From: Fábio Madeira Date: Thu, 18 May 2017 11:04:07 +0000 (+0100) Subject: JWS-109 New fixes and updated looks as suggested by Geoff. Added new section about... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9da1a3ca004ceec4f6c14f5ca533814f2acb543b;p=jabaws.git JWS-109 New fixes and updated looks as suggested by Geoff. Added new section about elixir, fixed the top bar and added a MSA figure. Also bumped the date, and fixed the links to some of the downloads. --- diff --git a/website/about.jsp b/website/about.jsp index 686b96a..58897c0 100644 --- a/website/about.jsp +++ b/website/about.jsp @@ -26,8 +26,8 @@ at the School of Life Sciences, University of Dundee. Development by: - Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, - Suzanne Duce, Fábio Madeira and Geoff Barton. + Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira, + Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

@@ -77,12 +77,17 @@

- Peter V. Troshin, James B. Procter and Geoffrey J. Barton - + Peter V. Troshin, James B. Procter and Geoffrey J. Barton (2011) Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS - Bioinformatics 2011. 27 (14): 2001-2002. doi: + Bioinformatics 27 (14): 2001-2002. doi: 10.1093/bioinformatics/btr304.

+

+ Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017) + JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure. + Paper in preparation. +

diff --git a/website/download.jsp b/website/download.jsp index 40e2d38..36fd9f2 100644 --- a/website/download.jsp +++ b/website/download.jsp @@ -98,14 +98,17 @@

The command line client displays help when executed without arguments, @@ -171,7 +174,7 @@

@@ -205,10 +208,13 @@ <%----%> <%-- download (92M)--%>

  • + + The complete project
    • +
  • JABAWS source
  • - + Binaries of the programs included in JABAWS
  • JABAWS Git repository http://source.jalview.org/git/jabaws.git diff --git a/website/getting_started.jsp b/website/getting_started.jsp index df22a01..ee0616d 100644 --- a/website/getting_started.jsp +++ b/website/getting_started.jsp @@ -103,7 +103,7 @@ (version 1.7)
  • Provided that you have the Java ready to run, you can get command line help by changing to the directory where you downloaded the client jar, and typing:
    - 
    java -jar jaba-client.jar
    + 
    java -jar jabaws-full-client-2.2.0.jar

    • diff --git a/website/index.jsp b/website/index.jsp index 9e40bf8..57f793c 100644 --- a/website/index.jsp +++ b/website/index.jsp @@ -15,44 +15,51 @@

    -

    Welcome to the JABAWS website

    +

    Welcome to the JABAWS 2.2 website

    -

    -

    - - JAva Bioinformatics Analysis Web Services (JABAWS) - is free software which provides web services conveniently packaged to run on your local computer, server or cluster. -

    -

    - Services for multiple sequence alignment include - Clustal Omega, - Clustal W, - MAFFT, - MUSCLE, - T-Coffee, - ProbCons, - MSAProbs, and - GLProbs. - Analysis services allow prediction of protein disorder with - DisEMBL, - IUPred, - Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and - GlobPlot; and calculation of amino acid alignment conservation - with AACon. - The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the - Vienna RNA package. -

    -

    - JABAWS web-services can be accessed through the Jalview desktop - graphical user interface (GUI) (version 2.8 onwards) or the JABAWS Command Line Interface (CLI) client. - In this way you can perform computations on your sequences using the publicly available servers - running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis - limited only by your own computing resources, by running it in your local computer, server or cluster. -

    -

    - -

    +
    +
    +

    + JABAWS is free software which provides web services conveniently + packaged to run on your local computer, server or cluster. +

    +

    + Services for multiple sequence alignment include + Clustal Omega, + Clustal W, + MAFFT, + MUSCLE, + T-Coffee, + ProbCons, + MSAProbs, and + GLProbs. + Analysis services allow prediction of protein disorder with + DisEMBL, + IUPred, + Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and + GlobPlot; and calculation of amino acid alignment conservation + with AACon. + The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the + Vienna RNA package. +

    +

    + JABAWS web-services can be accessed through the Jalview desktop + graphical user interface (GUI) (version 2.8 onwards) or the JABAWS Command Line Interface (CLI) client. + In this way you can perform computations on your sequences using the publicly available servers + running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis + limited only by your own computing resources, by running it in your local computer, server or cluster. +

    +

    + The public server based on JABAWS 2.0 at the University of Dundee has been in production since + November 2013 and serviced over 430,000 jobs for users worldwide. +

    +
    +
    + Jalview: Sequence Alignment +
    +
    @@ -141,7 +148,7 @@

    You can access our public JABAWS web services with Jalview, JABAWS CLI, or - with your own program. + with your own program. The latest versions of Jalview (version 2.9 or later) are fully compatible with JABAWS 2.2 and are configured to use the public JABAWS server by default.

    @@ -153,36 +160,41 @@

    These web services accept submissions of less than one thousand sequences. - Should you find this to be insufficient for your needs, or if you are concerned about privacy - or you are on an unreliable network connection, then you can - download and + Should you find this to be insufficient for your needs, or if you are concerned about privacy, + then you can download and run the JABAWS WAR on your own hardware.

    -<%--
    --%> - <%--
    --%> - <%--
    --%> - <%--
    --%> - <%--

    JABAWS version 2.2

    --%> - <%--
    --%> - <%--
    --%> - <%--

    --%> - <%--The current JABAWS version is 2.2.0 released on XX March 2017. We advise you to update to JABAWS 2.2 as this version is fully backward compatible with JABAWS v1.0, v2.0 and v2.1.--%> - <%--Please consult the documentation pages--%> - <%--for the changelog and more information on compatibility between versions.

    --%> - <%--<%–

    Should you require them, however, old versions of JABAWS are available here:

    –%>--%> - <%--<%––%>--%> - <%--
    --%> - <%--
    --%> - <%--
    --%> -<%--
    --%> +
    +
    +
    +
    +

    New in JABAWS 2.2

    +
    +
    +

    + The current JABAWS version is 2.2 released on 19 May 2017. Among the new developments in JABAWS 2.2 are: +

    +
      +
    • Several programs included in JABAWS, including Clustal Omega, ClustalW, Mafft and T-coffee, were updated. +
    • AACon + was also updated to the latest release, version 1.1.
      • +
    • The website looks were updated to use the Twitter Bootstrap CSS framework, + and documentation pages are now generated with Sphinx. +
      • +
    +

    + More information about the changes introduced in the latest release can be found in the + changelog pages. +

    +
    +
    +
    +
    +
    @@ -191,15 +203,71 @@

    - Peter V. Troshin, James B. Procter and Geoffrey J. Barton - + Peter V. Troshin, James B. Procter and Geoffrey J. Barton (2011) Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS - Bioinformatics 2011. 27 (14): 2001-2002. doi: + Bioinformatics 27 (14): 2001-2002. doi: 10.1093/bioinformatics/btr304.

    +

    + Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017) + JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure. + Paper in preparation. +

    +<%----%> +
    +
    +
    +
    +

    ELIXIR-UK

    +
    +
    +
    +
    + + ELIXIR UK + +
    +
    +

    + We are pleased that alongside with + Jalview and + Jpred, JABAWS is a proud member of + ELIXIR - + the European-wide project providing high quality and sustainable infrastructure for biological information. + Following a strict selection procedure, JABAWS has been identified as a "Tier 1" + resource by ELIXIR-UK, as part of the Dundee Resources. +

    +
    +
    + + UK BBSRC + +
    +
    + + JALVIEW + +
    +
    + + JPRED + +
    +
    +
    +
    +
    +
    +
    +
    \ No newline at end of file diff --git a/website/static/img/aligment.png b/website/static/img/aligment.png new file mode 100644 index 0000000..863745b Binary files /dev/null and b/website/static/img/aligment.png differ diff --git a/website/static/img/elixir_uk.png b/website/static/img/elixir_uk.png new file mode 100644 index 0000000..3d853e2 Binary files /dev/null and b/website/static/img/elixir_uk.png differ diff --git a/website/static/img/jalview.svg b/website/static/img/jalview.svg new file mode 100644 index 0000000..fc571df --- /dev/null +++ b/website/static/img/jalview.svg @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/static/img/jpred4.svg b/website/static/img/jpred4.svg new file mode 100644 index 0000000..bc83bbc --- /dev/null +++ b/website/static/img/jpred4.svg @@ -0,0 +1,814 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/template_footer.jsp b/website/template_footer.jsp index e3781ef..6c40a60 100644 --- a/website/template_footer.jsp +++ b/website/template_footer.jsp @@ -93,7 +93,7 @@

    - Site Last updated: 21 April 2017. This site was built using the Bootstrap framework. + Site Last updated: 19 May 2017. This site was built using the Bootstrap framework.

    diff --git a/website/template_header.jsp b/website/template_header.jsp index ba9f2b1..ef02afb 100644 --- a/website/template_header.jsp +++ b/website/template_header.jsp @@ -55,17 +55,22 @@
    -
    -
    - Barton Group Logo -
    -
    - University of Dundee Logo + +
    +
    + Barton Group Logo
    -
    - Barton Group Banner +
    +
    + + Barton Group Banner
    +
    +
    + University of Dundee Logo     +
    + <%--
    --%> @@ -103,6 +108,9 @@
    • + Table of Contents +
      • +
    • Getting Started
    • @@ -169,9 +177,9 @@