General:
 What is SilicoCyte?
SilicoCyte is a microarray based gene expression analysis solution. It is used to manage a data warehouse of microarray experiments of an enterprise.
Why and who should use SilicoCyte?
SilicoCyte is capable of processing; storing and mining microarray data from a variety of microarray platforms, this makes it ideal for use by organizations and individual researchers working with microarrays.
How can I evaluate SilicoCyte?
The latest version of SilicoCyte is available for download. Once the download is completed install the software (both client and server) and then get the trial activation keys for the software (both client and server).
How long can I evaluate SilicoCyte?
The trial version of SilicoCyte can be evaluated for 21 days from the day the activation keys are generated.
Can I upgrade my Trial version of SilicoCyte?
Once you have decided to purchase SilicoCyte you need to send the new set of hardware keys (both server and client). The new hardware keys are used to generate the activation keys for either the enterprise version or desktop version.
How do I obtain the client and server activation keys for SilicoCyte?
If you have obtained a trial version, you can email the hardware key to support@silicocyte.com or contact the nearest distributor. To upgrade your license to a Desktop edition or the Enterprise edition, contact your distributor.
How do I install loopback adapter on windows XP?
To install SilicoCyte on a stand alone system with windows XP you need to have a loopback adapter. please follow the below given instructions to insall the loopback adapter :- - Click on Start - Settings - Control Panel to open Control Panel options.
- Double click on Add/Remove Hardware to open the hardware options.
- Click on Next to continue with Add / Remove Hardware Wizard.
- Select Add/Troubleshoot a device and click on Next to proceed with the installation.
- Windows attempts to locate the new hardware.
- Click on Add a new device and Next to proceed with the installation.
- Select No, I want to select the hardware from a list option and click on Next to proceed with the installation.
- Select Network adapters and click on Next.
- Select Microsoft from the Manufacturers list and Microsoft Loopback Adapter from the Network Adapters list.
- Click on Next to proceed with the installation.
- Click on Next to start the hardware installation.
- Click on Finish to complete the hardware installation.
Technical Questions:
What operating systems does SilicoCyte run on?
SilicoCyte runs on Windows 2000 Professional, Windows 2000 Server and Windows XP. If you are planning to use MS-SQL Server then Windows 2000 Server is required (only for installing the server). Is SilicoCyte available for Linux?
No! SilicoCyte is not available on Linux. We are planning to support Linux in the future.
Is SilicoCyte a client/server application?
SilicoCyte is a 2-Tier client/server application. In the Desktop edition, the client and server can reside in the same machine. In the Enterprise edition, the server can reside on a remote machine with the client machines connected to it.
What are the different databases, which can be used in SilicoCyte?
SilicoCyte by default installs MSDE, if MS-SQL Server is already available then SilicoCyte can make use of this.
Can I use SilicoCyte with PostgreSQL or MySQL?
No! SilicoCyte does not support either PostgreSQL or MySQL. We have plans to support this in the future.
Basic Questions: How can I login into SilicoCyte?
SilicoCyte creates a default user "silicocyte" with password "silicocyte" during the installation. You can use this to login into SilicoCyte. This user ("silicocyte") has all the administration permission.
What type of image file format does SilicoCyte support?
SilicoCyte supports 16-bit grayscale TIFF images only.
How many channels or images can SilicoCyte process at a time?
SilicoCyte supports dual channel image analysis. Does SilicoCyte support single channel experiments?
SilicoCyte 1.2 does not support single channel experiments.
Balancing dual channel experiment data:
Why is Microarray data balancing required?
Microarray data balancing is used to correct the signal differences in Cy3 and Cy5 channels. To correct these errors, each probe (Cy5) signal value is multiplied by a balance coefficient in order to normalize the signal data relative to the expression of a set of elements on the Microarray. The normalization can be performed using a Gene Group (a subset of microarray elements), using all elements on the Microarray, or with a user supplied balance coefficient.
How do you perform microarray adjustments?
The Microarray Adjustments dialog allows the user to balance and filter analyzed data on a per Microarray basis. The Microarray Adjustments dialog is invoked by clicking on Adjustments in the Experiment window.
An analyzed microarray must be adjusted before its data can be viewed.
Filtering microarray data:
Why is microarray element filtering done?
Microarray Element filtering is used to help the user to exclude data that may not be interesting in the experiment. By allowing the user to remove data with very low signal values in both the Cy3 and Cy5 channels, more interesting data is more easily viewed.
Signal and Background values are computed independently in the Cy3 and Cy5 channels. The Element Area used for computation is an identical region in both channels; therefore A% will always be the same for both Cy3 and Cy5 channels.
What happens if the microarray element filtering condition is changed?
SilicoCyte checks each element in the microarray to see if it meets the element acceptance criteria set by the user. Differential expression will be computed only for those elements that meet the filtering criteria in at least one channel.
How can I change the default values for the STB?
Default values for new microarrays can be edited in the utilities/Preferences Dialog.
How can I change the element area percentage?
Default values for new microarrays can be edited in the utilities/Preferences Dialog.
What is a Location map?
Location map is an interactive tool that helps in showing the physical distribution of elements on a microarray. Each element is color coded in this window. This window is useful for detecting positional influence on differential expression, such as differential expression caused by an area of high background on the microarray.
What are Thresholds?
This helps in filtering the elements based on the filter conditions provided by the user. Usually thresholds are set negative for "Low" and positive for "High". Elements differentially expressed in the positive direction (balanced Cy3/Cy5 signal greater than the high threshold value) are green. Elements differentially expressed in the negative direction (balanced Cy3/Cy5 signal less than the low threshold value) are red.
What can I do with Element location window?
The element location window is used for visually identifying the following elements: - Accepted Elements
- Rejected Elements
- Differentially Expressed Elements
- Invalid Elements
- Controls
Import and Exporting Data: What export formats does SilicoCyte support?
SilicoCyte exports data in a comma-separated file, which can be further imported by Excel. It also supports exporting of some data in MAGE-ML format.
What import formats does SilicoCyte support?
SilicoCyte supports data import from Excel, tab-separated and comma-separated files. SilicoCyte can import some parts of dual channel data stored in MAGE-ML format. | 
