New biosequence data is implemented. This change
is primarily for better/easier software and schema
maintence going forward and to enable uniform tool
implementation.
2006-July
SMD Release 1.11
Doping controls may now be included during experiment loading
Quality plots are now available fr HEEBO arrays
Web service is available for obtaining ontology data
2006-March
SMD Release 1.10
SMD can accept data produced from HEEBO/MEEBO arrays.
Background
Correction Options For GenePix experiments it is now possible to
use a second set of spot backgrounds and do normalization using these
new values.
Quality graphs are available for MEEBO arrays.
Many bugs fixed and several new usability features included.
2005-October
SMD Release 1.09
SMD can accept data produced from HEEBO/MEEBO arrays.
Background
Correction Options For GenePix experiments it is now possible to
use a second set of spot backgrounds and do normalization using these
new values.
Download archived original scan files. This is available from the
'Display Data' page.
2005-June
SMD Release 1.08
Gene Alignment A new tool has been added to SMD that will
take a gene identifier(s) as input (clone, gene name, accession, etc)
and return the genomic alignment as given by goldenPath at UCSC.
Web Services It is now possible to access data within SMD
remotely via web services using Simple Object Access Protocol (SOAP).
SMD Tools Page Locate SMD Tools fast by checking this list
of tools, their functions and instructions on how to find them.
NimbleGen support SMD now accepts NimbleGen Systems
microarray designs and single-channel data.
Zero-time point transform A new option on the "gene
filtering" page of data retrieval allows zero-time point
transformation of time-course data.
Merge PCL files A new PCL merging tool, accessed from the
"All Programs" list, allows merging and translation of multiple data
files from any source.
Publication link to Repositories The publication list now
has a new column with a direct link to Geo and/or ArrayExpress
repositories if associated data are available in the repositories as
mage-ml files.
2005-April
SMD Release 1.07
Faster Search The Advanced Search tool has been made
significantly faster.
Expanded Array Comparisons The array comparison plot has
been extended to Agilent and Affymetrix data, and is more
configurable.
"Synthetic Gene" Annotations The synthetic gene tool
(accessed from the repository) can now add annotations, such as
cytoband or cancer module, to existing .pcl files.
New Ontology support
Taxonomy, EVOC, GO, MGED, and Disease ontologies are loaded and
browsable.
Treeview support The treeview applet has been integrated
into the analysis pipeline. The applet may be optionally launched at
the end of the analysis pipeline.
We have noted difficulty with the FireFox browser in that the
treeview launch button sometimes does not appear. The solution is
that FireFox's cache must be completely empty. We have discovered
that pressing the clear cache button in the preferences dialog does
not completely clear the cache, so that the cache files must be physically
deleted.
Combimatrix Support SMD now supports Combimatrix array
designs and data.
2004-Dec-6
SMD Release 1.06
Affymetrix and Agilent Publications
Experiments using data from Affymetrix and Agilent arrays may now be
organized into experiment sets, published on the SMD website, and
exported to ArrayExpress and GEO.
New Normalization Options
Normalization options have been added for GenePix, ScanAlyze, and
SpotReader data, including M-A (intensity-dependent) loess
normalization. See the help page for details.
Source Code Release
The complete source code for SMD version 1.06 has been publicly released.
New User Interface
SMD has a new look! This is an attempt
to unify the look and feel of SMD and facilitate better navigation.
Much of the old navigation is still in place Lists->All Programs.
2004-November-18
GO-TermFinder
0.7 released. Major math code replaced with C++ implementation.
For long running batch jobs, it is now up to 3x faster. See release
notes and README for details.
2004-Nov-17
Caryoscope 0.3.10 is released. This adds a Y axis ruler
to the display. Grab it from the Get it!
page.
2004-Oct-12
SMD Release 1.05
KNNImpute
This application will fill in missing values from a
data set. The program is available from the repository
and is always enqueued into the Job Queue for execution.
Interactive GoTermFinder
The GoTermFinder application has been integrated into SMD and may be applied
to all organisms SMD currently supports with sufficient GO
annotation.
A word of caution: not all
organisms contain complete annotation necessary to produce the
graphical view.
Experiment Text Search
Experiments may be searched by the text in the experiment description.
This is a Google-style search such that a query of 'foo bar' will
return experiments containing 'foo bar', 'bar foo', 'bar', and 'foo'.
Spotreader Experiments
Experiments analyzed by Spotreader may be loaded into SMD.
Misc
There have been numerous other small bug fixes, improvements, and
infrastructure changes included in this release.
2004-Sep-15
SMD Release 1.04
New Hardware
The only changes were to support the new hardware.
2004-August-11
GO-TermFinder
0.63 released. Another minor bug fix release - GO nodes should
now be correctly colored by the GO::View module.
2004-July-28
GO-TermFinder
0.62 released. Minor bug fix release - see Changes file on
GO-TermFinder for more details.
2004-July-26
Caryoscope 0.3.9 is released. This adds several settings
affording users much finer control over the colors and general
appearance of the display. Grab it from the Get it!
page.
2004-July-20
Caryoscope 0.3.8 is released. This version has an
updated command line interface and help documentation describing how
to run Caryoscope from the command line. Grab it from the Get it!
page.
2004-July-13
Caryoscope 0.3.7 is released. This version eliminates
the Numerical data regex setting, which most of our users found to be
unnecessary. Grab it from the Get it!
page.
2004-Jun-28
SMD Release 1.03
Ontology Browser The SMD ontology browser is based on
the Amigo Ontology browser from the Gene Ontology Consortium. We have
extended the browser to include a few new search features. The
browser is available from the script index page.
View DataExperiments that contain clones/genes with GO
annotation have an active link in the View Data experiment display.
This link will cause the Ontology Browser to be invoked and
information about that particular clone or gene will be displayed.
Cluster Image Clone DisplayClustered clones/genes with GO
annotation have an active link. This link will cause the Ontology
Browser to be invoked and information about that particular clone or
gene will be displayed.
Cluster Image Tree Display The tree nodes contain
additional (green) links. These links cause the GOTermFinder to
be invoked with the genes/clones in the specified cluster. It
should be noted that the annotation necessary to produce a
GOTermFinder graph may be inadequate for many organisms.
Array-specific Filters Users may now specify spot-quality
filters, on a per-array basis, using "Result Set Lists" in their
loader account. The online result set list (formerly arraylist)
creation tool will guide the user through specifying filters for each
array, if desired. See the arraylist/result set list help document for details of this new
feature.
Calculation of Q-ScoresThis program calculates a quality score
(Q-Score) for an array as the function of a selected spot quality
filter. This tool currently is only for human arrays, since the score
is based on the measured log ratios of unigene clusterids that are
represnted by more than one cloneid on the array. The result of the
Q-Score calculation is displayed on several representative graphs.
2004-May-7
GO-TermFinder
0.61 released. An optimization to the calculation of the p-value
now makes it twice as fast (or half as slow)
2004-May-5
GO-TermFinder
0.60 released. The multiple hypothesis correction is no longer
done using the custom method, but instead uses a Bonferroni
correction. Correcting p-values by running simulations is now
available, to allow you to control the Family Wise Error rate. Added
the ability to calculate the False Discovery Rate, as a potential
means of avoiding the whole p-value problem.
2004-Apr-08
Caryoscope 0.3.5 is released. We implemented progress
bars that show up during long-running tasks so you don't just get an
empty screen. See the Get
it! page.
2004-Mar-31
Caryoscope 0.3.4 is released. We have added a bunch of
enhancements: scroll wheel and keyboard support for moving about in
your data; zoom level feedback; "recent files" and "reopen"
menus. And, we completely rewrote the help (which is also available as
a PDF or HTML "user manual" -- see the Documentation
page). As usual, grab the new software from the Get
it! page.
2004-Mar-29
SMD Release 1.02
A job queue has been implemented. This allows long
running tasks to be serialized - run in the background and not require
a browser connection. Many potentially long running tasks give the
user the option of placing the task in the job queue. The results are
placed in the user's repository.
Average data by UniGene cluster. A new tool has been
added to the repository. Click on the "synth" icon to average a .pcl
file by UniGene cluster, genomic tilings, or several sets of
experimental "synthetic gene" lists. Clones will be averaged into
"genes" in the same way that spots are averaged into clones during
data retrieval. See the help page
for more details. This has so far been implemented only for human and
mouse arrays.
Raw Data Generation Improvements. Several bugs have been
fixed relating to raw data generation. Raw data retrieval should be
restored to previous performance levels (about five minutes for a
large human array).
Export data to public repositories. We have enhanced our
ability to export MAGE-ML documents to EBI's ArrayExpress microarray
repository. This is one way to satisfy some journals' requirement
that microarray data supporting a manuscript must be deposited in one
of the international databases. Email the curators for export of
publications or experiment sets.
Genome alignment of experiments. Our genome alignment
file export utility, used to generate input files for Caryoscope, has
been upgraded. We now provide tab- and comma-delimited spreadsheet
text formats, in addition to the GFF format. The spreadsheet formats
are compatible with your favorite spreadsheet program, allowing you to
compute new annotations to display in Caryoscope.
2004-Mar-15
SMD Awarded Shared Instrumentation Grant (S10 RR019375).
SMD has obtained funding from the National Center for Research
Resources, "System for the Stanford Microarray Database" to be
used to deploy a new system for SMD, including new servers, and new,
faster storage, with additional capacity. We expect to has this new
system deployed by September.
2004-Mar-08
Caryoscope 0.3.3 is released. This adds the ability to
import your data as tab- or comma-separated files, in addition to the
GFF format. This means you can manipulate data -- add and remove
annotations; compute new columns -- inside your favorite spreadsheet
program, and open them in Caryoscope! Grab the program from the Get
it! page, and be sure to look in the data folder for
new example files using the tab-delimited (*.txt) and
comma-delimited (*.csv) formats.
2004-Feb-25
Caryoscope 0.3.2 is released. The latest improvements
are (a) bug fixes and improvements in the PostScript and PDF output;
and (b) the ability to embed spaces and other characters in your GFF
files (if surrounded by double quotes). Grab it from the Get
it! page.
2004-Jan-08
Caryoscope 0.3.1 is released. This adds many
improvements in zooming and panning to boost performance with large
datasets. Grab it from the Get
it! page.
2003-Dec-16
GO-TermFinder
0.50 released. A version of Shuai Weng's (from SGD) GO::View
module has been added in, which can create a graphic representation of
the results of GO::TermFinder. This gives a much better way to
intuitively look at the results. A bunch of other stuff was added in
to support this, including a batch processor that will generate html
pages with a graphic for any number of input lists of genes. See
batchGOView.pl and examples.html in the examples directory.
2003-Dec-02
GO-TermFinder
0.40 released. Added in the ability to define a subpopulation of
genes as the background from which the interesting genes were drawn.
See pod for constuctor of GO::TermFinder for more details.
2003-Nov-26
GO-TermFinder
0.30 released. Extensive reworking of the code, such that it is
now case insensitive, with certain caveats. See the pod for that
module for more details.
2003-Nov-19
SMD Software Release 1_01.
GenePix 5. SMD now supports GenePix 5 data and also supports its
autoflagging feature. To use SMD filters to help you autoflag spots
on your arrays, just click on the gridded image icon you see when you
select "Display Data."
Affymetrix Data. SMD can now accept Affymetrix data generated by
users at Stanford (not off-campus SFGF customers). To load Affy data
into SMD, esults must be produced by either MAS5 or dChip and a cel
file will also be required. Data from Affy chips and printed arrays
cannot be analyzed together, but you will be able to analyze and
cluster Affy data using all of SMD's tools except "Ratios on Arrays"
(to examine potential spatial bias) and "Compare LogRAT2N with
experiment from same print".
Agilent Data. SMD can now accept data from Agilent arrays. You
can load data from GenePix or from the Agilent FeatureExtraction
software packages. You can use all SMD tools to retrieve, view and
analyze Agilent data with the exception of the "Ratios on Arrays" (to
examine potential spatial bias) and "Compare LogRAT2N with experiment
from same print" features.
Optimization. We've optimized performance of and added filtering options to "Plot
Data" and "Channel Intensities," which are both used to examine data
quality.
2003-Nov-13
Caryoscope 0.3.0 is out! This is our
first "end-user" release. Be sure to get it and try it out! Go
to the Get it! page. Caryoscope
displays expression and aCGH data from SMD (and, possibly, other
sources) aligned on the chromosomes of the relevant
organism. The home page for Caryoscope is: http://dahlia.stanford.edu:8080/caryoscope/.