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SASSIE-web: Basic Usage

Access


When you access the page you will see the following splash screen on the web page.


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Here one can either login or register if you are a new user. One can also access the documentation directly from here.


Register

Users must register to use software on SASSIE-web. To register you should click the Settings Manager icon, which is the white silhouette on the right side of the splash screen.

This will open the following pop-up window to enable your initial registration.


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Choose a user id (name), a password which is at least twelve (12) characters in length and a verifiable e-mail address, then click the "Register" button.

Registering with SASSIE-web will also enroll you in the CCP-SAS: SASSIE-web Google group. This will allow you to provide feedback from within the web application.

This completes the registration process. You must login to access the software using your new credentials.


Login

Registered users can login by clicking "Login" on the left side of the splash screen.

This will open the following pop-up window to enable you to login.


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Forgotten your password?

If you do not remember your password then enter your user id and check the "Forgot password" box and then click the "Login" button. This system will send you a temporary password at the e-mail address you entered during the registration process. You must login with the temporary password within one hour or you will have to begin the process again. Once you login you can change your password using Settings Manager.

After you are logged in, the main SASSIE-web screen is visible. The currently logged in user id (name) is shown in the upper right and two new icons are available.


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By default, roll-over help is "on" and therefore when your mouse passes over most icons and input fields a small amount of descriptive text will appear. At any time you can toggle help to be on or off.

The icon that looks like a filing cabinet is the File Manager that is used to inspect and download files and folders created while using SASSIE-web.

The icon that looks like two gears is the Job Manager that is used to inspect jobs (calculations carried out by SASSIE-web modules), check locked jobs, or re-attach to either running or completed jobs.

Multiple logins

You can login to as many browser windows on as many computers & devices as you wish. Note that by default, you can only submit and run one job at a time in a given project. See Job Manager.

Logoff

At any time, to logoff from SASSIE-web you can press the "Logoff" button. Alternatively, merely closing the browser tab/window also logs off the current user from that tab/window.


Settings Manager

The same icon that you used to register becomes the Settings Manager after you login.


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There are utilities to change your password and/or your e-mail address.

The "Share project" and "Allow other users to see your User id" check boxes are for future applications and are not currently functional.

Projects:

When logging in users are automatically placed into a workspace folder named no_project_specified. One can complete all work in this directory, or alternatively, one can create new project directories checking the "New project" box and entering a project name. Thus, in the future the new project will be available as a selection in the "Select project" list box.

If you create a new project then when you return to the main web page the current project name will be listed. For example, if you create a project named "demonstration" your current project would be indicated as shown below.


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Therefore, by default, if you do not see the word "Project" followed by a project name that you have created and/or selected, then your current project is always no_project_specified.

Beta and Retired modules:

One can choose to display beta and retired SASSIE-web modules in the main menu by selecting the corresponding "Beta" and/or "Retired" checkbox in the Settings Manager. This will allow you to access beta and/or retired SASSIE-web modules as part of your work flow.

Update colors:

One can change the background and foreground colors of your SASSIE-web screen by choosing the "Update colors" checkbox in the Settings Manager. The new colors are saved and will take effect each time the user logs in.

Main Menu

On the left hand side of the web page there is a series of vertically organized icons. Clicking on one of the six possibilities will open the appropriate sub-set of modules corresponding to that section. An overview of these sections and the modules that they contain can be found in the SASSIE modules at a glance page.


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One can minimize or expand the main menu at any time by clicking the three bar icon at the top of the image above. This icon can be found in the top left corner of every SASSIE-web page.

If the Beta or Retired menu options have been activated in the Settings Manager, they will appear in the main menu. The image below shows an example of the main menu with the Beta icon.


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Documentation

On the right hand side of the web page there is a tab labeled DOCS. Clicking on this tab opens a new window to the main page for SASSIE-web documentation.

If you click this tab after you have selected a specific section (i.e Tools, Build, Interact, etc.) then the specific documentation page for that section will open in a new tab.

If you click this tab after you have selected a specific module (i.e. Align, Data Interpolation, etc.) then the specific documentation page for that module will open in a new tab.


Basic Module Usage

SASSIE-web modules are designed to share similar interfaces and methods of user interaction despite their diverse functions. The purpose of this section is to introduce some of these usage abilities without worrying about the goal of any specific module.

run name

Each module requires a user to define a "run name" which serves as the name of a folder within the current project directory that will contain the results of a given calculation.


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Within each "run name" directory, the files and folders that are generated by the specific module are placed into a folder with the same name as the module in question. For example, when running the "data_interpolation" module where the "run name" entered is run_0 the results will be written to a folder called

run_0/data_interpolation/

inside the current project directory.

The selected "run name" must be compatible with allowed path names on computer systems. The following characters are not allowed

<  > | \\ : ( ) & ; # ? * or blank space

or an error message will be presented. The first character can not be a period, ".". Any files or folders with the same name that pre-exist the run will be overwritten. The characters mentioned above are also not allowed for any file name that exists on the server.

file input

Two options are given for each file input.


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The "Choose File" option on the left corresponds to a file you wish to upload from your local computer/device.

The "Browse server" option on the right corresponds to a file you wish to upload from the server that hosts SASSIE-web.

Selecting either option will open a pop-up window for you to select the desired file from the chosen system.

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path input

A few modules process all files that are located in a single directory. In these cases, there is no option to upload a directory of files to the SASSIE-web server. In these cases an option is provided to select a path on the server


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Clicking the "Browse server for a path" will open a pop-up window to select the path from the server that hosts SASSIE-web.

input / output structure file types

In many modules the input trajectory files (files that contain structure(s) to be analyzed or used in some way) can either be in text file format (PDB) or binary file format (DCD). For a typical input such as


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the user will select either a PDB or DCD file. The module will determine the file type from the last four characters


*.pdb -<center> PDB file input

*.dcd -<center> DCD file input

where the preceding "*" is at least one allowed character (see above for allowed characters).

Likewise, for modules that request the name of an output trajectory file such as the input such as


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the software will determine the required output type by the last four characters as described above.

dynamic text area and progress bar

When a job is submitted in a module a message will be displayed under the progress bar. It will state


starting job

Soon afterwards a white text box will appear and provide any module / run specific output, for example


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If a submitted job does not start the progress bar and/or the text area is not displayed completely, then check the status of the job using Job Manager. It could indicate that a run has failed due to an error in SASSIE-web software and/or the input files of the user and should be reported using Feedback.

plots

A few modules summarize the results of a run in graphical form. For example,


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Users can zoom using your scroll-wheel on your input device, drag by clicking your mouse on the graph and moving while maintaining the click. Plots can be re-sized to their original view by clicking on the title or axis labels. One can also view values from the graph by placing the mouse pointer at any points on the plot.

molecular viewing

A few modules allow the display of three-dimensional structures. Right clicking on the viewer menu will open a pop-up menu with viewing options. SASSIE-web uses JSMol to represent structures on the web application. See the JSMol documentation for further information regarding visualization options.


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File Manager

Each user has their own persistent file system. Your files will exist after you logout and they are backed up on a regular basis on our secure server.

Files are uploaded only within SASSIE-web modules from your local machine to the server. Files and directories are created by running modules and they are stored within the "project" directory that was current when the job was submitted.

The role of the File Manager is to enable users to download files in their file system on the server to their local machine. In addition, one can remove files and folders from their file system.

One can access the File Manager by clicking the filing cabinet icon at the top right of the web page.


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This will open the following pop-up window that lists the persistent file system for the logged in user.


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The current time on the server is listed along with the "User file tree" containing the project directories. To open or close a given folder one can click on the arrow to the left of the empty box adjacent to the folder name.

For example, a test calculation was done using the Align module within Tools in the project "demo". Thus, clicking on the arrow next to the "demo" folder reveals the files and folders within.


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This reveals a folder called "_logs" and a folder called "run_0". Once a job has been run within a project directory the "_logs" directory will exist. The files within this folder are mainly for debugging purposes as discussed in the Feedback below. The "run_0" directory contains the pertinent output from our test calculation. More information regarding the internal file structure within a project can be found in Basic Module Usage.

File / Folder Download

In this example we will download contents of the folder "run_0" as a compressed tar file. In the image below the selection of the run_0 folder is shown along with the list-box display of compression options.


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Clicking the download button will create a link to a compressed file that, once pressed, will download the compressed file to your local machine. The status of the compression is noted and once completed a link to the compressed file is presented as shown below.


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Clicking on the link will then enable you to download the file. The compressed file / folder will be saved in the same folder structure that existed in the user file tree. In other words, saving the folder "run_0" and it's enclosed folders and files will show up as

demo/run_0/align/ac7.dcd
demo/run_0/align/ac7.dcd.minmax
    

Thus, for this example, "run_0" contained a folder called "align" that contained two files "ac7.dcd" and "ac7.dcd.minmax".


File / Folder Refresh and Remove

Selecting a file or folder and "right-clicking" on your input device (i.e. mouse) will pop up a small window with an option to either "Refresh" or "Remove" the selected file or folder.

Choosing "Refresh" is useful if you expect that contents in a folder have been updated, such as occurs in long running jobs.

Choosing "Remove" will spawn a message box to confirm if you wish to remove the folder and it's contents.

Notes


Job Manager

When one performs a calculation by submitting a job in one of the SASSIE-web modules the calculation is sent to the server for execution. A list of all jobs that have been submitted by the current user can be observed in the Job Manager. One can access the Job Manager by clicking the two-gear icon at the top right of the web page.


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This will open the following pop-up window that lists the jobs run by the user.


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One can scroll to the right and inspect the various fields and note the color of the job

Module section & module that the job was submitted

Project name of project used for job submission

Start, End, Duration time statistics for the job (Universal Time)

Remote IP internet address of the local machine from which the user submitted the job

Resource name of node on the cluster the job was run on.

If a job has finished (either normally or not) it will appear white.

If a job is running and locks the project directory that it originated it will be red.

If a job is locked by a run in a different project directory it will be yellow

There are options to "Refresh" the list, "Clear Lock" to allow multiple jobs to run in the same project directory, "Remove Job" to clear the information from the list, and "Reattach" which allows users to connect to a job submitted previously whether it has finished or not.


Feedback

On the right hand side of the web page there is a tab labeled FEEDBACK. Clicking on this tab opens a pop-up window


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SASSIE-web will supply the e-mail address associated with your account. Your feedback will automatically be posted to the CCP-SAS: SASSIE-web Google group page.

If you are reporting feedback regarding specific job(s), then you can click the "Select a job or jobs" button which will open a pop-up window such as


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where for illustrative purposes we show the expanded tree structure. The folders are shown in chronological order "year - month", which has "day" as an interior folder. In the example, only one job has been run by this test user:

data interpolation module was run in the no_project_specified project on May 5, 2015

Clicking this job and pressing OK then attaches the _logs for this particular run and attaches them to the feedback e-mail as shown below.


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The _logs are useful in order to debug error reports. Their inclusion is not necessary for general feedback.


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