IMAGEne Release Notes

http://image.llnl.gov/image/imagene/4.9/bin/search

The data for this release was obtained on the following dates:

Human - OCT-10-2006
Mouse - OCT-11-2006
Rat - OCT-12-2006
Bos taurus - OCT-09-2006
Xenopus tropicalis - OCT-10-2006
Zebrafish - OCT-12-2006

October 13 2006 The 'Bos taurus' and 'Xenopus tropicalis' species were added to IMAGEne. The results are available in this release.
The definition for predicted fulls has been updated.

http://image.llnl.gov/image/imagene/4.8/bin/search

The data for this release was obtained on the following dates:

Human - DEC-23-2005
Mouse - DEC-22-2005
Zebrafish - DEC-25-2005
Rat - DEC-22-2005

December 21 2005 The species rat was added to the IMAGEne build. The results are available in this release.
The Alignments Java Applet will now display in Mozilla/Firefox for the Mac.

The data for this release was obtained on the following dates:

Human - JAN-06-2005
Mouse - JAN-05-2005
Zebrafish - JAN-05-2005

The data for this release was obtained on the following dates:

Human - MAY-27-2004
Mouse - MAY-26-2004
Zebrafish - MAY-26-2004

May 5 2004 - Corrected a semantic bug in the aligment process that allowed, in a small set of cases, the reverse complement of a high quality sequence match to be aligned to the reference sequence, even if the reverse was a poorer match than the original. A side effect of correcting this error was that the KG process was performance optimized due to a reduced number of calls to the SIM alignment algorithm needed to align ESTs and clones to the reference sequence.
May 5 2004 - Updated the display JavaScript so that the red highlighting for the current contig works in non-IE browsers (Mozilla, Netscape).
May 5 2004 - Updated the display JavaScript to correct a problem with the pull-down menus for the Java display. The "Show Alignments" menu will no longer automatically reset to "by clone" if "by est" is selected, and the contig is changed.
May 7 2004 - Fixed the format of data sent to the HTML and Java displays. The data displayed is not affected.
May 11 2004 - Rewrote part of the L2 clustering algorithm to remove a cluster-singleton overlap problem.
May 19 2004 - Updated the FTP README.

The data for this release was obtained on the following dates:

Human - MAR-16-2004
Mouse - MAR-15-2004
Zebrafish - MAR-15-2004

March 15 2004 - Added zebrafish to the list of species processed by IMAGEne.
March 15 2004 - Fixed a bug that caused the data in the *-Candidate_gold and *-Master FTP files to be swapped.

http://image.llnl.gov/image/imagene/4.4/bin/search

The data for this release was obtained on the following dates:

Human - DEC-19-2003
Mouse - DEC-19-2003

June 3 2003 - A bug in the generation of the Tissues in IMAGEne XML file was causing some lines to be ommitted, resulting in an improperly formatted XML file. This affected both the web-accessible version, as well as the downloadable version of the file. All versions of the XML files prior to 4.4 contain this error.

The data for this release was obtained on the following dates:

Human - JUN-08-2003
Mouse - JUN-07-2003

June 3 2003 - A subtle bug was causing problem clones to be allowed into the CG build.
June 3 2003 - Minor changes to the queries that collect sequence data from the database that were needed because of some improvements made to the production pipeline schema in the last of couple of months.
June 12 2003 - Changes made to the alignments applet to handle the occurence of duality sequences (for lack of a better term... the sequences that can represent one or another nucleotide, eg. R for Purine which could be either an 'A' or a 'G' ). These types of sequences are extremely rare, as such we've chosen to represent them with a dash. This allows us to maintain the highly compressed data stream used to transmit data to the applet (which is what allows it to load so quickly over the internet).

The data for this release was obtained on the following dates:

Human - JAN-31-2003
Mouse - JAN-31-2003

Jan 13 2003 - A problem with Megablast that allowed it to miss identifying sequences that were too closely related, because the CG process compares ESTs against other ESTs and itself, it was possible for Megablast to miss identifying an EST as homologous to any sequence, including itself, which would cause it to fall out of the build. This happened with primarily ESTs that had too many repeats in them. We worked with NCBI to identify the problem and verify that the patch they gave us fixes the problem.
Jan 13 2003 - Two portions of the CG build were optimized: the first, previously taking 10 hours was reduced to 3 and the second, taking 14 hours was reduced to 2. Both speed ups were attained through decreasing I/O requirements (i.e. less hard disk access).
Jan 16 2003 - Added code to the beginning of the build to update our list of predicted fulls to include any new clones in the IRAK or IRAL collections
Feb 4 2003 - Fixed a problem where blast searching against all species would not return results from human matches.
Feb 4 2003 - Further optimizations were made to distributed portions of the build, reducing total build time to 55 hours for a full NxN build of both human and mouse.

The data for this release was obtained on the following dates:

Human - OCT-07-2002
Mouse - OCT-08-2002

Oct 15 2002 - Megablast replaces BLAST as primary local alignment tool in initial similarity search for KG process
Oct 15 2002 - Megablast replaces BLAST as primary local alignment tool in L1 clustering for CG process
Oct 15 2002 - The Search Results page has been enhanced. It now searches the Singletons data set when searching by accession, clone ID or sequence. When searching by clone ID or accession it logically groups database hits by section from which they come (ie KG, CG, Singleton or Not found). For an example try searching version 4.1 for these accessions (AA101995 AA632285 BM951361 H15813 AA000000) and with "All" for species.
Oct 15 2002 - The Build Procedure document revised for clarity and an overall flowchart of the process has been added to complement the document.
Oct 15 2002 - Singletons FASTA data added to the FTP site. See FTP data.
Oct 15 2002 - We compiled a list of related links that relate to IMAGEne
Oct 15 2002 - A number of enhancements were made to help reduce build times, coupled with our adoption of Megablast and with hardware enhancements, we reduced the time down to 106 hours for a full NxN build of both human and mouse.

The data for this release was obtained on the following dates:

Human - JUL-10-2002
Mouse - MAY-28-2002

Aug 9 2002 - We now have clusters for mouse sequences!
Aug 9 2002 - The description line for candidate gene clusters now includes fields for species and number of contigs in the cluster
Aug 9 2002 - The 'Show Alignments' pull down was moved from the search page to the applet frame of the display page. Making it much more interactive.
Aug 9 2002 - We created a new document describing the build process, which is linked from the FAQ, and the navigation bar, or just click here.
Aug 9 2002 - Singletons data added to the FTP site. See FTP data.