Invoking Flicker from HTML -
The Flicker Applet API

Table of contents

There are several ways to invoke Flicker. The simplest is to use one of the scrollable list of images listed in Examples of Flicker in the Flicker Server or the scrollable lists of twp gels from the 2DWG meta-database and ANY Web image URL. You can directly specify two images directly by ANY image URL.

Alternatively, you can write HTML specific for the Applet. When invoked, it will start Flicker on the two images you specify. The Applications Interface (API) is specified below. There are two PARAM values image1 and image2 which must be specified. In addition, there are a number of optional parameters which may be used from the list below which control the startup behavior.

1. The Flicker Applet <PARAM> API

The Flicker applet uses the Applet <PARAM> constructs to communicate from the user's HTML document commands to be processed by the Applet. These are broken into two types of parameters: Required and Optional.

Required <Applet> PARAM parameters to run Flicker

NAME VALUE
image1" either file name of GIF file in Flicker server of image URL.
image2" either file name of GIF file in Flicker server of image URL.

Optional <Applet> PARAMeters to adjust Flicker when it starts

These are optional parameters which will either default to the values shown or will not be invoked.
canvasSize "220". Size of left, right and flicker windows in Flicker. Legal size is 100 to 300 pixels.
defaultDelay "200". Default initial flicker delay [0:1000] mSec (0 to 1.0 seconds).
objColor "yellow". Color of the image cursor. Legal colors are: black, white, red orange, yellow, green, blue, cyan, magenta.
clickableCGIbaseURL "url-base-address". URL Base address of CGI-BIN program in an database associated with the image. If the clickable checkbox was set, the URL will be invoked as a GET method with the addition of the comma separated image name (where it was clicked), x and y. It assumes the CGI program can lookup the coordinates and return HTML which analyzes it in some way. Flicker will insert ",pixName,x,y" after the URL before trying to access it.
clickableCGIbaseURL1 "url-base-address". URL Base address of CGI-BIN program for image 1. This overides clickableCGIbaseURL and Flicker does not insert "pixName," before inserting "x,y" after the URL before trying to access it.
clickableCGIbaseURL2 "url-base-address". URL Base address of CGI-BIN program for image 2. This overides clickableCGIbaseURL and Flicker does not insert "pixName," before inserting "x,y" after the URL before trying to access it.
clickableCGIbaseURL1pix "url-base-address". URL Base address of CGI-BIN program for image 1. This overides clickableCGIbaseURL and Flicker inserts ",pixName,x,y" after the URL before trying to access it.
clickableCGIbaseURL2pix "url-base-address". URL Base address of CGI-BIN program for image 2. This overides clickableCGIbaseURL and Flicker inserts ",pixName,x,y" after the URL before trying to access it.
useProxyServerBaseURL "url-base-address". URL Base address of CGI-BIN "get" proxy server program. This overides NCI proxy server and allows the proxy server to reside on other computers. It will insert the url you are trying to load after this URL before trying to access it. If you use a copy of the NCI proxy server, the base address might be "http://host-name/cgi-bin/simpleProxyServer?". Note, the simpleProxyServer CGI program looks at ../conf/gIBW.conf for configuration information.
zScale "10". Pseudo3D scale factor range [0:50] percent.
eScale "20". Edge enhancement scale factor range [0:50] percent
angle "15". Pseudo3D projection angle range [-45:45] degrees.
magnification "1". Zoom scale factor range [0:8] X.
contrast "10". Contrast transform scale factor range [0:100] percent.
brightness "0". Brightness transform scale factor range [0:100] percent.
maxKeepaliveTime "600". Default amount of time to keep Flicker Java program alive when the browser visits another web location. If you set it to -1, then it kills it instantly.
flickerFlag "false". Set to "true" to start Flicker when it first starts up
gangScrollFlag Enable gang scrolling when you press the CONTROL key and click on the mouse. This presets the "Gang Scroll Imgs(T)" toggle menu item.
init_iPixFlag Preset the "Disp. Gray Val(T)" toggle menu item. This lets you view the pixel gray values of an image as you move the mouse over the image.
i1PosX position of Image 1 X coordinate when it first starts up
i1PosY position of Image 1 Y coordinate when it first starts up
i2PosX position of Image 2 X coordinate when it first starts up.
i2PosY position of Image 2 Y coordinate when it first starts up.
xLM1a "0". If predefine Landmark A, then Image 1 X coordinate > 0.
yLM1a "0". If predefine Landmark A, then Image 1 Y coordinate > 0.
xLM2a "0". If predefine Landmark A, then Image 2 X coordinate > 0.
yLM2a "0". If predefine Landmark A, then Image 2 Y coordinate > 0.
xLM1b "0". If predefine Landmark B, then Image 1 X coordinate > 0.
yLM1b "0". If predefine Landmark B, then Image 1 Y coordinate > 0.
xLM2b "0". If predefine Landmark B, then Image 2 X coordinate > 0.
yLM2b "0". If predefine Landmark B, then Image 2 Y coordinate > 0.
xLM1c "0". If predefine Landmark B, then Image 1 X coordinate > 0.
yLM1c "0". If predefine Landmark B, then Image 1 Y coordinate > 0.
xLM2c "0". If predefine Landmark B, then Image 2 X coordinate > 0.
yLM2c "0". If predefine Landmark B, then Image 2 Y coordinate > 0.

1.1 Examples using the Applet <PARAM> construct

This section gives some examples illustrating the HTML used to access the Flicker Applet.

Example 1: simplest Flicker applet invocation

<APPLET 
   NAME=Flicker 
   CODE=FlkJ2.class  ARCHIVE=FlkJ2.jar
   CODEBASE="http://www.lecb.ncifcrf.gov/flicker"
   WIDTH=650 HEIGHT=700 
   ALIGN=absmiddle
   ALT="You need a java-enabled browser to see 
        Flicker applet here."
>
<PARAM NAME=image1
   VALUE=URL for image 1>
<PARAM NAME=image2
   VALUE=URL for image 2>
</APPLET>

Example 2: This example sets the canvasSize and defaultFlickerDelay

<APPLET 
   NAME=Flicker 
   CODE=FlkJ2.class  ARCHIVE=FlkJ2.jar
   CODEBASE="http://www.lecb.ncifcrf.gov/flicker"
   WIDTH=650 HEIGHT=700 
   ALIGN=absmiddle
   ALT="You need a java-enabled browser to see 
        Flicker applet here."
>
<PARAM NAME=image1
   VALUE=URL for image 1>
<PARAM NAME=image
  2 VALUE=URL for image 2>
<PARAM NAME=canvasSize
   VALUE=220>
<PARAM NAME=defaultFlickerDelay
   VALUE=300
</APPLET>

Example 3: This example sets the clickableCGIbaseURL which holds for both of the gels

<APPLET 
   NAME=Flicker 
   CODE=FlkJ2.class  ARCHIVE=FlkJ2.jar
   CODEBASE="http://www.lecb.ncifcrf.gov/flicker"
   WIDTH=650 HEIGHT=700 
   ALIGN=absmiddle
   ALT="You need a java-enabled browser to see 
        Flicker applet here."
>
<PARAM NAME=image1
   VALUE=plasmaH.gif>
<PARAM NAME=image2
   VALUE=plasmaL.gif>
<PARAM NAME=clickableCGIbaseURL 
   VALUE=http://www.lecb.ncifcrf.gov/cgi-bin/dbEngine/plasmaDB,ismapTable
</APPLET>

Example 4: This example sets different clickableCGIbaseURL's for each of the gels

<APPLET 
   NAME=Flicker 
   CODE=FlkJ2.class  ARCHIVE=FlkJ2.jar
   CODEBASE="http://www.lecb.ncifcrf.gov/flicker"
   WIDTH=650 HEIGHT=700 
   ALIGN=absmiddle
   ALT="You need a java-enabled browser to see 
        Flicker applet here."
>
<PARAM NAME=WebServer
   VALUE=http://www.lecb.ncifcrf.gov/>
<PARAM NAME=image1 
   VALUE=http://www.lecb.ncifcrf.gov/flicker/PLASMA_HUMAN_id.gif>
<PARAM NAME=image2 
   VALUE=plasmaL.gif>
<PARAM NAME=defaultFlickerDelay VALUE=300>
<PARAM NAME=clickableCGIbaseURL1 
   VALUE=http://www.expasy.ch/cgi-bin/map3/PLASMA_HUMAN?>
<PARAM NAME=clickableCGIbaseURL2 
   VALUE=http://www.lecb.ncifcrf.gov/cgi-bin/dbEngine2/plasmaDB,ismapTable,plasmaL,>
</APPLET>

Example 5: sets WebServer and ImgCodebase when not NCI defaults

This example sets the WebServer and ImgCodebase when they are not the default values http://www.lecb.ncifcrf.gov and http://www.lecb.ncifcrf.gov/flicker respectively. 
<APPLET 
   NAME=Flicker 
   CODE=FlkJ2.class  ARCHIVE=FlkJ2.jar
   CODEBASE="http://zorch.org/flicker"
   WIDTH=650 HEIGHT=700 
   ALIGN=absmiddle
   ALT="You need a java-enabled browser to see 
        Flicker applet here."
>
<PARAM NAME=image1 VALUE=myPix.gif>
<PARAM NAME=image2 VALUE=yourPix.gif>
<PARAM NAME=WebServer VALUE=http://zorch.org>
<PARAM NAME=ImgCodebase VALUE=http://zorch.org/xyzzy/Gifs/>
</APPLET>

2. Use of the CGI genFlkPair program to generate Applet HTML code

Because users really require the flexibility of dynamic selection of Applet HTML rather than hard-wired HTML for specific images, we developed the genFlkPair CGI program. This is used primarily with scrollable lists of gel images, but can be used for other interfaces. There are several ways for images to be specified using the CGI-BIN (NAME,VALUE) pairs from the form. Two images are required: These include:
NAME VALUE
"PARAM.<name>" (opt) generate a <PARAM NAME=name VALUE=value> for the APPLET
"PARAMS.list" n1=v1;n2=v2;...;nk=vk. This lets you pack k (N,V) pairs of PARAM.<name> entries into a single parameter which is useful for SELECT lists. These are unpacked and used as if they were entered separately.
"WebServer" (opt) Use this Web server base address instead of NCI' F.S. eg. <PARAM NAME=WebServer VALUE=http://www.lecb.ncifcrf.gov
"relDir" (opt) Add this to the WebServer instead of "." The alternative is eg. <PARAM NAME=ImgCodebase VALUE=http://www.lecb.ncifcrf.gov/otherDB/Gifs/
"ZoomImg" (opt) Zoom size 1X to 8X. eg. <PARAM NAME=ZoomImg VALUE=1
"CanvasSize" (opt) Change the default canvas size from 220 to new size with a max value of 352 pixels (1.6X) if not 220, then resize HEIGHT and WIDTH by height= 650 + 2*(canvasSize - 220)); width= 700 + 2*(canvasSize - 220); eg. <PARAM NAME=CanvasSize VALUE=220
"image1" the gif image relative to /flicker/ in F.S. eg. <PARAM NAME=image1 VALUE=a00001.gif
"image2" the gif image relative to /flicker/ in F.S. eg. <PARAM NAME=image2 VALUE=a00002.gif
Radio Buttons
"leftImage" "image1_FS", "image1_2DWG", "image1_SEL_URL", "image1_URL"
"rightImage" "image2_FS", "image2_2DWG", "image2_SEL_URL", "image2_URL"
Single instances
"image1_FS" gif image (w/o ".gif") rel. to /flicker/ in F.S
"image1_2DWG" full [-cp] http:// or [-cp] ftp:// URL
"image1_SEL_URL" full [-cp] http:// or [-cp] ftp:// URL
"image1_URL" full [-cp] http:// or [-cp] ftp:// URL
"image2_FS" gif image (w/o ".gif") rel. to /flicker/ in F.S
"image2_2DWG" full [-cp] http:// or [-cp] ftp:// URL
"image2_SEL_URL" full [-cp] http:// or [-cp] ftp:// URL
"image2_URL" full [-cp] http:// or [-cp] ftp:// URL
multiple instances (exactly 2)
"image_FS" gif image (w/o ".gif") rel. to /flicker/ in F.S
"image_DWG" full [-cp] http:// or [-cp] ftp:// URL
"image_SEL_URL" full [-cp] http:// or [-cp] ftp:// URL
"image_URL" full [-cp] http:// or [-cp] ftp:// URL

2.1 Examples of using the CGI genFlkPair program to generate Applet HTML code

Example 1. for images residing on scrollable SELECT lists on the Flicker server. Eg. fasFlkPair.html

<FORM METHOD="POST" ACTION="/cgi-bin/genFlkPair?fasDB">

<INPUT type="hidden" NAME="sampleTitle"
       VALUE="Fetal Alcohol Syndrome plasma proteins study">
<INPUT type="hidden" NAME="authorHref" 
       VALUE="mailto:jem1@cdc.gov">
<INPUT type="hidden" NAME="authorName" VALUE="Jim Myrick, Mary Robinson">

<INPUT TYPE="reset" VALUE="Reset form">
<INPUT TYPE="submit" VALUE="Go Flicker"> 

<SELECT NAME="CanvasSize">
<OPTION VALUE="220 SELECTED"> 1.0X (default)
<OPTION VALUE="176"> 0.8X
<OPTION VALUE="198"> 0.9X
<OPTION VALUE="242"> 1.1X
<OPTION VALUE="264"> 1.2X
<OPTION VALUE="286"> 1.3X
<OPTION VALUE="308"> 1.4X
<OPTION VALUE="330"> 1.5X
<OPTION VALUE="352"> 1.6X
</SELECT>Canvas Size,

Left Image:<BR>
<INPUT type="radio" NAME="leftImage" VALUE="image1_FS" Checked> 
NCI Flicker Server image (left)<BR>

<SELECT NAME="image1_FS" SIZE=3>
<OPTION SELECTED>plasma-Human-FAS-F9Case-s00010-Flicker-NCI  - sex:F age:9  Case
<OPTION>plasma-Human-FAS-F9Ctrl-s00015-Flicker-NCI  - sex:F age:9  Control
<OPTION>plasma-Human-FAS-F10Case-s00001-Flicker-NCI - sex:F age:10 Case
<OPTION>plasma-Human-FAS-F10Ctrl-s00006-Flicker-NCI - sex:F age:10 Control
<OPTION>plasma-Human-FAS-M9Case-s00012-Flicker-NCI  - sex:M age:9  Case
<OPTION>plasma-Human-FAS-M9Ctrl-s00018-Flicker-NCI  - sex:M age:9  Control
<OPTION>plasma-Human-FAS-M10Case-s00011-Flicker-NCI - sex:M age:10 Case
<OPTION>plasma-Human-FAS-M10Ctrl-s00016-Flicker-NCI - sex:M age:10 Control
<OPTION>plasma-Human-FAS-M11Case-s00013-Flicker-NCI - sex:M age:10 Case
<OPTION>plasma-Human-FAS-M11Ctrl-s00004-Flicker-NCI - sex:M age:10 Control
</SELECT><P> 

Right Image:<BR>
<INPUT type="radio" NAME="rightImage" VALUE="image2_FS" Checked> 
NCI Flicker Server image (right)<BR>

<SELECT NAME="image2_FS" SIZE=3>
<OPTION>plasma-Human-FAS-F9Case-s00010-Flicker-NCI  - sex:F age:9  Case
<OPTION SELECTED>plasma-Human-FAS-F9Ctrl-s00015-Flicker-NCI  - sex:F age:9  Control
<OPTION>plasma-Human-FAS-F10Case-s00001-Flicker-NCI - sex:F age:10 Case
<OPTION>plasma-Human-FAS-F10Ctrl-s00006-Flicker-NCI - sex:F age:10 Control
<OPTION>plasma-Human-FAS-M9Case-s00012-Flicker-NCI  - sex:M age:9  Case
<OPTION>plasma-Human-FAS-M9Ctrl-s00018-Flicker-NCI  - sex:M age:9  Control
<OPTION>plasma-Human-FAS-M10Case-s00011-Flicker-NCI - sex:M age:10 Case
<OPTION>plasma-Human-FAS-M10Ctrl-s00016-Flicker-NCI - sex:M age:10 Control
<OPTION>plasma-Human-FAS-M11Case-s00013-Flicker-NCI - sex:M age:10 Case
<OPTION>plasma-Human-FAS-M11Ctrl-s00004-Flicker-NCI - sex:M age:10 Control
</SELECT><P>

<INPUT type="radio" NAME="rightImage" VALUE="image2_URL">
Enter any image URL (http:// or ftp://) (right)<BR>
<INPUT type="text" NAME="image2_URL" VALUE="" SIZE=50><P>
</FORM>

HR

Example 2. using both a SELECT list and a URL text input. Eg. spFlkPair.html

Note the images in the SELECT list reside out on the network. The use would need to type in a legal GIF image URL. 

<FORM METHOD="POST" ACTION="/cgi-bin/genFlkPair?swissProtDB">

<INPUT type="hidden" NAME="sampleTitle"
       VALUE="SWISS-2DPAGE Clickable Database">
<INPUT type="hidden" NAME="authorHref" 
       VALUE="http://www.expasy.ch/">
<INPUT type="hidden" NAME="authorName" VALUE="SWISS-2DPAGE">

<INPUT TYPE="reset" VALUE="Clear">
<INPUT TYPE="submit" VALUE="Go Flicker">

<SELECT NAME="CanvasSize">
<OPTION VALUE="220 SELECTED"> 1.0X (default)
<OPTION VALUE="176"> 0.8X
<OPTION VALUE="198"> 0.9X
<OPTION VALUE="242"> 1.1X
<OPTION VALUE="264"> 1.2X
<OPTION VALUE="286"> 1.3X
<OPTION VALUE="308"> 1.4X
<OPTION VALUE="330"> 1.5X
<OPTION VALUE="352"> 1.6X
</SELECT>Canvas Size,<BR>

<INPUT type="hidden" NAME="leftImage" VALUE="image1_FS"> 
1. Select SWISS-2DPAGE gel:
<SELECT NAME="image1_FS">
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/CEC_HUMAN/CEC_HUMAN"> Human  Colorectal_epithelia_cells
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/CSF_HUMAN/CSF_HUMAN"> Human Cerebrospinal_Fluid
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/ELC_HUMAN/ELC_HUMAN"> Human Erythroleukemia_Cell
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/HEPG2_HUMAN/HEPG2_HUMAN"> Human HepG2
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/HEPG2SP_HUMAN/HEPG2SP_HUMAN"> Human HepG2_Secreted_Proteins
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/HL60_HUMAN/HL60_HUMAN"> Human Promyelocytic_leukemia_cells
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/LIVER_HUMAN/LIVER_HUMAN"> Human Liver
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/KIDNEY_HUMAN/KIDNEY_HUMAN"> Human Kidney
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/LYMPHOMA_HUMAN/LYMPHOMA_HUMAN"> Human Lymphoma
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/PLASMA_HUMAN/PLASMA_HUMAN"> Human Plasma
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/PLATELET_HUMAN/PLATELET_HUMAN"> Human Platelet
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/RBC_HUMAN/RBC_HUMAN"> Human Red_blood_cells
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/U937_HUMAN/U937_HUMAN"> Human Macrophage_Like_Cell_Line
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/LIVER_MOUSE/LIVER_MOUSE"> Mouse Liver
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/ISLETS_MOUSE/ISLETS_MOUSE"> Mouse Pancreatic_islet_cells
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/MUSCLE_MOUSE/MUSCLE_MOUSE"> Mouse Gastrocnemius_muscle
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/EFP_MOUSE/EFP_MOUSE"> Mouse Epididymal_fat_pad
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/ECOLI/ECOLI"> <I>Escherichia_coli</I>
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/ECOLI4.5-5.5/ECOLI4.5-5.5"> <I>Escherichia_coli</I>(4.5-5.5)
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/DICTYSLUG/DICTYSLUG"> <I>Dictyostelium_discoideum</I>
<OPTION VALUE="http://www.expasy.ch/ch2dgifs/YEAST/YEAST"> <I>Saccharomyces_cerevisiae</I>
</SELECT><P>

2. Enter URL of gel image URL (http:// or ftp://)<BR>
(eg. http://www.lecb.ncifcrf.gov/flicker/plasmaL.gif):<BR>

<INPUT type="hidden" NAME="rightImage" VALUE="image2_URL">

<INPUT type="text" NAME="image2_URL" VALUE="" SIZE=50><P>
</FORM>

HR

Example 3. access to a CGI Web DB for image1, and using both a SELECT list and a URL text input. Eg. swissProtFlkPair.html

Note the images in the SELECT list reside out on the network. The use would need to type in a legal GIF image URL. Because the SELECT can only pass one argument and we need to pass two (clickableCGIbaseURL1, image1_FS), these are passed as a PARAMS.list which lets us encode a list of (N,V) pairs. 
<FORM METHOD="POST" ACTION="/cgi-bin/genFlkPair?swissProtDB">

<INPUT type="hidden" NAME="sampleTitle"
       VALUE="SWISS-2DPAGE Clickable Database">
<INPUT type="hidden" NAME="authorHref" 
       VALUE="http://www.expasy.ch/">
<INPUT type="hidden" NAME="authorName" VALUE="SWISS-2DPAGE">

<INPUT TYPE="reset" VALUE="Clear">
<INPUT TYPE="submit" VALUE="Go Flicker">

<SELECT NAME="CanvasSize">
<OPTION VALUE="220 SELECTED"> 1.0X (default for SVGA)
<OPTION VALUE="176"> 0.8X
<OPTION VALUE="198"> 0.9X
<OPTION VALUE="242"> 1.1X
<OPTION VALUE="264"> 1.2X
<OPTION VALUE="286"> 1.3X
<OPTION VALUE="308"> 1.4X
<OPTION VALUE="330"> 1.5X
<OPTION VALUE="352"> 1.6X
</SELECT>Canvas Size,
<BR>

<INPUT type="hidden" NAME="leftImage" VALUE="image1_FS"> 

1. Select SWISS-2DPAGE gel:<BR>
<SELECT NAME="PARAMS.list">

<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/CEC_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/CEC_HUMAN/CEC_HUMAN"> Human  Colorectal_epithelia_cells
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/CSF_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/CSF_HUMAN/CSF_HUMAN"> Human Cerebrospinal_Fluid
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/ELC_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/ELC_HUMAN/ELC_HUMAN"> Human Erythroleukemia_Cell
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/HEPG2_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/HEPG2_HUMAN/HEPG2_HUMAN"> Human HepG2
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/HEPG2SP_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/HEPG2SP_HUMAN/HEPG2SP_HUMAN"> Human HepG2_Secreted_Proteins
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/HL60_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/HL60_HUMAN/HL60_HUMAN"> Human Promyelocytic_leukemia_cells
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/LIVER_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/LIVER_HUMAN/LIVER_HUMAN"> Human Liver
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/KIDNEY_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/KIDNEY_HUMAN/KIDNEY_HUMAN"> Human Kidney
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/LYMPHOMA_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/LYMPHOMA_HUMAN/LYMPHOMA_HUMAN"> Human Lymphoma
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/PLASMA_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/PLASMA_HUMAN/PLASMA_HUMAN"> Human Plasma
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/PLATELET_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/PLATELET_HUMAN/PLATELET_HUMAN"> Human Platelet
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/RBC_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/RBC_HUMAN/RBC_HUMAN"> Human Red_blood_cells
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/U937_HUMAN?;image1_FS=http://www.expasy.ch/ch2dgifs/U937_HUMAN/U937_HUMAN"> Human Macrophage_Like_Cell_Line
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/LIVER_MOUSE?;image1_FS=http://www.expasy.ch/ch2dgifs/LIVER_MOUSE/LIVER_MOUSE"> Mouse Liver
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/ISLETS_MOUSE?;image1_FS=http://www.expasy.ch/ch2dgifs/ISLETS_MOUSE/ISLETS_MOUSE"> Mouse Pancreatic_islet_cells
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/MUSCLE_MOUSE?;image1_FS=http://www.expasy.ch/ch2dgifs/MUSCLE_MOUSE/MUSCLE_MOUSE"> Mouse Gastrocnemius_muscle
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/EFP_MOUSE?;image1_FS=http://www.expasy.ch/ch2dgifs/EFP_MOUSE/EFP_MOUSE"> Mouse Epididymal_fat_pad
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/ECOLI?;image1_FS=http://www.expasy.ch/ch2dgifs/ECOLI/ECOLI"> <I>Escherichia_coli</I>
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/ECOLI4.5-5.5?;image1_FS=http://www.expasy.ch/ch2dgifs/ECOLI4.5-5.5/ECOLI4.5-5.5"> <I>Escherichia_coli</I>(4.5-5.5)
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/DICTYSLUG?;image1_FS=http://www.expasy.ch/ch2dgifs/DICTYSLUG/DICTYSLUG"> <I>Dictyostelium_discoideum</I>
<OPTION VALUE="PARAM.clickableCGIbaseURL1=http://www.expasy.ch/cgi-bin/map3/YEAST?;image1_FS=http://www.expasy.ch/ch2dgifs/YEAST/YEAST"> <I>Saccharomyces_cerevisiae</I>

2. Enter URL of gel image URL (http:// or ftp://)<BR>
(eg. http://www.lecb.ncifcrf.gov/flicker/plasmaL.gif):<BR>

<INPUT type="hidden" NAME="rightImage" VALUE="image2_URL">
<INPUT type="text" NAME="image2_URL" VALUE="" SIZE=50><P>
</FORM>

Example 4. setting up Flicker to run as a mirror site with images from the mirror site in the "htdocs/flicker" directory

   *** TODO ***

Example 5. setting up Flicker to run as a mirror site with images from the mirror site NOT in the "htdocs/flicker" directory

   *** TODO ***

3. NCI proxy image server simpleProxyServer CGI gIBW.conf API

The NCI proxy image server is used to fetch images from arbitrary URL web addresses - not residing on the Flicker server. It also does image conversion from other image formats to GIF using Image Magick. The simple proxy server in the Flicker Mirror distribution does NOT do image conversion and thus does not require Image Magick. It does however require wget. 
# File: gIBW.conf configuration for in Web server conf/
# This file is read by cgi-bin/simpleProxyServer

# Edit this for a particular server.
# P. Lemkin, NCI-FCRF
# Date: 1997/06/23 17:52:59  / Revision: 1.7 $

# NOTE: you MUST edit lines with "# [***EDIT THIS***]". You probably
# should leave the other defs alone.
# NOTE: pay attention to trailing '/' or lack thereof!!!!

#  Disk location of top of Web server directory tree
#  (we use the NCSA 1.5.x tree conventions) with the server directory called
# httpd.
#  [***EDIT THIS***]
BASE_PATH: /home/httpd

#  Web URL location of server
#  [***EDIT THIS***]
BASE_SERVER_URL: /http://host-name

#  Directory where intermediate images are kept during conversions
#  Relative to BASE_PATH 
USE_TMP_PATH: htdocs/tmpImg

#  Precomputed default error message image.
#  Relative to BASE_PATH
DEFAULT_ERROR_IMAGE: htdocs/getImageFailed.gif

# Tmp image used during image format  conversion
DEF_OUTPUT_FILE: TMP_WGET.gif

#  Base address of the temporary image directory when wget'ing or
#  converting images.
#  Relative to BASE_SERVER_URL
DEF_OUTPUT_URL: tmpImg/

#  Where the GNU 'wget' program lives on the Web server
WGET_PATH: /usr/local/bin

#  Where the ImageMagick 'convert' program lives on the Web server
CONVERT_PATH: /usr/local/bin

#  Maximimum timeout allowed by wget (seconds). Note 180 = 3 minutes
TIME_OUT: 180

#  Maximimum image size allowed by wget calls (Kbytes)
MAX_IMAGE_SIZE: 1500


# List of alternate names for this server so can bypass wget to get the image.
# Syntax: ALT_BSE: host-name
# Max of 200 names
# [***EDIT THIS***]
ALT_BSE: host-name
ALT_BSE: host-name.org
ALT_BSE: alt-name-of-host
ALT_BSE: 123.123.123.123

# Add mappings from /~user/ to /~user/public_html ON SERVER machine
# Syntax: USER_MAP: ~name=full_path
# MAx of 200 names
# [***EDIT THIS***]
USER_MAP: ~user=/home/user
USER_MAP: ~user2=/home/user2
  
# --- the end ---

4. Downloading the Flicker Jar and CGI files for setting up a Flicker server

We are making the Flicker Java FlkJ2.jar JAR file, a sample HTML file, and related CGI support programs available for download for installation on researchers own Web sites. There is no fee or restrictions. The CGI binaries are available for Solaris.2.6 and Sunos.4.4.1. for genFlkPair and simpleProxyServer. The basic flicker program can be run with out the CGI programs if you intend to run it on other hardware. It only requires a Java enabled Web browser.

Last revised $Date: 2000/10/18 19:21:10 $ by P. Lemkin.
Send comments on this server to lemkin@ncifcrf.gov
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