(last updated February 27th 2013)
The CMSB-NBIC Rosetta Resolver system is a multi-user system for the storage and
analysis of gene expression microarray data. Experiments are stored and
analyzed on main frame multi-processor computers with more processing and
storage capacity than any ordinary desktop computer. Users upload, analyze and
access their data through client software on their own PCs using a unique user
account and password. Your data and analyses can be private, or shared with
your group or institute.
This web page aims at giving specific information on the implementation and coordination of the CMSB-NBIC Rosetta Resolver system hosted by the Leiden University Medical Center (LUMC) in Leiden and supported by the Centre for Medical Systems Biology (CMSB).
The CMSB-NBIC Rosetta Resolver system can be used free of charge by CMSB researchers. Licenses providing access to Rosetta Resolver are available for other users from Dutch academic institutes. For more information, please contact Petra van Overveld.
The collaborators within the CMSB are:
User groups outside the CMSB are:
The CMSB-NBIC Rosetta Resolver system is maintained and administrated by the Leiden Genome Technology Center (LGTC) for the Centre for Medical Systems Biology (CMSB). The administrator team consists of:
and is assisted by Floris Jan Sicking (Leiden Institute for Advanced Computer Science (LIACS)), who contributes his expertise by monitoring Rosetta Resolver's Oracle database backup and configuration.
Each institute has their local coordinator who keeps in contact with the administrator team, authenticates new users from their institute and is the local expert on access and use of the system:
The CMSB-NBIC Rosetta Resolver system uses concurrent licenses to access the database. That means that the total number of users that can connect to the system at the same time is limited to the number of licenses issued to a specific user group. If you recurrently fail to login due to all accounts being used, please contact the database administrator.
Out of consideration for other users, please always log out of Rosetta when you are done working or taking a break!
If you have a problem using Rosetta Resolver, please follow this route:
New users are adviced to apply for a user account and to access Rosetta Resolver using a client computer in their departments/groups. To get acquainted with Rosetta Resolver, please follow the user training guide. Ask your local contact person about additional training possibilities.
In order to use Rosetta Resolver successfully in your department/group, the computer chosen to run the client software should:
1) meet these requirements
2) be registered to get access to the Rosetta Resolver server. To register, please send an email with the IP address and the name of the group/department and coordinator to the system administrator. You will get a response within three working days.
When your IP address has been registered, you can connect to the server website: http://184.108.40.206/ and download the client software from the Rosetta Resolver system.
Once the software has been successfully downloaded and installed on your PC, start the Rosetta Resolver client via Start >> Programs >> Rosetta Biosoftware >> Rosetta Resolver. The client will automatically connect to the server and you can log in with your user name and password.
If you can't locate the Rosetta Resolver client, look for it in the default installation location, which should be "C:\Program Files\Rosetta Resolver\Biosoftware\Resolver.exe". If you can't find it there, search the system for "Resolver.exe". If you can't find it this way, then the client is probably not installed (or not properly installed) on your computer.
All new users on the system need to be authenticated by their local coordinator. The minimum information required to register a user account is:
This information should be sent to your local coordinator for validation and authentication. Your coordinator will forward the information to the system administrators for registration.
After your information has been registered the system administrator will confirm this to the local coordinator, and you will in turn be informed by e-mail about the registration.
User accounts will be locked after 5 failing login attempts. Contact your local lab manager or coordinator to restore access. Users are not allowed to load patterns and their accounts will be locked if they try. Please ask your local manager or coordinator to load patterns and provide him with clear description of the array (contents and origin of the library on the array, array version and spotting date). Patterns of general commercially available arrays (Affymetrix, etc.), which should be available to many users, will be loaded by the administrator on request.
Keep your user name and password confidential!!!
The table below lists required components on Resolver client computers. We strongly encourage you to use the recommended requirements for best productivity.
|CPU||800 MHz||1.4 GHz|
|Operating system||Windows XP, Windows NT Workstation 4 with Service Pack 5, or Windows 2000||Windows XP, Windows NT Workstation 4 with Service Pack 5, or Windows 2000|
|Browser||Microsoft Internet Explorer 5.0||Microsoft Internet Explorer 6.0 or higher|
|RAM||512 MB||1024 MB|
|Drive space available||50 MB||200 MB|
|Monitor||17 inch||21 inch|
|Pixels||1024 x 768||1280 x 1024|
The Rosetta Resolver database comes with a number of standard options for species and experimental annotation. According to the users' needs, we can extend most of these. If you run into something you would like to have but do not find, please contact our administrators. Some examples:
Pattern names and description: Local home-spotted arrays should be named as follows: Institute abbreviation_Organism abbreviation_Array type/size_part number (e.g. LUMC_Hu19K_Sigma-oligo partI) with a clear description containing Clone/oligo library source, organism name, gene number, array manufacturer, part number, print date and other information (e.g. Sigma/Compugen human oligo library LGTC 18,861 60-mers partI) to allow users to choose the correct pattern.
Adding options to drop-down menus
Adding sequence annotation
When uploading profiles, please also keep a local back-up of your input files.
Before you can load a profile, you NEED TO MAKE A CHIP BARCODE!!! Go to Chips in the Annotation tab and make all the New Chip Barcodes you need. Then select them when loading profiles. Optionally, you can also define Hybs and Preps in the Annotation tab, and add a lot of experimental annotation data to your Profile.
Loading Illumina data into Rosetta Resolver requires a correct preparation of the data files with Illumina BeadStudio. Instructions can be found here
Importing MAGE files
Unfortunately, MAGE file import via the Rosetta Resolver client does not work properly. Please ask your lab manager for help to load MAGE data. When pictures of the scans are to be included, make sure that their file name is exactly the same as that in the XML file. Your lab manager can request ftp access to the MAGE directory to import data using the AutoImporter.
If you forget your password, the password can be reset to your user account name. For security reasons this reset has to be authorized by your local coordinator. The local coordinator as well as the user will always be notified by e-mail of this event.
Nota bene: If the system administrator knows you in person, then (s)he can reset your password by a direct request from you.
If it has been working before: Reboot your computer and try again, or contact your local coordinator.