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Release Notes

2017-04-24
Version v.20170410 released to the public.
2017-04-11
Sample and NMR Experiment Views added to Sundial.
2017-04-10
Sesame ported to MySQL release 5.7. Code and schema maintenance. Action and Protocol Tree based item searches and popups changed. Search ORFs in a Work Group By ID now allows multiple IDs to be defined as a search criteria. Bug fixes, minor changes, and performance enhancements. Version number changed to v.20170410.
2017-02-24
New cell for displaying User or PI info. Used in Views for Fields like Created By Date, Modified By Date, PI Name, etc. Couple small improvements.
2017-02-20
New Time Request Searches: By User Permit, and By Lab Permit. Spectrometer field added to By User, and By Lab, Time Request Searches. New Schedule Search: For Timeslots By Lab Permit.
2017-02-14
Time Request modified to allow to select only one (Spectrometer) Probe instead of multiple ones. New Time Request Reports: Sample Info, Publications, User Data, Training And Assistance, and Experiments. Minor improvements in web schedule.
2017-02-02
Decomissioned field added to Spectrometer. 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. Bug fixes, minor changes, and performance enhancements. Version number changed to v.20170204 and released to the public.
2017-01-10
ORF ID (Database No - must start with 'GO.', Main ID, or Lab ID) field added to Search Antigen Binder By Content, Search Mass Sample By Content, Search Metal Assay By Content, Search Plasmid By Content, and Search Sample By Content. New Search Primer By Content, and Search Protein By Content. New indexes added to the schema.
2017-01-04
Which Ones (All, In HI Assays, Not In HI Assays) dropdown added to HI Assay Report Samples, and Antigen Binders popup. Code maintenance.
2016-12-29
Lab field added to Search Report List By Owner. Major changes in HI Assay Report Samples. New HI Assay Reports: Antigen Binders, and Cross References. New HI Assay Report for an item viewed: Assay Data (More Than You See), and Inventory. Components and Dilution Ratio fields removed from B Sample. Amino Acid Mutations field added to Sample Search By Content. New Antigen Binder Search By Content. Storage Date, Expiration Date and Storage Temperature added to Balance Only, and Balance and Location inventory reports. Code maintenance and improvements.
2016-12-05
New Lab Resource: Amount Units. Bug fixed.
2016-12-03
Videos published: Using Actions Fields, and Using Linked Items Fields.
2016-11-29
Video published: Using Amount Fields.
2016-11-23
Video published: Using Files Fields.
2016-11-21
Video published: Using Text Area Fields.
2016-11-11
User search for issuing invitations changed. Code maintenance.
2016-11-07
Probe and Assitor added to the html timeslot rendering. Changes and improvements in Memberships View. Other minor changes and improvements. Bugs fixed and code maintenance.
2016-11-01
Video published: Managing Memberships.
2016-10-16
Video published: Adding and Removing Lab Members.
2016-10-11
Videos published: Making a Sesame Application Desktop Icon in Windows 10, and Removing a Sesame Application in Windows 10.
2016-09-29
Video published: Searching and Viewing Existing Records.
2016-09-20
Video published: Creating and Updating Records.
2016-08-30
Table reqabstr converted to reqabstract. Everything JobRequest whatever (classes, methods, structures, tables, directories, etc.) renamed to Task whatever. Everything Post whatever (classes, methods, structures, tables, directories, etc.) renamed to Notebook whatever. Code miantenance and improvements.
2016-08-19
Video published: Opening a New View.
2016-08-02
Table gencode converted to geneticcode table. Table treqgencode converted to treqgeneticcode table. All TargetTrack tables converted to CLOB tables. Bug fixes and small improvements.
2016-07-22
Started replacing in the Oracle schema the deprecated LONG RAW data type with CLOB, converting the database, and making the changes across the codebase necessitated by this change. The PostgresSQL schema was synched, and the database converted. Table labtextrscdata converted to a new recipe table, with new columns added: authors, reference, and url. 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. Other minor improvements.
2016-06-18
Bug fixes and enhancements.
2016-06-15
Every Time Request and Schedule related search and report popup containing the Billing Periods field was improved using new, context sensitive, methods to load the Billing Periods. Time Request View improvements. Improved access control to images and files attached to various requests. Bug corrections.
2016-06-07
STAFF 'Can Do' string replaced with OPERATOR and ASSISTER strings. Lab Resource PI bug eliminated.
2016-05-30
Bug corrections and Time Request verification strenghtened.
2016-05-23
Version v.20160402 released to the public.
2016-05-13
NY Instance. Was in Harlem. Here now.
2016-05-05
Bug corrections and small improvements. Footers added to the generated web pages. New TimeRequest and Schedule error messages.
2016-04-29
New Schedule Reports: Open Timeslots, Taken Timeslots, and Penalty Timeslots. To report the unused, used and penalty timeslots in a billing period. The Penalty Timeslots report replaced the Penalty Timeslots Lab Resource. 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: now, it can generate html pages (data streams) that contain the today's or tomorrow's schedules for multiple spectrometers. 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.
2016-04-25
Citation, Notebook, Recipe and Task Views and the requisite Lab Resources added to Sundial. Bug corrected and minor improvements.
2016-04-22
New menu item in Time Request Edit menu: Permit to Investigators. This adds the PI and the User from the selected Permit to the Investigators field. Code maintenance and performance enhancements.
2016-04-20
A web server has been added to Sesame's 2nd tier. 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 schedules in a browser are view only; to manipulate them, use Sundial. 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. Code improvements.
2016-04-08
Time Request View and the needed Lab Resources added to Camel. Vendor columns added to all Inventory Reports to show the vendors linked to the items in the report. Bug fixes and minor enhancements.
2016-04-02
From the beginning, there were two security sandbox models for data in Sesame: the 'Lab', and the 'Site - PI'. 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: Sites become Labs; every PI become a Lab Resource PI at every Lab that parallel a Site the PI was in relation with; Site Managed PIs become Lab Resource PIs; every PI issued or Site Managed Permit become a Lab Resource Permit; Time Requests and Schedules have been moved from Sites to Labs; etc. 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: to understand the concepts, and to set up Labs. New Lab Resources: Assistance, Billing Periods, Consoles, Open Periods, Permits, PIs, Scheduler, Spectrometers. New Lab Items: Time Request, Schedule. New Lab Profile fields: Full Lab Name, URL, Accept Time Requests, and a bunch of Time Request and Schedule related fields. New User Profile fields: URL, Info. Version number changed to v.20160402.
2015-11-05
Bug fixes and minor improvements.
2015-10-31
New inventory report for Citations. 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. New, simpler, 'Search and Add Investigators' functionality for Time Request Investigators field.
2015-09-28
The Citation View is completely redone. 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.
2015-09-18
Version v.20150912 released. New Installing Sesame and Upgrading Sesame web pages. New URL cell with a display button on its right side.
2015-09-01
New HI Assay report: Samples. This is a comprehensive report of samples used in hemagglutination inhibition assays in the default lab.
2015-08-24
A Sesame instance now can be set up so that self registration is not enabled, using the new 'jnlp.sesame.RegisteringEnabled' property in jnlp files, and the new 'sesame.registeringenabled' property in SesameMain.properties file. 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.
2015-07-27
The known bugs were eliminated and small improvements were made in screens.
2015-06-21
Bait View made into a regular view: bunch of new fields, searches and reports. The Target Request Category and Target Status Lab Resources are modified to support different Request types. 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. Code cleaning. The known bugs were eliminated and other small improvements were made.
2015-04-24
Bunch of new help pages, and many existing ones updated and improved. Work in progress nonetheless.
2015-04-21
Improved error messages and new error checks for Time Requests.
2015-04-15
In main application window's Search Result Tree, the 'NEW item' branch root nodes have been renamed to 'ARISEN item' to better reflect that they collect not only new items but all the items of a particular type, that are not elsewhere in the Search Result Tree.
2015-04-08
Amino Acid Mutations field added to Protein and Mass Sample Views.
2015-04-05
Amount Field added to Protein, B Sample, Mass Sample, Plasmid, Primer, Primer Plate, V Screen, Water Sample, WorkGroup, Software and Hardware Views, and to Genomic Library and Y2H Library Lab Resources. Room, Rack and Shelf Fields added to Software and Hardware View. Search By Location and By Amount, and Report Inventory added to all the items above, if missing. Changes in the ViewSesameItem superclass and in the abstract AbstractPluggable superclass. The changes were propagated to the many subclasses. DONOTDIGEST fields/rows added to RTable and DisplaySesameItem, to be able to exclude some fields/rows from the digest, and to prevent some unnecessary saves when closing an inner window in the Board, or exiting or logging out from a Module. REQUEST changed to TIMEREQUEST, to be in accord with TARGETREQUEST, Y2HREQUEST, etc. A lot of code maintenance and improvements.
2015-03-19
New shortcuts for data entry in HI Assays for well number format: '0', '0+' and '0/' is equivalent to '<1'; 'N/', 'N+', 'N.' and 'N.x' (e.g. 'N.5', 'N.3') are equivalent to 'N/(N+1)'. 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. Code cleaning.
2015-03-16
Version number changed to v.20150224. The workaround for an old Apple bug that existed for long, is removed from the codebase. New Field: Reference in Sample View and in Search Sample By Owner popup. The Fusion report for HI Assays is modified to put the Reference Samples at the top of the table. Couple other small changes.
2015-03-10
Amino Acid Calculator code improvements.
2015-03-07
The Action Field in Hemagglutination Inhibition Assay View now works. New HI Assay report: Fusion. This reports the joint of multiple assay tables.
2015-03-04
The linkSesameItems method has changed to allow to control if the ORFs linked to the dragsource item should be also linked to the droptarget item. 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.) The known bugs were eliminated and other small improvements were made.
2015-02-23
New View in Rukh: HI Assay, for handling Hemagglutination Inhibition Assays. To add Samples and Antigen Binders, use drag and drop. Labs can define custom Dilution Lists in the new Dilution List Lab Resource. The assay data can be entered either in well numbers (on a plate) or in dilutions. To convert among them, see the Edit menu. Both the well and dilution data allow the '<' (for first well and dilution only), '>' (for last well and dilution only), and '/' characters. 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.
2015-02-16
Sesame web pages converted to HTML5, redesigned, new style sheets, new floating menu, etc.
2014-12-23
The names of files uploaded into Sesame containing "weird" characters will be stored in Sesame in a modified form, where the "weird" characters are replaced either by a space or an underscore, to assure that the files will be downloadable on the supported platforms. Code refactoring, both on client and server side.
2014-12-08
The Screen Type, Screen No, Screen Plate No, Well No, Droplet No and Well Label fields were eliminated from Crystal and Antigen Binder Views. 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: Clear Mutations Data, and Clear ORFs. To set the ORFs in the Sequences table, drag and drop ORFs or ORFs from WorkGroups. Changes in Create Sample Records specifications implemented. Drag and drop of V Screen wells to Samples and Antigen Binders implemented. Drag and Drop of Screen and EM Screen wells to Crystals implemented. Further improvements in error checking and messages, and in creating different records from different screens. New icons, and couple changed ones.
2014-11-23
Amino Acid Mutations field added to Sample. New menu item in V Screen menu: Create Sample Records. This creates Samples from the selected V Screen wells (in Screen or Sequences table). The AA Mutations from the Sequences table will be copied to the Amino Acid Mutations field of the Sample. 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.g. Samples from V Screen wells. In Lab Resources Item View Preferences the handling of newly added Fields in Views is improved. The known bugs were eliminated and other improvements were made.
2014-10-17
Clear Selection added to ORF(s) View's Edit menu.
2014-10-13
The Board's initial sizing modified to handle multiple monitor setups. Protein View added to Rukh.
2014-09-11
New {DBID.} and {.DBID} variables added to URL base definition strings, and the Show URL method for External References and Database References Fields is updated to handle them. Using this, we can now show the webpages for UniGene IDs also. User Profile View code improvements.
2014-09-02
Major changes in the user interface for handling and managing associations and memberships in Sesame: simpler and more intuitive. The (old) Associations View (and menu item in Options menu) is gone. The Membership View is improved. The new GUIs and menu items are: New Lab, New Site, and New PI in the Options menu; Lab Members in the Lab Resources; Site PIs, Site Staff in the Site Resources; Apply To Site, PI Group Members in the PI Resources. 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: Cell, Virus, DNA, RNA, Other. (The Sample View's configuration changes depending on the category.) The JOBREQUEST item was renamed to TASK. Handling of PFAM Domains and DB References improved in Bulk ORF Upload and Bulk ORF Update. Show URLs, Show Files in Associated Applications, and Show Images in Associated Applications is now operational in Linux too. The framework for defining and building the menus for Modules changed. The known bugs were eliminated and miscellaneous improvements were made.
2014-06-13
Search By Number for Target Requests, Y2H Requests and Time Requests replaced with Search By List. Other server side code improvements for Time Requests. More code improvements for popups. Tier 2 code refactoring.
2014-06-01
Bunch of new popup classes that handle queries (sublasses of AbstractPopUpQuery) and reports (subclasses of AbstractPopUpReport) were created/extracted from the classes that manage the searching and reporting business at item level at the client side. Other code improvements. Couple reports improved at the server side.
2014-05-22
Big changes in the popup framework that affected all popup classes (more than 250) and resulted in a huge decrease in startup time (around 10 times faster) on the client side of the Modules. 'Can Do' checking speeded up. Changes in Resource Event Listener and handling. New GUI component, CellDisplaySpectrometer, used in Sundial. The known bugs were eliminated and a bunch of small changes. Version number changed to v.20140525.
2014-04-11
Faster login. Jars re-signed with a new Code Signing Certificate and re-deployed.
2014-04-04
'New Item' submenu was removed from the Board's Windows menu. 'New [Item]' menu item was added to the Views' main menu to create and add a new View to the Board. A new item View (of the given type) can be also obtained by double clicking on an "item type" node, e.g. 'SAMPLE', just below the root node of the Search Result Tree in the main window, or by 'drag and drop'-ing the node to the Board. Delete Notebook Page was redone. Framework improvements.
2014-03-28
Second tier object dispenser changed from "pool" to "on demand" type. Security enhanced for the critical dispenser methods. Calendar related bug corrections and improvements. New overlay icons. Other small changes.
2014-03-21
Major changes in Calendar and Calendarslot Views, both in GUI and functionality. For example, all-day events can be scheduled, new options for repeating events, new fields, etc. See the Help Pages for all the details. Practically, both the client and the server side for these views is new. New GUI component: ColumnTableRenderer.
2014-02-18
Improved error handling and messages for Timeslot management in Schedules. Site Staff can, from now on, reserve and release Timeslots in Schedules for Site Users, but only in Open Time Periods. Other small improvements were made.
2014-01-16
Jar deployment process modified according to the new, further enhanced security model (starting with Java 7_51), that mandates the Permissions manifest attribute in jars. The jars were recreated and redeployed.
2013-11-11
TargetTrack schema changes.
2013-10-18
Java 7_45 Oracle and Apple screwups related to system getProperty, setProperty, and key namings in jnlp files are taken care of.
2013-09-30
The Component Count report for 2d Xtal Screens is practically a new report due to extensive changes. The Details report for 2d Xtal Screens is extended with the details for the crystals.
2013-09-24
New 'csvtabledata' structure that alows to define the column types for CSV data, thus permitting to correctly sort the columns of the table presenting the data. 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.
2013-09-16
New 2d Xtal Screen report: Details. In addition to the All report, this includes all the details for the elements of ternary mixture.
2013-09-10
New 2d Xtal Screen report: All. It includes the ternary mixture and crystallization buffer data also.
2013-08-02
New 2d Xtal Screen reports: Crystals, and Publications. New 2d Xtal Protein report: All. 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.
2013-07-29
The Calculate menu item is new in the 2d Xtal Screen's Edit menu. This calculates the lipid mixture parameters (lipids negative charge, lipids positive charge, lipids charge, lipids molecular weight, lipids tail length (mean), lipids tail length (std), lipids unsaturation (mean), lipids unsaturation (std), lipids unsaturation %, lipids PC headgroup %, lipids PE headgroup %, lipids PG headgroup %, lipids PA headgroup %, lipids PS headgroup %, lipids CA headgroup % and lipids other headgroup), the protein charge at the pH, the LPR (mol/mol), and the estimated LPR (mol/mol) for every crystal. 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.
2013-07-23
The font for the menus, popup buttons, headers, dropdowns, and all the components that have text element, is changed from bold to plain for a more modern look and feel. 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.
2013-07-15
New View in Jafar: 2d Xtal Screen. 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. To add 2dx Xtal Detergents, Lipids or Proteins to a 2dx Xtal Screen's Ternary Mixture, use drag and drop. New 'All Accepted' reports for 2d Xtal Detergents and 2d Xtal Lipids.
2013-06-18
New View in Jafar: 2d Xtal Protein. 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.
2013-06-04
New Views in Jafar: 2d Xtal Detergent, 2d Xtal Lipid. 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.
2013-05-21
New Views in Lamp Module: 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. The Person records linked (d&d) to Water and B Samples can be declared as 'bill to', 'site', and/or 'collected by' persons, locations or institutions. Rush field added to Water Test/Service Lab Resource. Source field added to Sample View. The Sample Form, Sample Kind and Water Sample Source Lab Resources were made more general, and they are now used by all three Sample (Sample, B Sample and Water Sample) Views. Additional items that can be DB Dumped: C Screen, Library Sample, Mass Sample, WorkGroup, Combinatorial Library, Plate. The reported bugs were eliminated and improvements were made across the codebase.
2013-05-01
Past Access field added to Site Profile, to let sites allow timeslot manipulations in the past, up to 30 days. 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: Antigen Binder, Primer, Protein, Sample, Action, Labfund, Lab Protocol. Text reports modified to not export the empty fields, thus making them more readable and more compact. Report All added to Water Test/Service. 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: Mutations, Root ORFs. New report in ORF Details View: TargetTrack (TT) Trials.
2013-04-10
New Lab Resources: Water Test Reason, Water Test/Service, Water Well Construction, Water Sample Source. County and Professional License fields added to Person and User Views. New fields added to Lab Profile: Mailing Address, Email, Phone, Fax, Accept Water Test Request, Water Test Guideline, WDNR ID, WDATCP Certificate, EPA ID. Storage Date and Expiration Date fields are added to every view that contains storage location fields. Multiple Look and Feel related modifications and adjustments, mostly necessitated by changes in OS X L&F. Now the Sesame modules can again use the native Aqua L&F on OS X. 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.
2012-12-10
Barcode printing added to Stock Solutions and Robot Racks. 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. Improved table editor/renderer autosizing, and row height calculation for RTables. Couple unused fields removed from the detailed ORF view and the orf tables, and the changes were propagated across the codebase. New Antigen Binder View in Sheherazade and Rukh Modules, for handling antibodies, etc. New Application Lab Resource, currently used by the Antigen Binder View only, but it can be easily added to other views if/when needed. 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.
2012-09-27
The upper limit of the Notebook editability is increased to 30 days. Improvements in well level barcode printing for screens. For debugging purposes, one can now send the barcode data to the Java console, by defining and selecting a barcode printer with 'DEBUG' name and 'DEBUG' IP address. 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). New V Screen Report, Get Genealogy. Two new menu items in the main menu of the Genealogy View: Show All Nodes, and, Show Main Nodes. The maximum amino acid sequence length is extended to 16000 characters. New ORF No, and WorkGroup Well columns in the V Screen's Sequences table, and a new, Set ORFs, menu item to set them, in the Edit menu. Couple new, and couple modifed, TT Rationale and TT Annotations Reports, for ORFs and for Complexes. New Lab Resource Bulk Load menu items, Verify Bulk Update ORFs, and, Bulk Update ORFs. 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. Couple bugs were eliminated and other improvements were made.
2012-08-03
'Measurement' added to the protocol node I/O types. The TargetTrack deposition method is updated to handle the different I/O types. 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. The nodes with no I/O type will be not exported, nor the nodes that have no value. For the details, see the TargetTrack deposition 'how to' page. New Barcode variables for V Screens: {WELLCOORD}, {WELLPREVC}, {WELLROOTC}, {WELLLABEL} for well level barcode and/or label printing. At least one of these variables have to be used in the barcode definition, to toggle the well level mode. In this case, {JRNO} will be interpreted at well level. 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.
2012-07-24
New field added to the Person View, TargetTrack (TT) Contact Reference, a table of labfund-ORF# pairs. The Person will be listed in the contactInfoRefList element for the targets with the selected ORF#-s, in the TT deposition for the labfund. The ORFs have to be linked to the Person. New Person report: TT Contact References. The TT Target View, in Jafar, now shows the 'flow' attribute in the Partnerships field. New ORF reports: TT Target Categories, TT Target Protein Types, TT Target Contacts, TT Target Labs, TT Target Partnerships, TT Target Rationales, TT Target Annotations. These reports generates parts of the TargetTrack depositions in a more human readable form. New Complex reports: TT Target Rationales, TT Target Annotations. New TT Target reports, in Jafar: Target Categories, Target Protein Types, Target Contacts, Target Labs, Target Partnerships, Target Rationales, Target Annotations. These reports are generated from the TT data, for the selected PSI center. 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.
2012-07-08
Support for Java 1.5 dropped. Lot of code upgrades to use Java 1.6 features. Update ORF added to the ORF(s) View. New Notebook menu items: Add New Child Page, Add New Reply Page. 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 Person reports: Address Book, TT Roles, TT Partnership Roles. New V Screen Edit menu item: Create Child Screen Table. Couple bugs were squished.
2012-05-09
The TargetTrack report is now specification v1.4 compliant. Everything related to the now defunct PepcDB and TargetDB has been removed from the codebase. The TargetTrack Views are removed from Sheherazade. The V Screen sequences table is modified to handle segments, maximum 8 per well. Couple small changes.
2012-04-08
New 'Primer Plate' View. 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.
2012-03-31
Drag and drop of a PepcDB or TargetTrack Protocol to a Lab Protocol will copy the content of the dragged item to the drop target. The Lab Protocol and Action lab resources are added to Jafar. New ORF(s) menu items: Create Protein Records, Create Sample Records. New WorkGroup menu item: Create Sample Records. The new TargetTrack v1.4 specification partnership role details flow attribute is now supported both by the Action Lab Resrouce and the Person View. Some bugs were eliminated and couple small improvements were made.
2012-03-22
The TargetTrack XML files, all or some of them, now can be uploaded to Sesame. New Views added to Sheherazade and Jafar, to handle the TargetTrack data: TT Contact, TT Protocol, TT Target and TT Trial. 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. If the TargetTrack XML files contain proper database references to Sesame ORFs in the databaseRefList elements, and, if the Sesame instance where the PepcDB data is uploaded contains the Sesame ORFs referenced, the Sesame ORFs, the TT Targets, and the TT Trials will be linked together. The TargetTrack data is accessible to every Sesame User. At this Sesame instance, the TargetTrack data will be reloaded weekly, after the new TT XML files are released.
2012-03-01
Sequences tab added to the V Screen View, to handle AA and NT mutations and sequencing, or, any other type of well level files. New Edit menu items for bulk upload of mutations, and bulk upload and download for files. New Report menu item for mutations. Pull Plate Read Data added to the Edit menu, for transfering the plate read data from the parent V Screens. Sundial Schedule View modified to send email notification only when a Timeslot is released. New menu item in WorkGroup's Edit menu, Load Selection, for loading the well selection from a file. Target Rationale field added to the bulk ORF upload popup.
2012-01-23
Support for two generic type plate read files, 'Well Coordinate and Value CSV Lines' and 'Value per Well Lines' is added to C Screens and V Screens. 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.e. 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. For Library Samples, like for C Screens, multiple reports, including Worklists, can be generated. ORF# column added to the TT Partnership Role table in Person View. New 'Cells' and 'Virus' Sample Component Lab and System Resources. New Labfund edit menu items: Add Category, Delete Category, to modify the budget table. New Labfund Report: All, to generate a budget report for all funds in the lab. Couple small improvements were made, and the known bugs were eliminated.
2011-12-08
New Bulk Load menu item, 'Add TT References', for adding the TargetTrack references to the ORF's DB References table. The ORFs can now be uploaded or created as lab visible only. The ORF related queries and reports can be restricted to lab visible ORFs. The 'targetPartnershipList' element is added to the TargetTrack report. New TargetTrack system resources. New menu item for ORF and ORF(s) Views, to set an existing, lab owned, ORF's visibility to lab only, or, to everybody. Multiple plate reads can be attached to C Screen wells. The 'Amount' field is added to the C Screen View. Couple small improvements were made, and the known bugs were eliminated.
2011-11-22
Unit, i.e. the laboratory at a Department, field is added to the User Profile View, and to the long registration popup. The value of this field is used for the 'lab' element in TargetTrack reports. New fields added to the Action Lab Resource: TargetTrack (TT) Lab, TT Partnership Role and TT Protein Type to allow mapping lab actions to these TartgetTrack elements. 'Blue Eye' right hand side button added to Lab Protocol's Action field. New Jafar module for browsing the PepcDB data. Jafar only handles the four PepcDB items; the PepcDB Contacts, Protocols, Targets and Trials. New 'Person' View, for keeping track of collaborators. In the Person View, the 'TT Role' and 'TT Partnership Role' fields are TargetTrack report specific. To make a Person (collaborator) TT target specific, link it to the appropriate ORF(s). New 'TT Target Rationale' and 'TT Target Annotation' fields added to Complex and ORF Views. These fields are lab specific for ORFs too, i.e. only the members of the lab that entered them can see them. New additions to the TargetTrack report: the 'targetProteinType' element is supported; the 'targetPartnership' element is supported; non-Sesame lab members, i.e. out of PSI center collaborators can be added to the contacts and targets using the Person View; the 'lab' element can be defined for both Sesame users and external collaborators; statuses with out-of-center 'lab' element can be added to the trials via lab action mappings; the 'targetRationale' element is supported; the 'targetAnnotation' element is supported; the 'protocolDescription' element is supported.
2011-11-13
New TargetTrack System Resources: Partnership Name, Partnership Role and Target Protein Type. The Linked Items field now shows the links between Samples and V Screens, and Samples and C Screens also.
2011-11-10
New Search By ID List for PpepcDB Contact and Protocol. Schedule Mailing List field added to the Site Description Site Resource. 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.
2011-11-03
New 'C Screen' View added to Rukh. Used for handling combinatorial screens, e.g. phage display, yeast display, etc. The C Screens can contain multiple samples per well, a library sample, and multiple stock solutions. The Samples and the Library Samples are added by drag and drop to the table in the Screen Tab. 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. Data from Tecan Infinite M1000 and Thermo Scientific Multiscan Ascent plate reader files can be attached to C Screen wells. 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 48000 per C Screen. The Robot Racks content (tubes) are now built by dragging a Stock Solution from the Stock Solution Lab Resource's search result 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: add an empty tube, move a tube up or down, and, show the stock solution in a tube. Compound added to the Stock Solution Type (SS Type). The Source Organism tables are now sortable by double-clicking on a column's header.
2011-09-23
New 'Complex' View, for handling complexes of different kinds. 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.
2011-09-09
Two new PepcDB Target Reports: Progress, and Rivalry. 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. Couple small bugs were eliminated.
2011-08-29
New 'V Screen' View added to Rukh. 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. Data from Tecan Infinite M1000 and Thermo Scientific Multiscan Ascent plate reader files can be attached to V Screen wells. If a different plate reader needs to be supported, let us know. Generic worklists can be generated for parent-child V Screens. Different Hit picking strategies are implemented. The editable columns can be set by right clicking on the column's header. The number of wells is at the moment limited to 48000 per V Screen. Dilution Ratio (1/x) is added to the Sample View, to record the denominator, an integer, of the dilution ratio. 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. Couple small improvements were made, and the known bugs were eliminated.
2011-06-24
TargetTrack deposition generator added to Report ORF menu. The PepcDB related System Resources were updated to support the new TragetTrack schema. The Duration (in days) column is added to the Lab Protocol Lab Resource's Action field. The values that corresponds to the actions that maps to NIH Actions will be reported in TargetTrack's stepDurationDays element.
2011-05-13
Users can now attach Images and Files to ORFs, like to other Sesame Items. They are only visible in the lab they were attached from.
2011-04-11
Material Repository report updated to submission format v19. 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.
2011-03-13
New I/O type field for protocol tree nodes, so they can be classified as input (experimental variable) or output (measurement) nodes, or they can be left unclassified. Beside alerting the users visually, the input and output nodes will be exported to PepcDB depositions. A new right side button is added to the Protocol Tree cell in Lab Protocol View, to allow one to edit the name and the I/O type of an existing node. 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. 'Blue Eye' added to the ORF(s) cell in WorkGroup View, to show the details of a selected ORF. 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. 'Today Only' option is added to open timeslots search and report. Export Metal Assay Data to CSV report added to the Metal Assay View. 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.
2011-01-11
The PepcDB XML files, all or some of them, now can be uploaded to Sesame. New Views to handle the PepcDB data: PepcDB Contacts, PepcDB Protocols, PepcDB Targets and PepcDB Trials. These Views are read only. 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. If the PepcDB XML files contain a proper database reference to a Sesame ORF in the databaseRefList, and, if the Sesame instance where the PepcDB data is uploaded contains the Sesame ORFs referenced, the Sesame ORFs, the PepcDB Targets and the PepcDB Trials will be linked together, and they will be shown in the affected records view's linked items cell. The PepcDB data is accessible to every Sesame User. At this Sesame instance, the PepcDB data will be reloaded weekly, after the new PepcDB XML files are released. Components cell added to the Library Sample View. A minor change in Leginon Image Bulk Load to support the latest version of the Leginon software. 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.
2010-11-09
Labfund column added to the Contact table in the Labprotocol View, to allow different roles for the same person depending on the labfund. The PepcDB report generator will use the roles associated with the selected labfund, and only those. New Combinatorial Library Lab Resource in Rukh. New Library Sample View in Rukh. Couple improvements were made and couple bugs were eliminated.
2010-10-30
Rack and Shelf fields added to every item with location fields that haven't had them.
2010-10-24
New Lab Resource Can Do functionality and GUI. 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. Gene Locus, and Number of Predicted Transmembrane Segments are added, and Number of Cysteines, e280, and Absorbance are removed from the Workgroup ORF(s) cell table, and from ORF(s) View. Create ORF menu item added to the Target Request 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. Create ORF menu item added to the ORF(s) 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 selected ORF, set as a parent, or clear if no ORF is selected. The created ORF will be automatically added to the ORF table. When a new ORF is created in the database in any way, the NCBI Taxonomy ID will be automatically added to the Database References field. The Target Requests in a lab are now searchable by the PI Name also. Couple improvements were made and couple bugs were eliminated.
2010-10-03
The Signal Peptide Lenght ORF field is now bulk uploadable, like DB References. The Signal Peptide Lengths file can be verified before the upload by every Lab Member. The Signal Peptide Lengths are only attachable to lab owned ORFs, only by the Lab Master, and those who Can Do. Couple improvements were made and couple bugs were eliminated.
2010-09-27
New 'PEPC' fields have been added to Labfund to conform with PSI:Biology related PepcDB requirements. The PepcDB and TargetDB report generators have been modified accordingly. The (Number of) Transmembrane Seqments ORF field is now bulk uploadable, like DB References. The Nof Transmembrane Segments file can be verified before the upload by every Lab Member. The Nof Transmembrane Segments are only attachable to lab owned ORFs, only by the Lab Master, and those who Can Do. Transmembrane Segments filed is added to the Search ORFs By Characteristics popup. Couple improvements were made and couple bugs were eliminated.
2010-09-01
The Labfund field is added to the Administrative Use Only part of the Target Request View and to the Search By Lab popups. New fields in Search by ID popups for Hardware and Software. In ORF Details View, the Database References field is editable by the Labmaster and those who have cando for bulk loading DB references. There is a new menu item in the ORF menu, Save DB Refernces, to save the changes. New Report menu item for WorkGroup and ORF(s) Views, Export ORFs To CSV (More Than You See), to create a file that is very close both in content and format to a file that can be used to bulk load ORFs from a CSV file. The bulk load ORFs from CSV file is changed, the gcodetable column has been added to it, and the format of the parent_no field has been made more flexible. 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. will transfer the Labfund from the parent item to the newly created items. Many small improvements were made.
2010-08-07
New right side small button for EM Screen score images for showing the image viewer with the thumbnails of the images attached to the particular well for the particular scoring. The tooltip of a thumbnail shows the filename. A click on the thumbnail will show the full image. Couple small improvements were made.
2010-08-02
The Primer Calculator class have been rewritten, to allow one to apply new constraints on the calculated primers. The same new options have been added to the Search ORF by Criteria popup. For the new options, a default value can be set for labs through the Lab Profile Lab Resource.
2010-07-18
CrystalFarm and Leginon DB related default values 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. Couple small improvements were made.
2010-07-11
New Leginon Image Bulk Load menu item in EM Screen's Edit menu, for attaching images and image related data to a scoring column from a Leginon. New Source DB Distribution report for ORFs in main window's Report menu. The report shows the ORF uploads. New Source DB Start Date and Source DB End Data fields were added to some ORF queries and reports, so they can be restricted to ORF uploads. Couple small bugs were eliminated and couple small improvements were made.
2010-06-16
New in Screen View: clone and remove rows now works for multiple selection. Clone rows will add the new rows to the end of the table. Move Up and Move Down a row in Screen and Droplet tables. 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 -1. 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: clone and remove rows now works for multiple selection. Clone rows will add the new rows to the end of the table. 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. 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 Crystal View's Cryo field: clone and remove rows now works for multiple selection. Clone rows will add the new rows to the end of the table. 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. Couple small bugs were eliminated and couple small improvements were made.
2010-06-08
New Image Bulk Load menu item in EM Screen's Edit menu, for attaching images to a scoring column from the file system. 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.
2010-05-23
New location fields added to Workgroup View. Any (asterisk) Labfund related bug in TargetDB report eliminated. Couple small bugs were eliminated and couple small improvements were made.
2010-05-09
The Labfund field has been added to every fitting query and report, thus allowing to easily handle multiple projects inside a Lab. Couple small improvements were made.
2010-03-11
Major changes in the Screen GUI and data structures. Fields and columns added, a tab is eliminated, new and improved functionality, support of the more general plate types, etc. New Electron Microscopy (EM) Screen item. It is almost a Screen with only one droplet. But not quite. And not for long. All the Screen functionality is available for EM Screens too, Inventory reports improved. Bunch of new fields added to Plasmids. New Cloning Method, Clone Type, Expression System and Negative Selection Lab Resources in Plasmid Components group. Sample Category, Sample Form and Sample Kind moved from System Resources to Lab Resources Sample Components. 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. Material Repository Files is a new WorkGroup level Report. Screen Type field added to Crystal. New Columns in the Cryo field. Couple bugs were eliminated and a bunch of small improvements were made.
2010-01-17
New columns added to the ORF Surgery Definition table to increse the options for ORF surgeries. New C-term deletion and C-term addition fields in Plasmid View, that are used in Create Proteins methods for Cleaved AA Sequence determination like the N-term deletion and N-term addition fields. New fields added to the Plate Lab Resource to enable more general plate geometry description. Couple bugs were eliminated and couple improvements were made.
2010-01-13
Storage Temperature field added to every item with location fields. 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.
2010-01-10
New PEPC Stop Status System Resource. It contains the list of the PepcDB stopStatus values. The PEPC Stop Status field is added to the Action Lab Resource, so some of the lab actions can be associated with a PepcDB stop status. New Genomic Library Lab Resource, to keep track of the plates of genetic material, used for example in amplificaton reactions. New workgroup report: Genomic Library Worklist. The Amount and Location cells are added to the Stock Solution View. 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. The Compound, Recipe and Vendor records are now linkable to the Stock Solution records. Multiple improvements and updates in PepcDB report generator. Couple bugs were eliminated and couple improvements were made.
2009-12-20
The Labfund field is added to most of the Views, thus making it possible to more easily track multiple projects inside a Lab. The Labfund is an already existing Lab Resource in Salary And Effort group. 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. New Pfam cell in detailed ORF View: the table now consists of two columns, and a show URL button is added to the right side. The format of the ORF bulk upload was changed to support the new Pfam format, and to handle the KEGG db references. 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: Lipid and Detergent. Used by the Screen and Crystal Views. New Morphology Lab Resource. Used by the Crystal View. New ORF Search: By DB Reference List. Sesame looks good and runs good on Windows 7 too. Couple bugs were eliminated and couple improvements were made.
2009-11-11
New fields and columns in Employee Record and Labfund Views in Bazaar. New Salary And Effort Details report. The Status and Type Lab Resources are now orderable using the Move Up and Move Down menu items and buttons. The Plasmid descriptor line in search result tree has been changed. The Plasmid genbank_id and Primer biotech_no fields have been moved to the External ID table. 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. The Genetic Code Table and Genetic Code Error fields have been added to the Plasmid and Target Request Views, and to the AA Calculator. New ORF types have been added to the ORF Type System Resource. Native N-term Chunk is an ORF with N-term and no C-term, Native C-term Chunk is an ORF with C-term but no N-term, and a Chunk is an ORF with no N-term and no C-term. 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. Improved error messages all around. The latest changes in PostgreSQL jdbc driver have been accomodated. The URL Base System Resource is made more flexible by allowing one to specify the position of the DB ID in the URL Base string using the {DBID} variable. Couple bugs were eliminated and many small improvements were made.
2009-08-10
Create Primer default parameters can be set for labs through the Lab Profile Lab Resource. The functionality of couple cells in Labfund and Employee Record Lab Resources was modified. New Address Book and Salary Data Reports in Employee Record View. Search ORFs By List improved. Improved exception handling and more detailed error messages for network related problems. Couple bugs were eliminated and couple small improvements were made.
2009-07-14
Many updates and improvements in Rukh. Barcode lab resource structure and GUI modified. Couple bugs were eliminated.
2009-06-05
Support for TECAN Infinite M1000 plate reader added to Rukh.
2009-05-25
Major changes in Sundial: The GUI for the PI Permit View (PI Resources) has been modified to use the current framework for Resources of this type. The two new Site Resources, Site PI and Site Permit, allows the Site Administrators to maintain a list of PIs that have access to the Site, and to maintain everything related to those PIs: their contact info, the info about the funds needed to pay for the services provided by the Site, the PI's group, and the Site Permits permits issued to the group members. It is up to the Site and the PI to decide if they want to use this new mechanism to control the access to the Site, or if they want to use the legacy mechanism where the PI creates a Sesame User account, and manages his group and the related resources. The new Site PI entities are not Sesame Users, and they don't exist in a Sesame Instance, except for the Site that created them. A real PI can exist both as a regular PI and as a Site PI in a Sesame Instance. A Sesame User can be a group member of both a regular PI and a Site PI, and can have Permits to access a Site from both kind of PIs. The main difference between the two types of PIs is that the regular one is a Sesame User, while the Site PI is not. Hence, while the regular PI can access all the Requests of his group, create different Request related reports, and view the Schedules, a Site PI can not. However, the Site Administrator can provide all this info for the Site PIs. So a regular PI has more work to do, but has more control, while a Site PI delegates both to the Site Administrators. A Permit Type field is added to the Requests, and it shows if the Permit associated with the Request was issued by a PI or by a Site. The Permit field will show Permits of both kind. The Gene locus field has been added to Search ORF By Content, Criteria, ID, DB Reference, and Characteristics popups. Target Requests can now be linked like any other items. The new QIAGEN BioRobot Slot Lab Resource allows one to name the source and destination slots. The new QIAGEN BioRobot Worklist in the Report menu of the WokrGroup View allows one to generate a BioRobot 8000 worklist for workgroup reformatting with the current WorkGroup as the destination. The Create ORF Variants popup now allows one to control the reattachment of the start and stop codons to the ORFs obtained by surgery. If either one was missing before the surgery, it will be missing after the surgery too. WorkGroups now can be designated as Appendix workgroups. Appendix workgroups can not have children, nor other items linked to them. Hence not every workgroup can become an Appendix WorkGroup. A new field has been added to the GUI that indicates if a WorkGroup is Appendix or not. Use the Set Appendix On and Set Appendix Off menu items in the WorkGroup's Edit menu to set/reset the value of this field and the appendix status of the workgroup. If possible. A typical use of Appendix workgroup would be to keep track of after the fact reformattings. The actions attached to Appendix workgroups will be reported as actions attached to the parent workgroups, and will not create new PepcDB threads. New Salary And Effort Lab Resource: Employee Record. It is part of the Bazaar Module only. It allows tracking of salary, salary with fringe, effort, and related data for employees. New report for ORFs: Export To CSV File. This report creates a CSV file with a format and content very close to the file that can be used to bulk load ORFs from a CSV file. Due to atrocious Aqua look and feel for Java under OS X 10.5, the default look and feel for the Sesame Modules has been changed to Metal, to the default Java look and feel. Couple bugs were eliminated and many small improvements were made.
2009-04-01
Category, Kind and Form fields added to Search Sample By Owner, By Content, By Action, By Amount, By Date, and By Protocoltree popups. Create ORF Variants method tuned a bit.
2009-03-26
New menu item in ORF(s) View: Create ORF Variants. Enabled only for those who can upload and delete ORFs. The ORF Variants will be created for the selected ORFs in the table based on the selected ORF Surgery List. The ORF Surgery List is a new Lab Resource that describes how the ORF Variants will be created from an existing ORF (number of amino acids to be cut from the N-terminus and C-terminus, nucleotide sequences to be added to the 5' and 3' ends.) New module, Bazaar, targeting Lab Administration related tasks. New, and unique to Bazaar, resources are the Budget Category System Resource, and the Salary And Effort Lab Resources: Employee Category, Labfund and Pay Period. Couple bugs were eliminated and couple improvements were made.
2009-02-15
The ORF(s) View that shows the results of ORF searches in Board now supports drag and drop from one ORF(s) View to another ORF(s) View, thus allowing one to combine the results of multiple searches and to sort the combined result by a table column. New global report for Schedule to report Open Timeslots for all Spectrometers in a Facility from Now through all the defined Billing Periods. When the User is not loggid in, only the Public Facilities will be shown in the dropdown. WHen the User is logged in, only those will be shown that the User has access to. Like for Calendars, a click on the empty part of a day's title bar in a Schedule will toggle between day and month views. New Search and Reports were added to the Schedule View.
2009-02-09
New Calendar View. There are three types of Calendars: for owner's eyes only, lab viewable, and lab modifiable. There are different search and reporting options both at Calendar (current) and global (across all the Calendars in the default lab) level. The global search and report functions respect privacy. The calendars are linkable to other items, and vice versa. A single click on a calendarslot will show more details on the inner window's status bar, a double click will bring the calendarslot up allowing one to reserve, update, delete, or replicate it with a shift. A click on the empty part of a day's title bar will toggle between day and month views. Because of the new Calendar View, the formerly known Calendar View from Sundial has been renamed to Schedule View. New, global search functionality has been added to Schedules. These work across all the Spectrometers at a Site. The maximum number of selectable actions for Search By Action queries has been increased to 30. New report at a WorkGroup level: DB Reference counts. The selection scores field in detailed ORF View has been eliminated. The same info is accessible in WorkGroup View. The Heat field is added to the detailed ORF View and to WorkGroup's ORF field. The Heat value has been defined by Craig Bingman. The Heat is based on DB References, and it is automatically recalculated after every DB Reference upload. The Selection Heat column in WorkGroups is the frozen heat value at the time the ORF was added to the WorkGroup. Search ORF By ID has been modified. New Search ORF By DB Reference. Sort by Heat added to Search ORF By Content and Search ORF By Criteria. Heat added to Search ORF By Characteristics. New Report ORF, to report Heat distribution. New Lab Resource: ORF Modification. ORF Modification field has been added to detaild ORF Views and to Target Request View. The ORF Modification is bulk uploadable, either from ORF csv file (new format alert, see the help pages,) or, separately, like DB References. The ORF Modification file can be verified before the upload. ORF Modifications are attachable only to lab owned ORFs. New Lab Resource: Target Request Category, e.g. internal, external, extraterrestrial. Request Category field added to Target Request View, and some Target Request queries. Start and End Date added to Report Actions By List, and the itemlist field now alows DB No Lists to be selected. ORFTYPE added to the FASTA description line in Report ORF Export To FASTA. New Barcode variables: {WELLCOORD}, {WELLPREVC}, {WELLROOTC}, {WELLLABEL} for well level barcode or label printing for WorkGroups, and {NAME} for all the items Barcodes are definable. In Board, the inner window's title bar now shows the item's name. The corresponding window selection menu item too. JPEG-EXIF files, i.e. photos from digicams, are now uploadable to Images cells. The TargetDB report now creates an err file too. The functionality of the Custom Report has been improved. The Help menu now coupled to the new Help Pages. The jnlp files are now also versioned. On some operating systems, this might require a restart from the particular Sesame instance's home page and/or reinstallation of the desktop icon. Couple bugs were eliminated and couple improvements were made.
2008-11-01
Improved next active window selection, when a window is closed in the Board. New menu item in Associations: Report Memberships. Couple small improvements, and the initial sizing of couple popups that were missed has been adjusted.
2008-10-25
New Lab Resources Bulk Upload menu item: Verify DB References. It is enabled for every lab member, and it allows one to check if the format of the file is correct before attempting to upload it.
2008-10-21
Sesame is now fully functional in Windows Vista, and it looks good too. The initial sizing of the popups has been improved in every operating system. New Search By Location for Screens. New Create Crystal Records menu item in the Screen menu, for creating Crystal records for the selected Droplets. Also, the Droplets are now drag and droppable to Crystal records for linking purposes. New Add/Delete Droplet Additive menu items for modifying existing Droplet tables. New Search By Date For User and Search By Date In Lab for Target Requests. The ORF rows in the WorkGroup View's ORF(s) cell are now drag and droppable to every item for linking purposes. New Lab Resources Bulk Upload menu items: Verify ORFs From CSV File and Report Duplicate ORFs. The Verify ORFs From CSV File menu item is enabled for every lab member, and it allows one to check if the format of the file is correct before attempting to upload it. Report Duplicate ORFs is enabled only for those users who have LAB_RSC_ORFLOAD cando. This report will list all the ORFs in the default lab or in the system that are the same based on either the amino acid or nucleotide sequence. The maximunm length for the main_id and lab_id columns in ORF CSV files is now 30 characters. The file format for Attach DB References has been changed. See the Help Pages for details. New Lab Resources PEPC Nolist, to list ORFs that should be exempt from TargetDB and PepcDB reports, and to list Root Workgroups and Root Wells to prevent action threads from showing up in TargetDB and PepcDB reports. The PepcDB report now works at Workgroup level. Handling of items after Workgroups (Proteins, Samples, etc.) remains to be implemented. The maximum length of the Username has been increased to 32 characters. Change Default Site added to Options menu in Sundial. A server side Grim Reaper has been implemented to reclaim the inactive/orphaned connections and the related resources. The default grace period for inactivity, i.e. no server side access, is 24 hours. For Sesame Administrators, new functionality was added to the System Resources Alibaba Manager: lock/unlock a user account, quick user profile view, report locked users and report new users after a date. New System Resources: Plasmid Components Selectable Marker and Sample Components. These System Resources are drag and droppable to the corresponding Lab Resources. Framework and codebase improvements both on the client and the server side. Postgres related improvements. Couple bugs were eliminated and many small improvements were added.
2008-07-02
ORF Details View's Gcode err field has been changed to show the nucleotide sequence related errors in text format. In the same View, a new column, Database Date, has been added to the Database References field, hence the file formats for 'Attach DB references' and 'Load ORFs from CSV File' have been changed. See the Help Pages for details.
2008-05-14
New field in Action Lab Resource: PEPC Target Category. Allows one to tie the PepcDB's targetCategory to an action. The Actions can be searched based on this new field. The new PEPC Target Category System Resource contains all the possible values for this field. The Lab Protocol's Contact field now allows multiple contacts per lab protocol, and lets one define their roles. The list of roles is maintained through the new PEPC Contact Role Lab Resource. This resource is used to determine the value for PepcDB's role tag. Examples for roles: PI, co-director, co-investigator, scientist, archiver, etc. New field in Lab Protocol Lab resource: Parameters. The Parameters are tag/value pairs. Consider them as constants for the protocols, because unlike the tree nodes, they can not be changed through the views that use the protocol. One should put here values typically buried in the body of the protocol, that needs to be accessible for different reports, depositions, or data mining. The Tags for the Parameters are defined through the new Protocol Tag Lab Resource. New column in WorkGroup's ORF(s) cell: Root Coord. It is empty for root wells, i.e. those wells that have no parent. For other wells, it contains the root well's coordinate. If applicable, the Linked Items field will contain [root] links to root workgroups. New fields added to the Search WorkGroup By Number popup: Root workgroup number, and Root well coordinate. Roots And Branches report added for individual workgroups, hence it is accessible through the Report menu in the Board, when a workgroup window is active. It works for selected wells, or, for every well, if none is selected. This reports will show for the root wells of the selected wells all the branches extending to a leaf well. For a selected well, the root well's coordinate is either in the Root Coord column, or, if it is empty, then in the Well Coord column. At every well along a branch extending from a root to a leaf, all the actions attached to the particular well will be shown ordered in time. The actions are prefixed by the item through (and to) which they were attached, and by the lab protocol used. If there is one, the corresponding NIH action is also shown.
2008-04-30
Sundial's Permit View has been modified to monitor permit changes, and to warn the user when the changes might be lost.
2008-04-26
Two new reports, accessible from the main application window's report menu for workgroups: NIH Selected At Root, and, Leaves And Roots. Enabled for Lab Masters and users with the appropriate Can Do. NIH Selected At Root for every leaf well in workgroups backtracks to the corresponding root well, and checks if there is an action at the root well that maps to NIH's selected action. Leaves And Roots for every leaf well in workgroups returns the last and previous to last action in time that has the leaf well's coordinate (i.e. the last action could have been added to a protein linked to the ORF in that particular well), then backtracks to the root well, and shows the first action (in time) attached to the root well, and the ORF No in it. The leaf and root workgroup well coordinates, and the mapped NIH actions are also shown.
2008-04-24
NIH Selected report added for individual workgroups, hence it is accessible through the Report menu in the Board, when a workgroup window is active. It shows if an action was added that maps into the NIH selected action along the backtracked path.
2008-04-06
Sesame now handles multichain targets, i.e. targets with more than one polypeptide chain. Add Chain and Remove Chain are new menu items under Edit menu for View Protein, Sample, Mass Sample, Metal Assay and Target Request Views. While linking ORFs to a Protein, Sample, Mass Sample or Metal Assay, one can select the chain into which the data from the ORF will be transferred. A place for the chain already needs to exist for the transfer to happen. The Screen View has been also modified to support adding multichain Samples to Droplets. Isotope Labeling is now chain level. The XML Dumps for all the above mentioned Views are changed due to the underlying data structure change. Linking say a Protein to Sample will transfer all the chains if selected. Adding an action to a multichain record, i.e. a record that has multiple ORFs linked to it, will add the action to every linked ORF. Similarly removing the last action will remove it from the every linked ORF. If multiple ORFs are linked to the Parent, i.e. the Drag Source, in the linking process, if the Child, i.e. the Drop Target, contains the Actions cell, all the ORFs linked to the Parent will be transferred and linked to the Child. The same will happen while creating a new Child Record (Save As Child menu item). The right side small button containing an "=" for calculate is removed from amino acid and nucleotide sequence cells. The values to be calculated will be automatically calculated when one clicks to a different row in the View, or, while the record is saved. Cluster Seed field added to Search ORF By Id, Content, Criteria and Characteristics. Cluster Seed also added to Action Total, Last Action and Elbow Grease Reports. New ORF search, By Sequence. By Amino Acid, or Nucleotide Sequence, however, full sequence search only. Retrace report added for individual workgroups, hence it is accessible through the Report menu in the Board, when a workgroup window is active. It will trace back every well to the root well, and list all the actions and their translations to NIH actions along the path. Detergent added to Sample Components Lab Resource. In Sundial, Accepting Applications from PIs is now a configurable option for Sites. New Site Resources added, Spectrometer Console and Assistance. Allows the Sites to configure choices for Console Experience and Assistance cells in Requests. Couple bugs were eliminated, and couple small improvements were added. Framework improvements both on client and server side.
2008-02-07
Website revamped.
2007-12-09
New menu item in Report menu, Bulk XML Dump, for dumping all the selected items in the lab.
2007-12-03
New Clone and Submit functionality added to Sundial Time Requests, for Site Administrators and Staff only.
2007-11-15
New small button added to Images and File cell, to allow loading from URL addresses starting with "http://". Bulk upload from CrystalFarm now also allows URL access to images.
2007-10-29
New Post View. Allows labs to have a discussion board. Posts are linkable to other items. New CSV file format for ORF upload. Couple bugs were eliminated, and couple small improvements were added.
2007-10-18
New Caliper LabChip Input File menu item added to WorkGroup View's Report menu, to create an input file for Caliper LabChip Automated Electrophoresis System, for all, or for selected ORFs. Antimicrobial and Protease Inhibitor added to Lab Resource Sample Components. Labs can now control if the Job Requests sent to a user will be shown after login. Total makeover of Sundial's Schedule View in Site Resources, with new functionality added.
2007-10-08
New CrystalFarm menu item added to Lab Resources Bulk Load View's Bulk Load menu, to load and attach scores and images from Bruker Crystal Farm to Sesame Screens.
2007-10-01
Multi key selection added to ordered dropdown lists.
2007-09-19
Search ORFs by ID now allows one to search the ORFs based on the attached external db reference.
2007-09-08
Sesame is now Java 1.6 compliant. And that is the recommended JRE version. It is significantly faster. Java 1.4.2 is not supported anymore. Java 1.5 is still ok. Jafar has been retired. New Lab Resources: Item view preferences allows the lab master to define what rows in views are lab editable (by default all), what rows are visible (by default all) and the row order. Actions, where actions are defined. To attach them to lab protocols, they have to be dragged and dropped to one. Action order can be changed using the new Up and Down buttons on the side. Target status, to allow custom target statuses in target requests. 5'- and 3'-extensions are now nameable lab resources. Sample components, to define buffers, internal references, etc. for samples and metal assays. Stock solutions got a new GUI. Action maps are used by Mapped Actions Report, and they let one to replace a group of actions with a new one (only for the report), to obtain a simplified report. Flow Sampling Points allows to predefine sampling points for Flow Report. When a lab protocol is dumped to XML, one can choose to exclude the text in curly braces from body. New System Resources: Sample Form, Sample Kind, for the same named fields in samples. URL base, to form a valid URL in combination with external ids, or database references, and to allow to show them in a browser. Spectrometer Console, to define choices in the same field in Time Requests. Report List allows us to define custom configurations per labs used by Custom Report. Once we develop a tool to help building these configurations, it will become a lab resource. Until then, you have to send us an email to sesamelims@gmail.com if you need a configuration written for you. To give you an idea, this would allow one to show in Custom Report View a particular protocol tree node, action if exists, and the quality controlled amino acid sequence from a dropped protein (or for proteins defined by a list), and field(s) from say attached samples or mass samples to given proteins, etc. Basically it allows selecting any field from the Views, and from linked records, and even selecting them by some criteria. Probably it can not do everything, but it can do a lot. New Spectrometer Site Resource field: Choosable by User. If it is off, users can not submit a Time Request for the particular spectrometer. The Site Administrator for the site still can. The content of the Info field from Spectrometer resource is now visible in Time Requests View too. For the selected spectrometer. New View: Metal Assay. While linking a sample to it, a lot of data can be transferred. Take a look at the menu items to learn more about it. New functionality in Protein View: Create a cleaved protein (from this one.) New fields in Target Request View: Request Status History, and Target Status History, to keep track of status changes. New External ID fields in every View (where it makes sense.) Can show the associated URL (if there is a URL base defined for it in the system.) No more Collaborative Groups. None of the current stuff is using them. And we are heading to new direction. A lot of GUI changes: tabbing in protocol tree moves to next/previous node, right click now operational on OS X, buttons added to file and image cells to show the selected item using the associated external application and to edit the label and type, column sizing based on content, hitting a return when a Sesame Module starts up will bring up the login panel, with a focus in user name field, etc. New columns added to ORF cell in workgroups: well label, source organism, and last action. the last action column is the first one so one can easily see the last action (the last action is also in its right place, at the end of the row.) Auto sizing of the Visual Plate has been improved. The labeling too. New, Reformat By Previous Coordinate functionality added, to allow to keep the same format from plate to plate. If possible. New, Select Empty Wells menu item for ORFs in workgroup. Improved action based search for ORFs in a workgroup. "AND"-ing and "OR"-ing the actions is now supported. The ORFs in workgroups can now be searched based on "numbers," residue length, pI, number of Cys, etc. Smaller, bigger, from a range, etc. Different criteria can be combined, and the search can be restricted to a particular source organism. The ORF list is now autolocked for modifications, if an action is added to any of them, or, if any of them is linked to any other Sesame Item. When the ORF list is unlocked, i.e. while building a new workgroup, there are two new buttons on the right side for repositioning ORFs in the table. New Workgroup level reports: Worklist, to generate a worklist. Action totals, to get an action count for the workgroup (with a possibility to list the associated ORFs.) Genealogy, to generate a genealogy tree for the selected ORF. The nodes in the tree are double clickable and draggable to the board. There are some simple operations on the tree too, like route hiliting. This is the first version. The next one will use a graph instead of a tree. The Get Genealogy Report is also available in (single) ORF View, to obtain the genealogy for it. In the same ORF View, a button is added to the db references field, to show the associated URL (if everything is configured properly.) New and improved searches for most of the items: ORFs can be searched by numbers (like ORFs in a workgroup). Also items that have an amino acid sequence can be searched by numbers. Search by Action now let's one "OR" or "AND" the selected actions. Search by ID now handles the new external ids too. Source Organism has been added to orfs and actions report. New reports, for all the items the particular ones are applicable: Custom, described already above. Action totals allow to group (and count) actions by multiple criteria (action, user name, lab protocol, source organism), and it can be restricted by different criteria (start and end date, etc.) Last Actions, last one, or last two, restricted in a time interval, by protocol, on a source organism. Elbow Grease, returns the count of actions per items. Can be restricted by a time interval, lab protocol, or it can count only a particular action. Mapped Actions, for every item for the particular sesame item type will generate a (simplified) report based on action groupings defined in action maps. Every group of actions will be replaced by the group's name. The group order defines the column order. A Makeup can be applied. The actions in groups are defined by (lab protocol, action) pairs. The actions processed can be restricted to a time interval, source organism, etc. Flow report allows one to define a sampling points, each consisting of multiple )lab protocol, action) pairs. A sampling point defines all the items that have at least one action from the sampling point attached. When the Flow is Normal, the next sampling point is applied on top of the previous one (i.e. the results are "AND"-ed). As a result, there are no "holes" in the rows. When there is no flow, the sampling points are shown as is (independently from the previous one.) If there are missing actions, there will be no holes. Wish flow is like a wish sandwich. Two slices of bread, and you wish that there is something between. Or in case of actions, that there are no holes. Couple non-critical bugs were eliminated. As always, there are Framework improvements both on client and server side.
2007-01-29
Robot Racks Lab Resource not showing up in Board bug corrected. Count Selection menu item added to workgroup Edit menu and to button bar, Count Selections returns the number of selected orfs in ORF(s) cell.
2007-01-15
New argument added to Billings report popup in Sundial Requests. New small button added to scan the uploaded files for pulseprograms in NMR Experiment View. New Labprotocol Step lab resource, and a new Step field in Lab Protocol, to define the step (stage) in a multistep lab protocol thread. The new Linked Protocols field in Lab Protocol allows one to build labprotocol threads from labprotocol steps, by defining the previous and next step(s). Retired checkbox added to Lab Protocol's action. Selecting it, an action will become invisible when attaching actions to items, while the history and data consistency for reports will be preserved. New Search ORFs By Number added to the WorkGroup View's Search menu allowing one to search a workgroup's ORFs based on residue length, molecular weight, pI value, etc. Screen Optimization added to Screen View's Edit menu. Select one or more wells from an existing screen for a starting point. Add as many stock solutions to them as you want. The concentration points for every stock solution can be defined as a loop, or as a list. If you like the resulting optimization screen, save it, and link to it the original screen. The maximum number of wells for the Optimization Screen is 10000. Couple non-critical bugs were eliminated. Framework improvements both on client and server side.
2006-12-28
Billings report added to Sundial Requests. New NMR PulseProgram lab resource for mapping pulse programs to NMR experiment types. Experiment Type field in NMR Experiment View changed to table, to allow handling of multiple, different experiments attached to a single record. By Content search added to NMR Experiment View. While linking a Sample or an ORF to a Screen, one can now define a well range for every droplet, hence, the same droplet can contain different samples over different wells. New fields added to Plate lab resource, and the GUI has been changed from table to individual record format. ORF upload from CSV files has been updated to handle quoted fields, no space is required for empty fields, and the error messages have been improved. Commas are not allowed anymore in Lab Protocol lab resource Action strings. Couple non-critical bugs were eliminated. Framework improvements both on client and server side.
2006-11-26
Bunch of changes in Target Request View. New Barcode variables. New viewer for attached .sdf files. Couple non-critical bugs were eliminated. Framework improvements both on client and server side.
2006-11-13
Email to Sesame added to Options to contact the Sesame administrators. Set PI Info and Set Alternate Contact Info added to Target Request. ORFs are now deletable, if not used, by those who can upload them. New Time Request reports. Lab Protocol number to title conversion bug for non-choosable protocols corrected. Couple other non-critical bugs were eliminated. Framework improvements both on client and server side.
2006-10-31
Create Bait from Y2H Request bug in Rukh, and the Update/Save Lab Profile bugs were eliminated.
2006-10-15
Lamp is resurrected as the Metabolomics module. Category field (protein or compound) added to Sample and Mass-sample Views that control the GUIs content. New Job Request View, to handle job requests in a lab. Job request status suggestions: new, open, cannot reproduce, as designed, fixed, verified fixed, documented, duplicate, deferred. Some type options: software, publication, large scale production, hardware, screening, other, etc.Target Request View has been improved, and new functionality has been added. External id field added to Views. Email option and emailed column was added to Info field, to email to the owner of the record the selected info. New queries and reports added to some Views. Recipe changed to View from a lab resource. Search capability and more reports added to lab protocol, labeling pattern, robot rack, barcode, site spectrometer and choice list resources. Choosable field added to the same resources, that control their availability in dropdown lists. The Views now visually reflect the editability of the fields depending on the ownership, lab membership, etc. Y2H Screen exports improved. Some GUIs appearance improved. Show Board added to Options menu. Some Bulk Loads were made more robust, and better error messages were added. Email greeting added to newly registered users. Couple bugs were eliminated. Framework improvements both on client and server side.
2006-09-06
Lab Protocol View: Definitions added to actions.
2006-09-03
Couple Java 1.5 introduced bugs, and some other non-critical bugs were eliminated. Framework upgrade.
2006-08-22
Barcode printing for Compounds added.
2006-08-20
Screen View: Add Screen is now operational in Edit menu. Using this option one can add well-wise a screen to the current screen. WorkGroup View: Export ORFs to CSV added to the Report menu.
2006-08-11
Compound View added to Sheherazade. Target Request View: Couple new fields added. Couple "Export ... to CSV" menu items added to different View Report menus.
2006-07-12
Jar module resurrected, to handle Target Requests. New Search by List and Search By Linked Item List. New DBNo List View, to handle named item lists that can be used in Search by List and Search by Linked Item List. Printing of labels and barcodes for multiple items of the same type is operational again. The Create Protein Records from workgroups has been modified to handle optional modification of N- and C-terminal sequences and to add an optional tag sequence, and to automatically calculate the Cleaved, Un cleaved and Quality Controlled sequences. ORFs dragged from the search result tree, and dropped to a workgroup will be added to the workgroup's ORF list.
2006-03-19
Crystal View added to Sheherazade and Well. View REBASE URL menu item and button added to Restriction System and Lab Resources.
2006-03-12
Plasmid Resources added to System Resources. PNG type Images can be attached to different Sesame Items (beside JPEG and GIF), and viewed in the Board. New option added to file upload, that will upload the content of subfolders also. Temperature and Pressure fields added to NMR Experiment View. Couple bugs were terminated, and couple improvements were added.
2006-03-09
New queries and a new report added to Software and Hardware Views. Couple bugs were terminated, and couple improvements were added.
2006-03-08
Lab protocol added to Software and Hardware Views. View PUBMED URL added to Citation menu in Citation View. URL column added to Restriction, Tag and Cleavage Lab Resources.
2006-03-07
Selectable Marker, used by Plasmid View is now a lab resource. Couple bugs were terminated, and couple improvements were added. New Sesame logo.
2006-02-06
New version of Sesame LIMS released. Release notes, new help pages, and a buffed out website will follow. Until then, just go ahead, and check it out.
2003-11-16
Sheherazade: The Genie Views are now in Sheherazade also. Labmasters can generate email, phone and address reports for labs they manage. New membership invitation panel. New linking to ORFs or previous items, with transfer possibility. Improved reporting and printing. JDK 1.4.1 compliant. Many internal improvements, and a bunch of bugs eliminated. For news about the different views in Sheherazade, read the appropriate module news. Also the new things from Sheherazade are available in other modules. Genie: New fields added to detailed ORF view. Attach scores enabled for labmasters. New reports in Workgroup View, action stats for lab and users. Search by action in Workgroup View, both wg and ORF level. Search by action in ORF View. The output of ORFs and action report now contains the ORF and parent wg number. Ouroborus: New fields added to plasmid view. Amino acid calculator cell added. pI is not calculated at the moment. The field is editable though. Lamp: Three sequences are now associated with a protein record: cleaved, uncleaved and quality controlled. Each of them is in amino acid sequence calculator cell. pI calculation is not implemented yet. New sample cell, that shows all the linked samples from Jar. They can be viewed by pushing the blue eye. Jar: NMR sample view evolved into more general sample view. new fields added to the view, among others the three sequence cell (transferable from Lamp), and the volume transaction tracking cell (no entry can be deleted, in case of error a corrective transaction needs to be entered). Inventory reports added to reporting menu. The Mass Sample view also sports the new amino acid cells. Camel: Internal changes only. Well: Status field added to screen. Batch number added to stock solutions (and they propagate everywhere a stock solution is used). New robotrack report. Limited support for screen export to CrystalScore. Droplets are now linked to Jar instead of Lamp records. Robotracks open for lab. Jafar: Some details polished. New visualizations available due to changes in DEVise. Rukh: Version One. A lot of new and/or improved options. Sand: Internal changes and bug corrections. Sundial: New calendar handling. Multiple can be simultaneously viewed, and they can be printed.
2003-08-18
Sheherazade: The changes made in the other modules are in Sheherazade also. Genie: The update profile allows more user data to be entered. Any number of files can be attached to workgroups. File type added to lab resources. The info and location fields are now updateable by the lab members. Many framework upgrades. Ouroborus: The update profile allows more user data to be entered. Any number of files can be attached to primers and plasmids. File type added to lab resources. The info and location fields are now updateable by the lab members. The Plasmid View sports a new construct field. The Construct's components are now freely definable by the users. The maximum length of the amino acid sequence has been increased to 4000, and the length of the genetic code to 12000. ORF number and Workgroup number fields added to Search by Number pop-ups. Many framework upgrades. Lamp: The update profile allows more user data to be entered. Any number of files can be attached to proteins. File type added to lab resources. The info and location fields are now updateable by the lab members. Model and experimental amino acid fields added to protein view. Many framework upgrades. Jar: The update profile allows more user data to be entered. Any number of files can be attached to nmr- and mass-samples. File type added to lab resources. Model and experimental amino acid fields added to mass-sample view. The info and location fields are now updateable by the lab members. In addition, on mass-sample view, the instrument used, no spectrum, spectrum complex, measured mass, stdev mass, clean up steps, operator and exp AA sequence fields are updateable by the lab members. Many framework upgrades. Camel: The update profile allows more user data to be entered. Many framework upgrades. Well: The update profile allows more user data to be entered. Stock solution lab resource views updated. Stock solution selector for dropdowns based on robotracks added. Many framework upgrades. Jafar: Full release. The update profile allows more user data to be entered. Some details polished. Rukh: Beta version. Almost all of the process tracking is done. The fine tuning and adjustments are happening while Rukh is used in parallel with the classical approach. Sand: Major framework upgrades, still in progress on some views. The permit selector is now part of the time request table. Many resource panels have been redesigned. Sundial: Major framework upgrades, still in progress on some views.
2003-06-17
Rukh: Alpha version, partial functionality, mainly for testing.
2003-05-20
Sheherazade: The changes made in the other modules are in Sheherazade also. Genie: Stop/Start codon bug eliminated. Parent/child relations added for ORFs. One can export the genetic code from selected (or all) ORFs in a workgroup into a series of files (look under the Report menu). Many framework upgrades. Ouroborus: Many framework upgrades. Lamp: Parent/child relations added for Lamp records. New options in Search by Number. Many framework upgrades. Jar: Mass Spec Sample View added. Many framework upgrades. Well: Gilson robot control file generation related changes. Many framework upgrades.
2003-05-15
Jafar: Beta version, mainly for testing.
2003-02-17
Genie: BLAST input file (FASTA format) generation added. Lamp: For every protein entry the protein protocol can be updated by every lab member for a given lab. Well: For a selected screen, one can now generate a Gilson robot control file (.cye).
2003-01-16
Genie: Any number of images (.jpg) can be attached to workgroups. The image size limit has been relaxed. There is a new multiple image view panel with image processing capability. Labmembers can attach info to ORFs from the detailed view. There is a new target score field, while the old score related fields are eliminated. Some fields been eliminated from the ORF view table, while they are still visible in the detailed view. The column visibility control has been moved to the Edit menu. For selected ORFs in a workgroup, the digestion pattern can be calculated. Different reporting options added on workgroup and genome/lab level. Do not skip the stop codon is the default now. For labmasters, new edit option are added to the labresource tables: copy, cut, delete, paste and undo on multiple rows. NIH actions can be defined and associated with lab actions. Search by barcode added. Reporting has been improved. Multiple reports can be catenated, saved, or printed. There might be something else. Jar: Any number of images (.jpg) can be attached to nmr samples. The image size limit has been relaxed. There is a new multiple image view panel with image processing capability. For labmasters, new edit option are added to the labresource tables: copy, cut, delete, paste and undo on multiple rows. Search by barcode added.Reporting has been improved. Multiple reports can be catenated, saved, or printed. Sheherazade: Any number of images (.jpg) can be attached to primers and plasmids, proteins and nmr samples. The image size limit has been relaxed. There is a new multiple image view panel with image processing capability. For labmasters, new edit option are added to the labresource tables: copy, cut, delete, paste and undo on multiple rows. Search by barcode added. Reporting has been improved. Multiple reports can be catenated, saved, or printed. Ouroborus: Any number of images (.jpg) can be attached to primers and plasmids. The image size limit has been relaxed. There is a new multiple image view panel with image processing capability. For labmasters, new edit option are added to the labresource tables: copy, cut, delete, paste and undo on multiple rows. Search by barcode added.Reporting has been improved. Multiple reports can be catenated, saved, or printed. Lamp: Any number of images (.jpg) can be attached to proteins The image size limit has been relaxed. There is a new multiple image view panel with image processing capability. For labmasters, new edit option are added to the labresource tables: copy, cut, delete, paste and undo on multiple rows. Search by barcode added.Reporting has been improved. Multiple reports can be catenated, saved, or printed. Sundial: One can now log in hitting the return key. Well: Buffered precipitant is a new stock-solution type, and it can be selected as a screen component also. The volume calculations haven't been updated yet to use the buffered precipitant in the screen if exists instead of water. The add result assessment is now a floating panel instead of a pop-up, so a preset assessment can be easily added to multiple droplets. To every result assessment multiple images (.jpg) can be attached, and they can be viewed in the new multiple image view panel with processing capability. The bug that was hurting the robot rack definitions has been stomped. Sand: The bug that was affecting the PIs ability to add new members to the group has been eliminated. The report view now contains an option to generate the part of the annual report in xml format for electronic submission.
2002-12-03
Sundial: A major step toward the future look and feel of the modules. The time request panel sports a new GUI. To edit a cell in the table, just click on it. Sand: A major step toward the future look and feel of the modules. The time request panel sports a new GUI. To edit a cell in the table, just click on it.
2002-11-18
Well: The results of the crystallization process can now be recorded: add/view/delete droplet crystallization assessment added to the Edit menu of the Screen view. Multiple assessments can be attached to a droplet. Every assessment is username and time stamped. Camel: Couple minor bugs removed.
2002-11-15
Lamp: Info field added to General table.
2002-11-05
Sheherazade: Info field added to General table in Protein view. Genie: e280nm, pI and absorbance factor added to the detailed orf view, and to the workgroup orf table. Primer prefix mislabeling in create primer pop-up corrected. Well: Add component and delete component from screen table functions added.
2002-11-01
Well Help pages available.
2002-10-29
Genie: The "add action" bug (inability to attach actions to ORFs) has been squished.
2002-10-08
Lamp: Tree related bug in protein protocol is exterminated.
2002-10-07
Sheherazade: New fields, workgroup and orf number added to all views. Both numbers are from Genie. For now they have to be typed in. Detailed ORF view, Add Action and Delete Last Action are added to the appropriate menus. To be able to use the last two, both the orf no. and the wg. no. needs to be defined. A step toward the new GUIs. Ouroborus: New fields, workgroup and orf number added to primers and plasmids. Both numbers are from Genie. For now they have to be typed in. Detailed ORF view, Add Action and Delete Last Action are added to the appropriate menus. To be able to use the last two, both the orf no. and the wg. no. needs to be defined. A step toward the new GUIs. Lamp: Search by owner works again. New fields, workgroup and orf number added to protein. Both numbers are from Genie. For now they have to be typed in. Detailed ORF view, Add Action and Delete Last Action are added to the appropriate menus. To be able to use the last two, both the orf no. and the wg. no. needs to be defined. A step toward the new GUIs. Jar: Concentration for Components bug is gone. New fields, workgroup and orf number added to samples. Both numbers are from Genie. For now they have to be typed in. Detailed ORF view, Add Action and Delete Last Action are added to the appropriate menus. To be able to use the last two, both the orf no. and the wg. no. needs to be defined. A step toward the new GUIs. Genie: The ORFs in workgroup view and orf view are now numbered. Detail view has two new fields: molecular weight and amino acid count (number of amino acids in the sequence). Molecular weight added to the ORF tables also. New detailed view GUI, and GUI changes in many other places too. In ORF view, the ORFs can be searched by workgroup number to simplify the transfer of ORFs from old to new workgroups. Two new searches in workgroup view: search by id will find the workgroup that contains a particular agi id; the search orfs by id will hilite on the orf tab the orf with the given agi id. It is not possible to add more orfs into a workgroup than the plate can hold. Primers can be determined for any plate (and workgroup) size. ORFs and Actions report. Well: Tree related bug in result template is gone. Add/delete row on the screen table will modify the droplet table accordingly. The location lab resources (room, rack, etc.) are finalized, and can be used. The robotrack is still volatile.
2002-10-04
Well: Alpha2. New field mix. cycles added to stock solutions (set to 0 for existing ones). Screen view has 4 tab panels now. New field, screen type added to the general. Create screen wizard now allows to define the number of wells and one can use it to set up a initial value for total volume and mix. cycles (mix. cycles is a new field here also). The volume fields (except for the total) are not editable. There is "Calculate Volumes" menu item. whenever selected, the volumes will be recalculated. To create the droplet table, a screen has to exist. Then use the menu items to create, initialize, or drop the table. The forth panel is to map the screen to plates. The screens can be searched, saved, deleted, modified. Like in every other Sesame module: the existing screens can be used as templates, to create a new screen entry in the database one have to save it as new, and for updates save should be used. The robotrack and location lab resources are still volatile; if you enter something there today, it might be gone tomorrow. Help pages coming soon, until then, you are on your own. To report bugs, or if you have comments, use the link on the main well page. The recommended way to run well is through Java webstart.
2002-09-19
Well: Alpha version, partial functionality, mainly for testing.
2002-04-03
Genie: Help pages available.
2002-03-27
Genie: Beta2 version released.
2002-03-20
Genie is ready for Beta testing.
2002-02-15
Sheherazade: Multithreaded initialization has been added.
2002-01-30
Sand: This version has a multithreaded initialization and pop-up info windows at some places.
2002-01-29
Camel: This is a major release, with too many new things to list. Highlites: multithreaded initialization for fast startup, all the control files are viewable (both on the spectrometer and the database), more intuitive experiment upload and download.
2002-01-17
Camel Help pages released.
2001-12-12
Sheherazade: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. New fields added to Primers. Ouroborus: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. New fields added to Primers. Lamp: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. Jar: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. Sand: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. Sundial: The latest version is runnable under Java Web Start and on Mac OS 10.1 also. Added SA functionality.
2001-09-12
Sheherazade: Java2 version released. The new help pages are accessible from the module's help menu also. Clipboard access. Ouroborus: Java2 version released. The new help pages are accessible from the module's help menu also. Clipboard access. Lamp: Java2 version released. The new help pages are accessible from the module's help menu also. Clipboard access. Jar: Java2 version released. The new help pages are accessible from the module's help menu also. Clipboard access. Camel: Java2 version released. Sand: Java2 version released. The new help pages are accessible from the module's help menu also. Clipboard access. Sundial Java2 version released. The new help pages are accessible from the module's help menu also.
2001-04-24
Sand: A minor revision. Billing periods introduced, to make Sand more Sundial friendly. For a user, a billing period is e.g. the month a time request is submitted. Couple small bugs has been fixed and the cost info has been made clearer. Sundial: Couple small bugs fixed.
2001-04-03
Sundial help pages available.
2001-03-20
Sundial is ready for Beta testing.
2001-01-15
Sheherazade is functional. This version contains Ouroborus, Lamp and Jar.
2000-10-10
Jar: The user interface underwent a major surgery (menus, menubars, and other changes).
2000-10-09
A major new version of Sand. Too many new things to list. Couple teasers: The user interface underwent a major surgery (menus, menubars, and tons of other changes). Wanna know how much time you asked for, were given, actually used and how big hole did it burn in your pocket? And all that categorized by PI, user, spectrometer, project or site? Check out the Report View. Mike, you would have enjoyed using this one...
2000-06-16
Ouroborus: Primer management is a now included in Ouroborus. The primers can be linked to the plasmids.
2000-05-19
Ouroborus: The applet is now a signed one, hence fully functional: image loading and saving, and report generation and saving is operational now for Microsoft IE and Netscape browsers. Jar: The applet is now a signed one, hence fully functional: report generation and saving is operational now for Microsoft IE and Netscape browsers. Camel: The applet is now a signed one, hence fully functional for Microsoft IE and Netscape browsers. Tested on SGI-IRIX-XWINNMR-Netscape platform, not tested on PC-NT-XWINNMR-IE/Netscape platform. If the XWINNMR directory structures are the same on both platforms, Camel will work.
2000-05-17
Lamp: The applet is now a signed one, hence fully functional: image loading and saving, and report generation and saving is operational now for Microsoft IE and Netscape browsers.
2000-05-08
Lamp: Administration/Recipe tab is now operational. It contains a list of wetlab recipes, visible by lab members, and maintained by the lab master.
2000-05-05
Ouroborus: All Sesame Modules upgraded to sense the operating system and browser identity in use by the client. A report will be displayed to the user listing the probable behavior that can be expected of the Module under the current operating environment. User MUST have Javascript enabled in their browser for this feature to work. Lamp: All Sesame Modules upgraded to sense the operating system and browser identity in use by the client. A report will be displayed to the user listing the probable behavior that can be expected of the Module under the current operating environment. User MUST have Javascript enabled in their browser for this feature to work. Jar: All Sesame Modules upgraded to sense the operating system and browser identity in use by the client. A report will be displayed to the user listing the probable behavior that can be expected of the Module under the current operating environment. User MUST have Javascript enabled in their browser for this feature to work. Camel: All Sesame Modules upgraded to sense the operating system and browser identity in use by the client. A report will be displayed to the user listing the probable behavior that can be expected of the Module under the current operating environment. User MUST have Javascript enabled in their browser for this feature to work. All Sesame Modules upgraded to sense the operating system and browser identity in use by the client. A report will be displayed to the user listing the probable behavior that can be expected of the Module under the current operating environment. User MUST have Javascript enabled in their browser for this feature to work.
2000-03-20
Ouroborus: View to Lamp, to see the proteins created from the given expression plasmid. Lamp is now functional, except the figure and report related methods. Lamp is connected to Ouroborus and Jar. Jar is functional, except the report generation. Connected to Lamp.
2000-02-29
The Sand Tutorial is now on-line.