Questions about UltraScan-in-a-Box (USiaB):

Index:

  1. What is UltraScan-in-a-Box (USiaB)?
  2. How do I obtain USiaB system information from the Linux command line about the hardware?
  3. What makes USiaB so secure?
  4. How does data flow in USiaB?
Return to FAQ Main Index

  1. What is UltraScan-in-a-Box (USiaB)? -  UltraScan-in-a-Box is a Linux server that provides all UltraScan components, including the Optima AUC integration and data acquisition module, in a server environment that is remotely accessed via ssh and VNC using Windows, Macintosh, Linux, Android and Iphone clients. There are two types of USiaB solutions available: A high-end server or cluster solution with large storage, high memory and at least 128 core CPU capability that includes parallel computing, LIMS service and batch mode operation all in one server. USiaB is commercially supported by AUC Solutions, please visit AUC Solutions on the web for additional information. This version is appropriate for installation in corporate environments and cGxP laboratories. The second version does not include supercomputer hardware or LIMS service inside of the USiaB server, but insteads connects to the cloud and HPC services from AUC Solutions and NSF Access, respectively. The second version will work with an ordinary PC or a modest VM with a minimum of 4 cores and 16 GB of RAM, or more if multiple users access the system simultaneously. All USiaB servers are accessed via ssh (port 22), which must be opened to the users. In addition, for the second USiaB server type, outgoing ports 3306 and 443 need to be unblocked to communicate with the remote infrastructure.
    Return to Index

  2. How do I obtain USiaB system information from the Linux command line about the hardware?

    • Total storage, free storage and used storage available on the system: 'df -h'
    • Total number of drives installed on the system (if not part of a hardware RAID): 'cat /proc/diskstats'
    • Software RAID devices, RAID levels, RAID status, and participating drives: 'cat /proc/mdstat'
    • Processor details: 'cat /proc/cpuinfo'
    • RAM (total/used/free/shared/buffered/cached/available): ‘free’
    • Operating System: ‘cat /etc/redhat-release’
    • Kernel version: ’uname -a’
    • Network interface information: ’/sbin/ifconfig’
    • Mounted drives, including networked mounted shares: ’mount’

    Return to Index

  3. What makes USiaB so secure? - USiaB is designed to be more secure than your tyical Windows computer. First, the USiaB system is typically installed within a secure laboratory environment, where physical access is well controlled. The server is installed on a private network, internal to the company, and not in the cloud. All components are executing on the server itself, not on a remote system outside of your control. Second, USiaB uses two separate networks. The first is used iby the user to connect to the server, the second is a private, non-routable network to communicate with the Optima AUC whose operating system is no longer up-to-date with the latest security standard. Communications on all networks are encrypted, and the first network can only communicate over port 22 (secure shell), and uses a multi-factor authentication: 1. username, 2. public/private RSA digital key pairs, 3. source IP address validation, and 4. optionally a passpharase. VNC is used to transport the GUI information efficiently even over a slower network, but the connection is end-to-end encrypted by forcing the connection through a ssh tunnel. Similarly, the remote maintenance by AUC Solutions is performed using a reverse ssh tunnel to AUC Solution's secure server, which avoids opening any ports on the outside of the corporate firewall - the server is therefore invisible on the Internet. Additional information is available through the UltraScan-in-a-Box overview video
    Return to Index

  4. How does data flow in USiaB? - After logging into their account, the user starts their USiaB desktop environment and starts the UltraScan software. Here, the first step is to select the GMP Data Acquisition" module from the GMP menu. A experimental protocol is created and stored in the MySQL database in read-only format, and submitted to the target Optima AUC. An operator selects the protocol from the touchscreen on the Optima and initiates an experiment. The Beckman data acquisition software consumes the Optima-specific portions of the protocol and executes an experiment, saving data into the Optima's PostgreSQL database. The UltraScan Optima data acquisition service monitors the ongoing experiment, providing status updates to the UltraScan software running on the USiaB server. At the end of the experiment, UltraScan transfers a binary copy of the data into the MySQL database on the USiaB server, and performs data editing and passes the data to the MPI module for analysis. Any manual steps are documented by collecting necessary electronic signatures. After analysis is complete, data analysis reports, spreadsheets, plots, etc. are stored in the MySQL database and a GMP report is generated, which is signed and also stored in the MySQL database. On a user-configurable schedule in the crontab service, the MySQL database and selected directories on the USiaB server are pushed to the network attached storage unit using appropriate rsync logic for archival long-term storage. Original data as well as any metadata analysis result can be recalled and retrieved from the MySQL database at will. A data flow diagram is available here.
    Return to Index