SMD : SMD News

 

• SOURCE has been updated with a new BATCH SOURCE that can now accept common microarray identifiers from Affymetrix, Agilent, Illumina, Heebo/Meebo platforms, as well as chormosomal coordinates (human and mouse) and aanotate them. All organisms in SMD are supported in SOURCE.
• GenePattern has been updated to include sparse clustering and SNP capabilities

2009-April

• Load Illumina expression data into smd.
• Gene Expression Scope: Log ratio scales and image intensity scales are included as options on the display.

2009-March

• Gene Expression Scope: This is a spot history replacement. It is gene-centric rather than spot/reporter-centric and also displays relative significance.

2008-December

• New face for SMD
• SOURCE Enhancements - probe/reporter displays
• Load non-split/non-cropped images from Agilent multiplex arrays

2008-September

• SMD installed new servers and other hardware. The new hardware should improve performance and increase availability.

2008-July

• Expression Connection: from a publication data set the user is allowed to view and manipulate the cluster and the expression correlations. Currently only available for Tuberculosis and Streptomyces.
• GenePattern: GenePattern modules are available through registered users' repositories or for retreived datasets for public users.

2008-February

2007-November

• Primarily a bug-fix deployment

2007-August

• 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

• 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 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

• 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

• 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.
• Data Retrieval using GO-terms It is now possible to retrieve genes using GO-terms or GOIDs during data retrieval.
• 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

• 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

• 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 InterfaceSMD 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

• 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

• New Hardware The only changes were to support the new hardware.

2004-August-11

• 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

• 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