SEURAT Version 5.4.3 July 07, 2009

Improvement

Bug

 

SEURAT Version 5.4.2 June 26, 2009

Improvement

Bug

SEURAT Version 5.4.1 June 22, 2009

Improvement

Bug

 

SEURAT Version 5.4 May 26, 2009

 

 

 

{"experiment", "Expt Batch Number", "#hardcoded1#to_char(customer_table.customer_column)", "varchar"},\

 

 

New Feature

Improvement

Bug

SEURAT Version 5.3.3 March 6th 2009

Bug

Improvement

 

SEURAT Version 5.3.2 February 27th 2009

PLEASE NOTE: Existing customers upgrading from SEURAT 5.2.x or earlier will need to update their database(s) to be compatible with the latest version of SEURAT 5.3.x. Instructions on the steps to follow to upgrade your database(s) can be found in the “Upgrading your database tables for use with SEURAT 5.3” guide on the documentation page of our website.

 

Bug

Improvement

 

SEURAT Version 5.3.1 February 14th 2009

Bug

 

SEURAT Version 5.3 February 10th 2009

Bug

Improvement

New Feature

Refactor

 

SEURAT Version 5.2.2 November 6th 2008

Features added and Improved in SEURAT 5.2.2

 

Bug Fixes in SEURAT 5.2.2

 

 

SEURAT Version 5.2 October 8th 2008

IMPORTANT NOTES ABOUT UPGRADING TO SEURAT 5.2.x from SEURAT 5.1 or earlier

Please read and follow the instructions given in this section immediately after upgrading to SEURAT 5.2 but before you try to run SEURAT 5.2.

Update your Compound Whiteboard Tables

SEURAT 5.2 requires changes to the tables that hold the compound structure definitions stored in the database tables that support the Compound Whiteboard functionality in SEURAT.

 

In order to update these table definitions you need to do the following:

 

  1. Open a cmd window (Windows Installations) or a unix window and change directory into the SEURATServer directory of the SEURAT Server installation.
  2. Issue the command
    1. java –cp seurat-server.jar chemaxon.jchem.JchemManager
    2. At the connection dialog presented enter the following information

 

For ORACLE

 

JDBC Driver

oracle.jdbc.driver.OracleDriver

URL of database

jdbc:oracle:thin:@//localhost:1521/xe

or

jdbc:oracle:thin*:*@ localhost:1521:sidname

Property Table

jchemproperties 

Login name

seurat

Password

seurat (usually)

 

For PostgreSQL

 

JDBC Driver

org.postgresql.Driver

URL of database

jdbc:postgresql://localhost:3247/synaptic

Property Table

jchemproperties 

Login name

postgres

Password

<your password> (chosen during install)

 

  1. You will be asked if you would to update your table definitions. Choose yes.
  2. Once updated you will be asked if you want to update the data in those tables. Choose yes.

 

This will bring you database table definitions in-line with the latest version of SEURAT. If you experience any difficulties in upgrading your table definitions please contact Synaptic Science at support@synapticscience.com or on 301 915 0274.

Features added and improved in SEURAT 5.2

 

Bug fixes in 5.2

SEURAT Version 5.1 August 11th 2008

Features added and improved in SEURAT 5.1

Bug Fixes in SEURAT 5.1

SEURAT Version 5.0 April 6th 2008

NOTE: Version 5.0 of SEURAT requires a 1.5 JVM or greater to run. If you want to run under a Java 1.4 JVM then you will have to use version 4.5.1 or earlier.

Features added and improved in SEURAT 5.0

  1. SEURAT now supports single sign-on. Customers can now configure SEURAT to authenticate users via any LDAP directory (e.g. Active Directory). See the SEURAT administrators guide for details of the configuration file entries required to enable this feature.
    1. NOTE: The scheme prior to version 5.0 of using the underlying databases authentication is still available and remains the default for backward compatibility.

 

  1. The SEURAT Server can now be configured to periodically refresh its database constants. Database constants form the basis around which pick lists are built by the SEURAT Client upon each login.
    1. By default periodic update is turned off
    2. To enable periodic update of database constants you must set the System Property “db.constants.refresh.interval” and set its value to the number of minutes that should pass between each refresh.
    3. An example setting for refresh every hour would be -Ddb.constants.refresh.interval=60

 

  1. Two new features for organizing/clustering a sparse table of data have been added to the Assay Display. These new options are found under the Edit->Organize table option. The three sub options are:
    1. Data existence

                                                              i.      A fast way to bring the most assayed compound to the top and then the most often run assays to the left so that all “interesting” data is closer to or in the visible region of the table

    1. Euclidean distance->Automatic

                                                              i.      Will compare all quantitative columns using a nearest neighbors calculation based on Euclidean distance

                                                            ii.      NOTE: The Euclidean distance calculations are slower than the data existence method.

    1. Euclidean distance->Manual

                                                              i.      Same as above but only for the subset of columns you choose in the dialog presented when this option is selected

 

  1. SEURAT can now be configured to send bug reports from the Server rather than client to get around environments where Java Mail send from the client is blocked. Two new properties were introduced to support the server send of bug reports and feature requests:
    1. syn_bug_report_sender which can be either “client” or “server”
    2. syn_bug_report_server_script which is syn_bug_report_sender is “server” gives the name of the script that should be called to effect the sending of email.
    3. The script will be called with –s <subject> <report_file_name>

 

  1. Tables in SEURAT forms are now sortable by a single click on a column header. Sorting on multiple columns at the same time is possible to break sorting ties in the preceding column.

 

  1. Tables in SEURAT Forms can now be defined to show only a subset of assay data by providing a list of partial or full assay name matches in the second row of the table model painted via NetBeans (or another editor). Entries like PK_%, %TRFRET% would populate a table only with assays that had a name starting with PK_ or had the term TRFRET somewhere in the assay name.

 

  1. SEURAT forms now support two or more tables at the same level and subject in a form in case you want to split very large (number of columns) tables into 2 or more tables to avoid users needing to scroll.

 

  1. New administrator tools are now provided that allow the SEURAT administrator to run a set of jobs by their job numbers and to be presented with a GUI showing for each job

 

    1. Job ID
    2. Owner
    3. Title
    4. Description
    5. Path to job in job bookmark outline
    6. The script to run the admin tool for running an inspecting jobs by job id are in the SEURATClient directory (C:\Program Files\SynapticScience\SEURATClient by default)

 

  1. A new administration script is provided in the SEURATServer/bin directory for parsing cache builder log files for details on which jobs failed and how long re-cache of each job took. The script is called genCacheBuilderReport.py and is called passing two arguments:
    1. Arg 1 = path to a cache builder file
    2. Arg 2 = name of the file to which output of the script should be written
    3. The output of the script is written to the file designated in Arg 2 where the CSV file produced contains a header row of:

                                                              i.      “Job ID,Seconds To Cache,Megabytes To Cache,Success/Error?”

 

  1.  It is now possible to add an “All Assays” add column operation to an existing SEURAT job. This makes it easier to combine a cutoff query (e.g. Ki < 0.05 uM) with a post addition of all assay data such that running the job in the future will always find all new assay results for those compound matching the initial search criteria.

 

  1.  The SEURAT memory meter has been removed from the List Manager page as it had caused many users to think that SEURAT was still loading. The memory meter is now only shown if the property seurat.test is set to true.

 

  1. A new menu option for running a job by its id has been added to the View menu of the ListManager.

 

  1. Customers can now set the order of buttons on the toolbar of the ListManager. They can also remove any of the buttons decide where the vertical separators should be placed that group toolbar buttons or remove the toolbar altogether.

 

  1. Customers can now define their own search portal page to be used in conjunction with the SEURAT main List Manager window. The Search Portal page is designed by customers using any WYSIWYG GUI builder tool for java (like for example NetBeans) to paint a JPanel that also implements the Synaptic Science supplied SearchPortal interface. The SearchPortal interface allows the search portal author to tell SEURAT which panel should contain the compound structure for search, which should accept a list of corporate ids.

 

  1. Users can now double click on the compound structure pane in the Structure tab of the Advanced Search (aka Template Form) window to access the structure sketching view.

 

  1. A new assay search can now be launched from within the Assay Display based on the current selection in the table from a right mouse click over any table cell and selecting the “New Assay Search (all selected columns) option.

 

Bug Fixes in SEURAT 5.0

 

  1. CWB Cache builder now correctly deletes the cache results for any job that fails to run to completion during the cache rebuild process. Without this fix the next time a user tried to run the job that failed from cache they would see no results and would have to remember to run from scratch manually (right mouse option) to see their latest results.

 

  1. Jobs that included Add Property Columns for properties that no longer existed in the DB Mappings file would cause the cache builder to fail to complete often tying up large amounts of DB resources. Now even if such jobs exist and fail during the cache rebuild process, they will not stop the cache builder from completing cleanly and releasing its resources.

 

  1. SEURAT now properly ignores “bad” or null compounds and continues to render any in a hit list / analysis set that are valid.

 

  1. Rendering of the SEURAT GUI would sometimes become slow and sporadic after closing a heat map in SEURAT visualization suite. This issue has been corrected.

 

  1. SDF export from windows used to only put a line feed at the end of each line rather than the carriage return and line feed windows / DOS expects. This has been corrected such that SEURAT will output the appropriate end of line characters for each operating system.

 

  1. SEURAT client would often hang when launched from a URL on dual and quad core machines due to some threading issues. This has been resolved.

 

  1. Very long assay names used to cause the Advanced Search window to have scrollbars obscuring the magic wand button which gives access to the Assay Selection Dialog. SEURAT not employs stepped combo boxes to avoid the scrollbar appearing for very long assay names.

 

  1. Add column operations would fail (in 4.5.1 version of SEURAT only) if there existed two or more assay names where one assay name was a subset of another longer name. This has been corrected.

 

SEURAT Version 4.5.1 February 25th 2008

Bug Fixes in SEURAT 4.5.1

  1. Save of Assay Display sometimes fails when prompted to save after close window: after changes have been made in the Assay Display and a user clicks on the Windows close button (top right hand corner) they are prompted to save their work. Sometimes when saving just before closing the window the cached copy of the results would not get written out properly. This could have the following effects from the users perspective:
    1. When re-run from cache none of the updates for the job can be seen
    2. A visualization snapshot created before the save is no longer available from the Tools->Visualizations menu.

 

  1. Improved memory management and instrumentation in SEURAT Server: Installations of SEURAT with thousands of SEURAT jobs, especially when many of those jobs represent the results of loading large SDF and/or CSV files into SEURAT to share across projects, were starting to consume a lot of memory. Now the SEURAT Server can support many more jobs in a much smaller memory footprint and has been instrumented to give additional information as to which jobs are causing the greatest memory consumption.

 

SEURAT Version 4.5 February 18th 2008

Features added and improved in SEURAT 4.5

  1. 3x to 5x speed improvement for retrieval (from database) and rendering of compounds
  2. Assay Display cut and paste enabled (e.g. between SEURAT and Excel): Cut and paste operations now work within the Assay Display. This allows for cut and paste between the SEURAT Assay Display and Microsoft Excel amongst other applications. Data can be pasted directly into SEURAT user defined columns from Excel, other applications and from any of the other columns in the AssayDisplay itself.
    1. User defined check box columns will accept integer values (0 = false, non zero = true) values as well as the words true/false during a paste operation

 

  1. Right mouse on column header to hide column: It is now possible to hide a column by selecting the “Hide Column” menu item from a right mouse click with the mouse over the column header of any column in the Assay Display within SEURAT.

 

  1. Java 1.6 compatibility: SEURAT can now be run under Java 1.6 as well as Java 1.5 and 1.4

 

  1. Heat Map Coloring can be controlled on a per Assay Type basis: The SEURAT Heat Map now supports the ability to designate the data range, scaling (linear, exponential, e to the X and natural log) and hot and cold colors the heat map will use when coloring assay results on an assay type by assay type basis (as well as per column). These options can be accessed and controlled via the right mouse click “Heat Map Color Settings” menu with the mouse over any of the column headings of the heat map.

 

  1. Can now specify JChemBase structure and properties table names: Two new properties have been added to support the use of JChemBase structure searching that allow the customer to tell SEURAT the name of their JchemBase structure and properties tables. Those properties and their default values (suitable for use with the Synaptic Science native schema) are:

 

    1. syn_struct_search_jchembase_table=SYN_STRUCTURE
    2. syn_struct_search_jchembase_prop=JCHEMPROPERTIES

 

  1. New property to allow support for overlay images in AssayDisplay: A new property syn_use_overlay_url has been introduced that when set equal to “true” will cause SEURAT to call a single image producing url passing the assay results as a comma separated argument to that URL. When syn_use_overlay_url is set to “false” or undefined then multiple urls, one for each assay result will be called and a table of images displayed within a single cell of the Assay Display.

 

  1. Improved logic when operators excluded from aggregate results across lots in the Assay Display: Now when the user requests to exclude assay results with operators from the calculation of aggregate values (e.g. arithmetic mean, geometric mean, min, max) in the Assay Display the following logic applies:

 

    1. If all the values have operators then all those values are included so that at least the user knows assays have been run. The value is followed by “++” to show two or more values have operators.
    2. If assay results are a mix of values qualified by operators and values that are not qualified the aggregate value is calculated using only the values without operators. Mouse over however shows the complete range of values so the user is aware that qualified values with operators exist.
    3. NOTE: This change in rendering logic means that for any existing cached job results where the column contained only qualified values and the aggregation policy was to exclude values with operators then the cell will now display >null (single value) or null++ (multiple values all qualified) until the job is re-executed from scratch.

 

  1. Excel converter host and port can now be specified through system properties: In addition to being able to set the excel converted hostname and port number through the “Prefs…” button on the login screen the SEURAT administrator can centrally override and change these properties by specify the excel.host and excel.port system properties in the resources section of the SEURAT WebStart client JNLP file. The entries would look like:
    1. <property name="excel.host" value="somehostname"/>
    2. <property name="excel.port" value="80"/>

 

  1. First four Quick Searches can now be edited using the edit job button: Previously an attempt to edit a saved job that was the results of running one of the first for quick search’s (all results for a corporate id(s), prep data for corporate id(s), background data for corporate id(s), all results for an assay) generated a dialog indicating editing was not supported for quick search jobs. Now users can edit jobs created using the first four quick search options.

 

  1. New properties and command line args for controlling the Cache Rebuilder:
    1.  The database username and password can now be passed as arguments 2 and 3 to the cache re-builder (previously it always ran as the special user SEURAT).
    2. In addition a new system property cache.dontupdate.regression if set to true instructs the cache re-builder not to update jobs under the “Regression Testing” jobs folder of the user under which the cache builder is run.

 

  1. Redesign of the Combine Jobs Form: The form used to invoke a combine job has been redesigned to be more intuitive.

 

Bug Fixes in SEURAT 4.5

  1. First digit of number of molecules obscured in status bar: in some circumstances the first digit of the number of molecules reported in the status bar of the AssayDisplay would be obscured making it seem like less compounds were present in the display then was actually the case. This has been corrected.

 

  1. Search for “All Assays” during given time period not working: A Template Form (Advanced Search) specifying “All Assays” and an experiment date constraint would generate a dialog box saying insufficient constraints have been set. This has been corrected and now the search runs as expected.

 

  1. Search for “All Assays” combined with a Structure Search slow: Searches that combined a request for all assay results against a set of compounds identified by a structure search was extremely slow and would sometimes cause the SEURAT Client (and very occasionally SEURAT Server) to run out of memory. This has been corrected such that the query runs much more efficiently and the out of memory issues have been resolved.

 

  1. Assay counts not working when multiple/sub mapped databases used: When syn_show_counts_per_assay=true SEURAT provides a count of the number of results available in the database(s) for each assay. This was not working correctly when SEURAT was configured to access more than one database or a single database multiple ways (sub mappings). This has been corrected.

 

  1. Search for quantitative assay value cutoff combined with lot constraint still returns all lots: When a search involving a cutoff on a quantitative assay value was combined with a request for only a particular lots worth of data SEURAT would return all lots. Now SEURAT correctly returns only those values that are both for the lot specified and pass the quantitative cutoff constraints.

 

  1. Add assay column operations fail for assays including ‘(‘ in name/type: Some naming conventions used by customers that made use of the ‘(‘ and ‘)’ characters in either the assay name, assay type or both would cause add assay column operations to fail due to parsing errors. This has been corrected and customers are now free to name their assays and assay types without restriction.

 

  1. Add property and user defined columns to file loads with auto id: SEURAT used to only create the Result Display for a file loaded into a job that was using auto identifier generation supplied by SEURAT. Now opening a file into SEURAT using auto identifiers correctly creates the Assay Display from which property calculations and user defined columns can be added to augment the file data.

 

  1. Add database columns to file loads with corporate id: Previously could not add database columns to the results of loading a file (SDF or CSV) into a job when SEURAT was configured to access multiple/sub-mapping databases unless syn_add_columns and syn_properties were identical in all mapping files. This has been corrected and in addition in a multiple/sub-mapping database environment is much more efficient.

 

SEURAT Version 4.4 January 2nd 2008

Features added and improved in SEURAT 4.4

  1. Improved support for forms: Forms can now be used to extend SEURATs ability to access additional data from your federated data sources.
    1. Added example In Vitro Summary (averaged) results and In-Vitro Raw (including Well information) results forms as a means of showing how SEURAT can support master detail tables in forms built using the SEURAT form builder mechanism to any level.
    2. Form designs can now specify multiple join conditions and the order of the joins to be applied when SEURAT reacts to selection events in a master table within a form to populate a subordinate table.
    3. Forms now appear in a Tabbed Pane layout to make it easier to switch from one form to another. The “current molecule” and molecule sort order is synchronized between forms and first and last molecule navigation buttons have been added.

 

  1. Geometric mean / Improved Averaging Control: Customers can now configure SEURAT to calculate the geometric mean of experimental results across lots and protocols in addition to the already supported arithmetic mean, median, max and min functions. In addition:
    1. Can configure at the global level which aggregate function to use by default and override on an assay by assay basis
    2. Can configure at the global level whether values with operators should be included in aggregate calculations or not and override on an assay by assay basis.

 

  1. Improved PyMol integration: It is now possible to load information about pdb and pse files into the Synaptic Science schema from sdf and csv files that includes atom display and atom selection paths which can then be use to incrementally overlay multiple objects into a single PyMol session using the first Protein sent into PyMol as the frame of reference.

 

  1. It is now possible to search on multiple protocols at once: The SEURAT Template Form search GUI now allows the designation of multiple Assay Protocols as search criteria in any initial search.

 

  1. Display assay and/or assay / assay type counts: SEURAT can be configured to show the number of compounds that have been run in a give assay and/or assay and assay type combination whenever those assays are presented for selection during search construction. This makes it clearer where the holes are in current assay data.

 

  1. Greater flexibility when displaying images in Assay Display: Customers can now choose to configure SEURAT to interpret as images any assay result using a much wider range of match techniques those being indexOf, lastIndexOf, equals, equalsIgnoreCase, startsWith and endsWith

 

  1. Added ability to not update cache files: Customers requested a way to exclude certain SEURAT jobs from the overnight cache rebuild process so that the jobs “snapshot in time” cache could be used to compare these results to a job that retrieves the most recent data for the same constraints.

 

  1. Similarity sort re-enabled: Similarity sort based on similarity to the currently selected compound in the Assay Display has been re-enabled either using SEURATs own native tanimoto calculation or via a script provided by the customer.

 

  1. SAR Analysis and Matrices Work on Compound with Salts: it is now possible to perform an SAR Analysis on compounds including salts.

 

  1. Can now control who bug / feature reports are sent to: it is possible to designate who will be the recipient of bug and feature requests submitted through the SEURAT bug report window. In addition customers can configure through which SMTP server, messages should be sent.

 

  1. The link followed from the main Help menu is configurable: by default SEURAT takes you to the on line version of the SEURAT users guide from the help menu. This can now be overridden by each customer to send a help request to any web addressable URL.

 

  1. Easier license file management: License checks are now performed on the server rather than on the client. This makes deployment of updated or new licenses easier.

 

  1. Globally control formatting of assay results for display: it is now possible to specify via SEURAT configuration settings (using the syn_df0… syn_df10 properties) the number of decimal places that should be displayed for quantitative assay values. Different formatting rules can be applied depending on the magnitude of the assay result.

Bug Fixes in SEURAT 4.4

  1. New assays missing after upload file data to DB: Occasionally new assays introduced during an upload of data from an SDF or CSV file into the database did not appear in the drop down lists of the SEURAT GUI until after a SEURAT Server restart. Now the new assays appear after the file upload.

 

  1. Add rows not calculating column values when run on results from Quick Search: Add rows operations now work consistently regardless of whether the job to which rows are being added was created using Quick Search.

 

  1. All rows hidden when job with some hidden rows is duplicated:  Sometimes when a job that was saved with hidden rows was duplicated and re-executed the new copy of the job would mistakenly end up with all of its rows hidden. This has been corrected.

 

  1. Add rows to job with saved hidden rows not working: there were several situations where adding rows to a job that already had hidden rows would result in incorrect behavior (too many rows hidden, added row not showing up because it was itself hidden). These problems have been corrected.

 

  1. Pasted structure for search only recognized after open editor: Even though it has always been possible to paste a structure directly into the structure tab of the Template Form the structure was not recognized as a search parameter until opened into the compound sketching window (via the magic wand button). This has been corrected such that all that is needed is a paste into the structure tab for a structure search.

 

  1. Unable to clear lot date registered and prepared constraints once set: now clicking on the Clear All Tabs or Clear This Tab buttons in the Template Form correctly clears the Lot Date Prepared and Lot Date Registered fields if set.

 

  1. Units not displayed in headers until an Add Data operation performed: now the units display in the header correctly at all times without the need for an add data operation.

 

  1. Copy and paste of structures into office documents: In version 4.3 some jars were missing that allowed the correct copy and paste semantics between SEURAT and office products such that the paste operation would fail. This has been corrected in version 4.4.

 

  1. Hidden columns folder sometimes missing: for jobs with hidden columns sometimes the hidden columns folder of the add data dialog did not appear to allow the hidden columns to be added back to the job. This has been corrected.

 

  1. Improved memory management when running CWB Cache Rebuilder: The molecule caching mechanism could on occasion exhaust the SEURAT Servers memory or leave it will too small an amount of memory after a CWB Cache rebuild. Now a new system property max.cached.molecules has been introduced that can be passed to the CWB Cache Reuilder scripts java command to set the maximum number of molecules that can build in the cache before the cache is flushed. If the system property is not passed to the cache rebuilder the default maximum is 500 compounds.

SEURAT Version 4.3 September 10th 2007

Features added and improved in SEURAT 4.3

  1. Support for forms added: SEURAT now supports a form based view of compound data. A sample “Chemistry data” form has been supplied in this release as an example of the kind of forms that can be created for use within SEURAT. In the next SEURAT release users will be able to define their own forms covering any combination of chemical, biological and preclinical data already accessible through SEURAT.
    1. SEURAT forms are accessed through the View menu of the Assay Display created from the execution of a SEURAT process pipeline (job).
    2. The form names and the class that gets instantiated to provide the form content and layout are controlled via properties in the pri_mappings.properties file of the SEURAT Server.

 

  1. Better performance and user notification regarding failover: SEURAT’s failover mechanism now informs the user when they have been switched to a failover or backup server as well as when they have been switched back to the primary SEURAT server. Customers had requested this feature to ensure users were at least aware that they were being routed to a backup server in case that server was less performant (due to inferior hardware resources) or had the potential to be slightly out of date (due to customers own policies for SEURAT job replication) in terms of the serving of SEURAT process pipeline (job) information.

 

In addition failover logic is now only activated when the property backup.server.url is defined so that in the case where no failover server is specified there is no performance penalty for “keep alive” pings to the SEURAT server.

 

  1. New debug options to make mapping SEURAT to Databases easier: two new properties syn_query_builder_debug and syn_query_comp_struct_debug were added to allow customers to request that SEURAT output a high level of debug information during testing of a new mapping file (e.g. pri_mappings.properties for a third party database).

 

  1. Allow use of different database for compound retrieval: a new property syn_cmpd_diff_database (along with 7 additional related properties) allows customers to specify that compound structure data be retrieved from a different database than that of the database containing chemical, biological and preclinical data related to a compound. This increases the degree of flexibility that SEURAT can support when mapping its query, analysis and reporting functions to work against data residing in existing databases.

 

  1. Register biological data against compounds registered external to SEURAT: a new property syn_external_struct_registration allows customers who use an application other than SEURAT to register their compound structures to still use SEURAT to register lot, protocol, biological assay, preclinical and property data against those same compounds using the SEURAT “load file data into database” capability.

 

  1. Compound retrieval, averaging and job save performance improved: when dealing with a relatively large number of compounds (> 4000) in the Assay Display SEURAT now calculates average values, loads compound structures and saves a copy of any process pipeline results in the background allowing customers to continue working on other tasks.

 

Bug Fixes in SEURAT 4.3

  1. Incorrect constraints on Add Assay Column: when the new property syn_sce_assay_queries was set to “true” incorrect constraints were generated when adding assay columns to the Assay Display resulting in longer query times than were necessary. This has been resolved.

 

  1. Duplicate Observation Types (aka Assay Types) Generated: under some “load file data into database” situations duplicate observation type entries were generated into the Synaptic Science native database. This issue has been corrected and a commands supplied in the updateSchema.sql script (in the postgresql or oracle SEURAT Server sub directories), which SEURAT administrators need to run after each upgrade, to remove the duplicates.

 

  1. Unable to unload data loaded into database: when more than one file was loaded that referenced the same protocol number of a given assay name there was a bug that would stop the unload of any of these related files. This has been corrected such that now any of the files that share the common observation protocol can be unloaded to completely reverse a “load file data into database” operation.

 

SEURAT Version 4.2.3 July 27th 2007

Features added and improved in SEURAT 4.2.3

  1. Java 1.5 compatibility; SEURAT can now be run under Java 1.4 or Java 1.5 JRE’s.

 

  1. Easier to configure database connection settings; Database connection settings which you could set centrally to seed client first login settings are now honored each time a user logs in. This means that a SEURAT administrator can change database connection settings centrally in the pri_mappings.properties file (or equivalent) and have these automatically propagated to all client users.

 

  1. Database mapping configuration file syntax extended to support hardcoded values and data pivoting: Now when a SEURAT administrator is configuring SEURAT to access an existing database they can make use of the #hardcodedN# and #pivotedN# statements within the pri_mappings.properties file to tell SEURAT that a literal value should be returned or column values pivoted into rows respectively. More details can be found in the comments section of the latest pri_mappings.properties.example file in the SEURAT Server installation directory.

 

  1. Database mapping performance improved: When database values are split across a large number of tables SEURAT can be instructed using the new syn_sce_assay_queries property in the pri_mappings.properties file to only search tables known to contain particular assays by name when a query is constrained by assay.

 

Bug Fixes in SEURAT 4.2.3

  1. List manager table now sorts and refreshes correctly when click on column headers; The initial List Manager table can now be sorted by single clicking in the column headers in the same manner as sorting is supported in the Assay Display.

 

  1. Importing from CSV last column exclusion; There was a bug that stopped imports from a CSV file into the database from working when the user elected to exclude the last column in the CSV file from the import. This issue has been resolved.

 

NOTE: Due to differences between Java 1.4 and Java 1.5 if you have an existing installation of SEURAT running under Java 1.4, plan to move to run under Java 1.5 and have SEURAT jobs involving the use of User Defined Scaffold Columns then you need to do the following when upgrading:

 

  1. Install version 4.2.3
  2. Run the new version (client and server) initially still under Java 1.4
  3. Run the CWB cache rebuilder or manually run and then resave all jobs that include User Defined scaffold columns.
  4. Once this has been done you can then start running the client and server under Java 1.5

SEURAT Version 4.2.2 May 24th 2007

Features added and improved in SEURAT 4.2.2

  1. Background loading of images in Assay Display; SEURAT will now load images (for things like IC50 thumbnails and compound annotation information) in the background leading to significant performance improvements.

 

  1. Add Column Names can be changed; The name of the database columns and property columns that can be added as new columns in the Assay Display can now be changed without breaking existing jobs that reference the old deprecated names for those same database columns and properties.

 

  1. Better color separation when coloring on categories in visualizations: When coloring by a “categorical” column (like for example scaffold class) in SEURAT visualizations, better color separation is achieved to make each category more visually distinct from every other category or cluster.

 

  1. Rubber band / marquee selection: All visualizations now support marquee selection as well as multiple selections through Shift-Click operations.

 

  1. Save images of visualizations more easily: Menu items have been added to each visualization that makes it easier to save a PNG image of any SEURAT visualization.

 

  1. Can map some database columns to null: When configuring SEURAT to access a 3rd party database if there is no equivalent in that database for a concept SEURAT is able to retrieve and analyze, then that concept can be mapped in the pri_mappings.properties file (or equivalent) to always retrieve “null”.

 

  1. New structures only checkbox during load into database: SEURAT can now be instructed, during load of data from an SDF file into the SEURAT native database, to load only structures and their identifiers. Previously the user had to make several changes either to the SDF file to remove properties or in the file import to database dialog to uncheck for import many columns.

 

Bug Fixes in SEURAT 4.2.2

  1. Corrected import of compound from smiles for structure search; When an existing compound is loaded into the compound sketching area to be used as a starting point for a structure search and the compound comes from a smiles string, SEURAT now renders the compound correctly by applying a clean2D operation.

 

  1. Added database columns sort correctly; The data type of columns being added to an existing Assay Display from the list of “addable” database columns is now controlled correctly by the type designation given for that column in the pri_mappings.properties file (or other mapping file for other databases). This means that sorting on columns denoted as number will work as expected rather than sorting alphabetically as they had done in the past.

 

  1. The axes of visualizations launched from the primary Celera Visualization suite window now scale dynamically in conjunction with dynamic filtering operations: Whenever a visualization is plotting an axis that is also being filtered dynamically the axis itself will change to plot only the remaining range based on the filtering operation. Previously only the first scatter plot opened would scale in this fashion.

SEURAT Version 4.2.1 March 9th 2007

Features added and improved in SEURAT 4.2.1

  1. Multiple Images Per Assay Display Cell; SEURAT can now support multiple images per cell in the assay display when configured to interpret a particular assays values as an image (either through a direct URL or a call to a cgi script) and that assay has values for multiple lots of a compound or multiple experiments against the same lot.

 

  1. Obsolete and Activate Scaffolds; Scaffold definitions can now be obsoleted / re-activated through menu options in the File menu of the Assay Display

Bug Fixes in SEURAT 4.2.1

  1. Manual Scaffold Definition Re-enableld; Several bug fixes and database schema changes were made to correct problems reported with manual definition of a scaffold for use in later analysis and visualizations. In Version 4.2 we had disabled the ability to manually define scaffolds that appear in the Add Data Dialog but now this feature has been enabled again.

 

  1. Test and Prod Server Same Machine; The server can now be run multiple times on the same machine by providing a different port number using the –Dserver.url= //localhost:5247/CompChemServer and –Duse.server.url.only=true directives during startup of the Server to specify a different port for the test versus production servers. Previously due to a bug the server was ignoring the –Dserver.url directive and using the same port number 5247 in all cases.

 

 

  1. Test and Prod Client Same Machine; The client can now be run multiple times on the same machine by providing at least one or both instances of the client with the property –Dserver.url= //localhost:5247/CompChemServer as well as the property –Duse.server.url.only=true. Previously the SEURAT Client was only able to connect using a per user set of preferences stored in the Registry on Windows or a hidden directory on Unix meaning you had to switch connection parameters between production and test each time you ran the client.

 

  1. Symbolic Link to Crystal Structure Files Allowed; Symbolic or hard links on UNIX or shortcuts in Windows can now be placed in the SEURATServer/sandbox/xtal directory in cases where you want more than one compound to provide a link out to the same set of crystal structure files. Previously links had been ignored.

 

  1. Correction to RS3 Structure Search Script; rs3structurequery.pl script used to strucrture search RS3 databases now correctly returns the Compound ID rather than the Corporate ID of matching compounds in a structure search.

 

  1. Forward Compatability of Load to DB Profiles; Saved profiles for setting during a load of an SD or CSV file into the database will now be forward compatible between different versions of SEURAT.

SEURAT Version 4.2 February 7th 2007

Features added and improved in SEURAT 4.2

  1. SEURAT can now be configured through multiple server configuration files, one per database to read information from multiple databases simultaneously.
    1. Map SEURAT to any medicinal chemistry database be it home grown or third party (IDBS, MDL, CambridgeSoft, Accelrys)
    2. If your assay data is split across different tables for different assay classes (screening versus inhibition for example) simply provide N configuration files and link them in a primary/sub database relationship. The separate assay tables can be in the same or different databases.
    3. Load partner, CRO or third party database data (e.g. ACD, WDI) from SD and CSV files through the SEURAT Client into the Synaptic Science native database and retrieve that data alongside your own corporate compound data.

 

  1. The SEURAT Assay Display can now display images for Assay Values. This is done by configuring SEURAT to interpret a set of assays designated by the SEURAT Administrator as representing a URL that is then used to depict images in the cells of the column for those assays.
    1. This can be done either by having the assay value itself be a URL that will produce an image or it can be done by specifying a base URL (typically a CGI script) to which the assay value will be passed as the first and only parameter
    2. The size of the image so produced can be controlled by the same configuration section in the SEURAT database mapping configuration file

 

  1. Data can now be loaded into the Synaptic Science native schema in two ways.
    1. First it can be loaded as was possible in this and all prior versions by presenting the data in an SD or CSV file whereby each record (SDF) or line (CSV) represented the Assay, Lot and Property data for a single compound. We refer to this as pivoted data loading because the data has been pivoted around the corporate identifier. Note that pivoted data loading corresponds to presenting data for loading in a format almost identical to that which is displayed in the SEURAT Assay Display
    2. Newly added in this version is the ability to load un-pivoted data. In this mode an SD file is used to load only the structure information about the compound. A CSV (or number of CSV) file is then used to load the Assay, Lot and Protocol data pertinent to each experiment run against a compound. This mode of data load allows a much finer grained control over the lot and protocol information against which each assay result it loaded. Note that un- pivoted data loading corresponds to presenting data for loading in a format almost identical to that which is displayed in the SEURAT Result Display

 

  1. Hide rows can now be made to persist during a save job / re-run job cycle. Previously a conscious decision had been made to not allow this capability because it was thought that people would tend to forget they had hidden data and think that SEURAT was producing incorrect results. Now:
    1. A new configuration file property syn_allow_hide_row_persistence in the SEURAT Server configuration file can be used to enable (set to true) or disable (set to false) the persisting of hidden rows

 

  1. A default height for the column headers in the Assay Display can be provided in the SEURAT Server configuration file via the syn_default_column_header_height property.
    1. If a user subsequently alters the value and saves the job then the user selected value for the height of the column header will override the default for that job.

 

  1. SEURAT has been upgraded to the latest version of JChem Base (3.2.3) from ChemAxon bringing SEURAT up to date with the latest features and bug fixes contained therein. In particular this allows the interactive loading of compound structures through JChem Manager (also known as jcman) into the syn_structure with designated identifiers for each structure. This means:
    1. Customers who want to structure search using JChem Base but don’t want to load their assay data into the Synaptic Science native database can now do so and have SEURAT link out to their existing tables for assay and property data in all other cases
    2. Batch loading of customer data will not be possible until ChemAxon fix a bug that is causing the linking of fields in an SD or CSV file to the cd_id column of a JChem Base structure table from working. ChemAxon have committed to providing such a fix in their next bug fix release.
    3. Don’t forget to check out the property calculation capabilities accessible by double clicking on a compound in the Assay Display and then selecting the calculation of interest from the Tools menu of the resulting window.
    4. You can run each such application once per SEURAT session. Additional licenses are required to remove this restriction

 

  1. To make the task of SEURAT administrators easier the database connection parameters that formerly had to be provided by every client user can now be configured in the SEURAT Server configuration file meaning:
    1. The first time a user logs in they will automatically use those settings for authentication and subsequent queries issued from SEURAT
    2. If the settings need to change at any time the administrator can make the change once in a centralized place and then each client need only click on the “Set to Defaults” button of the “Prefs…” dialog of the client to pick them up.
    3. The database tabs that appear in the “Prefs…” dialog are driven entirely by the contents of the xxx_mappings.properties SEURAT Server configuration files.

                                                              i.      This makes what the user sees more meaningful

                                                            ii.      The old tabs for “smpc”, “asc” and “tsi” were removed as they have been replaced by properties within the SEURAT Server configuration file(s) that indicate which database hosts each concept (smpc = simple molecule property calculator, asc = available screening compounds, both are tools that can be launched within SEURAT).

                                                          iii.      The tab names can now be made meaningful to the user community.

                                                          iv.      NOTE: You must have a primary file named pri_mappings.properties that contains the is_auth_db=true for backward compatibility if you already have SEURAT jobs saved.

 

  1. A new property syn_dont_average_assay_rules in the SEURAT Server configuration files has been introduced to allow customers to specify which assay results should not be average when multiple experimental results exist for a given compound across lots. Most typically this will be a specification of rules that identify Pharmacokinetics assay names. The rules allow:
    1. Designation of startsWith, indexOf or endsWith logic for matching
    2. A list of strings to which the startsWith, indexOf and endsWith logic will be applied.

 

  1. The Synaptic Science native schema has been upgraded to more widely track which data comes from which file during the load of SF and CSV data and has been improved in many other respects. If you use the Synaptic Science native database YOU MUST run the appropriate update script for your PostgreSQL or Oracle database to be able to use version 4.2 of SEURAT.
    1. For Oracle the update script can be found in the SEURATServer/oracle directory
    2. For PostgreSQL the update script can be found in SEURATServer/postgresql or can be launched form the Start->All Programs->SEURAT Server->Update Database Schema menu item
    3. You DO NOT have to run either update script if you are interfacing to your own or a third party vendors database even though you include the minimal set of SEURAT tables as no changes were made to the tables that comprise the minimal set.

 

  1. More user roles have been added to allow finer grained authorization control. The new roles are:
    1. CanLoadToDB: Can a user load SD and CSV data into a Synaptic Science native database schema
    2. CanSeeOthersJobs: Can a user open the “Other Users” folder, see other peoples jobs, run them and then save a copy of the job of their own to work with.
    3. CanSeePKReports: Can a user open and view PK reports when they are available for a compound
    4. CanSeeXtal: Can a user see and open crystal structures into PyMol for viewing.

 

  1. Added a dialog to inform the use if the SEURAT Client cannot locate the SEURAT Server upon startup that gives the user the option to alter their server connection parameters

 

For more information about the particulars of how to set any of the new features that rely on property settings in the SEURAT Server configuration file please refer to the SEURAT Configuration Guide on our website.

 

Bug Fixes in SEURAT 4.2

  1. Freeze pane now works for all column types. Assay columns would not present a right mouse click menu which includes the freeze pane option when the underlying column data type was numeric. This has been corrected.

 

  1. The Available Screening Compounds application now correctly connects to the database specified by the SEURAT Server configuration file containing the property setting “contains_asc=true”. Previously the ASC was trying to perform structure searches against a database that was assumed to be on the same machine as the client.

 

  1. During data load from a file SEURAT used to incorrectly create a new Protocol entry in the database for a given Assay for every result stored against that assay. This has been fixed by the introduction of the ability to load un-pivoted data into SEURAT from SF or CSV files.

 

    1. Un-pivoted data is data in the same or very similar format to that which is displayed in the Result Display of SEURAT where each experiment details appears in a row and a compound can appear many times in many different rows.

 

  1. Commented out an erroneous reference to a non existent SVL file from within the caclprops.py script that SEURAT uses to interface to property calculators that do not have a Java binding. This issue only related to the calculation of properties using the Molecular Operating Environment (MOE).

 

  1. Code that was trying to speed up queries whereby the same assay or assays had been added more than once as columns to a job by running only one of those duplicates were not distinguishing between different types for the same assay. Previously the addition of a second column for a different result type for an assay would not work properly when the SEURAT job was re-executed.

 

  1. Quick Searches that show aggregate results (List all Projects, List All Assay Result Types) that don’t require transformation of the Result Display into the Assay Display would try to display the Assay Display anyway after a save re-execute cycle. This made it appear as though not results had been returned because the results were actually in the Result Display which was closed to produce an empty Assay Display. The fix means only the Result Display is shown.

 

SEURAT Version 4.1.2 December 19th 2006

Bug Fixes in SEURAT 4.1.2

  1. The URL generated during the emailing of a link to a SEURAT job was mistakenly being set to “localhost” rather than to the name of the machine upon which a Web Server was running to serve up the SEURAT Client. The SEURAT administrator can now specify the URL that will be used by SEURAT as the base for linking to existing SEURAT jobs via an email message in a SEURAT Server configuration file.

 

  1. The Web Start client distribution mechanism was built atop of version 5 of the jetty web server. In order to use this same jetty web server as the mechanism for the support of the emailing of URL links to SEURAT jobs we had to upgrade to the use of jetty version 6.0.2 or later. Users that wish to make use of the jetty Web Server to enable the emailing of links to SEURAT job’s need to upgrade to this new version of the Web Start Client by downloading it from our website.

 

  1. Customers that were using a compound identification scheme that, after the prefix, contained non numeric characters were not able to import compounds into the compound sketch area from within the Template Form or the Sigma tool for column addition. This issue has been corrected. An example of a compound that would not have worked prior to this bug fix is ABC-12345A where the final A was the character that confused SEURAT.

 

  1. The Quick Search query for notebook information was fixed to no longer always reference the synaptic science schema column for the alternate_id for the notebook and instead properly maps to whichever column is specified by the customer in the syn_mappings.properties file.

 

  1. The right mouse popup menu when over a cell in the Assay Display for a column containing numeric assay values was not appearing. This has been corrected such that all popup menu options for things like freezing a column into a separate pane can now be performed on any column.

 

  1. The SEURAT Client would, very infrequently and in a difficult to reproduce manner, become unresponsive after the execution of an existing job from within the List Manager or just after adding a new column to the Assay Display. Both of these issues have been resolved.

 

Features added and improved in SEURAT 4.1.2

  1. Searches including one or more compound identifiers made in the Template Form and Quick Search dialogs can now include the “*” character to designate that a wildcard match should be performed.

 

  1. The sigma tool in the Assay Display now supports a new function called regex which allows expressions that include Java regular expressions to be evaluated in order to create a new column. For example, it would be possible to parse just the year out of a date based column with the column identifier of A that had values like 2006-05-12 with the following sigma tool expression:
    1. Year := regex(A, "(\\d{4})-(\\d{2})-(\\d{2}).+", 1)

 

  1. More log messages added to the Server log on particular client activities in order to allow better auditing of which functions are being used within SEURAT.

 

  1. Removed implicit rule that placed PK assays into folder based on the portion of the name after the last underscore into a folder with the name of that last portion or a folder named “Other” if the PK assay had no underscore in its name.
    1. Now new assay folder rule entries are allowable that can designate an “ends with” condition rather than a “starts with” condition so that all rules pertaining to how assays are assigned to folders can be controlled from within the syn_mappings.properties file

 

SEURAT Version 4.1.1 November 16th 2006

Bug Fixes in SEURAT 4.1.1

  1. Scientist name when supplied during a load of SD data into the database was being ignored and the name of the currently logged in user was being used for the scientist that created each lot instead. This has been fixed so that the currently logged in users name will only be used in the event that a scientist property is not provided in the SD file being loaded.

 

  1. SEURAT no longer produces a mixture of Oracle and ANSI outer join syntax when communicating with Oracle. The ANSI outer join syntax is only required for PostgreSQL and MySQL and in fact using a mixture of Oracle and ANSI outer join syntax when communicating with Oracle causes problems.

 

  1. A new assay column can be added for results in an Assay Display with > 1000 rows. A bug that prevented this was inadvertently introduced during the changes to make SEURAT database agnostic.

 

  1. Externalized remaining Synaptic Science native database schema specific Quick Searches that were missed in version 4.1. Those were
    1. All data on a notebook
    2. List of all projects, their description and comment information along with the count of assay results per experiment
    3. List of all result types along with a count of how many results exist for each assay type.

 

  1. When invoking an external script or executable to perform a structure search on a Unix platform SEURAT no longer incorrectly inserts “cmd.exe /c” before the program being called which was behavior specific for executing scripts on Windows. SEURAT now correctly switches on the type of operating system and only includes the “cmd.exe /c” if the SEURAT Server is running on windows.

 

  1. It is no longer necessary to provide a seurat.ini override file for property setting to the server when SEURAT is interfacing with an Oracle database in order for the saving of new jobs to work. SEURAT now correctly reads the database connection settings from Java preferences rather than from the chemwb.ini file used to bootstrap the database connection properties

 

  1. Multiple selection of compounds in the Human Kinome Tree Viewer although rendered correctly as the activity of each Kinase on the Kinome Tree simultaneously used to leave the viewer in an error state (unresponsive) until a single selection was once again made. This issue has been resolved so that the viewer will remain responsive during multiple compound selections.

 

  1. Corrected several situations where combinations of settings in each of the tabs within the Template Form (Assay & Compound, Lot and Structure) would produce incorrect search results when one or more of the tabs specified a search that should have caused the whole search to return no results.

 

    1. This was especially true of searches involving the structure tab in combination with the other Template Form tabs when the other tabs had settings that should have resulted in no results being returned.
    2. This was a difficult bug to find because if the constraints in each tab produced at least one row then the searching would work perfectly.

 

  1. Corrected several situations where a job would return different results after it had been saved and then was re-executed.
    1. Most typically this would happen for a job that returned no results when run initially but after being saved and then re-executed it would show some results that were from the substructure search part of the query.

 

  1. Copy of  a SEURAT job’s constraints when that job includes a property calculated on the client no longer throws an Exception

 

  1. A URL’s menu now correctly appears on a right mouse click over a cell in the Assay Display that contains a valid URL or URL’s. Each URL is presented as a separate menu item of the URL’s menu in the popup menu.

 

  1. Jobs created from the Template Form that have corporate rows added no longer return no results when saved and then re-executed in a subsequent SEURAT session. NOTE: That a bug still remains that is stopping “add rows” from working properly with jobs created by the Quick Search tool.

Features added and improved in SEURAT 4.1.1

  1. It is now possible to set the assay type, assay units and concentration units en masse not only to one of the values in the preconfigured list of values but also to an arbitrary value entered by the user.

 

  1. Scripts have been provided that can be modified by customers (to provide correct paths to 3rd part executables) in order to enable the following property calculations on a list of compounds from within the Assay Display (note the need for MOE, ACDLABS and Strand Life Sciences batch software licenses for these property calculations to work):

Property

Supported OS

Required Software Package

hERG Binder

Unix (tested on Linux and Aix)

Admetis Strand Life Sciences www.strandgenomics.com and www.admetis.com

ACDLabs logS (mol/l)

Unix, Windows

www.acdlabs.com

ACDLabs logS (uM)

Unix, Windows

www.acdlabs.com

Lipinski Filter

Unix

MOE www.chemcomp.com

Lipinski Score

Unix

MOE www.chemcomp.com

Veber Filter

Unix

MOE www.chemcomp.com

QSAR- CaCo-2 Cell Permeability

Unix

MOE www.chemcomp.com

QSAR- Human effective permeability

Unix

MOE www.chemcomp.com

Aromatic Atoms

Unix

MOE www.chemcomp.com

Aromatic Bonds

Unix

MOE www.chemcomp.com

VDW Volume

Unix

MOE www.chemcomp.com

 

           

  1. In addition a new section in the syn_mappings.properties file was added to allow control of the display name for each of these properties and to allow extension of SEURAT to support additional properties for which a customer may already have their own property calculators.

 

  1. Customers can now expand the list of Kinase name mappings known to SEURAT for use with their own company proprietary, UPSTATE or AMBIT assays that are used by the Human Kinome Tree Viewer to visualize Kinase selectivity.
    1. Customers can also control the assay name and assay type used in the search for compounds that have UPSTATE or AMBIT results

 

  1. The Expanded view which shows assay results per lot aligned so that it is easy to tell which lots for a given compound have been assayed has been re-enabled. It had been disabled in the prior release (4.1) because of the change of the lot id from a number to a string.

SEURAT Version 4.1 October 2006

NOTE: Due to incompatibilities in the way Lot number is stored between version 4.1 (String) and earlier versions (Integer) it is necessary to refresh any cached job results after installation of version 4.1

 

To do this simply select the Interactive Cache Builder option AFTER having started the SEURAT server. This will cause any cached jobs to be re-executed so that their format is compatible with version 4.1

Bug Fixes in SEURAT 4.1

  1. Add Rows functionality now correctly retrieves the compound structure when a corporate compound is added to a job that contains the results of loading the contents of an SD or CSV file into a job.

 

  1. CSV file load into the database no longer requires that the identifier column be named “Corporate ID” and be the first column in the file. The selection of the identifier column can now properly be made using the combo box at the bottom of the file import dialog.

 

  1. File import into database now does a much better job at parsing out standard deviation and concentration information that is specified within the value for an assay. Previously SEURAT only dealt well with concentration information when it was supplied as part of the assay name. SEURAT was failing to parse standard deviation information out of assay values.
    1. As part of this resolution a decision was made to only parse the first line of a multi-line property value from a property in an SDF file placing the remaining lines content in the comment for the assay result. The ramification of this is that SDF file properties that are numeric should only contain a single value. If you want to provide multiple values for different lots then the compound needs to be repeated in the file N times with each repeat specifying different assay values and optionally the lot number.

 

  1. Sorting on columns will now work even if after a file load into the database a mixture of number and string assay result values are created.

Features added and improved in SEURAT 4.1

  1. SEURAT is now meta-data configurable. All database table and column references have been externalized so that it is now possible to reconfigure SEURAT through changes to the meta-data properties file (syn_mappings.properties) to read from a database other than the native SEURAT database shipped with the platform. See the SEURATPersistenceLayer.doc guide for details on how this can be done.
    1. One caveat is that file load into the database currently only works against the native SEURAT database shipped with the platform

 

  1. It is now possible to save your settings for a file import into the database so that for file imports that occur often you do not have to reset the Assay name, type, unit and concentration information each time.

 

  1. It is now possible to set the assay type, assay units, assay concentration and assay concentration units en masse by selecting several rows in the import to database dialog and then using the popup menu from the right mouse and selecting the appropriate menu item.

 

  1. SEURAT now ships with scripts that can create the native SEURAT database either in PostgreSQL 8.1 or Oracle XE. SEURAT can switch at runtime via preferences between interfacing with a PostgreSQL or Oracle XE database.

 

  1. SEURAT can now be configured to perform structure searches using a script called by the SEURAT server rather than using the built in JChem Base solution. This allows customers with their own structure search solution to continue to use that solution within SEURAT.

 

  1. By popular demand the type of the lot identifier has been changed from integer to string allowing a lot more flexibility in terms of lot identifier format. As a result of this change the Expanded View is temporarily unavailable until the next minor release.

 

  1. The rules for mapping assay names into folders can now be configured through the syn_mappings.properties file. The default rules SEURAT has always used are in the file as a starting point. Once changes have been made to the way folders are mapped the SEURAT server will need to be restarted.

SEURAT Version 4.0.2 August 2006

Bug Fixes

 

  1. When the test cMet dataset is loaded but the corporate prefix is set to other than CRA then you could not:

a)      Double click on a CRA id in the corporate id column to see all assay results for that compound from within the Assay Display did not return any results

b)      Link to a crystal structure for a CRA compound that had a crystal structure did not retrieve the crystal structure.

c)      Quick search to "List all compounds with crystal structures" did not return valid CRA compound ids.

 

  1. File upload into the database could not be called from a client running on a remote machine.

 

  1. Could not initiate a sub-structure search from a remote client.

 

  1. Corporate identifies were always given a hyphen character during install even if one was not provided.

 

  1. Corporate identifiers were always assumed to be zero padded to a fix length of digits during server installation.

 

  1. Corporate identifier and hypothetical identifier prefix could not be left blank.

 

  1. Complex assay names produce an "Invalid Assay Format" exception when added via the add column function in the Assay Display.

 

  1. PDF export of Assay Display or Result Display results placed a "Celera Confidential" as the header of each page.

 

  1. XLS export does not produce a format compatible with Excel 2002.

 

  1. Cannot save SAR display to a CWB format. This issue has only been partially corrected because not all facets of the SAR display are reconstituted from CWB yet, like for example coloring.

 

  1. Overwhelming amount of debug messages generated to the client log file when you load a file into the database after having visualized some results.

 

  1. Visualization snapshots would not reopen when a new column was added or an existing column renamed in the Assay Display upon which the snapshot was saved.

 

  1. Could not specify "No Prefix" in the structure sketched views when trying to retrieve a compound as the basis for a substructure search or SMPC hypothetical compound addition.

 

  1. Notebook ID designated within an SDF file as property or a CSV file as a column was incorrectly being used as the id rather than alternate_id in the notebook database table. This meant non numeric characters could not be present in the notebook identifier.

 

  1. ASC tool was not launching correctly from a remote client.

 

Features added in SEURAT 4.0.2

 

1. A new search with the assay name, type and units automatically filled can be launched from the Assay Display via a right mouse click with the cursor over an Assay column by selecting the "New Search..." menu item from the resulting popup menu.

 

2. A new search with the cutoff value for the assay also set can be launched from a the Assay Display via a right mouse click with the cursor over a cell of any Assay column by selecting the "New Search..." menu item from the resulting popup menu.

 

3. A new preferences tab was introduced named asc that allows the database connection parameters for the asc tool to be set by the user.

 

4. A new preferences tab was introduced named “Excel 2002 Converter” that allows the hostname and port of the machine running the optional Excel 2002 Converter server to be specified by the user.