Main Page

<a name="_Toc127331825">Heading 1</a>

Format for body text: <st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place>

Format for headings (examples of each follow):

• * Heading 1
• * Heading 2
• * Heading 3

<a name="_Toc127331826"></a><a name="_Installing_GenePattern"></a>Heading 2

<st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place> for body text. Body text When you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for either local or distributed configurations.

<a name="_Toc127331827"></a><a name="_Starting_the_GenePattern_Java Clien"></a><a name="_Exiting_from_GenePattern"></a>Heading 3

<st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place> for body text.

Heading 4

Rarely used, but should be supported.

<a name="_Toc127331828">Bulleted and Numbered Lists</a>

For bulleted lists, use

* List Bullet

* List Bullet<br><br>List Continue

** List Bullet 2

** List Bullet 2<br><br>List Continue 2

* List Bullet

For numbered lists, use:

1.      List number.

2.      List number.

List Continue

1.      List number 2

2.      List number 2

List Continue 2

3.      List number.

1.      List number 2.

2.      List number 2.

4.      List number.

Numbered and bulleted lists can be mixed:

1.      List number:

·        List Bullet 2

List Continue 2

·        List Bullet 2

List Continue 2

2.      List number.

1.      List number 2

2.      List number 2

List Continue 2

3.      List number.

<a name="_Toc127331829"></a><a name="_Getting_Help"></a>Text Formats

Within paragraph text, we use a number of character formats:

·        Hyperlinks: hyperlink

·         Code and file names: br_code<o:p></o:p>

·        For GUI items, like menus and buttons: br_GUI<o:p></o:p>

·        For menus, we use angle brackets, which need to be preserved: File>Open.

·        For variables (this looks the same as GUI, but might in the future): br_variable<o:p></o:p>

·        For various reasons, most formats can be bold. So bold needs to be preserved.

Normal formats: <st1:city w:st="on"><st1:place w:st="on">Normal</st1:place></st1:city>, br_code, br_GUI, br_variable<o:p></o:p>

Bold formats: <st1:city w:st="on"><st1:place w:st="on">Normal</st1:place></st1:city>, br_code, br_GUI, br_variable<o:p></o:p>

<a name="_Toc127331830"></a><a name="_Working_with_Projects"></a>Header and Footer

The headers and footers would normally come over to html, but just for completeness, those formats would be

·        Header: header text

·        Footer: footer text<o:p></o:p>

<a name="_Toc127331831">Tables and Graphics</a>

Tables need to come over cleanly. It’s hard to capture all formats, but here’s a basic table:

<tbody> </tbody>

Column Header<o:p></o:p>	Column Header<o:p></o:p>
Blah, blah, blah. ·        Bulleted stuff, stuff, stuff. ·        Stuff, stuff, stuff.	Blah, blah, blah. 1.      Numbered stuff, stuff, stuff. 2.      Stuff, stuff, stuff.
Blah, blah, blah.	Blah, blah, blah.

<o:p> </o:p>

In Word, graphics are linked in files. They also need to come over:

<img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1025" />

In rare cases, graphics appear in tables. Here’s an example:

<tbody> </tbody>

<img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1026" />	Expression dataset (res)
<img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image002.gif" v:shapes="_x0000_i1027" />	Expression dataset (gct)
<img width="18" height="18" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image003.gif" v:shapes="_x0000_i1028" />	Expression dataset (pcl)

<a name="_Toc127331832">Content</a>

The introduction to each section that has subsections, should provide hyperlinks to the subsections.

This section describes how to work with project directories in GenePattern:

·        <a href="#_Opening_a_Project_Directory">Projects Pane</a>

·        <a href="#_Opening_a_Project_Directory_1">Opening a Project Directory</a>

<a name="_Toc127331833"></a><a name="_Opening_a_Project_Directory"></a><a name="_Projects_Pane"></a>Projects Pane

Blah, blah, blah.

<a name="_Toc127331834"></a><a name="_Opening_a_Project_Directory_1"></a>Opening a Project Directory

Blah, blah, blah.