From: Sasha Date: Tue, 2 Jul 2013 10:37:21 +0000 (+0100) Subject: Add funding page X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0713a22dde55639aaeaf872c6b74eb782582ff73;p=jabaws.git Add funding page --- diff --git a/website/contacts.html b/website/contacts.html index a238e47..2ca4a8b 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -25,13 +25,14 @@
diff --git a/website/images/bbsrc_flat.png b/website/images/bbsrc_flat.png new file mode 100644 index 0000000..991d2ec Binary files /dev/null and b/website/images/bbsrc_flat.png differ diff --git a/website/images/enfin.jpeg b/website/images/enfin.jpeg new file mode 100644 index 0000000..c1694f6 Binary files /dev/null and b/website/images/enfin.jpeg differ diff --git a/website/images/sulsalogo.jpg b/website/images/sulsalogo.jpg new file mode 100644 index 0000000..7e848ea Binary files /dev/null and b/website/images/sulsalogo.jpg differ diff --git a/website/images/wellcome.jpeg b/website/images/wellcome.jpeg new file mode 100644 index 0000000..814a7f4 Binary files /dev/null and b/website/images/wellcome.jpeg differ diff --git a/website/index.html b/website/index.html index 532c5d1..a495cde 100644 --- a/website/index.html +++ b/website/index.html @@ -35,7 +35,9 @@ Usage Statistics Services Status Contact Us - Barton Group
+ Barton Group + Funding +
@@ -59,7 +61,7 @@ and sequence analysis calculations limited only by your own computing resources.

For Users

- The Server: JABAWS Virtual Appliance: (440M) + The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M)

To use JABA Web Services on most operating systems, just download and install diff --git a/website/jabaws_funding.html b/website/jabaws_funding.html new file mode 100644 index 0000000..18efa24 --- /dev/null +++ b/website/jabaws_funding.html @@ -0,0 +1,81 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual + + + + + + +

+ + + + +
+ + + + +
+

JABAWS FUNDING

+

+The primary funding for JABAWS development is provided by the BBSRC Bioinformatics and Biological Resources Grant: +"The Dundee Resource for Protein Structure Prediction and Sequence Analysis" 2013 to 2018 (BB/J019364/1) to Prof. +Geoff Barton. Further support comes from Wellcome Trust Strategic Grant: 100476. +

+ +

+ Initial development was funded from a mixture of sources including: BBSRC grants (BBS/B/14434, BB/G022682/1), + Wellcome Trust Strategic Grant (No. 083481), European Commision Framework of Excellence ENFIN + (LSHGCT-2005-518254) and the Scottish Universities Life Sciences Alliance (SULSA). +

+ + + + + + + +
+
ENFIN
Wellcome Trust
SULSA
+
+ +
+
+ + + + + + + diff --git a/website/man_about.html b/website/man_about.html index 9d644d4..55cdc98 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -46,6 +46,7 @@ Services Status Contact Us Barton Group + Funding
@@ -62,7 +63,9 @@
  • What is JABAWS Client?
  • JABAWS versions compatibility and Jalview support
  • Programmatic access to JABAWS
    • - + + +

    What is JABAWS?

    @@ -82,17 +85,22 @@ in writing your own client, the JABAWS command line client is what you need.

    + +

    JABAWS Benefits

      -
    • Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
      • -
    • Comes complete with sources and binaries for all the bioinformatics programs that it runs.
      • -
    • Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
      • -
    • Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
      • -
    • Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, - your lab's server, or the publicly available services at the University of Dundee.
      • -
    • Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.
      • -
    • Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.
      • +
    • Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
      • +
    • Comes complete with sources and binaries for all the bioinformatics programs that it runs.
      • +
    • Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
      • +
    • Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
      • +
    • Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, + your lab's server, or the publicly available services at the University of Dundee.
      • +
    • Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.
      • +
    • Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.
    + + +

    JABA Web Services Programs

    JABAWS currently provides access to the following programs:

    Multiple Sequence Alignement

    @@ -103,8 +111,7 @@
  • Muscle (version 3.8.31)
  • Tcoffee (version 8.99)
  • Probcons (version 1.12)
    • - - +

    Protein disorder prediction

    • DisEMBL (1.5)
      • @@ -115,9 +122,12 @@

      Amino Acid conservation

      +
    + + +

    What is new in JABAWS 2.0.1?

    -

    JABAWS Version 2.0.1 includes several minor updates and bug fixes for JABAWS Version 2. These are listed below:

    +

    JABAWS Version 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2. These are listed below:

    • Disembl returned swapped strings for HOTLOOPS and REM465
    • Jronn failed to process jobs with more than 3 sequences
      • @@ -126,6 +136,7 @@ in one call
    • JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties
    • Default web security has been incompatible with Tomcat 7.0.31 and newer
      • +
    • Documentation has been updated
    JABAWS Version 2 (Released 16th Dec 2011)

    Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.

    It contains:

    • updates for all multiple sequence alignment services
      • @@ -139,10 +150,11 @@
    • Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
    • Improved web services client API
    • Simplified WAR package installation
      • -
    + + -

    What is JABAWS client?

    +

    What is JABAWS client?

    A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web @@ -154,21 +166,27 @@ provides a graphical JABAWS client. This client has the same functionality as the command line client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

    + + +

    JABAWS versions compatibility and Jalview support

    JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and v2.0 clients should also be able to use JABAWS 2.0.1 services. To access the analysis web services introduced in JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.

    + + +

    Programmatic access to JABAWS

    -JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language -or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home -page, and you can use this to automatically generate service bindings for your program. If you use Java, however, -then you may wish to use our client package to access JABAWS. -This package is based on the autogenerated source code produced by wsimport, which -is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify -working with JABAWS. For more information please refer to the data model javadoc. + JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language + or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home + page, and you can use this to automatically generate service bindings for your program. If you use Java, however, + then you may wish to use our client package to access JABAWS. + This package is based on the autogenerated source code produced by wsimport, which + is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify + working with JABAWS. For more information please refer to the data model javadoc.

    diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 822ec3b..0a39b38 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding
    diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html index 004da8b..5469bf7 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -45,6 +45,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html index 8313b9b..15824b5 100644 --- a/website/man_awscloud_ec2.html +++ b/website/man_awscloud_ec2.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_client.html b/website/man_client.html index a3f7718..dff5389 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_configuration.html b/website/man_configuration.html index d60ecb8..6c0877e 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_dev.html b/website/man_dev.html index bdd050c..3470fbc 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_server_dev.html b/website/man_server_dev.html index f5ef11b..bdac853 100644 --- a/website/man_server_dev.html +++ b/website/man_server_dev.html @@ -43,6 +43,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_servervm.html b/website/man_servervm.html index b96a9c1..228a1ae 100644 --- a/website/man_servervm.html +++ b/website/man_servervm.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_serverwar.html b/website/man_serverwar.html index 4445f07..0783417 100644 --- a/website/man_serverwar.html +++ b/website/man_serverwar.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/man_stats.html b/website/man_stats.html index 5574c60..f526be6 100644 --- a/website/man_stats.html +++ b/website/man_stats.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding diff --git a/website/quick_start.html b/website/quick_start.html index 5a384e1..91fa02a 100644 --- a/website/quick_start.html +++ b/website/quick_start.html @@ -29,7 +29,9 @@ Usage Statistics Services Status Contact Us - Barton Group + Barton Group + Funding + diff --git a/website/ws.css b/website/ws.css index 42a7e9d..3876f92 100644 --- a/website/ws.css +++ b/website/ws.css @@ -1,149 +1,95 @@ -#banner { background-color:white; } +#banner { + background-color:white; +} #mainpagefeatures { - margin: 0 2em 0 2em; + margin: 0 2em 0 2em; } #wrapper #mainpagefeatures table, #wrapper #mainpagefeatures th, #wrapper #mainpagefeatures td, #wrapper #mainpagefeatures tr{ - border:none; - border-collapse:collapse; - background-color: #fff; - padding-bottom:2em; + border:none; + border-collapse:collapse; + background-color: #fff; + padding-bottom:2em; } #jabaws_on_cloud img { - border:1px solid #6994AF; - clear:both; - margin: 2em 0; + border:1px solid #6994AF; + clear:both; + margin: 2em 0; } #wrapper #choicematrix table, #wrapper #choicematrix th, #wrapper #choicematrix td, #wrapper #choicematrix tr{ - border:1px solid grey; - background-color: #fff; - padding:1em; + border:1px solid grey; + background-color: #fff; + padding:1em; } #wrapper #choicematrix th { - background-image:url(images/brickhead2.jpg); - background-repeat:repeat-x; + background-image:url(images/brickhead2.jpg); + background-repeat:repeat-x; } .brick { -padding-bottom:1em; - border: 2px solid #999; - -webkit-border-radius:20px; - -moz-border-radius:20px; + padding-bottom:1em; + border: 2px solid #999; + -webkit-border-radius:20px; + -moz-border-radius:20px; border-radius: 20px; - background-image:url(images/brickhead2_line.jpg); - background-repeat:repeat-x; + background-image:url(images/brickhead2_line.jpg); + background-repeat:repeat-x; } + .brick_header { - display:block; + display:block; background:none; } .brick_header h2 { - font-weight: bold; + font-weight: bold; border:none; background:none; margin: 0.7em 0 0 0.5em; } .brick_content { - position:relative; - padding: 2em 1.5em 0em 1.5em; -} - - -/* -td.vm { -background-image:url(images/N_cell.jpg); -background-repeat:repeat-x; -} -td.button a { -display:block; -background:#069; -border:1px outset #069; -text-decoration:none; -font-weight:bold; -line-height:1.5em; -padding:0 .5em; -color:#fff; -} - -td.button a:hover { -background:#09c; -border-color:09c; -} -*/ - /* -#container .round { - display:block; - margin-right:10px; - background:#fff; - border: 1px solid #ccc; - -webkit-border-radius:20px; - -moz-border-radius:20px; - border-radius: 20px; - background-image:url(images/N_cell.jpg); - background-repeat:repeat-x; -} - - -#container .example5 div a { - padding:3px 20px; - border: 1px solid #ccc; - -webkit-border-radius:20px; - -moz-border-radius:15px; -} - -#container .example5 div a:hover { - background:#5d9ddd; - border:1px solid #2a7ecd; - color:#fff; -} -*/ -/* - - -webkit-border-radius:20px; - -moz-border-radius:15px; - -See index.html banner commented out code for an example of use -.uniicon { overflow: hidden; display:inline; padding:0; margin:0; float:right; position:relative; top:1em; } -.uniicon a img {border:none;} -*/ -#panel { - width:161px; - background:url("images/panel_bg_long.png") repeat-y ; + position:relative; + padding: 2em 1.5em 0em 1.5em; +} + +#panel { + width:161px; + background:url("images/panel_bg_long.png") repeat-y ; float:left; font-family:Verdana, Arial, Helvetica, sans-serif; padding-top:1em; - } +} -#content { - margin-left:170px; - border-bottom:solid 1px #6994af; - margin-right:0.9em; +#content { + margin-left:170px; + border-bottom:solid 1px #6994af; + margin-right:0.9em; } -#page { - margin: 0; - background-color:#fff; +#page { + margin: 0; + background-color:#fff; } -#copyright { text-align:right; - color:#999999; - font-family:Verdana, Arial, Helvetica, sans-serif; - font-size:smaller; - line-height:1em; - padding:0.3em 0.9em 1em 0; - } +#copyright { + text-align:right; + color:#999999; + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:smaller; + line-height:1em; + padding:0.3em 0.9em 1em 0; +} -#wrapper { - background:url("images/panel_bg_long.png") repeat-y left top; - margin:0; - padding:0; +#wrapper { + background:url("images/panel_bg_long.png") repeat-y left top; + margin:0; + padding:0; } ul { @@ -151,28 +97,27 @@ ul { } #panel a:link, #panel a:visited { - text-decoration: none; - display:block; - line-height: 1em; - padding:10px; - color:#000000; - } - + text-decoration: none; + display:block; + line-height: 1em; + padding:10px; + color:#000000; +} + #panel a:hover { - background-color: transparent; - text-decoration: underline; - } + background-color: transparent; + text-decoration: underline; +} #panel a.selected { - text-decoration:underline; - font-weight:bolder; + text-decoration:underline; + font-weight:bolder; } - #panel #submenu a { -margin-left: 1.5em; -margin-left: 20px; -padding: 5px; + margin-left: 1.5em; + margin-left: 20px; + padding: 5px; } strong { @@ -184,30 +129,20 @@ pre { font-family:Arial, Helvetica, sans-serif; } -p { +p { line-height: 1.4em; } - -.i { -font-style:italic; -} - -.hightlight { -font-style:italic; -font-family:"Courier New", Courier, monospace; +.i { + font-style:italic; } +.hightlight { + font-style:italic; + font-family:"Courier New", Courier, monospace; +} -/* -.about { -border-left: solid 4px #006633; -border-left-style:ridged; -padding-left: 1em; -}*/ - - -.code { +.code { color:black; background-color:#F5F5F5; font-family:"Courier New",Courier,monospace; @@ -218,7 +153,7 @@ padding-left: 1em; display:block; } -.box { +.box { color:black; background-color:#F5F5F5; font-family:Arial, Helvetica, sans-serif; @@ -229,74 +164,87 @@ padding-left: 1em; display:block; } -.u { text-decoration: underline; } +.u { + text-decoration: underline; +} -.headeru { - text-shadow:0 1px 3px black; - border-bottom: 1px solid white; -} +.headeru { + text-shadow:0 1px 3px black; + border-bottom: 1px solid white; +} -#banner h1 { +#banner h1 { font-family:Helvetica, Arial, sans-serif; white-space:nowrap; - color: white; + color: white; font-weight:bold; text-shadow:0 1px 3px #100F0E; - font-size: 27px; + font-size: 27px; } -h3 {border-bottom: 1px solid grey; margin-top: 2em; } +h3 { + border-bottom: 1px solid grey; + margin-top: 2em; +} -#headtitle { margin:0; padding-top:1em; text-align:center; color:#003b62; font-weight:600;} +#headtitle { + margin:0; + padding-top:1em; + text-align:center; + color:#003b62; + font-weight:600; +} -h2 {margin:1.8em 0 0 0; color:#003b62; font-weight:600;} +h2 { + margin:1.8em 0 0 0; + color:#003b62; + font-weight:600; +} /* Table styles */ - #wrapper table { - border-collapse: collapse; + border-collapse: collapse; border: 1px solid #666; margin: 20px 0 20px 0; width: 100%; } + #wrapper th, #wrapper td { margin: 2px 4px 2px 4px; padding: 0 5px; text-align: left; - vertical-align: top; border: 1px solid #666; } #wrapper table caption { - font: 1.5em Georgia, "Times New Roman", Times, serif; + font: 1.5em Georgia, "Times New Roman", Times, serif; padding: 1em; background-color: #9c9; } - #wrapper tr { - background-color: #eee; + background-color: #eee; } #wrapper tr:nth-child(odd) { - background-color: #ccc; + background-color: #ccc; } span.directory { -background: transparent url(images/dir.gif) no-repeat scroll left center; -color:#666666; -font-family:"Courier New",Courier,monospace; -font-style:normal; -padding:0 0 0 15px; + background: transparent url(images/dir.gif) no-repeat scroll left center; + color:#666666; + font-family:"Courier New",Courier,monospace; + font-style:normal; + padding:0 0 0 15px; } -.attention { -color:#993333; +.attention { + color:#993333; } /* open/closed box related styles */ -.source { +.source { border:1px solid #858789; display:block; margin:26px 0; @@ -308,9 +256,7 @@ color:#993333; background:#F5F5F5 none repeat scroll right 0; color:#434546; padding:7px 15px; -/* white-space:pre-wrap; */ white-space:normal; -/* word-wrap:break-word; # this prop does not exits*/ } .source .header { @@ -328,12 +274,12 @@ color:#993333; display:none; } -.source .header.collapsed { +.source .header.collapsed { background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center; padding:0 15px 0 15px; } -.body .code { +.body .code { margin:0; padding:0; border:0; @@ -343,20 +289,17 @@ color:#993333; body { font-family:Arial, Helvetica, sans-serif; - /* color: #494949; */ - font: 12px/170% Verdana; + font: 12px/170% Verdana; background-image:url(images/matrix_bg6.jpg); background-repeat:repeat; -/* background-color: #EAEAEA; */ line-height: 2em; min-width: 760px; max-width: 1100px; margin:0 auto; } - #banner table { - border-collapse: collapse; + border-collapse: collapse; border: none; padding:0; margin:0; @@ -367,23 +310,25 @@ body { width: 100%; } - -#banner td.bg { - border-collapse: collapse; +#banner td.bg { + border-collapse: collapse; background-image:url("images/banner_bg.gif"); - background-repeat: repeat-x; + background-repeat: repeat-x; background-color:transparent; background-position:inherit; } -img.logo { -/* border-top:1px solid #003b62; - border-left:1px solid #003b62; - border-right:none; - border-bottom: none; */ +img.logo { border:none; - margin:0; - padding:0; + margin:0; + padding:0; display:inline float:left; } + +.mid { + vertical-align:middle; + height:80px; + border:none; +} +