help]]</nowiki>
Doesn't link to the Help index, it adds the page to that category. To make a link to an index page, add a colon (:) before the PageName, like this:
:<nowiki>[[:Category:Help]]</nowiki>
to get
:[[:Category:Help]]
Again, you can pipe this to give a link to a [[:Category:Help|list of help pages]].

====External Links====
If you just place a URL in the text, it will be converted to a link:
http://example.com
However, usually you want the linked text to be something other than the raw URL. To do that, put the URL and the link text, separated by a space, inside square brackets like this:
:<nowiki>[http://ecoliwiki.org EcoliWiki home page]</nowiki>
becomes
:[http://ecoliwiki.org EcoliWiki home page]
This external link method will also work for links to other pages inside EcoliWiki. However, the internal link methods described above are preferred, because they allow the system to count how the pages link to each other. For example,
http://ecoliwiki.net/colipedia/index.php/Community_portal does not show up in "What links here" for the Community Portal page
====Interwiki Links====
There are some external sites that we will be linking to so often that it is useful to have shortcuts for them. These are called interwiki links.
===Formatting characters===
====Italics, Bold, and Bold Italics====
One of the most common edits will be to change E. coli to ''E. coli'', or to italicize a gene name. Occasionally, you may want to make '''bold''' text, or '''''bold italic''''' text. Here's how:
{|{{Prettytable}}
|-
|''italics'' ||<nowiki>''italics''</nowiki> Text is surrounded by two single quote (') marks on each side.
|-
|'''bold''' ||<nowiki>'''bold'''</nowiki> Text is surrounded by three single quote (') marks on each side.
|-
|'''''bold italics''''' ||<nowiki>'''''bold italics'''''</nowiki> Text is surrounded by five (three for bold, two for italics) single quote (') marks on each side.
|-
|'' 'italicized single quoted' '' ||<nowiki>'' 'italicized single quoted' ''</nowiki> Put a blank space in between the marks for italics and the single quotes you want to appear in the text.
|}
Most of the time on EcoliWiki, you should not need anything besides italics. But now you know how to do the other kinds.

===Subheadings===
One of the reasons you should not need to do much beyond italics is that you don't need '''bold''' or different font sizes to make subheadings. Subheadings at different levels are made by putting different numbers of '=' signs around text on a line, where the string of equals signs are the first thing on the line.

On EcoliWiki pages, the Page Title is a level 1 heading, so start any headings with two = signs, and increase the number for subheadings and sub-subheadings. Headings made in this way are automatically used to generate a table of contents for each page in outline format, like the one for this page:
===Categories===
To add a page to a category, use
:<nowiki>[[Category:CategoryName]]</nowiki>
This will not be rendered on the page, but will add a category link to the bottom of the page. For example, this page is in the Help category. A list of categories can be found at [[Special:Categories]]. Using a new CategoryName creates a new Category. Any given page can belong to multiple categories.

==More Info==
{{Help:Editing}}

User:Clements/Sandbox

2008-05-15T20:56:15Z

Clements:

#REDIRECT User:Clements

User:Clements/Sandbox

2008-05-15T20:55:48Z

Clements: Redirecting to User:Clements

#REDIRECT [[User:Clements]]

Main Page

2008-05-15T20:50:42Z

Clements: This was an ancestral Main Page. The home page of this wiki is "Welcome to EcoliWiki". This page now redirects to that.

#REDIRECT [[Welcome to EcoliWiki]]

Help:Editing:Basics

2008-05-15T20:47:49Z

Clements: /* Internal Links */ Added comments on using redirects to support multiple capitalizations.

[[Category:Help]]
[[Category:Editing Help]]
==Be bold!==
Remember,
*Content is more important than formatting. The wiki system allows more experienced proofreaders to clean up your entries if they don't have perfect formatting. Go ahead and put something in the wiki, and then [[Help:Asking for help|ask for help]] if you want someone to clean up the formatting or discuss the content with you. As you gain experience you can help others with their pages.
*You can try out different editing techniques in the [[Sandbox]].
*You can't mess up anything so badly that we can't go back to the previous version. EcoliWiki saves old versions of every page.
*Use the [[Help:Discussion Pages|discussion pages]] or the [http://ecoliwiki.org/phpbb2 bbs] if you're not sure about something.
*Editing is a collaborative effort that should strive for a neutral point of view ([[NPOV]]). We want links to your strong opinions, but these should be placed outside the main EcoliWiki site, where others can't edit them. See [[Help:Trackbacks]].

==Editing Existing Pages==
To edit a page, click either the edit tab on top of the display, or one of the edit links for a specific subsection. This will bring up an editing form.
==Starting New Pages==
There are different ways of creating new pages in EcoliWiki.

===Using the Page Generator===
The EcoliWiki team has created preformatted templates for different types of pages in the wiki, such as Gene Pages, Literature Pages, and Strain Pages. If you want to create a new page that corresponds to one of these types of pages, use the [[http://ecoliwiki.net/dev/index.php/Page_Generator Page_Generator]]. The Page Generator will create a new page that is already formatted with all the boxes ready to fill in.

===Following a Red Link===
Often, you will be reading a page that someone else created that has both Blue and Red text links. Links in red text are to pages that don't exist yet; whoever put in the link thought a page was needed, but didn't get around to creating one. If you click on such a link, you'll get an edit page for that page.

===Create new page from search results===
Before creating a new page, it is useful to see if a similar page already exists. If you search for a page and nothing comes up, EcoliWiki will offer you a chance to create a new page.

===What if I don't like the Page Name after I've saved it?===
Moving a page will rename it and create a redirect to the new name. If you can't move the page, [[Help:Asking for help|ask for help]] from one of our administrators. If you want to have a different Page name link to an existing page, you need to make a redirect. This is done by making a page with the desired nickname, containing ''only'' the following:

#REDIRECT link in internal link style
Where "link in internal link style" is how you would link to the target page with a normal wiki link.

For example: The page for the Protein Data Bank contains information about that database, on a page named [[Protein Data Bank (PDB)]]. We would like to create another page called [[Protein Data Bank]] that redirects the user to [[Protein Data Bank (PDB)]]. We create a new page with the page name Protein Data Bank, and then add the content
#REDIRECT [[Protein Data Bank (PDB)]]
In this case, the redirect page already exists.

Redirects are useful for cases where there are different ways of referring to the same thing. EcoliWiki uses redirects to make finding what you want easier.

==Working in Edit Mode==
[[Image:Edit_buttons.jpg|thumb|framed|right|Edit buttons at bottom of a page in Edit mode]]
Adding or editing is just like any other web form. Click or drag to select an insertion point, and just type away. Just remember '''don't use the TAB key''' to space your text. That will take you out of the editing box.

Note that you can preview your changes before saving them. This is useful, since things don't always come out as expected, but you should also be sure to save at regular intervals. If you don't, your changes could be lost if your session times out, or if someone else starts editing the page while you're working on it. The show changes button shows you what parts of the page you've changed. The Summary box allows you to put in a short description of why you edited the page. This is optional, but it can be useful for when you, or others, come back and edit the page again. For example, if you delete a material that you think is inappropriate for a page, you might want to explain that to keep others from adding it back without thinking about it. Others may disagree with you and add it back anyway, but in that case, you should work out a neutral consensus text with the other editors. Each page in the wiki has a [[Help:Discussion Pages|discussion page]] which is a good place to work things out.

Here's a common unintended effect:
If your text winds up in a box like this, it's because you started it on a line beginning with one or more blank spaces. So don't try to indent your paragraphs!

This is all you need to know to start editing. If you're just adding text or fixing typos, you can just go ahead and skip the rest of this tutorial.

===Adding Links===
One of the most important aspects of making a page useful are the links to other pages. These can be links to other pages in EcoliWiki or links to pages on other websites
====Internal Links====
To insert a link to another page in EcoliWiki, put the name of the page inside a pair of brackets.
:<nowiki>[[What's new?]]</nowiki>
creates
:[[What's new?]]
Note that this is case-sensitive. [[What's New?]], [[what's New?]], and [[what's new?]] all give red links, indicating no pages with those names. However, if you want different capitalizations to all lead to the same page you can create those pages and have them contain only a [[#What if I don't like the Page Name after I've saved it?|REDIRECT]] statement that points to the original page.
=====Piped Links=====
Often, it is useful to have link to a page using different text than the page name. For example, at the top of this page, there is a sentence that starts with:
<blockquote>Use the [[Help:Discussion Pages|discussion pages]] or...</blockquote>
This actually links to [[Help:Discussion Pages]], not [[discussion pages]]. The link as made using a pipe character (|) between the PageName and the text for the link:
:<nowiki>[[Help:Discussion Pages|discussion pages]]</nowiki>
=====Linking to a Subsection=====
To link to a subsection in the middle of the page, use the # sign after the PageName, followed by a subsection name. For example:
:<nowiki>[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]</nowiki>
gives
:[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]
which links to a subsection on this Help page. Of course, this can be used in a piped link too, as in [[Help:Editing:Basics#Italics, Bold, and Bold Italics|how to make italics]].

=====Linking to Category Indices=====
Pages can be placed into categories, and the index pages for different categories are very useful for finding content. The PageName for a Category index is Category:CategoryName, but making a link as
:<nowiki>[[Category:Help]]</nowiki>
Doesn't link to the Help index, it adds the page to that category. To make a link to an index page, add a colon (:) before the PageName, like this:
:<nowiki>[[:Category:Help]]</nowiki>
to get
:[[:Category:Help]]
Again, you can pipe this to give a link to a [[:Category:Help|list of help pages]].

====External Links====
If you just place a URL in the text, it will be converted to a link:
http://example.com
However, usually you want the linked text to be something other than the raw URL. To do that, put the URL and the link text, separated by a space, inside square brackets like this:
:<nowiki>[http://ecoliwiki.org EcoliWiki home page]</nowiki>
becomes
:[http://ecoliwiki.org EcoliWiki home page]
This external link method will also work for links to other pages inside EcoliWiki. However, the internal link methods described above are preferred, because they allow the system to count how the pages link to each other. For example,
http://ecoliwiki.net/colipedia/index.php/Community_portal does not show up in "What links here" for the Community Portal page
====Interwiki Links====
There are some external sites that we will be linking to so often that it is useful to have shortcuts for them. These are called interwiki links.
===Formatting characters===
====Italics, Bold, and Bold Italics====
One of the most common edits will be to change E. coli to ''E. coli'', or to italicize a gene name. Occasionally, you may want to make '''bold''' text, or '''''bold italic''''' text. Here's how:
{|{{Prettytable}}
|-
|''italics'' ||<nowiki>''italics''</nowiki> Text is surrounded by two single quote (') marks on each side.
|-
|'''bold''' ||<nowiki>'''bold'''</nowiki> Text is surrounded by three single quote (') marks on each side.
|-
|'''''bold italics''''' ||<nowiki>'''''bold italics'''''</nowiki> Text is surrounded by five (three for bold, two for italics) single quote (') marks on each side.
|-
|'' 'italicized single quoted' '' ||<nowiki>'' 'italicized single quoted' ''</nowiki> Put a blank space in between the marks for italics and the single quotes you want to appear in the text.
|}
Most of the time on EcoliWiki, you should not need anything besides italics. But now you know how to do the other kinds.

===Subheadings===
One of the reasons you should not need to do much beyond italics is that you don't need '''bold''' or different font sizes to make subheadings. Subheadings at different levels are made by putting different numbers of '=' signs around text on a line, where the string of equals signs are the first thing on the line.

On EcoliWiki pages, the Page Title is a level 1 heading, so start any headings with two = signs, and increase the number for subheadings and sub-subheadings. Headings made in this way are automatically used to generate a table of contents for each page in outline format, like the one for this page:
===Categories===
To add a page to a category, use
:<nowiki>[[Category:CategoryName]]</nowiki>
This will not be rendered on the page, but will add a category link to the bottom of the page. For example, this page is in the Help category. A list of categories can be found at [[Special:Categories]]. Using a new CategoryName creates a new Category. Any given page can belong to multiple categories.

==More Info==
{{Help:Editing}}

Help:Editing:Basics

2008-05-15T20:43:32Z

Clements: /* Internal Links */ Changed example to use "What's new?"page, instead of "Main Page". Main Page isn't used in this wiki.

[[Category:Help]]
[[Category:Editing Help]]
==Be bold!==
Remember,
*Content is more important than formatting. The wiki system allows more experienced proofreaders to clean up your entries if they don't have perfect formatting. Go ahead and put something in the wiki, and then [[Help:Asking for help|ask for help]] if you want someone to clean up the formatting or discuss the content with you. As you gain experience you can help others with their pages.
*You can try out different editing techniques in the [[Sandbox]].
*You can't mess up anything so badly that we can't go back to the previous version. EcoliWiki saves old versions of every page.
*Use the [[Help:Discussion Pages|discussion pages]] or the [http://ecoliwiki.org/phpbb2 bbs] if you're not sure about something.
*Editing is a collaborative effort that should strive for a neutral point of view ([[NPOV]]). We want links to your strong opinions, but these should be placed outside the main EcoliWiki site, where others can't edit them. See [[Help:Trackbacks]].

==Editing Existing Pages==
To edit a page, click either the edit tab on top of the display, or one of the edit links for a specific subsection. This will bring up an editing form.
==Starting New Pages==
There are different ways of creating new pages in EcoliWiki.

===Using the Page Generator===
The EcoliWiki team has created preformatted templates for different types of pages in the wiki, such as Gene Pages, Literature Pages, and Strain Pages. If you want to create a new page that corresponds to one of these types of pages, use the [[http://ecoliwiki.net/dev/index.php/Page_Generator Page_Generator]]. The Page Generator will create a new page that is already formatted with all the boxes ready to fill in.

===Following a Red Link===
Often, you will be reading a page that someone else created that has both Blue and Red text links. Links in red text are to pages that don't exist yet; whoever put in the link thought a page was needed, but didn't get around to creating one. If you click on such a link, you'll get an edit page for that page.

===Create new page from search results===
Before creating a new page, it is useful to see if a similar page already exists. If you search for a page and nothing comes up, EcoliWiki will offer you a chance to create a new page.

===What if I don't like the Page Name after I've saved it?===
Moving a page will rename it and create a redirect to the new name. If you can't move the page, [[Help:Asking for help|ask for help]] from one of our administrators. If you want to have a different Page name link to an existing page, you need to make a redirect. This is done by making a page with the desired nickname, containing ''only'' the following:

#REDIRECT link in internal link style
Where "link in internal link style" is how you would link to the target page with a normal wiki link.

For example: The page for the Protein Data Bank contains information about that database, on a page named [[Protein Data Bank (PDB)]]. We would like to create another page called [[Protein Data Bank]] that redirects the user to [[Protein Data Bank (PDB)]]. We create a new page with the page name Protein Data Bank, and then add the content
#REDIRECT [[Protein Data Bank (PDB)]]
In this case, the redirect page already exists.

Redirects are useful for cases where there are different ways of referring to the same thing. EcoliWiki uses redirects to make finding what you want easier.

==Working in Edit Mode==
[[Image:Edit_buttons.jpg|thumb|framed|right|Edit buttons at bottom of a page in Edit mode]]
Adding or editing is just like any other web form. Click or drag to select an insertion point, and just type away. Just remember '''don't use the TAB key''' to space your text. That will take you out of the editing box.

Note that you can preview your changes before saving them. This is useful, since things don't always come out as expected, but you should also be sure to save at regular intervals. If you don't, your changes could be lost if your session times out, or if someone else starts editing the page while you're working on it. The show changes button shows you what parts of the page you've changed. The Summary box allows you to put in a short description of why you edited the page. This is optional, but it can be useful for when you, or others, come back and edit the page again. For example, if you delete a material that you think is inappropriate for a page, you might want to explain that to keep others from adding it back without thinking about it. Others may disagree with you and add it back anyway, but in that case, you should work out a neutral consensus text with the other editors. Each page in the wiki has a [[Help:Discussion Pages|discussion page]] which is a good place to work things out.

Here's a common unintended effect:
If your text winds up in a box like this, it's because you started it on a line beginning with one or more blank spaces. So don't try to indent your paragraphs!

This is all you need to know to start editing. If you're just adding text or fixing typos, you can just go ahead and skip the rest of this tutorial.

===Adding Links===
One of the most important aspects of making a page useful are the links to other pages. These can be links to other pages in EcoliWiki or links to pages on other websites
====Internal Links====
To insert a link to another page in EcoliWiki, put the name of the page inside a pair of brackets.
:<nowiki>[[What's new?]]</nowiki>
creates
:[[What's new?]]
Note that this is case-sensitive. [[What's New?]], [[what's New?]], and [[what's new?]] all give red links, indicating no pages with those names.
=====Piped Links=====
Often, it is useful to have link to a page using different text than the page name. For example, at the top of this page, there is a sentence that starts with:
<blockquote>Use the [[Help:Discussion Pages|discussion pages]] or...</blockquote>
This actually links to [[Help:Discussion Pages]], not [[discussion pages]]. The link as made using a pipe character (|) between the PageName and the text for the link:
:<nowiki>[[Help:Discussion Pages|discussion pages]]</nowiki>
=====Linking to a Subsection=====
To link to a subsection in the middle of the page, use the # sign after the PageName, followed by a subsection name. For example:
:<nowiki>[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]</nowiki>
gives
:[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]
which links to a subsection on this Help page. Of course, this can be used in a piped link too, as in [[Help:Editing:Basics#Italics, Bold, and Bold Italics|how to make italics]].

=====Linking to Category Indices=====
Pages can be placed into categories, and the index pages for different categories are very useful for finding content. The PageName for a Category index is Category:CategoryName, but making a link as
:<nowiki>[[Category:Help]]</nowiki>
Doesn't link to the Help index, it adds the page to that category. To make a link to an index page, add a colon (:) before the PageName, like this:
:<nowiki>[[:Category:Help]]</nowiki>
to get
:[[:Category:Help]]
Again, you can pipe this to give a link to a [[:Category:Help|list of help pages]].

====External Links====
If you just place a URL in the text, it will be converted to a link:
http://example.com
However, usually you want the linked text to be something other than the raw URL. To do that, put the URL and the link text, separated by a space, inside square brackets like this:
:<nowiki>[http://ecoliwiki.org EcoliWiki home page]</nowiki>
becomes
:[http://ecoliwiki.org EcoliWiki home page]
This external link method will also work for links to other pages inside EcoliWiki. However, the internal link methods described above are preferred, because they allow the system to count how the pages link to each other. For example,
http://ecoliwiki.net/colipedia/index.php/Community_portal does not show up in "What links here" for the Community Portal page
====Interwiki Links====
There are some external sites that we will be linking to so often that it is useful to have shortcuts for them. These are called interwiki links.
===Formatting characters===
====Italics, Bold, and Bold Italics====
One of the most common edits will be to change E. coli to ''E. coli'', or to italicize a gene name. Occasionally, you may want to make '''bold''' text, or '''''bold italic''''' text. Here's how:
{|{{Prettytable}}
|-
|''italics'' ||<nowiki>''italics''</nowiki> Text is surrounded by two single quote (') marks on each side.
|-
|'''bold''' ||<nowiki>'''bold'''</nowiki> Text is surrounded by three single quote (') marks on each side.
|-
|'''''bold italics''''' ||<nowiki>'''''bold italics'''''</nowiki> Text is surrounded by five (three for bold, two for italics) single quote (') marks on each side.
|-
|'' 'italicized single quoted' '' ||<nowiki>'' 'italicized single quoted' ''</nowiki> Put a blank space in between the marks for italics and the single quotes you want to appear in the text.
|}
Most of the time on EcoliWiki, you should not need anything besides italics. But now you know how to do the other kinds.

===Subheadings===
One of the reasons you should not need to do much beyond italics is that you don't need '''bold''' or different font sizes to make subheadings. Subheadings at different levels are made by putting different numbers of '=' signs around text on a line, where the string of equals signs are the first thing on the line.

On EcoliWiki pages, the Page Title is a level 1 heading, so start any headings with two = signs, and increase the number for subheadings and sub-subheadings. Headings made in this way are automatically used to generate a table of contents for each page in outline format, like the one for this page:
===Categories===
To add a page to a category, use
:<nowiki>[[Category:CategoryName]]</nowiki>
This will not be rendered on the page, but will add a category link to the bottom of the page. For example, this page is in the Help category. A list of categories can be found at [[Special:Categories]]. Using a new CategoryName creates a new Category. Any given page can belong to multiple categories.

==More Info==
{{Help:Editing}}

User:Clements

2008-05-05T17:07:10Z

Clements: New page: = Dave Clements = __NOTOC__ I work for the [http://nescent.org/ National Evolutionary Synthesis Center (NESCent)] and since September 2007 I run the [http://gmod.org/GMOD_Help_Desk GMOD ...

= Dave Clements =

__NOTOC__

I work for the [http://nescent.org/ National Evolutionary Synthesis Center (NESCent)] and since September 2007 I run the [http://gmod.org/GMOD_Help_Desk GMOD Help Desk]. I telecommute from the [http://www.uoregon.edu/~pphil/index.html Phillips Lab] in the [http://ceeb.uoregon.edu/ Center for Ecology and Evolutionary Biology (CEEB)] at the [http://uoregon.edu University of Oregon]. See the [http://gmod.org/GMOD_Help_Desk GMOD Help Desk] page for an explanation of what I do for the [http://gmod.org/ GMOD project].

I am also partially funded by and work part time on [[Welcome to EcoliWiki|EcoliWiki]].

See my [http://gmod.org/User:Clements personal page at GMOD] for more on me.

== Contact Details ==

{| class="wikitable"
|-
! E-mail
| [mailto:clements@nescent.org clements@nescent.org]
|-
! Phone
| 1 541 914 6324 (9-5 Pacific time)
|}