CHANGES since the inital release of ArrayDB 2.0 -------------------------------------------------------------------------------- NEW TO VERSION 2.1.03 -------------------------------------------------------------------------------- This release of ArrayDB incorporated the backend changes made for 2.1.02 and made them work under Sybase. Apart from some basic SQL changes the following things have been done. o A fix in uploader.cgi that for a date related problem o A new program pathway.cgi that shows the metabolic pathways for a clone via the kegg database. o Added encryption to the authenticator modules. This makes it harder for someone to 'trick' arraydb into giving them access they shouldn't have. -------------------------------------------------------------------------------- NEW TO VERSION 2.1.02 - Oracle Version -------------------------------------------------------------------------------- This release of ArrayDB had some pretty signifigant changes to backend. The schema was changed in the following ways: 1. Every table was prefixed with adb_. The precalculated tables are the only tables to have capital letters in their name. All words in the table names are seperated with underscores. 2. The Intensities table and INTENSITIES view was dropped from the database. This was replaced with the adb_intensity table, that contains the information from the green and red channels in a single row. 3. Columns were renamed so they better reflected what they were, and to avoid using Oracle reserved words: o adb_clones table (Clones in the old schema) - Flags renamed to Set_id. This references Set_id in adb_sets o adb_clusters (Clusters) - Txmap changed size from 50 characters to 255 characters o adb_experiments (Experiments) - ExpId renamed to Exp_id to be consistent with every other table that has Exp_id in the schema - Date rename UploadDate because Date is an Oracle reserved word o adb_pictures (Pictures) - Pic_id renamed Exp_id o adb_plates (Plates) - Row renamed Plate_Row - Column renamed Plate_Column o adb_sequences (Sequences) - Sequence renamed Clone_sequence o adb_sets (Sets) - Type_id renamed Set_id o adb_slides_prints_order (SlidesPrintsOrder) - Row renamed Plate_Row - Column renamed Plate_Column 4. All programs were altered to use this new structure. 5. Common functionality was pulled out of the different programs and collected into modules. The programs that do loading into the database benefitted the most from this. 6. Queries that used temporary tables to operate were re-written not using temporary tables. o Made the Array Viewer applet smaller, so that it will better fit into the web browser. o Re-arranged the components in the options panel so that they better fit together. o Removed the "Change Confidence" button, you can change the Confidence percent value, by changing the number and pressing enter on your keyboard. o Changed the "Range" radio button to "Outliers", and re-wrote the code so that it now searches everything outside the selected range or confidence value. o Moved the status message bar up into the controls, and changed the messages to be more informative as to what is really happening with the program. o Added a "Keyword Search" button that will search for results by title keyword only, regardless of the intensity ratio or any other parameters specified. o Searching with the "Submit Query", or the "Query With Confidence Value" buttons and text in the keyword field will further narrow down the query results. o The result list, under the color microarray image, is now ordered according to the type of query performed. Less than searches are returned in ascending order by intensity ratio, while greater than and outliers searches are displayed in descending order. o Fix/Smooth out the scroll bar action. o Making a way to jump to a spot on the result image, rather than having to scroll around looking for the number of the clone that you are looking for. Change Log of functionality by file: Authenticator.pm Fixed the cookie problem with a better regular expression, to truncate the file name from the URL that the cookie gets set for. This way you will only have to log into ONE ArrayDB program, and you will be authenticated for all of them. array_viewer.cgi Changed the width of the APPLET tag to make the applet smaller, and fit on the page better. clone_info.cgi Updated the UniGene link at NCBI because they moved the page that we were pointing to. metabolism2.cgi Moved the file into the cgi directory from the jcb directory. Now all of the Image tags work, and since the cgi is viewed directly, it should have been here in the first place. AMremove.cgi and MAremove.cgi We no longer need this file, because the dl_file script will delete the temp file after it is downloaded. AMsave.cgi We no longer need this file, now we use the MAsave.cgi for both the Array Viewer, and the Multi-Experiment viewers. MAhisto_query.cgi Changed the code so thet the where clause is only generated for the parts that are needed based on the input from the applet, and changed the where clause generation so that the "range" query will return everything outside that range, instead of inside the range(query for outliers). I added some checks to determine the order that the results should be printed so that the most extreme result will be on top. Changed around the where clause generation so that if a range is selected the rows will be everything OUTSIDE that range, and not everything inside the range. This will make it easy to query for outliers that are either over or under expressed. Added a direction to the order by clause, so that greater than queries will show the highest ratio on top, and less than queries will show the lowest ratio on the top of the result list. dl_temp_file.cgi Added this file as a safe way toi download anything that it stored in the TEMP directory. It's only real use right now is to download the result set from a query of the histogram data. AMLogic.java Changed the code to use the new download and save scripts for downloading the result set and deleting the temporary files. MicroArrayFrame.java Changed the size of the thumb print on the list scrollbar so that it will scroll slowre, and also changed the page incrementer to be the same as the line incrementer. This should make the scrollbar behave better... Made some changes to the Query Result applet so that when you click on the spot's id (number from 1 to N results of your search), the spot on the image will be moved into the visible area of the result window, and the spot will be outlined with a blue square. If you double click on the spot ID the close up croped view of that spot only will be opened in the seperate frame, like the single click used to do. setupMicroArray.html Fixed the server file names, so that the pathway and download list buttons will work properly. arraydb_loader.plx Added the Image Magic convert command, so that when the uploaded tiff image is moved to it's final resting place in the arraydb/images/array_images/ directory it will be in jpg format ready to be displayed by the Java Applet. Cleaned up some stuff, and changed the program to use the system bcp, instead of the Sybase::BCP module... That module is a PAIN to install on Linux... update15KSet.plx Chnaged the way flat file names are stored, and removed all of the old code that used the Sybase::BCP module directly. This logic has now been moved out into the DBControl, and BulkLoader modules. add_administrator.plx Fixed a bug that caused a NULL value to be used as the password to encrypt, and removed the email address. Users will need to configure that on their own. Made the script conform to "use strict" guidelines. -------------------------------------------------------------------------------- NEW TO VERSION 2.0.02 -------------------------------------------------------------------------------- date: 1999/07/12 15:30:07; Fixed an error in the README file that said the ArrayDB documentation could be found in arraydb/docs, when it is really in arraydb/protected/docs. Also made the location of the INSTALL file a little more obvious. date: 1999/07/12 13:11:07; Removed the NHGRI sidebar images and JavaScript from the web pages, and changed all image links to be relative. I also included a few of the images that I forgot in the inital release of ArrayDB. All images on the web pages should work properly now. date: 1999/06/10 19:01:17; Added the guest.cgi script to the distribution, to give an example of how you can give public assess to selected experiments in ArrayDB. date: 1999/06/09 19:45:45; Seperated out the loading of the Pre-Calculated table data and titles, for some reason they weren't workingtogether, and they work fine appart. No time to worry about this right now, so I just broke it out... date: 1999/06/09 19:17:22; Changed the schema a little, changed indexes on the pre-loaded tables so they are not clustered, and added an index for the Exp_id field. Hopefully this will speed things up a little! date: 1999/06/08 17:59:00; fixed an error in arraydb/protected/LoadDB/arraydb_loader.plx line 573. changed $$ to $ in the array ref $ra_exp_names date: 1999/06/03 13:57:14; I updated the INSTALL file to let users know that they can download and use our Clones, Sequences, and Sets Tables. I posted the data to our web sitte, and gave instructions on how to bcp the data into the database. -------------------------------------------------------------------------------- INITAL RELEASE VERSION 2.0.01 -------------------------------------------------------------------------------- date: 1999/05/28; First release of ArrayDB 2.0