Running Flicker
  • Examples of Flicker
  • Compare URL with 2DWG
  • Compare URL images

    Flicker info

  • Flicker Reference Manual
  • Lemkin(1997)Electroph.;18:461
  • Extended '97 paper
  • Slide show Siena '96
  • Slide show ABRF '97
  • Slide show NCI '97
  • Slide show NMHCC '98

    2D gel Internet DBs

  • 2D gel Web DBs
  • 2DWG meta-DB
  • Protein Web tools

    Other Flicker DBs

  • Create Flicker Web Page
  • HSC-2DPAGE

    Caveats

  • Notice
  • Browsers required
  • Loading gel images
  • Flicker API description
  • Download Flicker
  • Setup Flicker locally
  • Status
  • Msg of day

    • NCI Flicker Web Server

    http://www-lecb.ncifcrf.gov/flicker


    Note: Flicker now works with Netscape 4 and
    Internet-Explorer 4


    FLICKER - Comparing images across the Internet

    Flicker is a method for comparing images from different Internet sources on your Web browser. Scientists around the world often work on similar image data. More of this data is being published on the Internet each year. In the case of 2D protein electrophoretic gel images, maps identifying proteins in these gels are becoming increasingly available. Visually comparing 2D sample gels against these 2D gel database maps may suggest putative protein spot identification in many cases. Flicker was originally developed for comparing 2D protein gels across the Internet.

    The Flicker image viewer is a Java applet which reads two images from the Internet and then displays them in the your Web browser. It allows you to enhance them in various ways and to compare them visually in a third window called the flicker window. The program uses the 'flicker method' used in GELLAB with (see ref. [1-3]) and with Xconf (see ref. [4]). The "flicker method" is the alternate display in the same visual space of two images being compared which are aligned by aligning similar morphologic features. Images may first be enhanced by spatial warping, pseudo 3-Dimensional projections, image sharpening, contrast enhancement and other transforms. The transformed images may then be presented using flickering. Papers describing the details on the Flicker program are given in (see ref. [5-6]) as well as the Flicker Reference Manual.

    When started, your Web browser first loads the Flicker Java program applet which then loads two the images specified. Be patient, since it may take a while to load the two images, especially over a modem connection. Note: you need a Java-capable Web browser to use Flicker. Since Flicker is doing image processing operations on your computer, it works much better on computers which have a fair amount of memory (i.e. 16MB or more - 64MB is comfortable if doing various transforms) and adequate "horsepower". You may also want to adjust the canvas size for all of the images displayed in Flicker prior to starting Flicker. You may want to resize your browser to a larger window before starting Flicker.

    1. Examples of using Flicker on images from the NCI Flicker Web server and the Internet

    The 2D gel image data presented in the following examples are generally samples of data from different laboratories. The conditions under which the samples were obtained, the gels were run and scanned may not be fully specified in the corresponding databases. Therefore, one should not necessarily interprete these gels as standard gels for that class of sample. Anonymous attribution is given when the data is unpublished, otherwise attribution is given to the source of the images.

    The following examples will each flicker two gels: Note that some of these images were reduced in size to shorten transmission times as well as to enable them to fit on users' computers which don't have a lot of memory. Other gel images which were too small were zoomed up to give Flicker a large enough region to scroll. If an image is too small to scroll, you can not move it in Flicker and so can't align it with the other image. These examples only work with a Java-capable Web browser.

    1.1 Examples of 2D images to compare

    Two images are required in order to do the flicker comparison. These may be specified in either of several ways:     A) the two images to be flickered may be selected from preconfigured sets of images using pre-defined pairs of images. You can select any of the SWISS-2DPAGE gels to compare against a 2D gel that you specify by its URL. In B) you can also click on a spot in one of the SWISS-2DPAGE database gels to have it lookup the spot identification if known. C) you can pick two images from scrollable lists in any of the following sample domains; We also lists scrollable lists of images D) from other biomedical image domains.

    A) Predefined pairs of 2D gel images

    These examples will load predefined sets of gels which are tied to proteomic databases which are accessed by clicking on a spot in the images.
    1. Plasma 2D PAGE gels, the plasmaH (Hochstrasser Lab, Geneva) vs plasmaL (Merril Lab, NIMH, Bethesda). The gels are linked to the plasmaDB plasma database.
    2. Labeled plasma 2D PAGE gels linked to plasmaDB database.
    3. Plasma 2D PAGE gels linked to both SWISS-2DPAGE and plasmaDB databases.

    4. Phosphorylation 2D studies in mouse B lymphocytes and is linked to the phosphoDB PhosphoProtein Database (PPDB).
    5. Phosphorylation G1-G2/M cell cycle 2D studies in mouse T lymphocytes.

    B) Comparing SWISS-2DPROT or YPD gels to any Internet Gel

    1. Any SWISS-PROT gel compared with any Internet Gel.
    2. Any SWISS-PROT gel (linked to the SWISS-2DPAGE database) compared with any Internet gel.
    3. Any SWISS-PROT gel with markers on known spots (linked to the SWISS-2DPAGE database) compared with any Internet gel.
    4. A YPD or SWISS-PROT yeast gel with markers on known spots (linked to the YPD or SWISS-2DPAGE yeast databases) compared with any Internet yeast gel.

    C) Lists of 2D PAGE gel images - you pick two from each list to compare

    1. Flicker compare 2D gels from 2DWG meta-database with ANY Web image URL
    2. Leukemia 2D gel study
    3. Cd toxicity 2D gel study (urine).
    4. Fetal alcohol syndrome 2D gel study (plasma).
    5. Heart ventricle and atrium 2D gel study
    6. T-lymphocyte phosphoproteins from IL-2/IL-4 dependent cell line 2D gel studies
    7. Breast cancer NCI drug resistance screen subset from MCF7 cell line, 2D gel study.
    8. Breast cancer, multiple labs, 2D gels
    9. Prostate Nuclear Matrix Proteins for normal and prostate cancer, 2D gel study.
    Where: indicates "under construction".

    D) Examples of other types of images to compare

    1. Differential display PCR (ddPCR) gels of rat embryos - 22 vs 18 day
    2. K-ras alterations in transformed NIH-3T3 2D DNA gel images
    3. Sequence Logos of CRP and FNR binding sites
    4. MRM (MRI microscopy)
    5. HPLC Amino Acids spectra
    6. RNA structure comparison dot matrices
    7. Five MRI images of a beating human heart
    8. 3D projections of molecular models
    9. Visible Human sagittal or coronal views
    10. Dental X-rays
    11. Two people

    2. Flicker requires a Java-capable Web browser

    Flicker requires a Web browser which understands the Java applet protocol. It requires a version of a Web browser such as Netscape 3.0 or Internet Explorer 3.0 or higher, or some other equivalent Web browser. You can download Netscape for free now from Netscape Corporations Web site if you wish. The new versions of the Web browsers (Netscape 4.5) are more efficient running Java, so Flicker runs faster and it is worthwhile to upgrade your browser if you have an older version.

    Because of the complexity of the Flicker graphical user interface, it requires a higher computer screen resolution than is available on some computers. It works adequately with a 1024x768 SVGA. With lower resolution screens, you will have to repeatedly scroll the screen. Even with a SVGA resolution, it helps to remove the (Netscape) tool-bar, directory-buttons and location to increase the total vertical space available.

    3. Invoking Flicker from HTML

    There are several ways to invoke flicker. The simplest way to see how it works is to use one of the scrollable list of images listed in Examples of Flicker in the Flicker Server. In addition, we have set up scrollable lists of 2D gels from the 2DWG meta-database. A gel from that list may be compared with ANY image URL. You can specify two images directly for ANY Web images by their URLs.

    Alternatively you can write HTML (eg. see example A) above), which when invoked, will start Flicker on the two images you specify. This is illustrated in the following Flicker API description of how Flicker is invoked from HTML as well as some additional various startup options.

    4. Flicker compare images from any two URLs

    You may Flicker Compare two images specified by typing in their URLs for image files located on any Web server. If your images are on your Web server, you can specify their Web address (URL) as http://internet-host/image-file. Alternatively, if your computer has an FTP server, you can compare your own images by copying them to your FTP server and just referencing them with a URL of the form ftp://internet-host/image-file.

    This section is also available on a separate Web page 

       http://www-lecb.ncifcrf.gov/flicker/urlFlkPair.html
    Self-publishing images: This means that users can self-publish their images on their own Web or FTP server. FTP servers are either included or are easily installed on Microsoft Windows95/98, Windows-NT, Macintosh and UNIX systems which are connected to the Internet via TCP/IP.

    Image formats: It handles GIF, TIFF, JPEG, XWD, PS, PS2 files - although GIF files are preferred since other formats are converted to GIF for use by Flicker. Images must be less than about 1.5 Mbytes or they will be rejected by our Proxy Server. If images are too small, you will not be able to scroll them very well which may make the comparison difficult or impossible. If this happens, increase the size of all images using your favor image manipulation program before copying them to your server.

    URLs allowed: Only http:// and ftp:// protocols are accepted. Note that image files specified by CGI-BIN locations may not work depending on what weird characters are used in the URL.

    Image loading times: Note loading may take a while (could be on the order of minutes) since the NCI proxy server may need to read the gels from the Internet and then pass them back to Flicker running on your Web browser. [This extra work is required because of the security restrictions in the current version of Java.]

    Notice: Because of resource limitations, the Flicker Server is to be used only for scientific data.

    Enter two images URLs:

    1. First specify two different URL images for the Left and Right images.
    2. You may want to change the image canvas size for images displayed in Flicker.
    3. Press Go Flicker to start a Flicker comparison of this pair of images.

    Canvas Size,

    Left Image:
    Enter any image URL (http:// or ftp://)

    Right Image:
    Enter any image URL (http:// or ftp://)


    5. Notice - Flicker is still being developed

    NOTE: Flicker is a Beta level program and is under improvement to add additional functionality and take advantage of new Java developments. Some functions either may not work very well, work incorrectly, are slow, or may gobble up memory and crash your browser. If that happens, just restart your browser. A list of known bugs is available in the Flicker Reference Manual.

    6. References

    1. Lemkin PF, Merril C, Lipkin L, Van Keuren M, Oertel W, Shapiro B, Wade M, Schultz M, Smith E (1979) Software aids for the analysis of 2D gel electrophoresis images. Computers and Biomedical Research 12:517-544.
    2. Lipkin LE, Lemkin PF (1980) Database techniques for multiple PAGE (2D gel) analysis, Clinical Chemistry 26:1403-1413. (GELLAB-II)
    3. Lemkin PF, Lester EP (1989) Database and Search Techniques for 2D Gel Protein Data: A Comparison of Paradigms For Exploratory Data Analysis and Prospects for Biological Modeling, Electrophoresis, 10(2):122-140. (GELLAB-II)
    4. Lemkin PF (1993) Xconf: a network based image conferencing system. Computers and Biomedical Research. 26(1):1-27. [Extended paper]
    5. Lemkin PF (1997) Comparing Two-Dimensional gels across the Internet. Electrophoresis, 18, 461-470. [Extended paper]
    6. Lemkin PF (1998) Comparing 2D Electrophoretic gels across the Internet Databases. In 2-D Proteome Analysis Protocols, Andrew Link (Ed), in Methods in Molecular Biology, Vol. 112, Humana Press, Totowa, NJ, pp 339-410.
    7. Lemkin PF (1997) 2DWG meta-database of 2D electrophoretic gel images on the Internet. Electrophoresis, 18, 2759-2773. [Extended paper]

    Go to [ 2DWG meta-database| LECB | NCI]

    Last revised $Date: 2000/04/20 21:25:52 $ by P. Lemkin.
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