Table of Contents
BumberDash is a tool created to allow users to evaluate MS scan data on their own machines. It runs silently in the background, using only computer resources that would otherwise go to waste.
Pause/Start Button: Clicking pause will prevent BumberDash from processing any further jobs on the queue. If a job is being processed it will be finished but no more jobs will be started. Clicking start will resume processing.
Full Log Button: While a job is running the log button will bring up a screen indicating the history of what the running programs have shown. The most recent five lines of output will also be shown in the Recent Log Events box for details at a glance.
File->Run: From this menu the Instrument Template editor (more on this later) and IDPicker can be run. BumberDash will try to detect the latest version of IDPicker, however if this is not successful or an older version is desired the location can be set manually. The location can be reset to defaults at any time. This action also serves as a quick way to have BumberDash find the latest version of IDPicker if an upgrade has been installed alongside the old version.
Pause/Resume Log Button: Clicking the pause button will temporarily stop displaying new log information, allowing the user to examine information without interruption. Clicking resume shows all information that was missed and starts showing new information again.
In the Bumbershoot system, which drives BumberDash, there are two options for examining MS data. The first option, which is selected by default, is to examine the input file through a database search (using MyriMatch). The second option is to use tag sequencing, which is carried out by first deriving tags from the input file (using DirecTag) and then reconciling those tags against a database using TagRecon. Once an option is selected BumberDash will provide boxes to allow the user to specify the configuration files for the requested choice and show what configurations are currently in place that differ from the default values. This extra information can be hidden by clicking the tall button next to the configuration box
The name field is not required but it allows the user to name the job so it can easily be distinguished in the queue. If the name field is left blank the output directory name will be used by default. The user can select one or more input files by clicking the browse button and selecting the files needed (multiple files can be selected in the same folder by holding down the ctrl button and clicking each one, or by simply dragging a selection box over the group). Previously run input files can be selected by clicking on the drop down list. Once an input file is selected BumberDash will automatically fill in the output directory box. If the folder the input files came from is not the desired location it can be changed by clicking the browse button or selecting a previously chosen path in the drop down menu. The FASTA database box works the same way as the input files box, except that only one file can be selected.
The configuration boxes accept either ".cfg" files, ".pepXML" files (MyriMatch or TagRecon), ".tags" files (DirecTag), or temporary configurations set in the editor. If no file is selected a new file or temporary configuration can be set by clicking the "New" button, which brings up the configuration editor. If a ".pepXML" or ".tags" file is selected BumberDash will automatically get the properties used and treat the file as a custom configuration set with the file name as its name. If a ".cfg" file or temporary configuration is selected it can be edited in the same manner, only the button will say "Edit" instead.
There is an option to limit the number of CPUs used during execution of the jobs by adjusting the CPUs box on the bottom right; however the default "Auto" setting is recommended to expedite the process. Also to prevent overwriting of results the checkbox next to the "Name" box can be selected, placing results in their own directory within the output directory.
This screen can be accessed while adding a job by clicking the button next to "Browse" in the configuration section (this button will say "New", "Edit", or "Convert" depending on the situation). If no prior configuration is specified the configuration editor shows the internal defaults of the program it is creating a configuration for.
Some fields will be grayed out unless the "Use Advanced Mode" box (lower left corner) is checked, in which case all fields will be editable and an additional tab will become available with more options.
Any configuration that differs in value from the default will change its label color to green, allowing for quick identification of what is changed. If an instrument template is selected from the upper left box more colors can be displayed depending on the contents of the template. Blue text indicates that the value is consistent with the default values; however it differs from what is in the instrument template. Purple text indicates that a value is different from both the instrument and the default. If the "Load" button is clicked, all values will be reset to the contents of the instrument template.
"Save as New" will create a new ".cfg" file and select that as the current configuration, while "Use Once" will prompt the user for a name (which can be left blank to use the job name) and only use the configuration in the current run without saving as a file.
Full documentation on configuration parameters can be found at http://fenchurch.mc.vanderbilt.edu/bumbershoot/index.html. In addition, information can be quickly accessed by clicking on the blue question marks that appear next to documented parameters.
The instrument template editor looks exactly like the standard configuration file editor with the exception of the bottom bar, which now contains interface options for working with instrument templates. The program selection combo box will change what program mode is being worked on upon selection. The "Save Template" button will either save a new template or update an old template, depending on which is selected in the instrument box. Delete and rename work as expected, but must be accessed by first clicking the "More" button to show the popup menu. For obvious reasons the "New" instrument template cannot be deleted or renamed.
Import and Export can be used to backup templates or distribute them among colleagues. Upon clicking one of the two, BumberDash will ask where the file is located or where it is to be saved. After that is filled a screen like the following will appear.
While importing the top box shows the list of templates available in the selected file, and while exporting it shows all templates that are stored locally. The contents box shows what configuration settings differ from the default in the instrument template. In this particular case the selected template contains only default settings. Templates can be moved between the two boxes using the four buttons in the middle. Only templates in the bottom box will be imported or exported.
To create a new job either click on the bottom row in the queue (Labeled "Click to add new job") or go to File->"New Job". This will bring up the Add Job form where parameters of the job can be specified. Once all parameters are correct the "Run" button will place the job on the queue. If there is a problem with one or more of the parameters the field will be highlighted in red and the job will not be queued until they are fixed and "Run" is clicked again.
As long as BumberDash is not paused, jobs will be processed one at a time until there are no more unfinished jobs in the queue.
Right-clicking any job in the queue will bring up a menu containing a few options. "Lock" will tell BumberDash not to process the job selected. A locked job will turn a different color and will be pushed down if the queue comes to it. Locked jobs can be unlocked through the right-click menu, allowing them to be processed again. Only jobs which have not been processed and are not running can be locked. Likewise the "Edit" option will only function on jobs that have not been processed and are not running. Edit will bring up the job configuration form and allow the user to make changes. While jobs are being edited they will be treated as if they were locked for processing purposes. Clone works on any job visible, and will bring up a configuration form with the job’s parameters copied in. From there the job can be changed as necessary and placed as a new item in the queue.
The delete function can be accessed either by clicking on the "X" on the very right hand side of a job or by clicking "Delete" in the right-click menu. Delete can be used on any item in the queue, but its behavior changes depending on the status of the job it is being called on. If the job has been completed in the past BumberDash will ask if it is to delete the result (".pepXML" and/or ".tags") files that are associated with the job. Clicking "No" will delete the job without deleting the files, and clicking "Cancel" will delete nothing. If the job that is being deleted has not started BumberDash will just confirm that the job is to be deleted. If the job is in the process of running the user is given the option of deleting the files that have been produced to that point. If the user does not cancel the delete BumberDash will further give the option to save the job for later in a locked state. If the job is saved it will restart back to the beginning and set its state to "Locked". A job that has been saved and locked can be unlocked and run again, but any progress made on processing the file will have to be redone.