1. How will Iobion GeneTraffic be deployed in my lab?
2. What are the benefits of the client-server model?
3. What software platform does GeneTraffic require?
4. What are GeneTraffic hardware requirements?
5. What software technology is used by Iobion GeneTraffic?
6. What type of data files does an Iobion GeneTraffic microarray project require?
7. What file formats does Iobion GeneTraffic support?
8. How can I ensure that my statistical analysis produces relevant results?
9. What types of normalization are available in GeneTraffic?
10. Does Iobion GeneTraffic support dye-reversal and other replicate hybridizations?
11. How many microarrays can an Iobion GeneTraffic server hold?
12. Can I examine the microarray image?
13. How difficult is it to obtain a detailed description of the hybridization?
14. Can I visualize my data using graphical representation methods?
15. How do I annotate my projects?
16. Can I relate my work to public database annotation?
17. Can I safely share data with my colleagues?
18. I don't need my data now, but I may need them again in the future. Can I archive the data?

1. How will Iobion GeneTraffic be deployed in my lab?
The Iobion System is a comprehensive platform designed to take full benefit of the client-server architectural paradigm. Its operating environment consists of a single application server and of one or more client computers. The server runs application software, stores individual user preferences and houses databases required by Iobion System applications. All of these are accessible from the client computers distributed over a local area network.

Iobion GeneTraffic software consists of one comprehensive microarray data analysis application designed for the client-server architectural model as implemented by the Iobion System. [top]

2. What are the benefits of the client-server model?
Iobion GeneTraffic multi-tier model ensures accessibility and manageability of the stored information, while preserving highest industry standards with respect to data security and integrity. Any client computer can be used to configure the software located on the server, which further optimizes hardware investment and user training costs, for increased convenience and cost-efficiency. [top]

3. What software platform does GeneTraffic require?
No system software is required on the GeneTraffic server?the Iobion System installation CD installs all software necessary to run both the Iobion System and the GeneTraffic application.

Each GeneTraffic client requires Windows 98, Windows ME, Windows NT4 or Windows 2000 as its main operating system as well as the Microsoft Internet Explorer 5.5 browser and Macromedia Flash 5 browser plug-in. [top]

4. What are GeneTraffic hardware requirements?
Listed below are minimum hardware specifications required for a successful installation of Iobion GeneTraffic, [top]

5. What software technology is used by Iobion GeneTraffic?
To provide its customers with a competitively priced leading-edge software package, Iobion Informatics relies on the firmly established results of one of the most dynamic software initiatives in recent years—the open source movement.

A custom-built kernel of Red Hat Linux, an operating system famous for its reliability, stability and security, lies at the core of the server's operating environment.

Bioinformatics applications hosted by the Iobion System are served to the users by the latest version of the Apache Web server, a fast and secure network solution. Project data generated by the applications are stored using the PostgreSQL object-relational database management system.

Much of the computationally intensive statistical data analysis performed by Iobion System applications is carried out by routines coded in R, an open source relative of the S statistical language, known for its flexibility and power.

Support for other platforms, most notably Solaris, is planned for the near future. [top]

6. What type of data files does an Iobion GeneTraffic microarray project require?
The required data files for each hybridization experiment include two TIFF image files, generated for both dye channels, as well as a quantification data file. [top]

7. What file formats does Iobion GeneTraffic support?

We now support a couple of additional formats i.e. scanalytics. Please contact us directly for details. [top]

8. How can I ensure that my statistical analysis produces relevant results?
Two mechanisms are available to ensure validity of results: outlier elimination and normalization.

It is possible to flag spots and remove them from normalization and aggregate calculations. Flagged spots may be those that have intensity lower than a certain multiple of the local spot background, intensity lower than a certain multiple of the average background, or intensity lower than a given value.

Normalization attempts to eliminate local data perturbance, which may be hiding statistically valid patterns of data behavior. [top]

9. What types of normalization are available in GeneTraffic?
Normalization of microarrays can be achieved by a variety of methods. The normalization methods included with Iobion GeneTraffic software can be applied on either the global or the sub-array (grid) level. Global normalization is performed on the array as a whole and each qualified spot is included in the calculation. Sub-array normalization is performed on qualified spots in the individual print-tip groups (grids, sub-arrays, blocks) in order to account for systematic differences caused by the movements of the arraying robot and for surface defects on the printed slide. The following normalization methods are available:

1. Raw Intensity. Calculates a normalization value (N value) based on the ratio of the sum total intensity of qualified Cy3 spots to the sum total intensity of qualified Cy5 spots.
2. Log2 Ratio. Calculates an N value that is based on the average of the log2(Cy3/Cy5) intensity ratios of each qualified spot.
3. Reference Genes. Calculates a ratio-based N value on a smaller subset of spots that correspond to the set of reference genes.
4. Housekeeping Genes. Calculates a ratio-based N value on a smaller subset of spots that correspond to housekeeping genes.
5. LOWESS. The LOWESS (Locally Weighted Scatter Plot Smoother) function is a curve-fitting equation. It performs a local fit to the data in an intensity-dependent manner. The intensity value for each spot is normalized based on data distribution in the immediate neighborhood of the spot’s intensity (i.e. in a limited sub-range of the intensity scale, centered on the spot’s intensity value).
6. Custom Value. User-defined N value.

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10. Does Iobion GeneTraffic support dye-reversal and other replicate hybridizations?
Yes. A GeneTraffic project might involve, for example, expression profiling of a drug treatment at several time points (time-course), each time point being represented by a hybridization group including several replicate dye-reversal hybridizations. [top]

11. How many microarrays can an Iobion GeneTraffic server hold?
The number of complete microarray data sets an Iobion GeneTraffic server can store at any given time depends on the amount of disk space available on the server. Assuming availability of two 40-gigabyte disks, the server can hold data from 6000 five-thousand-spot microarrays or 2,500 twenty-thousand-spot arrays. [top]

12. Can I examine the microarray image?
Yes, you can. At any point in the process of analyzing your data you may consult a digitally-enhanced, false color microarray image. [top]

13. How difficult is it to obtain a detailed description of the hybridization?
Not difficult at all. For multiple types of objects contained in a hybridization, detailed description is but one click away. For example, clicking on a spot in the microarray image fetches the spot's unique ID, gene ID and description, spot position on the plate, intensity and ratio almost immediately. Range or equality queries (e.g. 'show me all spots with Cy3 intensity greater than 10,000 and log2 ratio greater than 2') bring up formatted lists of relevant genes. Every gene name in such a list is a hyperlink to a detailed Gene Report, showing mean log2 ratio, standard deviation, and coefficient of variation, calculated for qualified spots; also displayed are thumbnail images of the spots. [top]

14. Can I visualize my data using graphical representation methods?
Yes, you can.

Seven scatter plot types are available for immediate use. Preset 1 (default scatter plot) shows normalized data in logarithmic scaling. Presets 2 and 3 show raw data with and without background subtraction, allowing the user to assess the effect of normalization and background subtraction. Presets 4, 5 and 6 plots the data (normalized, raw, and background subtracted respectively) in an M versus A plot (the M versus A plot allows for rapid identification of skewed data). Preset 7 plots the normalized data in linear scaling and provides a sense of the intensity distribution.

Also provided is an interface to carry out hierarchical and non-hierarchical clustering of microarray data, using a variety of distance metrics and several visualization methods. Data sets can be imported into the clustering engine from third-party programs or exported into formats compatible with third-party software. [top]

15. How do I annotate my projects?
Iobion GeneTraffic project annotation is compliant with the Minimum Information About a Microarray Experiment (MIAME) standard. A project consists of hybridization groups, which in turn consist of related hybridizations. For example, a project might involve expression profiling of a drug treatment at several time points (time-course), each time point being represented by a hybridization group including several replicate dye-reversal hybridizations. The annotation of each hybridization includes all of the protocols and all of the materials listed in the diagram shown below. [top]

16. Can I relate my work to public database annotation?
A detailed Gene Report is available for every gene in a GeneTraffic project. The report provides multiple links to external gene databases: [top]

• NCBI UniGene
• NCBI GenBank
• NCBI LocusLink
• Stanford SOURCE
• SWISS-PROT
• BLASTn NR
• BLASTn HTGS
• BLASTn dbEST
• BLASTx SWISS-PROT
• OMIM
• GeneCards
• Saccharomyces Genome Database

17. Can I safely share data with my colleagues?
By default, when a GeneTraffic project is created, only the owner of that project can view the data it contains. Using permissions, users are able to collaborate in a safe and secure manner by sharing information and data within the GeneTraffic environment. Permission levels include: co-author (full editing access), reviewer (read-only access) and excluded (not allowed to access project).

For example, a principal investigator can name several students as co-authors of the project. The principal investigator can then define all the hybridization experiments necessary for the completion of the project. The students, granted sufficient privileges, can load the data for each hybridization experiment (and, if necessary, define new hybridizations) when the data becomes available. [top]

18. I don't need my data now, but I may need them again in the future. Can I archive the data?
Yes, you can. Iobion GeneTraffic allows you to archive completed projects to tape, file, or recordable CD-ROM. All of these are secure, reliable and cost-efficient methods of archiving rarely used project data. Moreover, archiving old projects allows you to reserve more space for current projects, thus streamlining the performance of Iobion GeneTraffic. [top]