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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE chapter 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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<!-- |
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$Id$ |
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8 |
|
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Copyright (C) 2008, 2011 Jari Häkkinen |
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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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13 |
|
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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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18 |
|
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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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23 |
|
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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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<chapter id="features" chunked="0"> |
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<?dbhtml filename="features.html"?> |
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<title>BASE features</title> |
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|
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<para> |
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The BASE application features many components; MIAME compliance, |
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multi-user, data sharing, data access management, array and |
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biomaterial LIMS, multiple array platforms, RNAseq sequencing |
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support, extensibility, configurable plug-ins, annotation |
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customisation, streamlined access to analysis tools, integration |
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of <ulink url='http://www.tm4.org/mev/'>MultiExperiment Viewer |
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(MeV)</ulink>, and more. To support all |
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components the underlying relational database has grown to become |
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very large and complex, especially since BASE itself works with |
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objects posing additional database tables to keep track of objects |
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stored in a relational database. Thus, rather than trying to |
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describe every feature in detail here, we highlight some of the |
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more important features. |
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</para> |
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|
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<sect1 id="features.webinterface"> |
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<title>Web interface</title> |
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|
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<para> |
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The entire system is accessed through a web-interface over the |
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Internet using a standard web browser, such as Firefox, Safari, |
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Opera, or Internet Explorer. Access privileges to a particular |
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BASE installation are managed by personal accounts through the |
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web-interface. A local administrator creates new user accounts |
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with specific roles and access privileges and has an overall |
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managerial responsibility for an individual BASE |
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installation. With exception for the administrator with global |
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data access, individual users have sole access to and control |
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their inputted data. Users have the possibility to share data |
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they own (or have share credentials for) to other users of the |
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same BASE installation. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.datamangement"> |
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<title>Information and annotation management</title> |
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|
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<para> |
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BASE features a biomaterial LIMS tracking biological material |
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from its source to hybridisation/sequencing and ultimately to |
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raw data and analysis. All events throughout sample handling are |
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tracked and information on used and remaining quantities, |
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physical sample locations, quality control information, and |
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sample relations is stored in BASE. Racks or boxes holding |
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biomaterials can be created as BioPlates and plate events are |
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easily performed for extraction or labelling events. Although |
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becoming less commonly used, the array production LIMS of |
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previous BASE versions is retained to support researchers with |
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spotting facilities, e.g., protein array production and BAC |
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array printing that may not be commercially available. |
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</para> |
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|
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<para> |
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Events in biomaterial and array LIMS are annotable with |
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protocols and event dates, and most items can be annotated with |
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customisable annotation types such as floats, integers, dates, |
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and Boolean flags. Change history for biomaterial items is |
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available if configured and can be used to track modifications |
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in the database. Annotations are either free form or from a |
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preset list of values, and can be marked as required for MIAME |
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compliance. The annotation system is searchable and the user can |
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select any annotations to be an experimental factors in analysis |
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whereby it becomes available to analysis plugins and plot-tools. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.sharingandprivacy"> |
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<title>Data sharing and privacy</title> |
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|
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<para> |
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One of the important features of BASE is its capabilities as a |
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local data repository. The repository functionality is amended |
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with data grouping, sharing, and privacy policies. A BASE |
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project is used to group items (biomaterial, raw data, and |
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experiments) into a logical entity, and a BASE experiment is a |
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collection of bioassays, e.g., array data, grouped logically |
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together for further analysis. All items can co-exist in several |
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projects and experiments without any unnecessary copying of |
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information. |
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</para> |
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|
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<para> |
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Data privacy is guarded by the data owner and BASE allows the |
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owner to set data access rules. To this end, each item in BASE |
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is owned by a user enabling him to share data with |
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colleagues. The grouping of data in projects allows the data |
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owner to simply include other users in a project in order to |
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share data. Each item can have different access levels even |
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within a project, and project members can have different |
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privileges. The data access rules are very flexible and can be |
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overwhelming since access levels on almost any item can be |
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individually set. However, using projects, the proper access |
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levels can be set at a single point of interaction. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.directorystructure"> |
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<title>File and directory structure</title> |
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|
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<para> |
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BASE has an integrated file system to provide the possibility |
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for researchers to collect all data files related to a project |
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in one single storage location. Data files are uploaded using a |
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web browser or an ftp client. The file storage is an integral |
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part of a strategy to store all experiment relevant data in |
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BASE, even data types not already supported in |
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analysis. Collecting all data allows future reuse of the data as |
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more data are produced, and new analysis tools becomes |
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available. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.plugininfrastructure"> |
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<title>Plugin and extension infrastructure</title> |
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|
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<para> |
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BASE features a hierarchically organised analysis interface that |
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allows data filtering, normalisation, transformation, and other |
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analyses. Parameters and settings are automatically stored for |
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each step in the analysis. The selection of analysis tools |
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depends on array type and available plug-ins where a wide range |
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of tools are pre-installed with BASE, and optional plug-ins can |
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be downloaded from the <ulink |
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url="https://baseplugins.thep.lu.se">BASE plug-in site |
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</ulink>. BASE capitalise from other software tools, such as |
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MEV, by integrating them into the user interface. Such |
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integration provide streamlined access to analysis modules in |
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external tools. BASE even features a rudimentary manual |
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transform creator that enables researchers to add analysis steps |
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within the hierarchical overview of analysis performed |
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independently of BASE. The transform creator enables storage of |
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result files and parameter information for archival, tracking, |
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and sharing purposes. |
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</para> |
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|
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<para> |
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The analysis of genomics data is continuously evolving with new |
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methods and techniques. To this end BASE provides extensions and |
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plug-in programming interfaces (APIs) to enable straightforward |
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additions of new analysis tools. The use of the APIs is well |
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documented and there are numerous examples on how to create |
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extensions. The MEV and ftp-server integration all utilise the |
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extension mechanism, and the automatically generated overview |
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plots available in the experimental analysis view are also |
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extensions. The plug-in API is used for all data imports and |
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exports, and most analysis tools, providing new developers a lot |
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of example code to examine when they create BASE plug-ins. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.batchdata"> |
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<title>Batch upload and download of data</title> |
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|
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<para> |
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File, annotation, and item upload can be done asynchronously as |
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data are generated or information becomes available. To relieve |
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researchers from the tedious task of entering data one by one a |
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set of batch import were created; the information generated |
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throughout the experimental work is uploaded to BASE in plain |
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tab-separated files. These files are supplied to batch importer |
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plug-ins that parse the files and create items and associations |
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according to the information in the files. The same plug-ins can |
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be used to batch update many items. Similarly, annotating items |
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is done by creating tab-separated files with annotation |
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information, uploading these to BASE, and loading the file |
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content into the database using annotation importers. If needed, |
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annotations are easily updated with the same mechanism. |
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</para> |
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|
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<para> |
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Files uploaded to BASE are stored in the directory structure |
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within BASE and multiple files are easily transferred to BASE |
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either packaged in compressed files with a single upload action, |
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or by using an ftp client supporting transfer of file |
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structures. Similarly, downloading multiple files is |
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straightforward either using an ftp client or by a single click |
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in the BASE web interface. Download of items is done through |
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item listing views enabling users to filter and select what |
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information should be downloaded. |
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</para> |
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|
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</sect1> |
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|
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<sect1 id="features.supportedarrays"> |
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<title>Supported array platforms and raw data formats</title> |
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|
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<para> |
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There are many types of microarrays, techniques, and brands |
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available for researchers; one- or two-channel hybridizations, |
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spotted cDNA/oligo arrays, Affymetrix (GeneChip), Illumina (SNP, |
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DASL, WGEX, microRNA), aCGH, SNP, tiling arrays, and many |
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more. In addition expression data can be derived from sequencing |
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data, i.e., RNASeq. Data is produced in different file formats |
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that must be treated differently depending on type. |
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</para> |
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|
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<para> |
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Many platforms and experimental setups are supported in |
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downstream analysis but some microarray techniques cannot |
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currently be analysed within BASE simply because lack of support |
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in available plug-ins. The problem is resolved by creating new, |
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or extending available, plug-ins that add analysis capabilities |
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of platforms and techniques not readily supported in |
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analysis. Extending analysis capabilities to new technologies is |
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only a matter of local needs and resources. We add support for |
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platforms in use at the Lund University microarray facility and |
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make our tools freely available to the community. |
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</para> |
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|
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<para> |
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For two channel array platforms it is straightforward to |
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customise BASE for a specific array platform, the platform |
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simply needs to be adapted to the (BASE) Generic platform. The |
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adaptation is to create a raw data format definition and to |
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configure raw data importers, or make use of already available |
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raw data formats. However, it is not always possible to make an |
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natural mapping of a platform to the Generic platform. Platforms |
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such as Affymetrix and Illumina platforms cannot naturally be |
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mapped on to the Generic two channel platform. For Affymetrix, |
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BASE comes with a specific Affymetrix platform and Illumina can |
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be supported by customising BASE (go to the <ulink |
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nicklas |
259 |
url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina"> |
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01 Nov 11 |
jari |
260 |
Illumina package</ulink> web site for more information on adding |
5845 |
01 Nov 11 |
jari |
261 |
Illumina support to BASE). |
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01 Nov 11 |
jari |
262 |
</para> |
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01 Nov 11 |
jari |
263 |
|
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01 Nov 11 |
jari |
264 |
<para> |
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27 Aug 08 |
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265 |
How to adapt new array platforms to the Generic platform format |
4421 |
27 Aug 08 |
jari |
266 |
or how to create a new platform type in BASE can be read |
4421 |
27 Aug 08 |
jari |
267 |
elsewhere in this document. Here we list different array |
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01 Nov 11 |
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268 |
platforms used in BASE and also list raw data types supported by |
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01 Nov 11 |
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BASE. However, not all platforms nor raw data types listed below |
5846 |
01 Nov 11 |
jari |
270 |
are available out-of-the box and a BASE administrator must |
5846 |
01 Nov 11 |
jari |
271 |
customise his local BASE installation for their specific |
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27 Aug 08 |
jari |
272 |
need. What comes pre-configured when BASE is installed is |
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27 Aug 08 |
jari |
273 |
indicated in the lists below. |
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27 Aug 08 |
jari |
274 |
</para> |
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27 Aug 08 |
jari |
275 |
|
4421 |
27 Aug 08 |
jari |
276 |
<sect2 id="features.supportedarrays.platforms"> |
4421 |
27 Aug 08 |
jari |
277 |
<title>Vendor specific and custom printing array |
4421 |
27 Aug 08 |
jari |
278 |
platforms</title> |
4421 |
27 Aug 08 |
jari |
279 |
|
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27 Aug 08 |
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280 |
<para> |
4421 |
27 Aug 08 |
jari |
281 |
Not all array platforms listed below are available by |
4421 |
27 Aug 08 |
jari |
282 |
default. The comments to specific platforms explain how to |
4421 |
27 Aug 08 |
jari |
283 |
enable the use of the array platform in BASE. In some cases |
4421 |
27 Aug 08 |
jari |
284 |
there is no confirmed usage of a platform but we believe it |
4421 |
27 Aug 08 |
jari |
285 |
has been tested by anonymous users. |
4421 |
27 Aug 08 |
jari |
286 |
</para> |
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27 Aug 08 |
jari |
287 |
|
4421 |
27 Aug 08 |
jari |
288 |
<variablelist> |
4421 |
27 Aug 08 |
jari |
289 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
290 |
<term>Affymetrix</term> |
4421 |
27 Aug 08 |
jari |
291 |
<listitem> |
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27 Aug 08 |
jari |
292 |
<para> |
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01 Nov 11 |
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293 |
The Affymetrix platform comes pre-configured with a new |
5846 |
01 Nov 11 |
jari |
294 |
BASE installation. Affymetrix platform in this context |
5846 |
01 Nov 11 |
jari |
295 |
are the Affymetrix expression arrays. So far there has |
5846 |
01 Nov 11 |
jari |
296 |
been no reason for expanding the Array platform to other |
5846 |
01 Nov 11 |
jari |
297 |
chip-types. In principle any Affymetrix chip type can be |
5846 |
01 Nov 11 |
jari |
298 |
stored in BASE but current plug-ins will always assume |
5846 |
01 Nov 11 |
jari |
299 |
that expression data is stored and analysed. This can be |
5846 |
01 Nov 11 |
jari |
300 |
resolved by adding variants of the Affymetrix platform |
5846 |
01 Nov 11 |
jari |
301 |
but the Lund BASE team currently has no plans to create |
5846 |
01 Nov 11 |
jari |
302 |
Affymetrix variants. |
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27 Aug 08 |
jari |
303 |
</para> |
4421 |
27 Aug 08 |
jari |
304 |
</listitem> |
4421 |
27 Aug 08 |
jari |
305 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
306 |
|
4421 |
27 Aug 08 |
jari |
307 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
308 |
<term>Agilent</term> |
4421 |
27 Aug 08 |
jari |
309 |
<listitem> |
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27 Aug 08 |
jari |
310 |
<para> |
4421 |
27 Aug 08 |
jari |
311 |
</para> |
4421 |
27 Aug 08 |
jari |
312 |
</listitem> |
4421 |
27 Aug 08 |
jari |
313 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
314 |
|
4421 |
27 Aug 08 |
jari |
315 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
316 |
<term>Custom printing</term> |
4421 |
27 Aug 08 |
jari |
317 |
<listitem> |
4421 |
27 Aug 08 |
jari |
318 |
<para> |
4421 |
27 Aug 08 |
jari |
319 |
The array layout options are endless and imagination is |
4421 |
27 Aug 08 |
jari |
320 |
the only limitation ... almost. BASE can import many |
4421 |
27 Aug 08 |
jari |
321 |
in-house array designs and platforms. The custom arrays |
4421 |
27 Aug 08 |
jari |
322 |
usually fall back on one of the raw data types already |
4421 |
27 Aug 08 |
jari |
323 |
available such as GenePix. |
4421 |
27 Aug 08 |
jari |
324 |
</para> |
4421 |
27 Aug 08 |
jari |
325 |
</listitem> |
4421 |
27 Aug 08 |
jari |
326 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
327 |
|
4421 |
27 Aug 08 |
jari |
328 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
329 |
<term>Illumina</term> |
4421 |
27 Aug 08 |
jari |
330 |
<listitem> |
4421 |
27 Aug 08 |
jari |
331 |
<para> |
5846 |
01 Nov 11 |
jari |
332 |
There are several variants of the Illumina |
5846 |
01 Nov 11 |
jari |
333 |
platform. Using several variants allows BASE to adapt |
5846 |
01 Nov 11 |
jari |
334 |
its handling of different Illumina chip types. Illumina |
5846 |
01 Nov 11 |
jari |
335 |
platform support is not included in a standard BASE |
5846 |
01 Nov 11 |
jari |
336 |
installation but there is a <ulink |
7982 |
14 Jun 21 |
nicklas |
337 |
url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina"> |
5846 |
01 Nov 11 |
jari |
338 |
Illumina package</ulink> available for seamless |
4421 |
27 Aug 08 |
jari |
339 |
integration of the Illumina array platform to BASE. |
4421 |
27 Aug 08 |
jari |
340 |
</para> |
4421 |
27 Aug 08 |
jari |
341 |
</listitem> |
4421 |
27 Aug 08 |
jari |
342 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
343 |
|
4421 |
27 Aug 08 |
jari |
344 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
345 |
<term>ImaGene</term> |
4421 |
27 Aug 08 |
jari |
346 |
<listitem> |
4421 |
27 Aug 08 |
jari |
347 |
<para> |
4421 |
27 Aug 08 |
jari |
348 |
No successful use confirmed but ImaGene raw data is |
4421 |
27 Aug 08 |
jari |
349 |
available in BASE. |
4421 |
27 Aug 08 |
jari |
350 |
</para> |
4421 |
27 Aug 08 |
jari |
351 |
</listitem> |
4421 |
27 Aug 08 |
jari |
352 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
353 |
|
4421 |
27 Aug 08 |
jari |
354 |
<varlistentry> |
5846 |
01 Nov 11 |
jari |
355 |
<term>Sequencing</term> |
5846 |
01 Nov 11 |
jari |
356 |
<listitem> |
5846 |
01 Nov 11 |
jari |
357 |
<para> |
5846 |
01 Nov 11 |
jari |
358 |
Expression data from sequencing experiments. Cufflinks |
5846 |
01 Nov 11 |
jari |
359 |
raw-data type is available for expression values from |
5846 |
01 Nov 11 |
jari |
360 |
sequencing experiments. |
5846 |
01 Nov 11 |
jari |
361 |
</para> |
5846 |
01 Nov 11 |
jari |
362 |
</listitem> |
5846 |
01 Nov 11 |
jari |
363 |
</varlistentry> |
5846 |
01 Nov 11 |
jari |
364 |
|
5846 |
01 Nov 11 |
jari |
365 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
366 |
<term>Unlisted</term> |
4421 |
27 Aug 08 |
jari |
367 |
<listitem> |
4421 |
27 Aug 08 |
jari |
368 |
<para> |
5846 |
01 Nov 11 |
jari |
369 |
In principle any platform generating a matrix of data |
5846 |
01 Nov 11 |
jari |
370 |
can be imported into BASE. Simply utilise the available |
5846 |
01 Nov 11 |
jari |
371 |
raw data formats and data importers. |
4421 |
27 Aug 08 |
jari |
372 |
</para> |
4421 |
27 Aug 08 |
jari |
373 |
</listitem> |
4421 |
27 Aug 08 |
jari |
374 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
375 |
</variablelist> |
4421 |
27 Aug 08 |
jari |
376 |
|
4421 |
27 Aug 08 |
jari |
377 |
</sect2> |
4421 |
27 Aug 08 |
jari |
378 |
|
4421 |
27 Aug 08 |
jari |
379 |
<sect2 id="features.supportedarrays.rawdatatypes"> |
4421 |
27 Aug 08 |
jari |
380 |
<title>Available raw data types</title> |
4421 |
27 Aug 08 |
jari |
381 |
|
4421 |
27 Aug 08 |
jari |
382 |
<para> |
4421 |
27 Aug 08 |
jari |
383 |
Raw data comes in many different formats. These formats are |
4421 |
27 Aug 08 |
jari |
384 |
usually defined by scanner software vendors and BASE must keep |
4421 |
27 Aug 08 |
jari |
385 |
track of the different formats for analysis and plotting. BASE |
5846 |
01 Nov 11 |
jari |
386 |
supports many formats out the box, but some formats need to be |
5846 |
01 Nov 11 |
jari |
387 |
added manually by the BASE administrator (indicated in the |
4421 |
27 Aug 08 |
jari |
388 |
list below). |
4421 |
27 Aug 08 |
jari |
389 |
</para> |
4421 |
27 Aug 08 |
jari |
390 |
|
4421 |
27 Aug 08 |
jari |
391 |
<variablelist> |
4421 |
27 Aug 08 |
jari |
392 |
|
4421 |
27 Aug 08 |
jari |
393 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
394 |
<term>Affymetrix</term> |
4421 |
27 Aug 08 |
jari |
395 |
<listitem> |
4421 |
27 Aug 08 |
jari |
396 |
<para> |
4421 |
27 Aug 08 |
jari |
397 |
</para> |
4421 |
27 Aug 08 |
jari |
398 |
</listitem> |
4421 |
27 Aug 08 |
jari |
399 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
400 |
|
4421 |
27 Aug 08 |
jari |
401 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
402 |
<term>AIDA</term> |
4421 |
27 Aug 08 |
jari |
403 |
<listitem> |
4421 |
27 Aug 08 |
jari |
404 |
<para> |
4421 |
27 Aug 08 |
jari |
405 |
</para> |
4421 |
27 Aug 08 |
jari |
406 |
</listitem> |
4421 |
27 Aug 08 |
jari |
407 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
408 |
|
4421 |
27 Aug 08 |
jari |
409 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
410 |
<term>Agilent</term> |
4421 |
27 Aug 08 |
jari |
411 |
<listitem> |
4421 |
27 Aug 08 |
jari |
412 |
<para> |
4421 |
27 Aug 08 |
jari |
413 |
</para> |
4421 |
27 Aug 08 |
jari |
414 |
</listitem> |
4421 |
27 Aug 08 |
jari |
415 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
416 |
|
4421 |
27 Aug 08 |
jari |
417 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
418 |
<term>BZScan</term> |
4421 |
27 Aug 08 |
jari |
419 |
<listitem> |
4421 |
27 Aug 08 |
jari |
420 |
<para> |
4421 |
27 Aug 08 |
jari |
421 |
</para> |
4421 |
27 Aug 08 |
jari |
422 |
</listitem> |
4421 |
27 Aug 08 |
jari |
423 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
424 |
|
4421 |
27 Aug 08 |
jari |
425 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
426 |
<term>ChipSkipper</term> |
4421 |
27 Aug 08 |
jari |
427 |
<listitem> |
4421 |
27 Aug 08 |
jari |
428 |
<para> |
4421 |
27 Aug 08 |
jari |
429 |
</para> |
4421 |
27 Aug 08 |
jari |
430 |
</listitem> |
4421 |
27 Aug 08 |
jari |
431 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
432 |
|
4421 |
27 Aug 08 |
jari |
433 |
<varlistentry> |
5846 |
01 Nov 11 |
jari |
434 |
<term>Cufflinks</term> |
5846 |
01 Nov 11 |
jari |
435 |
<listitem> |
5846 |
01 Nov 11 |
jari |
436 |
<para> |
5846 |
01 Nov 11 |
jari |
437 |
</para> |
5846 |
01 Nov 11 |
jari |
438 |
</listitem> |
5846 |
01 Nov 11 |
jari |
439 |
</varlistentry> |
5846 |
01 Nov 11 |
jari |
440 |
|
5846 |
01 Nov 11 |
jari |
441 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
442 |
<term>GenePix</term> |
4421 |
27 Aug 08 |
jari |
443 |
<listitem> |
4421 |
27 Aug 08 |
jari |
444 |
<para> |
4421 |
27 Aug 08 |
jari |
445 |
</para> |
4421 |
27 Aug 08 |
jari |
446 |
</listitem> |
4421 |
27 Aug 08 |
jari |
447 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
448 |
|
4421 |
27 Aug 08 |
jari |
449 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
450 |
<term>GeneTAC</term> |
4421 |
27 Aug 08 |
jari |
451 |
<listitem> |
4421 |
27 Aug 08 |
jari |
452 |
<para> |
4421 |
27 Aug 08 |
jari |
453 |
</para> |
4421 |
27 Aug 08 |
jari |
454 |
</listitem> |
4421 |
27 Aug 08 |
jari |
455 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
456 |
|
4421 |
27 Aug 08 |
jari |
457 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
458 |
<term>Illumina</term> |
4421 |
27 Aug 08 |
jari |
459 |
<listitem> |
4421 |
27 Aug 08 |
jari |
460 |
<para> |
4421 |
27 Aug 08 |
jari |
461 |
The Illumina array platform usage is recommended to be |
4421 |
27 Aug 08 |
jari |
462 |
based on the <emphasis>Illumina Bead Summary |
4421 |
27 Aug 08 |
jari |
463 |
(IBS)</emphasis> raw data format below. |
4421 |
27 Aug 08 |
jari |
464 |
</para> |
4421 |
27 Aug 08 |
jari |
465 |
</listitem> |
4421 |
27 Aug 08 |
jari |
466 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
467 |
|
4421 |
27 Aug 08 |
jari |
468 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
469 |
<term>Illumina Bead Summary (IBS)</term> |
4421 |
27 Aug 08 |
jari |
470 |
<listitem> |
4421 |
27 Aug 08 |
jari |
471 |
<para> |
5846 |
01 Nov 11 |
jari |
472 |
Not available in BASE directly but it is added with the |
5846 |
01 Nov 11 |
jari |
473 |
<ulink |
7982 |
14 Jun 21 |
nicklas |
474 |
url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina"> |
4421 |
27 Aug 08 |
jari |
475 |
Illumina plug-in</ulink> that adds Illumina array |
4421 |
27 Aug 08 |
jari |
476 |
platform support to BASE. |
4421 |
27 Aug 08 |
jari |
477 |
</para> |
4421 |
27 Aug 08 |
jari |
478 |
</listitem> |
4421 |
27 Aug 08 |
jari |
479 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
480 |
|
4421 |
27 Aug 08 |
jari |
481 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
482 |
<term>ImaGene</term> |
4421 |
27 Aug 08 |
jari |
483 |
<listitem> |
4421 |
27 Aug 08 |
jari |
484 |
<para> |
4421 |
27 Aug 08 |
jari |
485 |
</para> |
4421 |
27 Aug 08 |
jari |
486 |
</listitem> |
4421 |
27 Aug 08 |
jari |
487 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
488 |
|
4421 |
27 Aug 08 |
jari |
489 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
490 |
<term>QuantArray Biotin</term> |
4421 |
27 Aug 08 |
jari |
491 |
<listitem> |
4421 |
27 Aug 08 |
jari |
492 |
<para> |
4421 |
27 Aug 08 |
jari |
493 |
</para> |
4421 |
27 Aug 08 |
jari |
494 |
</listitem> |
4421 |
27 Aug 08 |
jari |
495 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
496 |
|
4421 |
27 Aug 08 |
jari |
497 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
498 |
<term>QuantArray Cy</term> |
4421 |
27 Aug 08 |
jari |
499 |
<listitem> |
4421 |
27 Aug 08 |
jari |
500 |
<para> |
4421 |
27 Aug 08 |
jari |
501 |
</para> |
4421 |
27 Aug 08 |
jari |
502 |
</listitem> |
4421 |
27 Aug 08 |
jari |
503 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
504 |
|
4421 |
27 Aug 08 |
jari |
505 |
<varlistentry> |
4421 |
27 Aug 08 |
jari |
506 |
<term>SpotFinder</term> |
4421 |
27 Aug 08 |
jari |
507 |
<listitem> |
4421 |
27 Aug 08 |
jari |
508 |
<para> |
4421 |
27 Aug 08 |
jari |
509 |
</para> |
4421 |
27 Aug 08 |
jari |
510 |
</listitem> |
4421 |
27 Aug 08 |
jari |
511 |
</varlistentry> |
4421 |
27 Aug 08 |
jari |
512 |
|
4421 |
27 Aug 08 |
jari |
513 |
</variablelist> |
4421 |
27 Aug 08 |
jari |
514 |
|
4421 |
27 Aug 08 |
jari |
515 |
</sect2> |
4421 |
27 Aug 08 |
jari |
516 |
|
4421 |
27 Aug 08 |
jari |
517 |
</sect1> |
4421 |
27 Aug 08 |
jari |
518 |
|
5846 |
01 Nov 11 |
jari |
519 |
<sect1 id="features.supportedsequencing"> |
5846 |
01 Nov 11 |
jari |
520 |
<title>Supported sequencing applications</title> |
5846 |
01 Nov 11 |
jari |
521 |
|
5846 |
01 Nov 11 |
jari |
522 |
<para> |
5846 |
01 Nov 11 |
jari |
523 |
BASE was originally developed for management and analysis of |
5846 |
01 Nov 11 |
jari |
524 |
array based data. Recent version, starting at version 3, have |
5846 |
01 Nov 11 |
jari |
525 |
been adopted to support sequencing based data. Being a newly |
5846 |
01 Nov 11 |
jari |
526 |
developed feature it is not as mature as the array part of BASE. |
5846 |
01 Nov 11 |
jari |
527 |
</para> |
5846 |
01 Nov 11 |
jari |
528 |
|
5846 |
01 Nov 11 |
jari |
529 |
<para> |
5846 |
01 Nov 11 |
jari |
530 |
For sequencing data in general, BASE can be used for data |
5846 |
01 Nov 11 |
jari |
531 |
management and sharing. BASE currently has extended support for |
5846 |
01 Nov 11 |
jari |
532 |
sequencing applications such as RNAseq where data is transformed |
5846 |
01 Nov 11 |
jari |
533 |
to gene expression measurements. For such applications array |
5846 |
01 Nov 11 |
jari |
534 |
designs can be created based on gene structure defined in <ulink |
5846 |
01 Nov 11 |
jari |
535 |
url='http://en.wikipedia.org/wiki/Gene_transfer_format'>GTF |
5846 |
01 Nov 11 |
jari |
536 |
formatted files</ulink>. For example, GTF files for all RefSeqs |
5846 |
01 Nov 11 |
jari |
537 |
or known genes. |
5846 |
01 Nov 11 |
jari |
538 |
</para> |
5846 |
01 Nov 11 |
jari |
539 |
|
5846 |
01 Nov 11 |
jari |
540 |
</sect1> |
5846 |
01 Nov 11 |
jari |
541 |
|
5845 |
01 Nov 11 |
jari |
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<sect1 id="features.repositoryandstandards"> |
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<title>Repository and standards</title> |
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|
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<para> |
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The Microarray Gene Expression Data Society (MGED) develops and |
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maintains standards for data acquisition, representation, and |
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interchange such as the MIAME guidelines, the MAGE-TAB |
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interchange format, and the MGED Ontology for microarray |
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experiments. BASE does not enforce the use of the MGED standards |
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but support storage of information required by MIAME. BASE has |
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an experiment item overview functionality useful for validating |
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01 Nov 11 |
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information related to experiments. The validation level is user |
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selectable of which the option regarding MIAME compliance is |
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most relevant here. When users or server administrators create |
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annotation types in BASE these annotation values can be marked |
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as required by MIAME and optionally defined to be a list of |
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pre-defined values from a controlled vocabulary. Validation will |
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01 Nov 11 |
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check for inconsistencies and report errors, and give the user |
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an opportunity to fix issues immediately or later. After |
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resolving the issues raised by the validation, data can be |
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exported for submission to public repositories such as |
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ArrayExpress, Gene Expression Omnibus (GEO), and CIBEX. |
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</para> |
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|
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</sect1> |
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|
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</chapter> |