UltraScan Laboratory Information Management System (LIMS) Questions:

Index:

  1. What is UltraScan LIMS?
  2. What information is contained in the LIMS database?
  3. How is LIMS data accessed?
  4. Why is a LIMS instance required to submit jobs to a supercomputer?
  5. Who can use the public LIMS and HPC service?
  6. How do I obtain a  LIMS instance?
  7. How do I obtain a LIMS account?
  8. What are the user levels used in UltraScan and the LIMS system?
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  1. What is UltraScan LIMS? - The UltraScan LIMS system is a relational database system that uses a MySQL server to store a comprehensive list of AUC-related data that is relevant to the analysis of such data with UltraScan.
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  2. What information is contained in the LIMS database? - Data types stored in the LIMS system include raw data, edit profiles, finite element models, buffers and buffer component details, analytes, solutions, centerpiece geometries, Optima AUC instrument profiles, investigator contact information, rotor calibrations, analysis reports, electronic laboratory notebooks, GMP protocols, experimental designs, and supercomputer details.
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  3. How is LIMS data accessed? - UltraScan data stored in the LIMS system can be accessed either with the UltraScan GUI software, or from a web browser. The computer used for the access must have outgoing port 3306 opened to the LIMS server, as well as outgoing port 443 for https access.
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  4. Why is a LIMS instance required to submit jobs to a supercomputer? - Supercomputer analysis requires certain data located in the LIMS database to be transferred to a remote high performance computing (HPC) facility, available through the NFS Access program. These data include the raw openAUC-formatted data files, the corresponding edit profiles, and the analysis parameters and target HPC system, and source database. Once the data has been submitted to the selected resource, the jobs are queued and processed in batch mode, and the resulting models are transferred back to the requesting LIMS database. In order to assure that communications between database and HPC system are unimpeded by local firewalls and services, the database server must be hosted on an appropriately configured LIMS server. Those servers provide free storage and backups for AUC data for UltraScan LIMS users, and must be publicly available and accessible.
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  5. Who can use the public LIMS and HPC service? - The publicly hosted LIMS servers and the remote high performance computing (HPC) systems are intended for academic and not-for-profit use only. NSF Access makes multiple supercomputers available to researchers in the US, and the UltraScan development team continuously renews (since 2006) a community allocation grant to provide this resource to qualifying investigators. Currently, we have HPC servers available at the Texas Advanced Computing Center (TACC, Lonestar 6), Indiana University (Jetstream2), San Diego Supercomputing Center (SDSC, Expanse), Pittsburgh Supercomputing Center (PSC, Bridges2), and at Purdue University (Anvil).
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  6. How do I obtain a  LIMS instance? -  Before requesting a LIMS instance, please identify your geographic region and request access to the nearest LIMS server. Database connections between the UltraScan GUI software and the LIMS database are very chatty and are impacted by long distances, which cause delays when the distance is responsible for noticeable delays due to speed-of-light limits and jumps through multiple hops and gateways. A list of suitable LIMS servers can be found here. When requesting a new LIMS instance, follow the link entitled “Request a new UltraScan III LIMS Instance”. Please note that different regions provide different LIMS and HPC services. If your region is not supported, and you would be willing to provide such resources to your geographic community, please contact us and we will try to help you get set up (this service is not available for regions sanctioned by the US or Canada).
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  7. How do I obtain a LIMS account? - After selecting the appropriate LIMS instance from LIMS server that serves your geographic region click on the Login button in the left bar. Follow the link to “New Users: Sign up for a new account” and enter your information. A verification link will be sent to the supplied email address and you will need to click on this link to validate your account. In addition, a temporary password is indicated in your email, which you can use to log into your LIMS account for the first time. At this time, you should be able to log into the system and select the “Change my info” button to update your account information and user password. To update your user level (see below), you need to contact the administrator in charge of your LIMS instance. If you don’t know who your LIMS instance administrator is, feel free to contact us.
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  8. What are the user levels used in UltraScan and the LIMS system? - The UltraScan LIMS system uses user levels (ULn) to segregate user’s roles in a laboratory. 

    • UL0 is the IT admin, who is in charge of user and role management, including assigning who has reviewer and approver roles, as well as operator roles. Any UL >=2 can be operator, UL > 0 can be reviewer or approver. UL0 is not allowed to access any data, and can only execute the user management functions in the LIMS, or assign reviewers and approvers.
    • UL1 means "unprivileged user", no permissions except to view your own data in the LIMS, after UL3 has placed them there. UL1 is the default user level assigned to a new user.
    • UL2 is analyst level, analysts cannot access data owned by other people, only their own data. UL2 is allowed to submit jobs to the supercomputer.
    • UL3 is admin level, they can access their own data like UL2, but also data from other users on the system.
    • UL4 is superuser, can also perform MySQL functions on the database. UL4 is reserved for the developers.

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