http://wiki.biouml.org/index.php?title=Workflow&feed=atom&action=historyWorkflow - Revision history2024-03-29T00:41:26ZRevision history for this page on the wikiMediaWiki 1.20.3http://wiki.biouml.org/index.php?title=Workflow&diff=5482&oldid=prevYvkondrat@mail.ru at 09:54, 3 December 20132013-12-03T09:54:29Z<p></p>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Step 3.''' '''Joining elements''' on the diagram is done by clicking on the arrow symbol in the toolbar - a new window '''Create new edge''' will pop up. By clicking on the '''Table''' element in the workspace you select it as the '''Input node''' for this edge. Similarly, you click on the <del class="diffchange diffchange-inline">left table symbol </del>in the '''Filter table''' element to select it as the '''Output node''' of this new edge. After pressing '''OK''' a new connection (edge) appears.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Step 3.''' '''Joining elements''' on the diagram is done by clicking on the arrow symbol in the toolbar - a new window '''Create new edge''' will pop up. By clicking on the '''Table''' element in the workspace you select it as the '''Input node''' for this edge. Similarly, you click on the <ins class="diffchange diffchange-inline">input path (port) </ins>in the '''Filter table''' element to select it as the '''Output node''' of this new edge. After pressing '''OK''' a new connection (edge) appears.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram adding output table.png|thumb|Composing a workflow diagram - Step 4: adding an output table (A) and joining it to the method element (B)]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram adding output table.png|thumb|Composing a workflow diagram - Step 4: adding an output table (A) and joining it to the method element (B)]]</div></td></tr>
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</table>Yvkondrat@mail.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=4887&oldid=prevLan@dote.ru: Lan@dote.ru moved page Workflows to Workflow: Plural to singular2013-07-03T09:33:31Z<p>Lan@dote.ru moved page <a href="/index.php/Workflows" class="mw-redirect" title="Workflows">Workflows</a> to <a href="/index.php/Workflow" title="Workflow">Workflow</a>: Plural to singular</p>
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</tr></table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=4404&oldid=prevLan@dote.ru: +diagram type info and links2013-06-14T08:41:02Z<p>+diagram type info and links</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [[wikipedia:Bioinformatics workflow management system|workflow management systems]] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [[wikipedia:Graph (mathematics)#Directed graph|graph]], where each [[wikipedia:Vertex (graph theory)|node]] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [[wikipedia:Bioinformatics workflow management system|workflow management systems]] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [[wikipedia:Graph (mathematics)#Directed graph|graph]], where each [[wikipedia:Vertex (graph theory)|node]] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>BioUML provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[</ins>BioUML<ins class="diffchange diffchange-inline">]] </ins>provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In BioUML the workflow is a special {{Type link|diagram}} type, so you can edit it using the [[diagram document]]</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Pre-defined workflows==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Pre-defined workflows==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== See also ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== See also ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[:Category:Workflows|List of workflows]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[:Category:Workflows|List of workflows]]</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:Diagram types]]</ins></div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=3784&oldid=prevLan@dote.ru: wikipedia: namespace used2013-05-17T10:37:32Z<p>wikipedia: namespace used</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram script params.png|thumb|left|The dialog box of a new script]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram script params.png|thumb|left|The dialog box of a new script]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/</del>JavaScript JavaScript], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:</ins>JavaScript<ins class="diffchange diffchange-inline">|</ins>JavaScript<ins class="diffchange diffchange-inline">]</ins>], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into <code>$["…"]</code> otherwise. For example, the variable “TableColumn” can be accessed from a script either by name <code>TableColumn</code> or by <code>$["TableColumn"]</code>, but “Table column N1” should be accessed as <code>$["Table column N1"]</code>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into <code>$["…"]</code> otherwise. For example, the variable “TableColumn” can be accessed from a script either by name <code>TableColumn</code> or by <code>$["TableColumn"]</code>, but “Table column N1” should be accessed as <code>$["Table column N1"]</code>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>''Example 2. Run [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/Gene_Ontology </del>GO] classification for all tables in a folder''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>''Example 2. Run [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:Gene Ontology|</ins>GO<ins class="diffchange diffchange-inline">]</ins>] classification for all tables in a folder''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This workflow (see the figure) contains three input elements: '''InputFolder''', where one or more Tables should be placed; '''ResultFolder''' that will be created by the method <span class="plainlinks">[http://wiki.biouml.org/index.php/Create_folder_(analysis) '''Create folder''']</span>, and the data element '''Species''', required for table conversion and functional classification.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This workflow (see the figure) contains three input elements: '''InputFolder''', where one or more Tables should be placed; '''ResultFolder''' that will be created by the method <span class="plainlinks">[http://wiki.biouml.org/index.php/Create_folder_(analysis) '''Create folder''']</span>, and the data element '''Species''', required for table conversion and functional classification.</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=3783&oldid=prevLan@dote.ru: wikipedia: namespace used2013-05-17T10:35:58Z<p>wikipedia: namespace used</p>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:Bioinformatics workflow management system|</ins>workflow management systems<ins class="diffchange diffchange-inline">]</ins>] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:Graph </ins>(mathematics)#<ins class="diffchange diffchange-inline">Directed graph|</ins>graph<ins class="diffchange diffchange-inline">]</ins>], where each [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:Vertex </ins>(<ins class="diffchange diffchange-inline">graph theory</ins>)<ins class="diffchange diffchange-inline">|</ins>node<ins class="diffchange diffchange-inline">]</ins>] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/Bioinformatics_workflow_management_system </del>workflow management systems] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/Graph_</del>(mathematics)#<del class="diffchange diffchange-inline">Directed_graph </del>graph], where each [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/Vertex_</del>(<del class="diffchange diffchange-inline">graph_theory</del>) node] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes.</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=2081&oldid=prevLan@dote.ru: On variable editing /* Cycles and scripts */2013-05-03T13:15:17Z<p>On variable editing - <span dir="auto"><span class="autocomment">Cycles and scripts</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [http://en.wikipedia.org/wiki/JavaScript JavaScript], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [http://en.wikipedia.org/wiki/JavaScript JavaScript], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into <code>$["…"]</code> otherwise. For example, the variable “TableColumn” can be accessed from a script either by name <code>TableColumn</code> or by <code>$["TableColumn"]</code>, but “Table column N1” should be <del class="diffchange diffchange-inline">called </del>as <code>$["Table column N1"]</code>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into <code>$["…"]</code> otherwise. For example, the variable “TableColumn” can be accessed from a script either by name <code>TableColumn</code> or by <code>$["TableColumn"]</code>, but “Table column N1” should be <ins class="diffchange diffchange-inline">accessed </ins>as <code>$["Table column N1"]</code>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">It's also possible to change the workflow variable from the script. To achieve this you should perform the following steps:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"># Create an arrow which starts from the script workflow element and ends in variable node you want to change. Only variables connected with such arrows can be written.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"># Use <code>$["&lt;VariableName&gt;"] = &lt;new_value&gt;</code> in the script. Implicit type conversion may be performed if necessary.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Example 1. Print column names''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Example 1. Print column names''</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=2080&oldid=prevLan@dote.ru: <code> sections /* Cycles and scripts */2013-05-03T13:09:07Z<p><code> sections - <span dir="auto"><span class="autocomment">Cycles and scripts</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [http://en.wikipedia.org/wiki/JavaScript JavaScript], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''script''' workflow element represents a code written in [http://en.wikipedia.org/wiki/JavaScript JavaScript], which can be executed during the workflow run. To add a script user should press the '''analysis-script''' toolbox icon, click on the proper place in the workflow diagram area and type JavaScript code in the '''Script source''' field.</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into $[<del class="diffchange diffchange-inline">“…”</del>] otherwise. For example, the variable “TableColumn” can be accessed from a script by name TableColumn, but “Table column N1” should be called as $[<del class="diffchange diffchange-inline">“Table </del>column <del class="diffchange diffchange-inline">N1”</del>].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>All variables defined in a workflow (green and orange boxes) are available inside the script as JavaScript variables. If the name doesn’t contain spaces, it can be used as it is, the name should be put into <ins class="diffchange diffchange-inline"><code></ins>$[<ins class="diffchange diffchange-inline">"…"</ins>]<ins class="diffchange diffchange-inline"></code> </ins>otherwise. For example, the variable “TableColumn” can be accessed from a script <ins class="diffchange diffchange-inline">either </ins>by name <ins class="diffchange diffchange-inline"><code></ins>TableColumn<ins class="diffchange diffchange-inline"></code> or by <code>$["TableColumn"]</code></ins>, but “Table column N1” should be called as <ins class="diffchange diffchange-inline"><code></ins>$[<ins class="diffchange diffchange-inline">"Table </ins>column <ins class="diffchange diffchange-inline">N1"</ins>]<ins class="diffchange diffchange-inline"></code></ins>.</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== See also ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== See also ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[:Category:Workflows|List of workflows]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[:Category:Workflows|List of workflows]]</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=2014&oldid=prevStan.lo@dote.ru: /* Complex workflows */2013-04-26T08:13:57Z<p><span dir="auto"><span class="autocomment">Complex workflows</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram more complex.png|thumb|An example workflow diagram with additional steps]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram more complex.png|thumb|An example workflow diagram with additional steps]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>More complex workflows are created by adding next workflow steps and by connecting them through a common data element. As shown in the figure, the output element '''Table filtered''' of the first step is used as the input element of the second step of the workflow <span class="plainlinks">[http://wiki.biouml.org/index.php/Regulator_search_(analysis) '''Regulator search''']</span>. You can also see that a new input parameter '''Species''' has been added, which appears now among the workflow parameters upon starting the workflow. With this, you can select a taxonomic species (presently human, mouse or rat) for the table you are going to run through the workflow.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>More complex workflows are created by adding next workflow steps and by connecting them through a common data element. As shown in the figure, the output element '''Table filtered''' of the first step is used as the input element of the second step of the workflow <span class="plainlinks">[http://wiki.biouml.org/index.php/Regulator_search_(analysis) '''Regulator search''']</span>. You can also see that a new input parameter '''Species''' has been added, which appears now among the workflow parameters upon starting the workflow. With this, you can select a taxonomic species (presently human, mouse or rat) for the table you are going to run through the workflow.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[File:research diagram.png|thumb|Example of a research diagram]]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><div id="research diagram"></div></ins></div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">'''Note:''' During execution of a workflow a “research diagram” is saved (you can specify the name of this diagram before starting of the workflow). </del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[File:research diagram.png|thumb|left|Example of a research diagram]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">The research diagram contains the history of the workflow execution with the names of all input and output files. It also contains all the links to these tables, so that you can easily open them by clicking on the respective element in the diagram.</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Note:''' During execution of a workflow a “research diagram” is saved (you can specify the name of this diagram before starting of the workflow). </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The research diagram contains the history of the workflow execution with the names of all input and output files. It also contains all the links to these tables, so that you can easily open them by clicking on the respective element in the diagram.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Cycles and scripts===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Cycles and scripts===</div></td></tr>
</table>Stan.lo@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=2000&oldid=prevStan.lo@dote.ru at 06:17, 25 April 20132013-04-25T06:17:53Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram more complex.png|thumb|An example workflow diagram with additional steps]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram more complex.png|thumb|An example workflow diagram with additional steps]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>More complex workflows are created by adding next workflow steps and by connecting them through a common data element. As shown in the figure, the output element '''Table filtered''' of the first step is used as the input element of the second step of the workflow '''Regulator search'''. You can also see that a new input parameter '''Species''' has been added, which appears now among the workflow parameters upon starting the workflow. With this, you can select a taxonomic species (presently human, mouse or rat) for the table you are going to run through the workflow.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>More complex workflows are created by adding next workflow steps and by connecting them through a common data element. As shown in the figure, the output element '''Table filtered''' of the first step is used as the input element of the second step of the workflow <ins class="diffchange diffchange-inline"><span class="plainlinks">[http://wiki.biouml.org/index.php/Regulator_search_(analysis) </ins>'''Regulator search'''<ins class="diffchange diffchange-inline">]</span></ins>. You can also see that a new input parameter '''Species''' has been added, which appears now among the workflow parameters upon starting the workflow. With this, you can select a taxonomic species (presently human, mouse or rat) for the table you are going to run through the workflow.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Note:''' During execution of a workflow a “research diagram” is saved (you can specify the name of this diagram before starting of the workflow).  </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Note:''' During execution of a workflow a “research diagram” is saved (you can specify the name of this diagram before starting of the workflow).  </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Example 2. Run [http://en.wikipedia.org/wiki/Gene_Ontology GO] classification for all tables in a folder''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Example 2. Run [http://en.wikipedia.org/wiki/Gene_Ontology GO] classification for all tables in a folder''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This workflow (see the figure) contains three input elements: '''InputFolder''', where one or more Tables should be placed; '''ResultFolder''' that will be created by the method '''Create folder''', and the data element '''Species''', required for table conversion and functional classification.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This workflow (see the figure) contains three input elements: '''InputFolder''', where one or more Tables should be placed; '''ResultFolder''' that will be created by the method <ins class="diffchange diffchange-inline"><span class="plainlinks">[http://wiki.biouml.org/index.php/Create_folder_(analysis) </ins>'''Create folder'''<ins class="diffchange diffchange-inline">]</span></ins>, and the data element '''Species''', required for table conversion and functional classification.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram GO classification.png|thumb|A workflow diagram to GO classify all tables in a folder]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram GO classification.png|thumb|A workflow diagram to GO classify all tables in a folder]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Expression: $InputFolder$</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Expression: $InputFolder$</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>   </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Here, the cycle variable named '''Table''' will adopt the names of the tables in the InputFolder. Then it goes to the method '''Convert table''', and identifiers are converted to Ensembl genes, according to the analysis settings below:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Here, the cycle variable named '''Table''' will adopt the names of the tables in the InputFolder. Then it goes to the method <ins class="diffchange diffchange-inline"><span class="plainlinks">[http://wiki.biouml.org/index.php/Convert_table_(analysis) </ins>'''Convert table'''<ins class="diffchange diffchange-inline">]</span></ins>, and identifiers are converted to Ensembl genes, according to the analysis settings below:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input type: (Auto)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input type: (Auto)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Output type: Genes:Ensemble</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Output type: Genes:Ensemble</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The conversion result is taken as the input set for the '''Functional classification''' analysis:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The conversion result is taken as the input set for the <ins class="diffchange diffchange-inline"><span class="plainlinks">[http://wiki.biouml.org/index.php/Functional_classification_(analysis) </ins>'''Functional classification'''<ins class="diffchange diffchange-inline">]</span> </ins>analysis:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Source data set: <same as the output table at the previous step></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Source data set: <same as the output table at the previous step></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Species: Human (Homo sapiens)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Species: Human (Homo sapiens)</div></td></tr>
</table>Stan.lo@dote.ruhttp://wiki.biouml.org/index.php?title=Workflow&diff=1999&oldid=prevStan.lo@dote.ru: /* Six steps to compose a simple workflow */2013-04-25T06:06:47Z<p><span dir="auto"><span class="autocomment">Six steps to compose a simple workflow</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Suppose you have specified the name and directory for your new workflow and its tab is active in the workspace,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Suppose you have specified the name and directory for your new workflow and its tab is active in the workspace,</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram adding input table.png|thumb|Composing a workflow diagram - Step 2: adding an input table]]  </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Editing workflow diagram adding input table.png|thumb|Composing a workflow diagram - Step 2: adding an input table]]  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''the first step''' is to '''add the analysis function''' to the workflow diagram. You can either drag and drop the '''Filter table''' method from the subdirectory '''Methods/Data''' in the '''Analyses''' tab of the navigation pane, or add the analysis-method item from the toolbox and choose '''Data/Filter table''' from the drop-down list of the '''Create new node''' dialog box. The item will appear on the diagram as a light blue rectangle labelled "Filter table".</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''the first step''' is to '''add the analysis function''' to the workflow diagram. You can either drag and drop the <ins class="diffchange diffchange-inline"><span class="plainlinks">[http://wiki.biouml.org/index.php/Filter_table_(analysis) </ins>'''Filter table'''<ins class="diffchange diffchange-inline">]</span> </ins>method from the subdirectory '''Methods/Data''' in the '''Analyses''' tab of the navigation pane, or add the analysis-method item from the toolbox and choose '''Data/Filter table''' from the drop-down list of the '''Create new node''' dialog box. The item will appear on the diagram as a light blue rectangle labelled "Filter table".</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Step 6.''' The workflow is now ready to be executed. To '''start the workflow''' please click on the '''Run workflow''' button ([[File:Run workflow icon.png|caption]]) in the toolbar of the operations field.   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Step 6.''' The workflow is now ready to be executed. To '''start the workflow''' please click on the '''Run workflow''' button ([[File:Run workflow icon.png|caption]]) in the toolbar of the operations field.   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the pop-up menu '''Workflow parameters''' you are to specify the input table. Navigate to the folder with your tables and select a table which has a column “Score” and press OK. The workflow will be executed and a new table with a new name and the appendix “filtered” will be created in the same folder as the input table.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the pop-up menu '''Workflow parameters''' you are to specify the input table. Navigate to the folder with your tables and select a table which has a column “Score” and press OK. The workflow will be executed and a new table with a new name and the appendix “filtered” will be created in the same folder as the input table.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Complex workflows===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Complex workflows===</div></td></tr>
</table>Stan.lo@dote.ru