Changeset 5795
- Timestamp:
- Oct 10, 2011, 12:08:12 PM (11 years ago)
- Location:
- trunk
- Files:
-
- 6 added
- 25 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/user/annotations.xml
r5782 r5795 59 59 <emphasis>Protocols</emphasis> 60 60 and 61 <emphasis>Bioassay sets</emphasis> 61 <emphasis>Bioassay sets</emphasis>. 62 62 </para> 63 63 … … 138 138 <para> 139 139 The <guilabel>Edit annotation type</guilabel> window is opened in a 140 pop-up. It contains four differenttabs.140 pop-up. It contains several tabs. 141 141 </para> 142 142 … … 176 176 database. This value can be used by tools that 177 177 need to update annotation types in BASE from external 178 sources. The value does not have to be unique. 178 sources. The value does not have to be unique and is not 179 used by BASE. 179 180 </para> 180 181 </listitem> … … 224 225 <listitem> 225 226 <para> 226 A short textual description of the227 A short textual description 227 228 to clarify the usage. 228 229 </para> … … 405 406 <para> 406 407 If the annotation type has been marked as a 407 <guilabel>Protocol </guilabel> parameter, these settings are408 <guilabel>Protocol parameter</guilabel>, these settings are 408 409 ignored, with one exception. If you wish to view parameter 409 410 values in the list view for a specific item type you must select … … 516 517 <title>Categories</title> 517 518 519 <figure 520 id="annotations.figures.annotationtype.categories"> 521 <title>Annotation type categories</title> 522 <screenshot> 523 <mediaobject> 524 <imageobject> 525 <imagedata 526 fileref="figures/annotationtype_categories.png" format="PNG" /> 527 </imageobject> 528 </mediaobject> 529 </screenshot> 530 </figure> 531 518 532 <helptext external_id="annotationtype.edit.categories" 519 533 title="Categories"> … … 534 548 button to remove the selected categories. 535 549 </para> 536 550 551 <tip> 552 <title>Create categories with the same name as item subtypes</title> 553 <para> 554 If you, for example, have defined multiple subtypes of extracts 555 (see <xref linkend="subtypes" />), 556 it usually so that some annotation types are only intended for 557 one subtype while some other annotation types are only intended 558 for the other subtype. If you create categories with the same name 559 as the item subtypes, BASE will automatically select the corresponding 560 category when annotating an extract with a subtype. This makes the interface 561 cleaner and easier to use since irrelevant annotation types are hidden. 562 Note that it is possible for annotations to be part of more than one 563 category so it is also possible to define annotation types that are 564 intended for all types of extracts by including them in both categories. 565 </para> 566 </tip> 567 537 568 <seeother> 538 569 <other external_id="annotationtype.edit">Properties</other> … … 544 575 </sect1> 545 576 546 <sect1 id="annotations.categories">547 <?dbhtml filename="categories.html" ?>548 <title>Annotation type categories</title>549 550 <para>551 <guilabel>Annotation Type Categories</guilabel>552 allow grouping of related Annotation Types, based on553 users requirements.554 </para>555 556 <para>557 For managing categories go to558 <menuchoice>559 <guimenu>Administrate</guimenu>560 <guimenuitem>Types</guimenuitem>561 <guisubmenu>Annotation Type categories</guisubmenu>562 </menuchoice>.563 </para>564 565 <example id="annotation_types.example.atcategory">566 <title>Annotation category examples</title>567 568 <para>569 <itemizedlist>570 <listitem>571 <para>572 A category <userinput>Hematology Descriptors</userinput>573 could be created to group together annotation types such as574 <userinput>Lymphocyte count</userinput> and575 <userinput>Hematocrite</userinput>576 </para>577 </listitem>578 579 <listitem>580 <para>581 A category <userinput>Plasma Clinical Descriptors</userinput>582 could be created to group together annotation types such as583 <userinput>ALT activity (UI/mL)</userinput> and584 <userinput>LDH activity (UI/mL)</userinput>585 </para>586 </listitem>587 </itemizedlist>588 </para>589 </example>590 591 <tip>592 <para>593 If you use the same name for a category as for an item subtype (see <xref linkend="subtypes" />)594 the annotations in this category will be selected by default when editing an item item595 by that subtype. This can be useful when you have two or more subtypes of the same596 main item type and a different set of annotations that should be used on each subtype.597 For example, <emphasis>Labeled extract</emphasis> and <emphasis>Library</emphasis>598 are subtypes of <emphasis>Extract</emphasis>, which probably have different annotation599 types.600 </para>601 </tip>602 603 </sect1>604 605 577 <sect1 id="annotations.annotating"> 606 578 <?dbhtml filename="annotating.html" ?> -
trunk/doc/src/docbook/user/jobs.xml
r5738 r5795 44 44 </para> 45 45 46 47 <sect1 id="jobs.properties"> 48 <title>Properties</title> 46 <para> 49 47 Click on 50 48 <menuchoice> … … 52 50 <guimenuitem>Jobs</guimenuitem> 53 51 </menuchoice> 54 to list your jobs. 55 <para> 52 to list your jobs. 56 53 Details of a single job is displayed in a pop-up window. This window opens either if you 57 54 click on a job's name from the list page of jobs or when a job configuration is … … 66 63 </para> 67 64 </helptext> 65 66 <figure id="jobs.figures.properties"> 67 <title>Job properties</title> 68 <screenshot> 69 <mediaobject> 70 <imageobject> 71 <imagedata fileref="figures/job_properties.png" format="PNG" /> 72 </imageobject> 73 </mediaobject> 74 </screenshot> 75 </figure> 76 68 77 <helptext external_id="job.view.properties" title="Job properties"> 69 78 <para> … … 115 124 <varlistentry> 116 125 <term> 117 <optional>118 126 <guilabel>Description</guilabel> 119 </optional>120 127 </term> 121 128 <listitem> … … 123 130 A description of the job. Like the name-property it can be set in 124 131 the job configuration. 125 </para>126 </listitem>127 </varlistentry>128 <varlistentry>129 <term>130 <guilabel>Type</guilabel>131 </term>132 <listitem>133 <para>134 The type of job, which is depending on the plug-in that is used. It135 can be one of these five:136 <itemizedlist>137 <listitem>Export</listitem>138 <listitem>Import</listitem>139 <listitem>Analysis</listitem>140 <listitem>Intensity</listitem>141 <listitem>Other</listitem>142 </itemizedlist>143 132 </para> 144 133 </listitem> … … 175 164 <listitem> 176 165 <para> 166 <emphasis>Preparing</emphasis> 167 - The job queue is preparing to executed the job. 168 </para> 169 </listitem> 170 <listitem> 171 <para> 177 172 <emphasis>Executing</emphasis> 178 173 - The job is being executed. … … 191 186 </para> 192 187 </listitem> 193 <listitem> 194 <para> 195 <emphasis>Preparing</emphasis> 196 - The job queue is preparing to executed the job. 197 </para> 198 </listitem> 199 <listitem> 188 c <listitem> 200 189 <para> 201 190 <emphasis>Aborting</emphasis> … … 205 194 </listitem> 206 195 </itemizedlist> 207 </para> 208 </listitem> 209 </varlistentry> 210 <varlistentry> 211 <term> 212 <guilabel>Status message</guilabel> 213 </term> 214 <listitem> 215 <para> 216 A message, given by the plug-in, with more information about the 217 status. 196 197 This field will also display any messages from the plug-in while it 198 is running and the final message after it's completion. 218 199 </para> 219 200 </listitem> … … 344 325 <listitem> 345 326 <para> 346 Retry a failed job with different . This feeture is supported by most but not327 Retry a failed job with different parameters. This feeture is supported by most but not 347 328 all plug-ins. It is very useful when the failure is due to a misconfiguration 348 329 and the job may succeed if it was configured differently. … … 374 355 375 356 </helptext> 376 </sect1>377 357 </chapter> -
trunk/doc/src/docbook/user/platforms.xml
r5783 r5795 37 37 Affymetrix platform (as defined in BASE) uses CEL files for 38 38 raw data and CDF files for array design information. 39 </para>40 41 <para>42 39 The concept of a platform is also tightly coupled to the 43 40 ability to keep data in files instead of importing it to … … 48 45 49 46 <para> 50 BASE comes pre-installed with two platforms; A generic platform 51 and the Affymetrix platform. Other platforms, such as Illumina, 47 BASE comes pre-installed with three platforms. 48 </para> 49 50 <itemizedlist> 51 <listitem> 52 <para> 53 A generic platform that can be used with almost any 54 type of data that can be imported into the database from 55 simple column-based text files. 56 </para> 57 </listitem> 58 59 <listitem> 60 <para> 61 The Affymetrix platform which keep data in CEL and CDF files 62 instead of importing into the database. 63 </para> 64 </listitem> 65 66 <listitem> 67 <para> 68 A sequencing platform which uses GTF files to define array designs 69 and FPKM counts as raw data. 70 </para> 71 </listitem> 72 73 </itemizedlist> 74 75 <para> 76 Other platforms, such as Illumina, 52 77 are available as non-core plug-in packages, see 53 78 <xref linkend="resources.plugins" />. An administrator may … … 60 85 </seeother> 61 86 </helptext> 62 63 64 87 65 88 <para> … … 189 212 <listitem> 190 213 <para> 191 This checkbox will modify the required flag for the192 selected file types.214 Mark this checkbox to indicate that the file is required for 215 the platform. 193 216 </para> 194 217 195 218 <note> 196 219 <para> 197 The requried flag is not a hard requirement. It is only 198 used for generating warnings when validating an experiment. 220 The requried flag is not enforced when creating items. It is 221 used for generating warnings when validating an experiment and 222 can be checked by plug-ins that may need the file in order 223 to run. 199 224 </para> 200 225 </note> 201 226 227 </listitem> 228 </varlistentry> 229 <varlistentry> 230 <term><guilabel>Allow multiple files</guilabel></term> 231 <listitem> 232 <para> 233 Mark this checkbox if it is possible to have more than one 234 file of the given type. In most cases, a single file is used, 235 but some platforms (for example Illumina) may split data into 236 multiple files. 237 </para> 202 238 </listitem> 203 239 </varlistentry> … … 285 321 Make it possible to validate and extract metadata from attached files. 286 322 This is done by extensions. Currently, BASE ships 287 with extensions for CEL and CDF files, but the administrator may have installed323 with extensions for CEL, CDF and GTF files, but the administrator may have installed 288 324 extensions for other file types. See <xref linkend="extensions_developer.fileset_validator"/> 289 325 for more information about creating extensions. -
trunk/doc/src/docbook/user/protocols.xml
r5738 r5795 124 124 <seeother> 125 125 <other external_id="protocol.edit.parameters">Protocol parameters</other> 126 <other external_id="annotations.edit">Annotations</other> 126 127 </seeother> 127 128 </helptext> … … 191 192 <seeother> 192 193 <other external_id="protocol.edit">Edit protocol</other> 193 <other external_id="annotations.edit">Annotations & parameters</other>194 <other external_id="annotations.edit">Annotations</other> 194 195 </seeother> 195 196 196 197 </helptext> 198 199 <para> 200 The <guilabel>Annotations</guilabel> tab allows BASE users to use 201 annotation types to refine protocol description. More about annotating items 202 can be read in <xref linkend="annotations.annotating" />. 203 </para> 197 204 </sect1> 198 205 </chapter> -
trunk/doc/src/docbook/user/reporters.xml
r5738 r5795 27 27 <chapter id="reporters" chunked="0"> 28 28 <title>Reporters</title> 29 <sect1 id="reporters.introduction"> 30 <title>Introduction</title> 29 31 30 <helptext external_id="reporter.view.properties" 32 31 title="About reporters"> … … 45 44 </para> 46 45 </helptext> 47 </sect1>48 46 49 47 <sect1 id="reportertypes"> … … 57 55 and qualification defined during the array design 58 56 specification. 59 </para> 60 </helptext> 61 62 <para> 57 <nohelp> 63 58 You can manage the reporter types by going to 64 59 <menuchoice> … … 67 62 <guisubmenu>Reporter types</guisubmenu> 68 63 </menuchoice>. 64 </nohelp> 69 65 </para> 66 </helptext> 70 67 71 68 <figure … … 122 119 <menuchoice> 123 120 <guimenu>View</guimenu> 124 <guimenuitem>Reporter </guimenuitem>121 <guimenuitem>Reporters</guimenuitem> 125 122 </menuchoice> to view and manage the reporters. 126 123 </para> … … 178 175 </para> 179 176 180 <sect3 id="reporters.properties">181 <title>Reporter properties</title>182 183 177 <figure id="reporters.figures.properties"> 184 178 <title>Reporter properties</title> … … 245 239 </seeother> 246 240 </helptext> 247 </sect3> 248 249 <sect3 id="reporters.extended_properties"> 250 <title>Extended properties</title> 251 241 252 242 <figure id="reporters.figures.extended_properties"> 253 243 <title>Extended reporter properties</title> … … 295 285 </seeother> 296 286 </helptext> 297 </sect3>298 287 </sect2> 299 288 … … 302 291 <title>Deleting reporters</title> 303 292 304 < important>293 <caution> 305 294 <title>Deleted reporters cannot be restored</title> 306 295 <para> … … 313 302 confirm before the reporters are deleted. 314 303 </para> 315 </ important>304 </caution> 316 305 317 306 <para> … … 463 452 should be included in the list. This option is only available 464 453 when creating a new reporter list, not when editing an existing 465 list. 454 list. The default is to create a list with <emphasis>all</emphasis> 455 reporters that are in the current list. 466 456 </para> 467 457 </listitem> … … 490 480 </helptext> 491 481 482 483 <sect2 id="reporterlists.merge"> 484 <title>Merging reporter lists</title> 485 486 <para> 487 It is possible to modify a reporter list by merging it with other reporter 488 lists. Go to the single-item view page for a reporter list. There should be 489 three buttons in the toolbar corresponding to three main merge variants: 490 </para> 491 492 <itemizedlist> 493 <listitem> 494 <para> 495 <guilabel>Union:</guilabel> Add all reporters from 496 the source lists to the destination list. 497 </para> 498 </listitem> 499 <listitem> 500 <para> 501 <guilabel>Intersection:</guilabel> Keep only reporters 502 that are present in all selected lists. 503 </para> 504 </listitem> 505 <listitem> 506 <para> 507 <guilabel>Complement:</guilabel> Keep only reporters that 508 are unique for the destination list. 509 </para> 510 </listitem> 511 </itemizedlist> 512 513 <para> 514 All three buttons open up the same dialog with different default selections. 515 </para> 516 517 <figure 518 id="reporterlists.figures.merge"> 519 <title>Merge reporter lists</title> 520 <screenshot> 521 <mediaobject> 522 <imageobject> 523 <imagedata fileref="figures/reporterlist-merge.png" format="PNG" /> 524 </imageobject> 525 </mediaobject> 526 </screenshot> 527 </figure> 528 529 <helptext external_id="reporterlist.merge" 530 title="Merge reporter lists"> 531 532 533 <variablelist> 534 <varlistentry> 535 <term><guilabel>This list</guilabel></term> 536 <listitem> 537 <para>Shows the name of the current reporter list.</para> 538 </listitem> 539 </varlistentry> 540 <varlistentry> 541 <term><guilabel>What to do</guilabel></term> 542 <listitem> 543 <para> 544 In this drop-down list you can select if you want to 545 <emphasis>add</emphasis>, <emphasis>keep</emphasis> 546 or <emphasis>remove</emphasis> reporters from the 547 selected list based on if a reporter is present in one 548 or all of some other reporter lists (selected below). 549 The image to the right gives an overview what will 550 happen for the currently selected alternatives. The 551 red-colored areas indicate which reporters that are 552 included in the final list. The white-colored areas 553 indicate reporters that doesn't pass the filter and 554 are excluded from the final list. 555 </para> 556 </listitem> 557 </varlistentry> 558 <varlistentry> 559 <term><guilabel>Reporter lists</guilabel></term> 560 <listitem> 561 <para> 562 You will need to select at least one more list 563 to merge with. 564 </para> 565 </listitem> 566 </varlistentry> 567 568 </variablelist> 569 570 571 </helptext> 572 </sect2> 573 574 575 492 576 </sect1> 493 577 </chapter> -
trunk/doc/src/docbook/user/subtypes.xml
r5738 r5795 53 53 This feature can be a real time-saver when used together with project default items 54 54 (see <xref linkend="project_permissions.project.defaults" />). 55 When creating new items (eg a biomaterial) BASE will search among the55 When creating new items (eg. a biomaterial) BASE will search among the 56 56 default items in the active project for protocols, hardware, software, 57 57 etc. and automatically select the best match based on the subtype of the new … … 123 123 the current subtype. The possible options depend on the which the 124 124 main item type is. For example, for <emphasis>biosource</emphasis> 125 there are no other related subtypes, but <emphasis>physicalbioassay</emphasis>126 can have a related p rotocol and hardware subtype as well as a127 related extract subtype.125 there are no other related subtypes, but a <emphasis>derived bioassay</emphasis> 126 can have a related physical bioassay and extract as well as protocol, hardware and 127 software subtypes. 128 128 </para> 129 129 </listitem> … … 157 157 <helptext external_id="itemsubtype.filetypes" title="File types"> 158 158 <para> 159 If the main item type for a subtype is a <emphasis>physical bioassay</emphasis> 160 or <emphasis>derived bioassay</emphasis> (which has support for linking 161 of data files) it is possible to select data file types 159 If the main item type for a subtype is a <emphasis>derived bioassay</emphasis> 160 (which has support for linking of data files) it is possible to select data file types 162 161 <nohelp>(see <xref linkend="platforms.datafiletypes"/>)</nohelp> 163 162 that can be used for items of the given subtype. This is very similar to how … … 176 175 </listitem> 177 176 </varlistentry> 177 <varlistentry> 178 <term><guilabel>Required</guilabel></term> 179 <listitem> 180 <para> 181 Mark this checkbox to indicate that the file is required for 182 all items of the given subtype. 183 </para> 184 185 <note> 186 <para> 187 The requried flag is not enforced when creating items. It is 188 used for generating warnings when validating an experiment and 189 can be checked by plug-ins that may need the file in order 190 to run. 191 </para> 192 </note> 193 194 </listitem> 195 </varlistentry> 196 <varlistentry> 197 <term><guilabel>Allow multiple files</guilabel></term> 198 <listitem> 199 <para> 200 Mark this checkbox if it is possible to have more than one 201 file of the given type. In most cases, a single file is used, 202 but some subtypes, for example Scan, may generate multiple images. 203 </para> 204 </listitem> 205 </varlistentry> 178 206 179 207 <varlistentry> -
trunk/doc/src/docbook/user/wares.xml
r5738 r5795 104 104 105 105 <para> 106 A hardwareis used in BASE to represent the software that is used to106 A software item is used in BASE to represent the software that is used to 107 107 process and analyze data outside of BASE. Analysis that is done inside 108 108 BASE is usually represented as plug-ins.
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