From CAGT

IRDB News

v2.14

• Added an action to download a cluster (sequences only in correct direction). Note, if saving as a set, direction is lost.
• now distribution table and clusters table can be added to a report
• added Set Comparison tool (TRDB only so far) to compare two sets ran at different parameters or with a different algorithm version

v2.13

• changes to IRDB reflecting IRF3.03 changes as extra fields and changed process form

v2.12

• changed copying/merging/saving/clustering/tools on sets to preserve comment,sub*pattern fields, polymorphism prediction tools, etc.

v2.11

• sub-pattern detection tool added (TRDB only)

v2.10

• new sequence selection dialog implmented
• support for GT match and Mirror repeats options programmed in (IRDB only)

v2.09

• added PRINTER FRIENDLY COLORS button to the repeat alignment page
• modified TRDB to display possible pattern fragments in the flanks when flanks are selected on the repeat alignment page
• modified IRDB to display flank alignments when flanks are selected on the repeat alignment page
• clustering revamped and moved to the computation cluster :)
• function for managing multiple remote jobs from the same client added
• modified IRDB GFF export file to include the UCSC custom track header, also it is now made of 2 parts (left and right arms) and not a continuous blob as before

v2.08

• added arm join tool (IRDB Only)
• added Multiple Sequence Summary display
• added removing yourself from a project as well as transferring ownership of a project
• now it is possible to delete a project and all its content in the same operation
• project and partition group are preserved when jumping around the pages
• when going to the browser from a particular repeat, that repeat is now surrounded by a red square
• also it is possible to switch between other sets that repeat is part of while staying on the same sequence position
• added save to report feature to flankcomp output
• now when saving a set or report, it is possible to create a new project on the fly
• process id of each transaction is now saved in the logs so it is easier to track run away processes
• fixed a few problems with the GU library (v1.05 now) (affects distributions graphs)

v2.07

• better statistics
• added a guest user type

v2.06

• added a gapper tool to IRDB
• implemented multiple set merge
• added scatter plot to the distributions page using our new graph library
• fixed the "view history" bug which caused errors in big displays due to pallete running out of colors

v2.05

• added preregister page to collect information about users before they register
• implemented automatic GENBANK sequence pull
• added a "veiw scheduler statistics" administrative tool

v2.04

• fixed a bug that incorrectly displayed repeat count when saving "as cluster" in IRDB.
• fixed a bug that prevented adding records from a cluster to a report
• added a comment field on the repeats table and an index on the repeats table to speed up some queries
• created a distributed version of the program (we now have a 4 node cluster to take advantage of that). Right now we

only use it for sequence processing, but soon other tasks as "clustering" will follow.

• added a new "Collaborator" user role that has some extended properties

v2.03

• created a joined preapproval table which is now a part of a centralized security system
• IRDB no longer keeps the loops saved. Loops and flanks can still be accessed if the original source sequence is not deleted. There is no visible difference for the user.
• browser, distribution and popups now do not jump away from the data after refreshing (except that it cause NS to freeze,

to it is only available for IE)

• found a bug in the browser that wasn't letting the user pick the zoom level in some cases
• redundancy tool (IRDB only)

v2.02

• new browser zooming selection options
• new way of browsing public sets (first an organism is selected with javascript and than the sets appear)
• added multiple alignment (IRDB)
• all annotations on the browser now have a link to a more detailed popup (unless the density of annotations becomes too high)
• fixed the browser stacking so it no longer produces huge unbalanced stacks
• added the "compare flanks" tool (TRDB only) as well as an alignments options to the account to be used by it
• added the Transcriptions Binding Factors Prediction tool (TRDB only)
• added the flanking display to repeat view
• modified the sequence download page so that masking and range select options are available
• added display of annotations to the browser
• some alignment corrections for MREPS found repeats and a new field called "Sensor" added (TRDB only)

v2.01

• completed DAS client and used it to annotate our public sequences. The client is now automatically run once a week.
• a new sensor for finding exact tandem repeats of unlimited size (MREPS) added to TRDB
• added "composable FASTA" set download option which lets the user to create a custom string from available DNA strings
• fixed a memory bug in image distributions
• fixed a bug in TRDB "copy labels" tool which caused copies to be mislabeled (TRDB only)
• added the DAS (annotation source) information to the sequence modify page (administrative only)
• created this update file and placed a link to it on the about page
• added REPORTS feature
• added positional view (browser) for repeats available from the distributions page)
• spelling error fix on filter page ("greater than or equal to")
• changed text on the download and primers forms for line termination to be more understandable
• the process of uploading a sequence is now simplified (organism is now optional and a default name is provided for the sequence)
• Fixed the bug in IRDB where loops where saved with some added garbage at the end. Run a script on the database to update affected rows.
• Added flanking sequences to the set download (before you could only get them from the primers page in TRDB)
• added a button to the "label copies" tool to download the copy definition FASTA file (TRDB only)
• Fixed "FASTA" set download (TRDB only)
• added textual pattern and sequence to the repeat viewer (TRDB only)

v2.00

• Major release. A common webcore is established (LBIwebbase) and 2 child databases (TRDB and IRDB.) Update file not yet kept.

v1.00

• First version. Update file not yet kept.