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Minor enhancements for multiple components. Bug eliminated and small improvements. Using the Scheduler Lab Resource. Couple small Scheduler improvements. New menu items added to Time Request View, for setting the given and used time fields from the linked timeslots. Search results tree node title changed for Recipes.
Schedule View Tutorial for Recipient Labs. Schedule View Tutorial for Users. Bug corrections, improved error messages, and small improvements. Code maintenance and improvements. Using the Billing Periods Lab Resource. Spectrometer Type is rolled into Lab Resource Type. Bug corrections, minor improvements, and code enhancements. Time Request View Tutorial for Users. Using the Permits Lab Resource. Using the Spectrometers Lab Resource.
Bug corrections and small improvements. By Content, and By Characteristics. Time Request verification strengthened. Major changes in 'Can Do' table and methods.
Using the Can Do Lab Resource. Bug fixes and performance enhancements. Size in Bytes column added to the Images and Files tables in Views. Code and schema maintenance. Action and Protocol Tree based item searches and popups changed. Bug fixes, minor changes, and performance enhancements. Version number changed to v.
For Timeslots By Lab Permit. New Time Request Reports: Minor improvements in web schedule. The Billing Period View is completely redone. New spectrline idl structure. Bunch of table columns and idl structure fields renamed, and the changes propagated through the codebase. New indexes added to the schema. New HI Assay Reports: Antigen Binders, and Cross References.
New HI Assay Report for an item viewed: Components and Dilution Ratio fields removed from B Sample. Using Text Area Fields. Changes and improvements in Memberships View. Other minor changes and improvements. Bugs fixed and code maintenance. Adding and Removing Lab Members. Searching and Viewing Existing Records. Creating and Updating Records. Everything JobRequest whatever classes, methods, structures, tables, directories, etc. Everything Post whatever classes, methods, structures, tables, directories, etc.
Opening a New View. Table treqgencode converted to treqgeneticcode table. Bug fixes and small improvements. The PostgresSQL schema was synched, and the database converted.
Table labtextrscdata converted to a new recipe table, with new columns added: The Recipe View and everything between was modified accordingly. New fields added to Search Recipe by Owner. Tables labprotocoldata and labprotocol converted to a new labprotocol table; the codebase was modified accordingly. Time Request View improvements. Improved access control to images and files attached to various requests.
Lab Resource PI bug eliminated. Footers added to the generated web pages. New TimeRequest and Schedule error messages. To report the unused, used and penalty timeslots in a billing period. It is a Lab Master report only. Time Requests can be linked to other sesame items and vice versa. New functionality added to the Sesame Web Server: The daily schedule for a spectrometer will be shown if the day is in an open period, and the spectrometer is public and operational.
The schedules in a browser are view only; to manipulate them, use Sundial. Bug fixes and various enhancements. Bug corrected and minor improvements.
Code maintenance and performance enhancements. Currently, the only functionality of the Sesame Web Server is to respond to specific HTTP requests and to generate HTML pages data streams that contain the schedule for a particular spectrometer for this contains today and the next open period, from the current data in the database. The schedules are only generated if the open periods exists and for spectrometers that are public and operational.
The Sesame Web Server classes are in the same package as the rest of the 2nd tier, and is using the existing classes. However, the web server is started separately, and runs separately, from the tier2 server.
Vendor columns added to all Inventory Reports to show the vendors linked to the items in the report. Bug fixes and minor enhancements. Now, there is only one left, the 'Lab'.
The Sites and the PIs of old are eliminated, however, all the Site and PI related data and functionality have been transmogrified: During these moves, additional functionality and can dos were added, and many changes and improvements were made to the Views and the underlying data structures and tables.
Having only one sandbox simplified the Sesame framework and codebase. Also, the unique sandbox made simpler for users to get started with Sesame: New Lab Profile fields: New User Profile fields: User label field added to Search Bait By Id. Couple system and site resources that were not used were eliminated. Code maintenance and improvements, mainly in Time Request related classes.
Compared to the previous incarnation, it is much simpler, thus making it easier for labs to create PDF or other electronic document or publication libraries. Couple Time Request and Permits related improvements.
New Installing Sesame and Upgrading Sesame web pages. New URL cell with a display button on its right side. This is a comprehensive report of samples used in hemagglutination inhibition assays in the default lab.
RegisteringEnabled' property in jnlp files, and the new 'sesame. A 'New User' menu item is added to Alibaba Manager for creating new users, that is enabled only for users with a Sesame administrator level can do. The known bugs were eliminated and more small improvements were made in screens. PHP added to the Sesame webserver to determine the remote IP addresses of the clients that are passed to the second tier. Java 6 support is dropped. At least Java 7 is needed to use Sesame.
The known bugs were eliminated and other small improvements were made. Work in progress nonetheless. The changes were propagated to the many subclasses. A lot of code maintenance and improvements. More data checking and error messages for HI Assay data entry. HI Assay Fusion report modified to allow to include the Sample Amino Acid Mutations, and to otionally keep all the Samples separate, even if they are duplicates.
The workaround for an old Apple bug that existed for long, is removed from the codebase. Couple other small changes. New HI Assay report: This reports the joint of multiple assay tables.
The unlinkSesameItems is updated to accomodate the changes in linkSesameItems method. These changes were propagated to the codebase, and all the places where auto-linking of ORFs was in effect were revisited and confirmed or changed. The empty Seqences table in V Screen it is not eliminated anymore during a save, thus allowing one to attach files to the wells even when the table is still empty.
Gives more freedom in the workflow. To add Samples and Antigen Binders, use drag and drop. The assay data can be entered either in well numbers on a plate or in dilutions. To convert among them, see the Edit menu. For no data, leave the cell empty. New methods added to CTablePanel class "classic" tables to make it configurable for column and cell selection, in addition to row selection of yore.
Code refactoring, both on client and server side. The known bugs were eliminated and other improvements were made. To link Screen wells to these items, drag and drop a Screen well to the particular item. Handling of actions for V Screens changed. New menu items in V Screen Edit menu: Changes in Create Sample Records specifications implemented.
Further improvements in error checking and messages, and in creating different records from different screens. New icons, and couple changed ones. New menu item in V Screen menu: The item linking framework refactored both at the client and the server side, and is extended to allow linking of Screen wells explicitly by drag and drop, or implicitly, by creating items from the selected wells, e.
Samples from V Screen wells. Protein View added to Rukh. Using this, we can now show the webpages for UniGene IDs also. User Profile View code improvements. The old Associations View and menu item in Options menu is gone. The Membership View is improved. The new GUIs and menu items are: The user search popup is completely redone and issuing invitations to become members of an association is much simpler.
See the Help Pages for all the details. New categories added to Sample Category, in addition to Protein and Compound: The Sample View's configuration changes depending on the category. The framework for defining and building the menus for Modules changed. The known bugs were eliminated and miscellaneous improvements were made. Other server side code improvements for Time Requests. More code improvements for popups.
Tier 2 code refactoring. Couple reports improved at the server side. Changes in Resource Event Listener and handling. The known bugs were eliminated and a bunch of small changes. Jars re-signed with a new Code Signing Certificate and re-deployed. A new item View of the given type can be also obtained by double clicking on an "item type" node, e.
Delete Notebook Page was redone. Security enhanced for the critical dispenser methods. Calendar related bug corrections and improvements. For example, all-day events can be scheduled, new options for repeating events, new fields, etc.
Practically, both the client and the server side for these views is new. Other small improvements were made. The jars were recreated and redeployed. The Details report for 2d Xtal Screens is extended with the details for the crystals. This structure is mostly used for reports created on the server side. All the existing reports that benefited from the use of this structure were modified to use it. In addition to the All report, this includes all the details for the elements of ternary mixture. It includes the ternary mixture and crystallization buffer data also.
New 2d Xtal Protein report: The 2d Xtal detergents, lipids, proteins and screens specific reports were modified to either use only the accepted records, or all the records visible to the current user. When a 2d Xtal Lipid or Protein is updated, all these values are recalculated at the server side for all the affected 2d Xtal Screens. New fields added to 2d Xtal Screen: Ternary Mixture, and Crystallization Buffer.
Amino acid data cell auto-sizing corrected. Couple bugs were eliminated and a bunch of other small changes, mostly 2d Xtal related, were made. Part of a public database of successful 2d crystallization trials that is under development, and will be maintained by the Cryo-electron Microscopy Facility at NYSBC.
They are part of a public database of successful 2d crystallization trials that is under development, and will be maintained by the Cryo-electron Microscopy Facility at NYSBC. Barcodes added for Antigen Binders. Water Sample, B Sample. The first one is for handling water samples, the later for other types of samples where the collection site might have to be recorded too, like biological, geological, soil, air, etc.
Source field added to Sample View. Additional items that can be DB Dumped: The reported bugs were eliminated and improvements were made across the codebase. New functionality added to Sesame, DB Dump, that allows one to bulk dump all the lab records for the selected item types into an SQLite database file a single, platform independent file.
Currently the next items can be DB Dumped: Text reports modified to not export the empty fields, thus making them more readable and more compact. The Custom Report definition language is expanded, allowing a new class of reports to be defined for V Screens. Two new reports for V Screens: New fields added to Lab Profile: Storage Date and Expiration Date fields are added to every view that contains storage location fields. Diamond icon added to the sortable table column headers.
New Barcode variables for V Screens. External References field added to Notebook pages. Improved error and exception reporting. The single protocoltree DB table was split up into multiple, item specific tables. Major tier2 codebase changes and refactoring.
Couple bugs were eliminated and other improvements were made. Barcodes can be also printed for the selected stock solutions in a robot rack. New barcode variables have been introduced to reference some of the stock solution and robot rack fields.
Couple unused fields removed from the detailed ORF view and the orf tables, and the changes were propagated across the codebase.
Pull Mutations Data added to V Screen View, to transfer the mutations data from the parent screens to the current one. The reported bugs were eliminated and miscellaneous improvements were made across the codebase.
Improvements in well level barcode printing for screens. New Replicate menu item in the V Screen Edit menu, to clone the selected wells doesn't have to be a continuous selection , well by well, or, the whole screen, by appending the whole screen to the end of the current screen. For screens and workgroups, Move Up, and, Move Down, now works on the selected wells doesn't have to be a continuous selection.
Two new menu items in the main menu of the Genealogy View: The maximum amino acid sequence length is extended to characters. These allows one to verify and to upload updates for every updateable ORF field from a csv file. One field per file. The verification is enabled for every lab member, while the bulk update is enabled only for those that can upload and create ORFs. Only the lab owned ORFs can be updated.
Couple, now redundant, ORF field specific bulk update menus were removed. The 'Input' nodes are exported to the protocolDetails elements. The 'Output' nodes are exported to the trialOutcome elements.
The 'Measurement' nodes are exported to trialMeasurement elements. If a 'Measurement' node has a 'Measurement' parent or child, and the name of the node contains both the 'measurement' and 'procedure' substrings, its value will be exported to the measurementProcedure element for the connected trialMeasurement.
For the details, see the TargetTrack deposition 'how to' page. New Barcode variables for V Screens: At least one of these variables have to be used in the barcode definition, to toggle the well level mode. The barcodes will be printed for the selected wells only, or, if none is selected, for all. PI View added to the Schedule menu in Sundial. Couple bugs were eliminated and couple improvements were made.
The ORFs have to be linked to the Person. These reports generates parts of the TargetTrack depositions in a more human readable form. New TT Target reports, in Jafar: New field added to Notebook View, Private Page, to allow one to make private pages, not viewable by other lab members.
Two new Edit menu items, related to private pages in a notebook. When a lab member leaves a lab, or is kicked out, all his private pages becomes public for the lab. New field added to Calendar, Private Calendar, to allow the owner of a calendar to make it private.
The same functionality was before provided through the Type field. The Type field is now like the Type field in the other Views. Lot of code upgrades to use Java 1. New Notebook menu items: Body field added to the search Notebook by owner popup. The image viewer now correctly handles images with transparent background.
Delete start and stop codon options added to the material repository report popup. Hitpick for V Screen and C Screen now allows for interval, half interval, equal, and not equal criteria. Labfund added to search Person by owner.
New V Screen Edit menu item: Create Child Screen Table. Couple bugs were squished. The TargetTrack Views are removed from Sheherazade. The V Screen sequences table is modified to handle segments, maximum 8 per well.
The WorkGroup View's Create Primers menu item now creates a new Primer Plate record in the Board, that contains the primers generated according the criteria selected.
To set multiple rows in the editable columns of the primers table, right click on the column's header. Once a plate is selected, and the record is saved, different reports can be generated. The Lab Protocol and Action lab resources are added to Jafar.
New ORF s menu items: New WorkGroup menu item: The new TargetTrack v1. Some bugs were eliminated and couple small improvements were made. These Views are read only. Every TT item has couple Sesame style queries and reports, like query by content, query by sequence characteristics, query by status, report status totals, etc.
The TargetTrack data is accessible to every Sesame User. New Edit menu items for bulk upload of mutations, and bulk upload and download for files. New Report menu item for mutations. Sundial Schedule View modified to send email notification only when a Timeslot is released. Target Rationale field added to the bulk ORF upload popup. Due to new spec, that fits the combinatorial screening workflow better, the Library Sample View was completely redone.
It is now plate based and not vial based, while vials can still be handled as plates with only one well. The Library Sample records are associataed with a Combinatorial Library, a Lab Resource, and they are derivatives made after the selection stages.
A C Screen can contain mutiple starting and derivative libraries, i. Library Sample records, and Samples.
In the typical combinatorial screening step, one creates a Library Sample form the C Screen to track the elusion, then a child Library Sample to track the amplification, and finally using these Library Samples and the last C Screen, a new C Screen is created. In all the steps, and across the different record types, the connections, the content, multiple platereads, and the selections hit-pics are tracked at a well level.
New Labfund edit menu items: Add Category, Delete Category, to modify the budget table. All, to generate a budget report for all funds in the lab. Couple small improvements were made, and the known bugs were eliminated. The ORFs can now be uploaded or created as lab visible only. The 'targetPartnershipList' element is added to the TargetTrack report. New TargetTrack system resources. Multiple plate reads can be attached to C Screen wells.
The 'Amount' field is added to the C Screen View. The value of this field is used for the 'lab' element in TargetTrack reports. New fields added to the Action Lab Resource: New Jafar module for browsing the PepcDB data.
New 'Person' View, for keeping track of collaborators. These fields are lab specific for ORFs too, i. New additions to the TargetTrack report: A notification email is sent to the mailing list when a Timeslot is released or taken, and when a Schedule is opened. Couple small bugs were eliminated. Used for handling combinatorial screens, e. The C Screens can contain multiple samples per well, a library sample, and multiple stock solutions.
The Library Samples are associated with a Combinatorial Library, a Lab Resource, and are used to track the derivatives after the elusion and amplification steps in a combinatorial screening.
If a different plate reader needs to be supported, let us know. Generic worklists can be generated for parent-child C Screens. The editable columns can be set by right clicking on the column's header. The number of wells is at the moment limited to per C Screen. The Robot Racks content tubes are now built by dragging a Stock Solution from the Stock Solution Lab Resource's search results window and dropping it to the Robot Rack window's title bar.
New functionality, and right hand side buttons, are added to the tube field: The Source Organism tables are now sortable by double-clicking on a column's header. New Edit menu items for V Screens, Append Screen, to append a screen to the current one, and a new hit pick option.
New PepcDB Target report: Target Request PI Progress. The Rivalry report was modified. Couple improvements were made. New Edit menu item for V Screens, to add control wells to screens. Many screen operations now can be applied separately to control or non-control wells, or to all at once. New worklist generator, for Hamilton robots. If a different liquid handling robot needs to be supported, contact us. Used for handling receptor-binding, antigenic and polymerase screens. The V Screens are built from Samples, and optionally Glycans can be added to wells.
The Samples are added by drag and drop to the table in the Screen Tab. If needed, the V Screens will be modified to handle more stock solution types. Glycan is a new stock solution type. Generic worklists can be generated for parent-child V Screens. Different Hit picking strategies are implemented. The number of wells is at the moment limited to per V Screen. New field is added to the User Profile, the Default Query Item, to allow users to set the default item type for the quick query selector, the drop-down on the button bar of the main window.
They are only visible in the lab they were attached from. The Post Item is renamed to Notebook, and a Status field is added to it. Couple queries have been updated, and some other improvements were made. Couple bugs were eliminated. Beside alerting the users visually, the input and output nodes will be exported to PepcDB depositions. The edit will be propagated to the identical nodes already attached to sesame items.
The Custom Report definition language is expanded, allowing a bigger variety of reports to be defined. When the main application window is in logged out state and in focus, hitting the return key will bring up the login popup. New 'Post Body Editable Time' field in Lab Profile, to limit the editability of the post's body between 0 and 24 hours after the post was created. The title bar of the main window and the Board now shows the name of the instance the client is connected to.
The main window's title bar also shows the logged in user's username. In Sundial, all the schedule searches for timeslots have been improved. For Screen and EM Screens, the scoring cell renderer now shows both the score and the quantity, and a camera icon if there are images attached to the well.
Improved verification error visualization for all requests. Big Framework changes, new table models, Oracle 11g supported, etc. Many small improvements were made, and the known bugs were eliminated. New Views to handle the PepcDB data: Every PepcDB item has couple Sesame style queries and reports, like query by content, query by sequence characteristics, query by status, report status totals, etc. Components cell added to the Library Sample View.
Many performance improvements in the codebase, both for the first and the second tier, including the tables that are one of the main classes of the Sesame Views. The PepcDB report generator will use the roles associated with the selected labfund, and only those.
New Library Sample View in Rukh. Couple improvements were made and couple bugs were eliminated. It allows the Labmaster to specify for every Lab Member, for not owned records, the not editable cells, for every item. These not editable cells are in addition to the not editable cells defined at the lab level. If the 'All But Show Buttons' virtuall cell is selected to be not editable, the not owned records will be view only, and the Save menu item will be disabled.
However, the not owned records can be still saved as new, or as a new child. In the Can Do View, there are couple menu items in the Edit menu to help to set up the 'Can Not Edit' table, and some specific reports in the Report menu. It is only enabled for users with ORF load can do. The fields are the columns from the ORF csv upload, and they are initialized from the target request fields.
The created ORF will be automatically linked to the target request. Biology related PepcDB requirements. See the help pages for the details.
New Fill Itemtype menu item in the Cell Order menu, to add the new fields to an existing order. The Labund is now transferable while linking items. Create proteins, crystals, etc. Many small improvements were made. The tooltip of a thumbnail shows the filename. A click on the thumbnail will show the full image. Couple small improvements were made. For the new options, a default value can be set for labs through the Lab Profile Lab Resource. They are only visible to the lab members.
The image and file tranfer class has been rewritten, and the focus grabbing progress popup has been eliminated. The transfer progress is now shown in the status bar. The report shows the ORF uploads.
Couple small bugs were eliminated and couple small improvements were made. Clone rows will add the new rows to the end of the table. If a Droplet table exists, moving a row in the Screen Table will move the coupled Droplet row s too. To set a value for whole column or a continuous section of a column in the Screen and Droplet tables, right click on the header of the column. The Droplet number for all droplets is A cutoff value for the Scores can be set in the Lab Profile lab resource.
The above and below the cutoff scores are differently rendered. Beside the score, now a quantity can be also recorded. New in EM Screen View: Move Up and Move Down a row in Screen table. To set a value for whole column or a continuous section of a column in the Screen table, right click on the header of the column. New in Crystal View's Cryo field: Move Up and Move Down a row in Reservoir table. To set a value for whole column or a continuous section of a column in the Reservoir table, right click on the header of the column.
Screen Optimization implemented for EM Screens. The handling of table changes and table model listeners is changed. Couple small bugs were eliminated and many small improvements were made.
Any asterisk Labfund related bug in TargetDB report eliminated. Fields and columns added, a tab is eliminated, new and improved functionality, support of the more general plate types, etc.
It is almost a Screen with only one droplet. And not for long. Bunch of new fields added to Plasmids. Material Repository Action is a new System Resource.
Material Repository Action field added to the Action Lab Resource, to map lab actions into material repository actions. Screen Type field added to Crystal. New Columns in the Cryo field. Couple bugs were eliminated and a bunch of small improvements were made. New fields added to the Plate Lab Resource to enable more general plate geometry description. External Id field added to Stock Solutions. Amount field added to the Screen's General tab. New, Inventory report for Screens. Couple bugs were eliminated and couple small improvements were made.
It contains the list of the PepcDB stopStatus values. New Genomic Library Lab Resource, to keep track of the plates of genetic material, used for example in amplificaton reactions.
Inventory is a new report for Stock Solutions. The Info field in Stock Solution View has been changed to a table, to allow multiple timestamped entries. Multiple improvements and updates in PepcDB report generator. The Labfund field has been also added to the Search By Owner queries.
It will be added to most of the existing queries and reports. The bulk upload of the db references was modified to handle the KEGG db references. Two choices for Melting Temperature Tm calculation in Primer calculation now. Nickname added to Source Organism.
Two new Stock solution types: Used by the Screen and Crystal Views. New Morphology Lab Resource. Used by the Crystal View. By DB Reference List. Sesame looks good and runs good on Windows 7 too. New Salary And Effort Details report. The Plasmid descriptor line in search results tree has been changed. New Genetic Table System Resource. It contains all the genetic code conversion tables listed at NCBI. The bulk ORF upload popup now allows one to choose the conversion table that will be applied to the ORFs in the file, resulting in better conversion and genetic code error determination.
These new types were needed for better genetic code error determination, which is also used in primer calculation. New tier2 startup error messages, to help new Sesame installations. The application of information and the impact of data submitted in this basis will depend on each individual's situation. If you detect errors, you can report these to us, Povot Park appreciates that very much! The following valuable additional facilities are also available, click on bleu tekst please for more information: Want to see more?
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