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QuickStart Guide

The installation procedure:

Download >> Install >> Activate >> Logon

DOWNLOAD:

1. Click on the link:
Click here to download

2. Fill the registration form and "Submit":

While typing in your First Name and Last name, use only characters (A-Z, a-z). Example: If your First Name is Leu-Tang, or Leu Tang, please enter as: LeuTang

While typing in the Telephone number and the zip code use only numbers. Do not use spaces, commas, hyphen, etc.
Example: If your telephone number is 34-91-5854918, enter it as 34915854918

3. The download starts immediately and will take 45 minutes maximum to download. The size of the file is 195 MB.

In case you have any problem in downloading the file, please mail us at support@silicocyte.com

INSTALL:

Double-click the SilicoCyte Application.

ACTIVATION:

In order to use the software, you will need to activate both the server and the client versions. To do this, copy the generated product software keys (both server and client) and send them in an email to support@silicocyte.com. Once you receive activation keys from us, they can be pasted in the corresponding products. Please note that the 21-day trial does not start until you paste the activation keys into the software pop-up boxes.

Activating procedure:

  • Generate Server Hardware Keys:
    1. Click on Start menu -> Programs -> SilicoCyte SilicoCyte Server-> Activate Server License.
    2. SilicoCyte Server License Authentication window opens up.
    3. The Server product key is displayed in the dialog box, which is a bunch of Alpha-numeric characters:
    Example: 1609 5L17273518/SEWE6T/2L789/5L32908245/5/L/00..
  • Generate Client Hardware Keys:
    1. Click on Start menu -> Programs -> SilicoCyte SilicoCyte Client-> Activate Server License.
    2. SilicoCyte Client License Authentication window opens up and the Client Product keys are displayed similar to the Server Activation Keys.
  • Mail both the Server and the Client hardware keys generated to support@silicocyte.com. And we will mail you back the respective activation keys.

    Once you receive the Activation keys, you can input the information in the activation keys text box of the SilicoCyte Server License Authentication and SilicoCyte Client License Authentication dialog boxes.

LOGIN:

1. Click on Start menu > Programs > SilicoCyte SilicoCyte™ > SilicoCyte™ 1.0 to launch SilicoCyte™.

2. Enter the user name and password to login into SilicoCyte™.


Default Login information
User Name: silicocyte
Password: silicocyte


You are now ready to use the software. For guidance on using the software, please view the SilicoCyte tutorial.

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Silicocyte Quick notes - Image Analysis

SilicoCyte™ is a Microarray based gene expression analysis solution. It is used in enterprises to manage a data warehouse of Microarray experiments. The capability to process and mine Microarray data from a variety of Microarray platforms makes it ideal for use by organizations and individual researchers, working with DNA Microarrays. You can learn to use SilicoCyte™ with the help of this document.

This document provides an introduction to performing Image analysis in SilicoCyte. Numerical data generated through image analysis is used as the main input for all data analysis methods. This document assumes the user has read "SilicoCyte Quick Notes - Microarray Experiment" document and is working with images representing Cy3 and Cy5 images for experiment described in this document. User can follow instructions provided in this document to perform Image Analysis.

Main tasks involved in Image Analysis

Image analysis process has three main stages; they are:

1. Gridding: addressing elements or spots
2. Segmentation: classification of image into foreground and background pixels
3. Data Extraction: background correction and collection of intensity information from the image per element.

Main tasks performed during image analysis in SilicoCyte listed below

1. Loading of a Pair of 16 bit gray scale tiff files into Image analysis module of SilicoCyte.
2. Perform Gridding. Gridiing can be classified into Automatic, Semi-automatic, Manual process indication level of manual intervention during gridding process
3. Perform element invalidation for bad spots
4. Perform Image analysis

Notes:
Please download tiff file Images from download page of http://www.silicocyte.com/imagesforevaluation.htm. Download the link labeled "Sanger_Meosis_H0" to download tiff images representing Hour 0 after induction of Meosis. The names of the images are "JM_0h_131-2_cy3.tif", and "JM_0h_131-2_cy5.tif".

Image Analysis Workflow:

Tasks listed above are described in following sections of this document.

1. Loading images in Image Analysis Module - Cy3 and Cy5 images

  • Click Experiment on the left tab in the main screen to open Experiment window.
  • Load Microarray with the name "S.pombe G1 phase Vs. Meosis" by using microarray name combo box provided in experiment window.

Loading of Cy5 image (Representing "S.pombe in G1 phase of Cell Cycle" sample)

  • Click Select Images on Experiment window.
  • Click ellipses on Select Images window. A file open window pops up.
  • Use this dialog box to locate and open "JM_0h_131-2_cy3.tif" image.


Loading of Cy3 image (Representing "S.pombe after induction of meosis" sample)

  • Click Select Images on Experiment window.
  • Click ellipses on Select Images window. A file open window pops up.
  • Use this dialog box to locate and open "JM_0h_131-2_cy5.tif" image.

Image Scan Resolution & Launching Image Analysis

  • Select 10 microns radio button
  • Click Analyze to launch Image Analysis window.

2. Perform Gridding

Gridding can be performed in three ways as described below.

Automatic gridding: Performed when the image is of high quality with very less noise. This is the default operation.

Semi-automatic gridding: Performed when some errors are generated during the automatic gridding operation. Minor corrections could be done manually.

Manual gridding: Could be performed when the image quality is low and automatic and semi-automatic gridding fails.
Semi-automatic gridding is recommended for analyzing the image files described in this document SilicoCyte™.

Automatic Gridding

  • Click Grid in the navigation bar of Image Analysis window to perform automatic gridding operation.
  • On successful execution of Automatic Gridding, a properly aligned image with grids arranged on all the zones will be displayed. Gridding succeeds if the quality of images loaded is good in Image Analysis module.
  • Visually check the grid placement and proceed with Image Analysis if the grid placement is correct.
If automatic gridding fails the following message is displayed:

You can then switch to semi-automatic or manual-gridding option to complete the gridding
process.

Semi-automatic Gridding

  • Click on the Info icon on the navigation bar of Inspect window
  • Select Manual Gridding option.
    The following window will be displayed

  • Click OK to save the configuration and return to grid in image analysis window.
  • Click on the grid located on a sub array in the image and use Arrow Keys to manually adjust the grid.
  • Click CTRL + Arrow Keys for fine adjustments. This process has to be repeated for all the sub arrays. Alignment of all the grids on the available sub arrays will result in successful semi-automatic gridding.
  • Visually check the grid placement and if the grid placement is correct then proceed with Image Analysis.

Notes:
Semi automatic gridding might fail for badly printed or scanned Microarray images. For such images, perform Manual Gridding.

Manual Gridding

Manual gridding is an advanced topic. Please refer to "SilicoCyte User Guide" for instructions to perform manual gridding.


3.Perform element invalidation for bad spots

Element Invalidation is an advanced topic. Please refer "SilicoCyte User Guide" for instructions to perform manual gridding.

4. Perform Image Analysis

Proceed with image analysis after successful completion of gridding operation.
Click Analyze in the image analysis main window to perform image analysis.
Successful completion of Image Analysis will display the following window.

Click Close to complete Image Analysis.

Warning:
Image Analysis is a computationally intensive operation. Analysis of large images may take a long time for completion. Other operations in SilicoCyte™ cannot be performed during image analysis. Perform image analysis when no other urgent activity is pending in SilicoCyte™.

Click Exit to close Image Analysis application. SilicoCyte™ window is enabled after clicking Exit.

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SilicoCyte Quick notes - Microarray Experiment

SilicoCyte™ is a Microarray based gene expression analysis solution. It is used in enterprises to manage a data warehouse of Microarray experiments. The capability to process and mine Microarray data from a variety of Microarray platforms makes it ideal for use by organizations and individual researchers, working with DNA Microarrays. You can learn to use SilicoCyte™ with the help of this document.

SilicoCyte™ provides a single user interface to manage Microarray experiment data. The data required to perform Microarray experiment analysis can be grouped into three categories.

1. Gene annotations: includes information about gene sequences located on Microarray that is used in the experiment

2. Probe annotations: includes information about biological samples used in the experiment, the label attached to the sample i.e. Cy3 or Cy5.

3. Experiment annotations: includes information on Microarray design, image analyzed Microarray data, details such as the experimental conditions, protocol followed, etcetera.

All the above-mentioned databases are required to analyze Microarray data that will be of biological significance.

Audience

This document is meant for a new user of SilicoCyte software. User will be able to perform a microarray experiment in SilicoCyte after reading this document.

Login

Click on Start > Programs > SilicoCyte SilicoCyte Client > SilicoCyte to launch SilicoCyte™.
Enter the user name and password to login into SilicoCyte™.
Note: Default Login information
User Name: silicocyte
Password: silicocyte

Functional Stages In MA Experiment

1. Purchasing or creating microarrays,
2. Creating Labeled probes from biological samples,
3. Performing Hybridization,
4. Scanning of microarray slides with laser scanners,
5. Digitization of image data through Image Analysis,
6. Data Analysis & Interpretation.

Main tasks in SilicoCyte

Types of tasks that can be performed in SilicoCyte can be grouped under five categories. They are listed below

1. Microarray Experiment data generation: This process includes creation probes per sample being studied, creation of microarray, LIMS data collection for hybridization, Image Analysis, Quality report generation, Reports and Visualization of microarray data.
2. Management of Annotations: Management of Gene Annotation data, Gene Sources, Gene Groups, Gene Hierarchies, Samples (Probes), probe groups, Microarrays and Microarray groups.
3. Data Analysis: Normalization of microarray data, Statistical analysis, Clustering, Generation and execution of data mining queries, Generation and execution of Venn queries, visualization and interpretation of data analysis results.
4. Project Management: Project Creation, Resource allocation, and tracking of individual tasks in a microarray project.
5. Administration: Database administration, Microarray design creation, user creation and access privilege management for each user etcetera.

SilicoCyte Microarray Experiment Workflow

Steps to perform microarray experiment in SilicoCyte:

1. Creation of a pair of Cy3 and Cy5 probes per sample being studied
2. Creation of microarray,
3. LIMS data collection for hybridization,
4. Image Analysis, and
5. Reports and Visualization microarray data.

These steps are described in the following sections of this document.

Wet Lab Objects Labels
Cy3 Probe (Reference Biological Sample) S.pombe in G1 phase of Cell cycle
Cy5 Probe (Reference Biological Sample) S.pombe after Induction of Meosis
Microarray S.pombe G1 phase Vs. Meosis

 

1. Creating a pair of Cy3 and Cy5 probes per sample being studied

Creating Cy5 Probe (S.pombe in G1 phase of Cell Cycle)

  • Click Probes on the left tab in the main screen to open probes window.

  • Click New on Probes Window.

  • Enter "S.pombe in G1 phase of Cell Cycle" in probe name field of New probe Window.
  • Select Cy5 in Label combo.
  • Click OK.

Creating of Cy3 Probe (S.pombe after induction of meosis)

  • Click New on Probes Window.
  • Enter "S.pombe after induction of meosis" in probe name field of New Probe window.
  • Select Cy3 in Label combo.

  • Click OK.
  • Each probe should be assigned a fluorescent label before it can be assigned to a microarray during hybridization stage. A pair of probes one with Cy3 label and another with Cy5 label is required to successfully complete a microarray experiment in SilicoCyte.

2. Creation of microarray

  • Click New to add a new Microarray based on the Microarray design ID.
  • Add New Microarray window will be displayed.
  • Select an existing Microarray design from the Microarray Design ID list box.Select "SANGER".
  • Enter "S.pombe G1 phase Vs. Meosis" in the name field of Add New Microarray window.
  • Enter Notes for the new Microarray Type "S.Pombe meosis microarray Hour 0".

3. LIMS data collection for hybridization

  • Click Hybridize in the Experiment window to open Hybridization window

.

  • Assign two probes created in previous step to the microarray. Select "S.pombe after induction of meosis" for Cy3 Probe in Available Probes Combo box. This probe gets displayed in Experiment Window's Probe1 field.
  • Select "S.pombe in G1 phase of Cell Cycle" for Cy5 Probe in Available Probes Combo box. This probe gets displayed in Experiment Window's Probe 2 field.

Entering Experiment Information

The Experiment details are grouped into two tabs namely Application and Take down. The Application tab holds information regarding the Hybridization initiation process and the take down tab collects the information available at the end of hybridization process.

The minimum production details namely Technician and Hybridization Date should be entered in the Application Tab.The minimum experiment details namely Take Down by and End Time should be entered in the Take Down tab.

Tips:
1. Place the cursor in Available Probes dropdown box and press F3 to select default probes.
2. Place the cursor in Production Detail table and press F3 to fill default values.
3. Press F5 to retrieve values from the cached template.
4. Click Close of Hybridization window.

4. Image Analysis.

Please refer to "SilicoCyte Quick Notes - Image Analysis" document for details regarding Microarray image analysis SilicoCyte.


5. Reports and Visualization microarray data.

  • Click Adjustments to launch Adjustments window that is used to perform dye0-bias normalization in microarray experiment.
  • Click QC Report to launch QC report available in pdf format for the microarray experiment. This report can be used to evaluate quality report for experiment.
  • Click Location Map to launch Element Location window that can be used to dynamically query for differentially expressed genes and to create pertinent gene groups that can be used in other data analysis procedures.



  • Click Graph to display various types of Cy3 Vs. Cy5 graphs and to visually interpret the data.


  • Click View element to launch Element Display window. Element display window is used to view textual report of image analysis data for a microarray.