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A
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Step-by-Step
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Guide
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to
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Create
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a
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MAGE-TAB
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Template
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Specific
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to
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RPLA
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Project
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Topic
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:
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caArray
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Installation
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and
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Upgrade
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Release
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:
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caArray
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2.4.0
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Date
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entered
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:
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04/20/2011
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{
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Introduction
Developed by Leandro Hermida, this step-by-step
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guide
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will
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help
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RPLA
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project
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user
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to
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create
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a
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RPLA
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specific
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MAGE-TAB
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template.
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Create
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new
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provider(s)
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Create
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RPLA
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providers
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in
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the
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contact
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table
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as
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for
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other
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array
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providers:
| Code Block |
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}insert into contact (discriminator, provider, name) values ('O', 1,'Zeptosens');{code} |
After
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the
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insert,
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use
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the
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statement
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below
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to
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find
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the
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ID
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for
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the
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contact
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just
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created:
| Code Block |
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}Select ID from contact where name ='Zeptosens';{code} h2. Create new Assay Type Create a new RPLA assay type in the database in the assay_type table: {code} |
Create new Assay Type
Create a new RPLA assay type in the database in the assay_type table:
| Code Block |
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insert into assay_type (name) values ('RPLA');{code}
h2. Check if caArray is a valid Term Source
Since a new technical term: * |
Check if caArray is a valid Term Source
Since a new technical term: reverse_phase_protein_array_features
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would
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be
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inserted
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into
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term_source
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table
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under
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the
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source
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of
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caArray,
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it
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is
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necessary
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to
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check
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if
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the
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source
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of
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*caArray*has
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already
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been
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added
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in
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term_source
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table.
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During
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the
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normal
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caArray
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installation,
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caArray
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should
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have
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been
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added
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to
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the
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term_source
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table
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with
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a
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default
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ID
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=4.
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To
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verify,
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apply
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the
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select
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statement
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below:
| Code Block |
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}select * from term_source where name='caArray'{code} If *caArray* is not a valid source in the |
If caArray is not a valid source in the term_source
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table,
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it
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should
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be
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added
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with
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the
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insert
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statement
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below:
| Code Block |
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}insert into term_source (name, version, url) values ('caArray','2.0','https://array.nci.nih.gov'){code} h2. Add a new terminology term After the source *caArray* has been added, use the SELECT statement above to find the ID for the source *caArray* just created in the *term_source* table. The id will be used in the insert statement below to add the new terminology * |
Add a new terminology term
After the source caArray has been added, use the SELECT statement above to find the ID for the source caArray just created in the term_source table. The id will be used in the insert statement below to add the new terminology reverse_phase_protein_array_features
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to
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the
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term
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table:
| Code Block |
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}insert into term (value, source) values('reverse_phase_protein_array_features', <id of term_source inserted above>);{code} |
Use
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the
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SELECT
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statement
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below
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to
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find
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the
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ID
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for
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the
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term
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just
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created:
| Code Block |
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}SELECT ID from term where value = 'reverse_phase_protein_array_features';{code} |
Use
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this
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ID
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in
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the
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INSERT
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statement
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below:
| Code Block |
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}insert into term_categories (term_id, category_id) values (<id of term inserted above>, 224);{code} h2. Create a dummy Array Design File for RPLA Create |
Create a dummy Array Design File for RPLA
Create MAGE-TAB
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ADF
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dummy
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array
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design
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files
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(.ADF
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files)
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for
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the
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array
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provider
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Zeptosens
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,
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created
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in
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Step
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1.
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The
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dummy
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file
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can
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be
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a
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empty
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file
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with
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a
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simple
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header.
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Upload
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the
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Dummy
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Array
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Design
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file
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in
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caArray
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Upload
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new
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array
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designs
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for
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each
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ADF
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using
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the
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caArray
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web
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application
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(For
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more
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details,
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please
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refer
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to
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).
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The
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new
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file
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will
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have
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the
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final
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status
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of
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"Imported
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no
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Parsed".
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Update
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Array_Design
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Table
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After
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uploading
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dummy
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array
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designs
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into
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caArray,
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update
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their
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array_design
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table
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entries
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in
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the
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database
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to
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lsid_authority
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to
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be
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Zeptosens.com,
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lsid_namespace
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to
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be
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PhysicalArrayDesign.
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This
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SQL
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statement
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will
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work
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only
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after
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the
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array
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design
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file
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is
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added
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to
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caArray.
| Code Block |
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}update array_design set lsid_authority = 'Zeptosens.com', lsid_namespace = 'PhysicalArrayDesign' where provider = <id of contact inserted above>;{code} h2. Create New File Types for RPLA data files The next step is to create new file types for the RPLA data file formats you have. This modification is not at the database level, but file level. The file is: {code} |
Create New File Types for RPLA data files
The next step is to create new file types for the RPLA data file formats you have. This modification is not at the database level, but file level. The file is:
| Code Block |
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caarray_src_2_3_1_1/caarray.war/src/main/java/ApplicationResources.properties{code}
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Following
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is
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an
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example
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the
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RPLA
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data
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file
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in
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text
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format:
| Code Block |
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}experiment.files.filetype.Zeptosens_TXT = Zeptosens TXT{code} |
After
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the
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properties
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is
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edited,
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caArray
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must
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be
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rebuilt
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and
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redeployed.
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Have
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a
...
comment?
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Please
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leave
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your
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comment
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in
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the
...
...
...
...
...
.
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