UltraScan LIMS Integration:

UltraScan-III can take advantage of local or remote high-performance parallel computing to accelerate data fitting and to yield higher resolution results and lower RMSDs for the fitted data. Using remote resources requires the use of a LIMS system which provides access to the NSF-funded UltraScan Science Gateway for US-based investigators and their collaborators. This LIMS system integrates a relational database backend to manage cloud-hosted data storage and a web interface to submit jobs to a supercomputer, and to facilitate collaborations. UltraScan-III software can be found here.

With UltraScan-III, you have the option to switch back and forth between using a local disk-based data management system, or one that uses a remote cloud-hosted MySQL database backend. If you choose to work with the remote MySQL database backend, you will need to connect to a LIMS instance for your work, which will provide you with a custom website for your institution where you can securely store your analytical ultracentrifugation data in the cloud. This option is also required if you plan to use the high-performance computing backend with UltraScan. Each institution has its own LIMS interface and database, and it is used to manage your AUC data through a web interface. If you can't find your institution in any of the listings for the various LIMS servers then you need to request a new instance on the server that is geographically closest to you. Public LIMS servers only offer service to local resources, which are separated by country or region based on the funder of the resource, and typically reserved only for users of this region. We will typically not grant access to LIMS resources to users who are not members of the supported group. Once your institution is listed in the LIMS list, you can create an account in your LIMS instance and gain access to the resources available through the LIMS. Each LIMS instance has a local manager with elevated privileges who can set up your permission level within the database to authorize activities such as submitting analysis jobs to the supercomputing infrastructure. A new user without elevated permissions does not have any permissions on the system, other than changing his or hers own information, so a higher userlevel needs to be set up before you can use the systems. More information about LIMS user leves is available on our FAQ page.

Steps that should be taken to get the UltraScan software integrated with the UltraScan LIMS system and configured are shown below:

  1. download the UltraScan software. You can get it from the UltraScan website at:

    http://www.ultrascan3.aucsolutions.com/download.php

    Please select your platform (Linux/Macintosh/Windows) and follow the installation instructions closely (esp. for Macintosh, which requires some additional steps):

    http://www.ultrascan3.aucsolutions.com/installation.php

    Once installed, you will need to request a license. Fill out the license form and submit the request. Once you received an e-mail response, click on the verification link in your email, then you should click the "Finish Registration" button in your UltraScan registration dialog to complete the installation. Next, please go to 

    Edit:Preferences:Master Password:Change:
    and enter a master password (you cannot retrieve it, so make sure you can remember it!)
  2. Request a new LIMS instance. If you already have a LIMS instance, you can skip to step 3. To determine if your institution is set up with a LIMS instances, please select the geographic region closest to your location and then consult the list to identify if your institution is already listed:

    https://uslims.aucsolutions.com/lims_servers.php

    If not, request a new instance on the server closest to your institution. The appropriate link can be found at the bottom of each region's list. Please fill in all of the requested information and I will take care of the rest and notify you when everything is ready to be used.

    Please note that we only support requests for institutions whose users are supported by the organization providing or funding the resources. For example, we cannot grant access to users from China on the US-based ACCESS infrastructure.

    If you cannot find or identify a resource, you can always install your own UltraScan Science Gateway using your own resources. This typically requires an adequately configured server on a network with appropriate ports open, and sufficient storage and computational resources. If you are planning to make this server publically available for your users and others in your region, we can assist with the installation of this resource. Please contact our support team for further instructions.

    The LIMS instance is used to store experimental data, review experimental reports, and to submit jobs for supercomputer analysis. UltraScan-III needs to have this back-end available to allow you to use the remote computational resources.

  3. Configure your UltraScan LIMS instance:

    Once you identified the correct LIMS instance, you should create an account on it by following the links under "Login:Sign up for a new account" (at the bottom of the login page. Once you filled out the account application form, a new password will be e-mailed to you, but you can change the password after the first time login. Once you are registered, request the appropriate LIMS user level from your LIMS instance's administrator to support the functions you need from the LIMS. To access the LIMS instance with UltraScan, your account must have at least user level 2. For more information on user levels please visit our LIMS FAQ.

    After your user level has been set to "2" or higher, log into your account again and select the "Database Login Info" button. This will show you a list of credentials that need to be transferred to your UltraScan installation.

    To do that, open up UltraScan. You will have to tell UltraScan to which LIMS instance it needs to connect. Select: 

    Edit:Preferences:Database Preferences:Change:
    Fill out the information in the database configuration panel by transferring the information in the website to the GUI dialog.

    Verify that the connection is successful, and then save your new entry. Now check that everything is working by going to: 

    Database:Manage Investigator Data
  4. Please note that your network should not block incoming port 3306 from the LIMS server on which your LIMS instance is installed. Once your database setup is complete, you can proceed with the actual data analysis. Data import and the steps for analysis refinement using US-III are explained in this document.

For additional detail please consult the UltraScan Quickstart Information Guide.