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Release Notes
=============
...
#Product:#
...
caArray
...
#Version:#
...
2.4.0.2
...
#Date:#
...
February
...
2011
...
Contents
...
--------
...
1.
...
Introduction
...
2.
...
Release
...
History
...
3.
...
Anticipated
...
Releases
...
4.
...
Features
...
and
...
Defects
...
Addressed
...
in
...
this
...
Release
...
5.
...
Known
...
Issues/Defects
...
6.
...
Bug
...
Reports,
...
Feature
...
Requests
...
and
...
Support
...
7.
...
Documentation
...
and
...
Files
...
8.
...
NCICB
...
Web
...
Pages
...
9.
...
Getting
...
Started
...
with
...
the
...
new
...
API
...
Introduction
...
---------------------------
...
caArray
...
is
...
an
...
open-source,
...
web
...
and
...
programmatically
...
accessible
...
array
...
data
...
management
...
system.
...
caArray
...
guides
...
the
...
annotation
...
and
...
exchange
...
of
...
array
...
data
...
using
...
a
...
federated
...
model
...
of
...
local
...
installations
...
whose
...
results
...
are
...
shareable
...
across
...
the
...
cancer
...
Biomedical
...
Informatics
...
Grid
...
(caBIG).
...
caArray
...
furthers
...
translational
...
cancer
...
research
...
through
...
acquisition,
...
dissemination
...
and
...
aggregation
...
of
...
semantically
...
interoperable
...
array
...
data
...
to
...
support
...
subsequent
...
analysis
...
by
...
tools
...
and
...
services
...
on
...
and
...
off
...
the
...
Grid.
...
As
...
array
...
technology
...
advances
...
and
...
matures,
...
caArray
...
will
...
extend
...
its
...
logical
...
library
...
of
...
assay
...
management.
...
...
Release
...
History
...
------------------------
...
- caArray v2.4.0.2
...
- – February 2011
- caArray v2.4.0.1
...
- – January 2011
- caArray v2.4.0
...
- – September
...
- 2010
- caArray v2.3.1
...
- – February 2010
- caArray v2.3.0.1
...
- – November 2009
- caArray v2.2.1
...
- – May 2009
- caArray v2.2.0
...
- – January 2009
- caArray v2.1.1
...
- – October 2008
- caArray v2.1.0
...
- – August 2008
- caArray v2.0.2
...
- – May 2008
- caArray v2.0.1
...
- – April 2008
- caArray v2.0.0
...
- – February 2008
Anticipated Releases
------------------------
...
- caArray v2.5.0
...
- – Q2 2011 (new
...
- features)
...
Features
...
and
...
Defects
...
Addressed
...
in
...
this
...
Release
...
-----------------------------------------------
...
This
...
release
...
represents
...
a
...
feature
...
release
...
of
...
the
...
caArray
...
2
...
software.
...
Highlights
...
of
...
caArray
...
2.4.0
...
are:
...
- Parsers
...
- for
...
- several
...
- new
...
- data
...
- types:
...
- Agilent
...
- raw
...
- TXT
...
- for
...
- aCGH,
...
- expression
...
- and
...
- miRNA
...
- assays.
...
- Agilent
...
- GEML/xml
...
- array
...
- designs
...
- Nimblegen
...
- pair
...
- Report
...
- TXT
...
- (raw
...
- and
...
- normalized)
...
- Nimblegen
...
- NDF
...
- array
...
- designs
...
- Illumina
...
- Sample
...
- Probe
...
- Profile
...
- TXT
...
- Illumina
...
- genotyping
...
- processed
...
- data
...
- matrix
...
- TXT
...
- Illumina
...
- BGX/TXT
...
- array
...
- designs
...
- Affymetrix
...
- CEL
...
- and
...
- CHP
...
- in
...
- AGCC/Calvin
...
- formats
...
- in
...
- addition
...
- to
...
- the
...
- old
...
- GCOS
...
- formats
...
- Affymetrix
...
- CNCHP
...
- copy
...
- number
...
- data
...
- (CN4
...
- and
...
- CN5)
...
- Copy
...
- Number
...
- data
...
- in
...
- a
...
- prescribed
...
- MAGE-TAB
...
- Data
...
- Matrix
...
- format.
...
For
...
- details
...
- about
...
- the
...
- parsing
...
- of
...
- these
...
- files,
...
- please
...
- refer
...
- to
...
- the
...
- chapter
...
- "Importing
...
- Data
...
- Files"
...
in
...
- the
...
- caArray
...
- User's
...
- Guide.
...
- If
...
- there
...
- are
...
- array
...
- design
...
- files
...
- or
...
- data
...
- files
...
- already
...
- in
...
- the
...
- system
...
- that
...
- are
...
- "imported
...
- not
...
- parsed",
...
- and
...
if
...
- there
...
- are
...
- new
...
- parsers
...
- available
...
- that
...
- allow
...
- those
...
- file
...
- types
...
- to
...
- now
...
- be
...
- parsed,
...
- the
...
- system
...
- provides
...
- the
...
ability
...
- to
...
- reimport
...
- these
...
- files.
...
- If
...
- you
...
- have
...
- copy
...
- number
...
- data
...
- that
...
- is
...
- not
...
- in
...
- the
...
- caArray-prescribed
...
- Copy
...
- Number
...
- MAGE-TAB
...
- Data
...
- Matrix
...
- format,
...
we
...
- provide
...
- a
...
- conversion
...
- utility.
...
- The
...
- conversion
...
- utility
...
- is
...
- found
...
- inside
...
- the
...
- cn2magetab.jar
...
- file,
...
- and
...
- is
...
- invoked
...
from
...
- the
...
- command
...
- line.
...
- Please
...
- see
...
- the
...
- README_copy_number_conversion.txt
...
- for
...
- more
...
- details
...
- on
...
- its
...
- operation.
...
- For
...
- experiments
...
- created
...
- from
...
- 2.4.0
...
- onwards,
...
- the
...
- experiment
...
- public
...
- identifier
...
- will
...
- be
...
- composed
...
- of
...
- the
...
string
...
- "EXP-"
...
- followed
...
- by
...
- a
...
- number.
...
- Already-existing
...
- experiment
...
- public
...
- identifiers
...
- will
...
- not
...
- be
...
- changed.
...
We
...
gratefully
...
acknowledge
...
our
...
collaborators
...
at
...
Yale
...
and
...
UPMC
...
for
...
their
...
contribution
...
of
...
the
...
Nimblegen
...
parsers
...
to
...
the
...
release.
...
The
...
2.4.0.2
...
release
...
addresses
...
the
...
following
...
issues
...
with
...
the
...
2.4.0
...
release:
...
- Fixes
...
- out-of-memory
...
- errors
...
- with
...
- the
...
- parsers.
...
- Fixes
...
- null
...
- pointer
...
- exception
...
- in
...
- the
...
- upgrade
...
- installer.
...
- Adds
...
- probe
...
- name
...
- validation
...
- to
...
- the
...
- data
...
- file
...
- parsers.
...
- Adds
...
- a
...
- security
...
- patch
...
- to
...
- Struts
...
- 2.1.x.
...
- Correctly
...
- validates
...
- Genepix
...
- GAL
...
- array
...
- designs
...
- with
...
- non-integer
...
- block
...
- header
...
- information.
...
- Fixes
...
- an
...
- error
...
- which
...
- causes
...
- copy
...
- number
...
- data
...
- to
...
- not
...
- parse.
...
- Addresses
...
- issues
...
- recently
...
- found
...
- with
...
- 2.4.0
...
- installers.
...
Known
...
Issues/Defects
...
------------------------
...
See
...
the
...
GForge
...
tracker
...
for
...
existing
...
open
...
defects,
...
community
...
requests,
...
resolutions
...
and
...
feature
...
requests.
...
The
...
following
...
issues
...
are
...
highlighted.
...
https://tracker.nci.nih.gov/browse/ARRAY
...
- The
...
- total
...
- import
...
- job
...
- size
...
- (defined
...
- as
...
- sum
...
- of
...
- uncompressed
...
- file
...
- sizes)
...
- must
...
- be
...
- less
...
- than
...
- 3GB.
...
- A
...
- collaborator
...
- cannot
...
- see
...
- files
...
- in
...
- the
...
- "Uploaded"
...
- state
...
- even
...
- with
...
- read-write
...
- permissions
...
- to
...
- the
...
- experiment.
...
- If
...
- you
...
- are
...
- still
...
- using
...
- the
...
- Legacy
...
- API
...
- and
...
- your
...
- query
...
- results
...
- in
...
- >10,000
...
- results,
...
- your
...
- transaction
...
may
...
- time
...
- out.
...
- The
...
- workaround
...
- is
...
- to
...
- modify
...
- your
...
- query
...
- into
...
- multiple
...
- queries
...
- that
...
- return
...
- smaller
...
- result
...
- sets.
...
- The
...
- installer
...
- does
...
- not
...
- support
...
- configuring
...
- SSL
...
- support
...
- in
...
- JBoss.
...
- After
...
- installing
...
- a
...
- local
...
- copy
...
- of
...
- caArray,
...
- you
...
- must
...
- go
...
- to
...
- http://<IP_address_or_host_name>:<port>/caarray
...
in
...
- order
...
- to
...
- test
...
- your
...
- installation.
...
- Even
...
- if
...
- you
...
- are
...
- running
...
- the
...
- browser
...
- on
...
- the
...
- same
...
- machine
...
- as
...
- your
...
- caArray
...
installation,
...
- you
...
- cannot
...
- go
...
- to
...
- http://localhost:<port>/caarray.
...
- Image
...
- files
...
- referenced
...
- in
...
- a
...
- MAGE-TAB
...
- SDRF
...
- cannot
...
- be
...
- validated
...
- or
...
- imported.
...
- Multiple
...
- MAGE-TAB
...
- imports
...
- can
...
- result
...
- in
...
- duplicate
...
- persons
...
- in
...
- the
...
- database.
...
- Experiments
...
- with
...
- multiple
...
- array
...
- designs
...
- may
...
- cause
...
- copy
...
- number
...
- data
...
- to
...
- be
...
- Imported
...
- (not
...
- parsed).
...
- For
...
- more
...
information,
...
- please
...
- go
...
- to
...
...
- Data
...
- import
...
- can
...
- fail
...
- if
...
- experiment
...
- is
...
- associated
...
- with
...
- multiple
...
- array
...
- designs.
...
- For
...
- more
...
information,
...
- please
...
- go
...
- to
...
...
- In
...
- IE
...
- browser
...
- only,
...
- pane
...
- overflows
...
- "Download
...
- Selected
...
- Experiment
...
- Files"
...
- leaf
...
- in
...
- Download
...
- Data
...
- tab
...
- so
...
- buttons
...
- are
...
- obscured.
...
For
...
- more
...
- information,
...
- please
...
- go
...
- to
...
...
- GUI
...
- installer
...
- suddenly
...
- quits
...
- when
...
- illegal
...
- characters
...
- present
...
- in
...
- password
...
- fields.
...
Bug
...
Reports,
...
Feature
...
Requests,
...
And
...
Support
...
------------------------------------------
...
Send
...
...
to
...
ncicb@pop.nci.nih.gov
...
to
...
request
...
technical
...
support.
...
To
...
report
...
a
...
bug
...
or
...
request
...
a
...
new
...
feature,
...
please
...
visit
...
the
...
Molecular
...
Analysis
...
Tools
...
Knowledge
...
Center
...
resources
...
at:
...
https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page
...
Existing
...
requests
...
and
...
resolution
...
may
...
be
...
viewed
...
at
...
the
...
caArray
...
issue
...
tracker
...
URL:
...
https://tracker.nci.nih.gov/browse/ARRAY
...
Documentation
...
And
...
Files
...
-----------------------
...
Please
...
note:
...
new
...
wiki
...
based
...
technical
...
guide
...
and
...
the
...
installation
...
guide
...
can
...
be
...
found
...
at
...
following
...
locations:
...
caArray
...
2.4.0
...
Installation
...
Guide:
...
...
caArray
...
2.4.0
...
Technical
...
Guide:
...
https://wiki.nci.nih.gov/display/caArray2/caArray+2.4.0+Technical+Guide+Wiki+Main+Page
...
caArray
...
2.4.0
...
API
...
Guide
...
(unchanged
...
for
...
this
...
release):
...
https://wiki.nci.nih.gov/display/caArray2/caArray+2.4.0+API+Guide
...
Links
...
to
...
all
...
other
...
documentation
...
and
...
files
...
can
...
be
...
found
...
at:
...
https://cabig.nci.nih.gov/tools/caArray
...
NCI
...
CBIIT
...
Web
...
Pages
...
---------------
...
- The NCI Center for Bioinformatics, http://ncicb.nci.nih.gov/
...
- NCI CBIIT Application Support,
...
...
- NCI CBIIT Download Center,
...
...
Getting
...
Started
...
with
...
the
...
caArray
...
API
...
------------------------------------
...
To
...
get
...
started
...
with
...
the
...
caArray
...
Service
...
API
...
v1.0,
...
please
...
download
...
the
...
client
...
libraries
...
(caarray-client-external-v1_0.zip).
...
Example
...
client
...
code
...
for
...
the
...
Java
...
API
...
is
...
available
...
in
...
java_api_client_examples_v1_0.zip.
...
Example
...
client
...
code
...
for
...
the
...
Grid
...
API
...
is
...
available
...
in
...
grid_api_client_examples_v1_0.zip.
...
Both
...
the
...
example
...
packages
...
contain
...
a
...
README.txt
...
that
...
will
...
get
...
you
...
started.
...
Please
...
note
...
that
...
applications
...
with
...
no
...
authentication
...
requirement
...
can
...
use
...
the
...
Java
...
API
...
or
...
the
...
Grid
...
API.
...
But
...
applications
...
needing
...
authenticated
...
access
...
must
...
use
...
the
...
Java
...
API.
...
We
...
will
...
add
...
authentication
...
support
...
to
...
the
...
Grid
...
API
...
in
...
a
...
future
...
release.
...
If,
...
for
...
some
...
reason,
...
you
...
do
...
not
...
wish
...
to
...
use
...
the
...
new
...
Service
...
API
...
yet,
...
you
...
can
...
continue
...
to
...
use
...
the
...
legacy
...
API,
...
but
...
you
...
must
...
upgrade
...
to
...
the
...
latest
...
version.
...
To
...
do
...
this,
...
please
...
download
...
the
...
client
...
libraries
...
(caarray-client-legacy.zip).
...
FEEDBACK
Please post feedback on the Molecular Analysis Tools Knowledge Center forum: https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page
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