UltraScan II Frequently Asked Questions:
Frequently Asked Questions
- What is UltraScan?
- What features does UltraScan support?
- I got an XL-A, I want UltraScan, what should I do?
- Is there a release log file?
- Is there a mailing list for UltraScan?
- Is UltraScan available for the Microsoft Windows© or Macintosh operating system?
- UltraScan License
- What support is available for UltraScan?
- What are remote updates?
- How do I install UltraScan?
- What is the current version?
- Can you add xyz-protocol to the analysis methods?
- Is there a limit on the number of scans in the analysis?
- What is the minimal hardware configuration for UltraScan?
- Where do I get the shared libraries?
- Is there a static version available?
- Is the 8-hole rotor (AN 50 Ti) supported?
- Are interference optics supported?
- Can I export the results of UltraScan to other applications (for example, Origin©)?
- Is the source code available?
- Where can I obtain UltraScan?
- Are older versions binary compatible with the current version?
- Can I use Origin© with UltraScan?
- I have a problem with my data, what should I do?
- I need help installing Linux (Unix, FreeBSD, etc.)
- What Linux kernel do I need?
- What Linux distribution should I use( i.e, RedHat, Slackware, S.u.S.e, Caldera, Debian, etc.)?
- Can UltraScan take advantage of my dual Pentium motherboard?
- Is parallel processing possible for finite-element calculations?
- Can I run UltraScan on my Unix Workstation (SGI, Dec Alpha, Solaris, HPUX, AIX, etc...)
- I am running UltraScan on an SGI/DEC Alpha and all the fonts look too large for the text fields of UltraScan - how can I fix this?
- The Beowulf Monte Carlo doesn't work - what's wrong?
- Where do I send bug reports?
-
What is UltraScan?
UltraScan attempts to be a comprehensive data analysis tool for the hydrodynamic studies of macromolecules and macromolecular assemblies with analytical ultracentrifugation experiments. The main goal of UltraScan is to provide an intuitive GUI which provides an integrated data editing and analysis environment. The software utilizes fast and highly efficient analysis algorithms that are easily applied. The software should be useful to the non-expert technician with little training in the field, as well as provide an efficient interface to the experienced user who has to analyze a large amount of data in the shortest possible time. To achieve this goal, every possible task that can be automated is implemented in the software and only tasks that can not be predicted a priori are left to the user. This is always a difficult goal to attain, since the software will need many diagnostics and error checks to assure the user is not overwhelmed and led to incorrect data interpretations. Therefore, extra care has been taken in the design of this software to assure that incorrect user actions are caught by the software and clearly indicated. Similarly, warnings will be provided to assist the user in correct result interpretation. Over time, I will attempt to include the majority of published methods as modules that can be used in this integrated data analysis environment.
- What features does UltraScan support?
- Unlimited number of scan files for any analysis method
- On-line context specific hyperlink help
- Compatible with Beckman's file format
- Multi-Platform support:
-
Free for academia, nonprofit and for profit:
- Linux, FreeBSD, NetBSD, OpenBSD (Intel, Mac-PPC, Alpha, Sparc)
- MS-Windows: 95, 98, NT, 2000, XP (Intel)
- Mac OS-X (Darwin/X11 support required)
- SGI Irix 6.5 (MIPS)
- Sun Solaris 7, 8 (Sparc, Intel)
- DEC OS/F (Alpha)
- Automatic remote update (Unix only)
- Remote data analysis (Unix only)
- Integrated SQL database
- Customizable postscript graph exporting (publication quality)
- Raleigh interference and UV absorbance support for velocity and equilibrium experiments
- Integrated parallel processing environment for symmetric multiprocessing (SMP) on multi-processor computers for multi-threaded nonlinear least squares fitting engine and Beowulf support for Monte Carlo analysis.
- Internationalization support
Editing:
- Automatic file structure analysis
- Automatic temperature diagnostics
- 4- and 8-hole rotor support (AN 60/50 Ti)
- Scan files excludable at analysis runtime
- Multiwavelength support
- Time-invariate noise and radial offsets removal during editing of interference data
- Full-featured editing environment with scan
(single and range) exclusion, temperature, speed and delta-t plots,
scan spike editing module and interference data support.
Velocity Analysis:
- finite-element whole boundary modeling with integrated shape modeling function and a choice of constrained or unconstrained fits. Two Jacobian calculation algorithms available: DUD and automatic differentiation.
- van Holde - Weischet Analysis with visual boundary cropping
- Second moment analysis
- dC/dt analysis
- dC/dr analysis
- Automatic skipped-scan indicator
- Smoothing using Gaussian kernel with reflecting frame on borders
Equilibrium Analysis:
- Predefined and user-defined monomer-Nmer-Mmer equilibrium models
- Global fitting of equilibrium data for multiple scans incorporating multiple wavelengths, multiple scans, multiple concentrations, and multiple speeds
- Equilibrium Analysis: ln(C) vs. R^2, MW vs. Concentration, MW vs. R^2,
single scan fitting
Simulation:
- Real-time finite-element simulations: Models: non-interacting (unlimited components), Monomer-Dimer self-associating system, isomerizing equilibrium (2 states), user selectable models (can be saved), concentration dependency of sedimentation and diffusion. Analysis methods: van Holde - Weischet, Second Moment, dC/dt, dC/dr. Shape modeling module, equilibrium self-association simulator for monomer-dimer, monomer-dimer-tetramer and monomer-tetramer models.
- Self-Association simulator
- Global equilibrium experiment simulator
- Estimator for time to reach equilibrium
- equilibrium speed simulator providing column length, column boundaries and volume for various centerpieces and AN50/60 Ti rotors.
- Hydrodynamic property simulator
Utilities:
- HTML analysis reports and webserver support
- Data archiving
- Data export
- Buffer tables and custom buffer file creation
- Automatic buffer and temperature correction of hydrodynamic parameters
- Peptide data analysis: molecular weight calculation, v-bar calculation, 280 nm extinction calculation, composition analysis.
- Global fitting of wavelength/extinction data
- Nucleic acid MW calculation module
- System Status Monitor on Linux w/ proc filesystem support with system load meter, measures CPU load, memory usage and system load.
- Data archive and data archive rebuilder for corrupted or out-of-sequence data files.
- van Holde - Weischet integral distribution combination plot utility
- Run merging utility
- Cell content identification renaming utility
- Copying of edited data
- Scan diagnostics
- Global extinction/wavelength fitter
Database:
- UltraScan integrates a relational SQL database engine (for a listing of supported
SQL database engines click here)
for XL-A/I data. The database includes tables for:
- investigator
- date
- cell
- buffer
- associated protein and nucleic acid sequences
- experiment type
- description information
-
I got an XL-A, I want Unix-based UltraScan,
what should I do?
Since Unix-based UltraScan requires Unix to run, and Beckman's data acquisition software requires Microsoft Windows, you will have to install a second operating system. You will not be able to concurrently run 2 different operating systems on the same hardware, so you either need two separate computers, or you'll have to install two operating systems on the same PC. So, you have two options:
1. You can install Linux on the XL-A computer that came with the XL-A/I. In most cases, that requires freeing up a minimum of 2 GB of diskspace for a Linux partition, configuring your PC as a dual-boot system, so you can run both Linux and Windows on the same system. If diskspace is low, a second drive is easily added to the computer that can accommodate Linux, and, because of the low cost of harddrives today, you'll probably end up getting a big drive. The disadvantage of this setup is that you can never run the XL-A data collection simultanousely with the UltraScan software, because each task requires a different operating system.
2. You can install UltraScan and Linux on a second PC, network both PC's over ethernet. The computer can aquire data and work just fine if you add an ethernet network interface card) and you can analyze data while aquiring it on the XL-A PC. This is the preferred method. Of course, you could also leave the computers without network connectivity and transfer files using a floppy disk, CD or tape. Linux runs happily on all Intel, Mac-PPC and Sparc hardware. You probably have an old Pentium laying around, why not add some memory, install Linux and you have a decent workstation for AUC data analysis. Also see section "Hardware required".
The last obstacle you may have to overcome is your fear of Unix. This is unfounded. Although Unix is quite a bit more sophisticated and complex than Windows, most distributions now available come with excellent installation programs that make installation a breeze and hide the complexity behind well-written installation and GUI configuration software that'll get you going in no time. In addition, they come with good reference manuals and excellent documentation, written for converting beginners. Your local bookstore may also have some good reference books on Linux that are worthwhile to keep around.
- Is there Release Log file?
- Is there a mailing list for UltraScan?
- Is UltraScan available for the Microsoft Windows© or Macintosh operating system?
-
UltraScan License:
Please click here for the UltraScan License
- What support is available for UltraScan?
- What are remote updates?
- How do I install UltraScan?
- What is the current version?
- Can you add xyz-protocol to the analysis methods?
- Is there a limit on the number of scans in the analysis?
- What is the minimal hardware configuration for UltraScan?
- Where do I get the shared libraries?
- Is there a static version available?
- Is the 8-hole rotor (AN 50 Ti) supported?
- Are interference optics supported?
- Can I export the results of UltraScan to other applications (for example, Origin©)?
- Is the source code available?
- Where can I obtain UltraScan?
- Are edited data from older versions binary compatible with the current version?
- Can I use Origin© with UltraScan?
- I have a problem with my data, what should I do?
- I need help installing Linux (Unix, FreeBSD, etc.)
- What Linux kernel do I need?
- What Linux distribution should I use?
- Can UltraScan take advantage of my dual Pentium motherboard?
- Is parallel processing possible for finite-element calculations?
- Can I run UltraScan on my Unix Workstation (SGI, Dec Alpha, Solaris, HPUX, AIX, etc...)
-
I am running UltraScan on an SGI/DEC Alpha and all
the fonts look too large for the text fields of
UltraScan - how can I fix this?
You need to adjust the fontpath to make sure that the 75 dpi fonts are loaded by default first. Please check here for detailed instructions. You can also adjust the fonts in File:Configuration:Fonts
- The Beowulf Monte Carlo doesn't work - what's wrong?
- Where do I send bug reports?
Back to Top
-
General:
Yes, the release log file is distributed along with the distribution, a current listing is available here. You can also obtain the latest version of this file from the download site
Yes, for details on how to subscribe, post messages and review the UltraScan archives please visit the UltraScan mailing list page.
Yes, an UltraScan version is available for Microsoft Windows 9x, ME, 2000, NT and XP, and for Macintosh OS-X with Darwin.
For support, please contact Borries Demeler directly.
Remote updates are a feature you can sign up for that will automatically update your software each time a new version is released. Since frequent updates will be forthcoming, this feature will provide the end-user with an easy update facility which doesn't require any interaction by the user. The updates will be done automatically by a program running on your server. Currently, only Slackware is supported.
Please read the INSTALL file for details on installations.
For the latest version number, please consult the release log file on the download page.
In most cases, yes. While I can't make any promises with regard to time, all suggestions are welcome and I will attempt to integrate all of them. Please forward all your suggestions to me personally. Experienced C++ programmers are also encouraged to contribute to this software project.
All memory limitations with regard to scan numbers, datapoints/scan, cell numbers, divisions, etc. have been removed. If you find any that shouldn't be there, let me know.
Minimum hardware configuration: Intel Pentium PII-450, 128 MB RAM,
2 GB diskspace, 8 MB Graphics Display, 1280x1024/16 bit display.
Please consult the download page.
No. Static versions are no longer provided since the software itself is using libraries and would become too large and inefficient if provided in a static version. You can download the required libraries along with the UltraScan software from the download page.
Yes.
Yes. A number of editing features automatically take care of issues such as time-invariant noise (refractive index heterogeneities across the windows), integral fringe shifts and baseline shifting (breathing).
Yes. All data files are exportable in ASCII format (both DOS and Unix format) and can directly be integrated in programs such as MS-Excell, Origin, SigmaPlot, DISLIN, Gnuplot, etc. For Linux users: VMWare (http://www.vmware.com) offers a product that allows you to run Windows under Linux. It works well and allows you to run your favorite plotting program simultaneously under Linux.
Yes. UltraScan is open source. Source code is available through the subversion source code control system. To check out a current copy of the code, use the following command:
svn co svn://bcf2.uthscsa.edu/ultrascan/trunk ultrascan
The current source can also be viewed at the UltraScan wiki.
Please check the download page.
Unfortunately not. Fortunately, editing is very simple, fast and efficient, so all you have to do is to re-edit your data once and your data is integrated into UltraScan.
Yes, UltraScan data directly imports into Origin, or if you have VMWare, you can run Windows under Linux. Please see also the information on data exporting.
You can post your problem to the UltraScan mailing list, and I will attempt to answer your question if time permits, or someone on the mailing list will. Please keep in mind that commercial customers will receive preferential treatment. If you have a support contract, you can also use the phone support option. For customers with support contracts, I will log directly into your computer and debug the problem remotely.
Linux comes with excellent documentation. Try contacting a local Linux User Group (LUG) for assistance.
Any Linux kernel from the 2.4.20 on upwards can be used for the Linux version of UltraScan. A recent 2.6 based Linux kernel is recommended.
All Linux distributions known to us are supported. Any current version of Gentoo, Ubuntu, RedHat, Slackware, S.u.S.e, Mandrake or Debian can be recommended. All Linux versions are available for free by downloading from the Internet or by purchase through a commercial outfit such as Linux Mall for a few dollars to cover the costs of burning the CD. We also offer our own distribution, which comes pre-installed with UltraScan. This distribution is based on Slackware, and is distributed as an iso image, which can be burnt to CDROM or DVD and creates a bootable disk for installation.
Yes, any multiprocessor and multicore SMP motherboards are supported by Linux. SMP capability is utilized through threading in the nonlinear least squares fitting algorithms, the Monte Carlo analysis, and many utilities.
Yes, see above.
If you can't find your particular hardware distribution available on the download page, contact me and I may be able to provide you with a port.
This is most likely due to 2 issues: First check to make sure that you can log into the remote beowulf nodes without a password using either rsh or ssh. In an insecure environment, ssh is the preferred method, then you would have to generate a public key and add it to your own authorized_keys files. This works well on an nfs-shared /home directory across the cluster. On a secure Beowulf you can use rsh, in which case you need to have rshd running with the appropriate flags, and also have installed an ~/.rhosts file with entries of all your nodes and authorized usernames. Please see the documentation for your specific Unix flavor for ssh and rsh for more details. The second issue is generally due to failed environment initializations. On linux, running bash, these have to be done in ~/.bashrc, not ~/.bash_login. Do not forget to set the LD_LIBRARY_PATH variable for Qt, QWT and the UltraScan library (for dynamic installations). The system directory also needs to be defined in the UltraScan configuration.
Please contact me directly if you find any bugs. Any contributions, comments or bug reports are welcome!.
www contact: Borries Demeler
This document is part of the UltraScan Software
Documentation distribution.
Copyright © notice
The latest version of this document can always be found at:
Last modified on October 24, 2009.