2D gel software survey

Babu Raman braman1 at gl.umbc.edu
Fri Jun 22 14:06:31 EST 2001

I'm doing a survey on the importance of various features in
2D-gel image analysis software.  Could you rate the following

   1 ----- 2 ----- 3 ----- 4 ----- 5
unimporant                       very important

============== 2D-Gel Software-Feature Survey ============

1. Image Cleanup options
   (eg, smoothing, background removal, contrast enhancement
   SCORE = ?

2. Spot Detection:

   2a. Availability of adjustable parameters
       (eg, min. spot area/size, partial threshold,
        confidence etc..)
   SCORE = ?

   2b. Availability of spot editing options
       (eg, adding, deleting, spliting, merging of spots
   SCORE = ?

3. Gel Alignment:

    3a. Speed of alignment:
        (consider automatic alignment vs landmarking
        technique etc..)
    SCORE = ?

    3b. Easy visualization of alignment
        (dual channel [two colour] display of gels etc.)
    SCORE = ?

4. Gel matching:
    (consider matching speed, easy visualization of
    qualitative/quantitative differences using different
    SCORE = ?

5. Composite Gel:
    5a. Adjustable parameters:
        (eg, number of gels which should have a spot for it
        to be entered in composite gel etc., also consider
        appearance of the composite gel)
    SCORE = ?

6. Reports:
    (consider options available for displaying various
    information, export capabilities, etc.)
    SCORE = ?

7. Quantitation:
    (consider calibration options, histogram for protein
    expression differences etc..)
    SCORE = ?

8. Statistical Analysis:
    (Availability of various statistical methods for
    data Analysis)
    SCORE = ?

9. Database Querying Option:
    SCORE = ?

General questions:

1. Which step do you think is the current bottleneck in
Proteomic gel analysis?

2. What is/are the software you have experience with and in
your opinion, what is one aspect of your software which
needs improvement?



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