1. What platform does Chitraka run on?
Chitraka needs Windows 2000,NT,Me or XP Operating systems. It is not supported on Linux or Mac yet.
2. What additional dlls are required to run Chitraka?
Make sure that "msvcp60.dll" exists in the system.Filedescription: Microsoft (R) C Runtime Library, v. 6.00.8168.0
3. How many microarray images can Chitraka work with?
Chitraka can work with multiple microarray images for independent experiments. In addition each of the experiments can have dual Cy3/Cy5 channels. There is no limit to the number of images that can be acquired simultaneously. The only constraint would be the amount of memory in the system.
4. Does Chitraka support image enhancement operations?
Yes. Chitraka allows for contrast,brightness, zooming and sharpness operations on the image. The operations on the images does not affect the actual intensity values of the originally acquired image on which operations are done.
5. Does Chitraka support automatic normalization during loading?
Yes. Chitraka does an automatic image normalization so that the hard to locate spots are easily viewed. Again, the operations on the intensity values in the original image remain unaffected.
6. Does Chitraka support any chip(array) layout files?
Yes. Chitraka is designed to read files such as GAL,Quant etc. In addition the users can create their own chip templates for new layouts.
7. Can Chitraka support microarrays that are skewed by rotation?
Yes, Chitraka allows users to rotate the images based on couple of operations so the image can be aligned for further gridding.
8. What kind of feature packing does Chitraka support?
At the moment Chitraka supports rectangular packing only.
9. Does Chitraka support multi-level blocks?
Yes, Chitraka support upto 2 levels of blocks.
10. How does Chitraka calculate background estimates?
Chitraka uses the rectangular cell defined by the region for computing the background mean. The normal and trimmed means are computed. In addition Chitraka can support user-specified background subtraction, background along the boundary and the median values also.
11. Does Chitraka support Scanner interfaces?
Chitraka can read all file formats (preferably TIFF) that are stored using the software built into scanners. Chitraka has been customized and extended to interface with proprietary scanners to control scanner operations. Please contact sales for additional information.
12. Does Chitraka support multiple image file formats?
At the moment, Chitraka supports 16 bit TIFF formats only. It can be easily extended to accommodate other image files.
13. What techniques does Chitraka provide to align grids?
Chitraka provides both manual editing and automatic tuning of grids at the block and sub-block level. We recommend that the user use the automatic tuning features for sub-block levels and then perform manual adjustments. In most of the cases manual adjustments are not required.
14. What are the different views for an experiment in Chitraka?
Chitraka provides workspaces for every individual experiments. Each microarray image is linked to a Spreadsheet view and a Graph view on which additional operations such as scatter plots and histograms can be performed. This avoids clutter of several views and at the same time provides a comprehensive workspace for the user.
15. Does Chitraka have some way to tag bad spots?
Chitraka does automatic bad spot recognition and flags it as bad. The user can manually flag spots as bad also.
16. What is a typical spot finding protocol in Chitraka?
Chitraka provides a wizard like icon interface to perform spot finding operations on microarray images. The GUI is very intuitive and in a few quick steps images can be analyzed automatically and accurately.
Start by specifiying the preferences using the icon. The preferences should minimally include the number of blocks along the rows and columns and also the number of features withing blocks. Next, draw the topleft grid and the bottom right grid to identify the end grids. Click the find grids to find the remaining grids automatically. Use the automatic grid tuning to perform automatic adjustment of grids. Use the find subgrids and auto tuning to correctly layout the subgrids. Press the find spots, and the spots are determined automatically and accurately. The spot statistics can be exported onto a spreadsheet by clicking the "X" icon ( for spreadsheet).
17. What is the difference between a chip layout (template) and a grid file?
The grid files can be stored during the middle of any operation and will store the geometry of the grids. It will not have any gene/label information. The chip layout file contains the gene/label information in addition to the block layout.
18. Do I need to specify a spot diameter in Chitraka?
Chitraka allows you to draw an approximate spot for diameter using simple ellipse editing operations. The user should make sure that the spot diameter covers a candidate spot on the image approximately.
19. What are the undo levels in Chitraka?
At present Chitraka supports "Undo All", which effectively returns the user to the original state after loading an image.
20. How do I open/close an experiment workspace in Chitraka?
Chitraka allows users to open a workspace by opening an image. Once an image is opened Chitraka will associate a Spreadsheet and Graph view along with it. To close simply choose the close option in the windows tab or the File Close option.
21. Computer - Minimum
- IBM-compatible computer with a Pentium 500 MHz or faster
- Windows NT, 2000,ME ,XP operating system
- 256 MB RAM
- Hard disk with 10 GB free
- CD-ROM drive for installation
- 1024 x 768 display system with 65K colors
22. Computer - Recommended
- IBM-compatible computer with a Pentium 1.7 GHz or faster (not Celeron)
- Windows 2000 or XP operating system (dual-boot systems are not recommended)
- 512 MB RAM or more
- Hard disk with 30 GB free
- Recordable/Rewriteable CD drive
- 1280 x 1024 display system with 16M colors
|
Technologies 
