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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE sect1 PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2007 Peter Johansson, Nicklas Nordborg |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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<sect1 id="experiments_analysis.derivedbioassays"> |
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<?dbhtml filename="derivedbioassays.html" ?> |
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|
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<title>Derived bioassays</title> |
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<para> |
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When you have processed your physical bioassay you can |
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register any information that you have gathered as |
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<guilabel>Derived bioassay</guilabel> items in BASE. |
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The derived bioassay can represent both a physical process, |
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such as scanning a microarray slide, or a software |
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process such as aligning sequence data against a reference |
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genome. It is even possible to register child derived |
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bioassays if there are multiple steps involved that you want |
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to register independently. Each derived bioassay can |
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specify a protocol (with parameters if needed) and the hardware |
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or software item that was used to create it. |
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</para> |
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|
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<para> |
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It is also possible to link one or more files to the derived |
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bioassay. This feature requires that a subtype is selected and |
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that the subtype has been linked with the file types that |
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are useful in that context. For example, the <guilabel>Scan</guilabel> |
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subtype is linked with <guilabel>Image</guilabel> files. |
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See <xref linkend="subtypes" /> for more information. |
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</para> |
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|
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<note> |
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<para> |
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A derived bioassay can only hold data in the form of files. |
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When the data has been processed enough to make it a sensible |
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option (performance-wise) to import into the database a |
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<guilabel>Raw bioassay</guilabel> should be created. |
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</para> |
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</note> |
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|
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<sect2 id="experiments_analysis.derivedbioassays.create"> |
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<title>Create derived bioassays</title> |
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|
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<para> |
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Beside the common way, using the &gbNew; button, a derived bioassay can be created in one of |
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the following ways: |
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</para> |
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<variablelist> |
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<varlistentry> |
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<term>from either physical bioassay list- or single view- page.</term> |
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<listitem> |
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<para> |
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A root derived bioassay is a bioassay that has one or more physical |
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bioassays as parents. Therefore, a natural way to create a derived bioassay |
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is to click on |
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<guiicon> |
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<inlinemediaobject> |
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<imageobject> |
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<imagedata fileref="figures/add.png" format="PNG" /> |
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</imageobject> |
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</inlinemediaobject> |
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</guiicon> |
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in the <guilabel>Derived bioassays</guilabel> column in the list view. There is also a |
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corresponding button, <guibutton>New derived bioassay…</guibutton> |
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in the toolbar both in the list and single-item view. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term>from either derived bioassays list- or single view- page</term> |
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<listitem> |
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<para> |
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A child derived bioassay is a bioassay that has one or more |
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derived bioassays as parents. Click on the |
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<guiicon> |
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<inlinemediaobject> |
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<imageobject> |
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<imagedata fileref="figures/add.png" format="PNG" /> |
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</imageobject> |
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</inlinemediaobject> |
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</guiicon> icon in the <guilabel>Child bioassays</guilabel> column |
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to create a new child derived bioassay. There is also a <guibutton>Merge</guibutton> |
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button in the list view and a <guibutton>New child bioassay</guibutton> |
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button in the single-item view. |
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</para> |
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</listitem> |
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</varlistentry> |
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</variablelist> |
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</sect2> |
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|
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<sect2 id="experiment_analysis.derivedbioassay.properties"> |
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<title>Derived bioassay properties</title> |
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|
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<figure id="experiment_analysis.figures.derivedbioassay"> |
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<title>Derived bioassay properties</title> |
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<screenshot> |
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<mediaobject> |
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<imageobject> |
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<imagedata |
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fileref="figures/derivedbioassay_edit.png" format="PNG" /> |
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</imageobject> |
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</mediaobject> |
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</screenshot> |
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</figure> |
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|
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<helptext external_id="derivedbioassay.edit" title="Edit derived bioassay"> |
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<variablelist> |
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<varlistentry> |
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<term><guilabel>Name</guilabel></term> |
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<listitem> |
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<para> |
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The name of the derived bioassay. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Type</guilabel></term> |
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<listitem> |
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<para> |
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The subtype of the derived bioassay. The list may evolve depending on additions by |
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the server administrator. Selecting the proper subtype is required |
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to be able to attach data files to the bioassay. It will also help BASE |
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to automatically guess the most likely subtype when creating child bioassays. |
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<nohelp> |
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See <xref linkend="subtypes" /> for more information. |
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</nohelp> |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Parent type</guilabel></term> |
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<listitem> |
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<para> |
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Select if the parent items should be physical or derived bioassays. |
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This option is only available when creating new derived bioassays. |
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Once created it is not possible to change the parent type. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Physical bioassays/parents</guilabel></term> |
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<listitem> |
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<para> |
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Use the <guibutton>Add bioassays</guibutton> and <guibutton>Remove</guibutton> buttons |
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to add or remove parent items. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Extract</guilabel></term> |
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<listitem> |
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<para> |
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Select the extract that this derived bioassay is linked with. The <guibutton>Select</guibutton> |
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button opens a selection list that is pre-filtered with all extracts that are |
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found on the parent physical bioassays including all parent extracts. |
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Do not select an extract if the derived bioassay represents more than |
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one extract at this stage. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Protocol</guilabel></term> |
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<listitem> |
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<para> |
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The protocol used in the process that created this derived bioassay (optional). |
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Parameters may be registered as part of the protocol. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Hardware</guilabel></term> |
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<listitem> |
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<para> |
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The machine used in the process that created this derived bioassay (optional). |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Software</guilabel></term> |
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<listitem> |
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<para> |
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The software used in the process that created this derived bioassay (optional). |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Description</guilabel></term> |
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<listitem> |
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<para> |
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A decription of the derived bioassay (optional). |
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</para> |
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</listitem> |
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</varlistentry> |
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</variablelist> |
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|
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<seeother> |
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<other external_id="datafiles.edit">Data files</other> |
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<other external_id="annotations.edit">Annotations</other> |
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<other external_id="annotations.edit.inerited">Inherit annotations</other> |
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</seeother> |
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|
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</helptext> |
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|
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<para> |
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The <guilabel>Data files</guilabel> tab allows BASE users to select |
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files that contains data for the derived bioassay. |
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Read more about this in <xref linkend="platforms.selectfiles" />. |
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</para> |
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|
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<para> |
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The <guilabel>Annotations</guilabel> tab allows BASE users to use |
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annotation types to refine bioassay description. More about annotating items |
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can be read in <xref linkend="annotations.annotating" /> |
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</para> |
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|
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<para> |
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This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
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that are inherited from the bioassay's parents. Information about working with inherited |
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annotations can be found in <xref linkend="annotations.inheriting" />. |
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</para> |
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|
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</sect2> |
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|
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|
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</sect1> |