Note: Updates to the JAVA security settings require users to configure a security exception in order to run DoMosaics. We will soon provide a certificate for DoMosaics, making this unecessary. In the meantime, read here on how to configure an exception (under "WORKAROUND").

About


DoMosaics (previously known as AnGSTD) shows you a tree with corresponding domain arrangements of the proteins at the same time. If you want to know where your domain was lost, whether a group of proteins differs in its domain arrangements, or what are the characteristic domains for a phylogenetic group, DoMosaics is for you. DoMosaics lets you also examine the domain annotations to see whether the domains have been correctly identified. You can create dotplots, run a context-dependent similarity analysis and more. Furthermore, you can also run some general phylogenetic profiling, create domain network graphs, find domain insertion/deletion events and, last but not least, simply visualize and manipulate phylogenetic trees. All output can be saved as PDF or as SVG (which can be viewed in Firefox or edited using e.g. Adobe Illustrator or Inkscape) as well as in a number of common bitmap formats.
Graphics
create highly customizable, publication ready graphics from annotation data
Annotate
easy-to-use batch access to InterPro, wrapper for local HMMER installation
Connect data
visualize domain architectures along phylogenies
Analyse
investigate domain gain and loss events along branches, collapse similar architectures, annotate domains with context, perform domain dotplots, access webservices @EBI, ...
Manage
manage multiple projects in parallel, merge projects, export selections to new projects, separate data types in different views, ...

NOTE: We will release DoMosaics to the public domain, and source code will be made available on github after we have released the first stable version.

Requirements


Any machine running a recent version of JAVA should be able to run DoMosaics. RAM requirements vary depending on data set size, but we recommend 512 MB or more. For running HMMSCAN, a dual core (or better) is recommended. If you should encounter any issues, please let us know. You can start the application below.

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Download


DoMosaics requires an up-to-date version of Java. Once installed, you can start DoMosaics using JAVA web start by clicking Start DoMosaics below. For most applications, the default memory settings should be sufficient. If you choose to enable the offline-mode, a link to the cached jar will be placed on your desktop and in your start menu. Find out more about Java Web Start here.
Java_logo
MB
Memory allocated to the Java Virtual Machine
Indicates whether the program will run when offline
By downloading this software, you agree with the following:

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Note: DoMosaics is licensed using the Apache License 2.0. For more information, please visit

http://www.apache.org/licenses/LICENSE-2.0

Description Type Version Location
JAR Binary rv 0.95 http://domosaics.net/download/domosaics.jar
TAR source files rv 0.95 http://domosaics.net/download/domosaics-src.tgz

Use JAVA web start to start the application. JAVA web start allows users to start Java applications from a web server. It also makes sure that the application is always on the latest version. Note that, prior to running DoMosaics, your JAVA version we be checked (and you will be redirect to the JAVA download page if none, or an insufficient version of JAVA was detected). You can sign up with a valid email to receive update information.

Important We will not use your email for anything but to inform you about updates.

You can also access the JAVA archive directly, or build DoMosaics from scratch by downloading the source files. We plan to release DoMosaics on GitHub in the nearer future. If you wish to contribute, please get in touch and we can set you up with git read access.

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Running DoMosaics


To run DoMosaics, click on Start DoMosaics above. DoMosaics requires JAVA 1.7. Your browser will download a JNLP file. Depending on your browser version and the availability of a JAVA plugin you should see a dialog indicating the progress of the download. After the download has completed, you will need to accept the permission level (and risk - see below).

  • Downloading the DoMosaics JNLP file on Linux

  • The security warning on Windows

  • Note: DoMosaics will ask for unrestricted access to your system. This is necessary to allow proper interaction with your system (e.g. starting jobs, writing files etc). That said, we guarantee that DoMosaics will not do anything hidden or harmful to your system in any way.
If you enabled the offline mode above, you should see a DoMosaics Icon on your desktop (and in your start menu). There is no installation (or deinstallation) necessary as the link points to a self contained java archive. When you are done with the application, you can simply delete the link. Once you have started DoMosaics, you will probably want to start with a set of fasta sequences, run the annotator (against InterPro) to annotate domains, and then associate the resulting domain architectures to leafs of a tree. A crude tree can be calculated using DoMosaics, but we recommend using proper software for that (eg. RaxML or FastTree ). For more information on how to do what, visit the documentation.

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Changelog


Please report any bugs you may find to domosaics[at]uni-muenster.de, or submit a bug report to http://iebservices.uni-muenster.de/bugzilla. Thanks for helping us improve DoMosaics!

    REVISION 0.92 (current release candidate)
    • Removed insertion/deletion prediction
    • Adjustments to protein search
    • Auto-update of legend upon name/acc change in Domain Views
    Known issues:
    • Remote scanning with interproscan is not working - version v4 of InterProScan (SOAP) has been phased out (see here). We have already implemented version 5 for domosaics, and are currently testing it. If you need an updated version urgently, drop a mail.

    REVISION 0.89
    • Window stacking issue solved
    • Fixed issue with unresponsive panels
    • Fixed issue which led to InterProScan jobs not being cancelled when requested
    • Fixed issue with failure during submission of InterProScan jobs
    • ...
    Known issues:
    • On windows, the "report exception" functionality can fail when operating behind Symantec Endpoint Protection. This does not influence the functionality of DoMosaics

    REVISION 0.79
    • Lots of bugfixes
    • Cleaned up UI and wizards
    Known issues:
    • the netbeans wizard API used in all DoMosaics wizards does not work properly with OpenJDK 1.6.0 (java-1.6.0-openjdk-amd64), which leads to freezes in all wizards (e.g. when creating a workspace). We do not know the reason for this, but an upgrade to 1.7 (java-1.7.0-openjdk-amd64) fixes the issue.
    • Some systems present problems with windows stacking (e.g. a pop-up window opens, but remains under the parent window). This can give the impression that DoMosaics has frozen (as the modal window in the background is waiting for input). We are working on fixing this issue.
    • A few users have reported issues with running interpro scans (in which the scan terminates right after submission, even if domains can be found in the query sequence). We have not been able to reproduce this issue. Please drop us an email if you experience this (and include the fasta file).

    REVISION 0.78
    • Complete overhaul of workspace management
    • Updated iprscan to reflect changes to EBI interproscan API
    • Angstd now supports all InterProScan methods (Superfam, Pfam, SMART, Panther, ...)
    • Updated local HMMSCAN and HMMPRESS interfaces
    • Incorporated GO mappings
    • Included CODD procedure to allow for context dependent annotation (see also PMID:19786484)
    • Cleaned up overlap resolution procedure (mostly GUI related)
    • Various updates to the user interface
    • ...
    Known issues:
    • Job management: submitted jobs do not cancel properly upon abort (in some special cases)

    REVISION 0.68 (first public release)
    Known issues:
    • Bug in SwingWorker for Java SDK versions 1.6.0_18 - 1.6.0_20; InterProScan does not work properly. We recommend updating to the newest Java version.

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Frequently asked questions


  • How do I clear my application cache?

    If you enabled the offline version of DoMosaics, every time you start DoMosaic a quick check is made whether there is a newer version of the program available. This check has a timeout which, in some cases, my lead to a new version going undetected. We have changed the JNLP settings to make sure the check does not timeout, however, to be sure you get the newest version of the program if you have an old JNLP file, you have to clear your webstart application cache. On Windows, you can clear the cache by opening 'Java' in the Control Panel, selecting 'General' and clicking on 'View'. In the cache viewer, select DoMosaics and press delete. On *unix systems, open a terminal and enter

    javaws
    and follow the Windows instructions. Finally, go to http://www.domosaics.net and launch DoMosaics.

  • When I start the application the JNLP file is displayed (and not started)

    It is likely that your browser is not set up to handle JNLP files. If so, when you start DoMosaics you will see a dialog asking you what to do with the file. In the window, click on Open with, select the javaws executable (depending on your operating system, the name can be different) and press OK. If the "open with" option does not display the Java Web Start executable, map the .jnlp file to Java Web Start manually. This procedure differs for different browsers - best google the right solution for your OS/Browser setup. Get in touch if the problem is persistent. Note: there is a known issue on ubuntu which relates to javaws pointing to the wrong JAVA version. See here for more information.

  • How is DoMosaics licensed?

    DoMosaics is open source and is released under the Apache License, Version 2.0 We plan to release the source code on github in the nearer future, until then you can download the sources from here. Alternatively, you can drop us a note and we can provide access to our git repo.

  • I am using DoMosaics under Windows...

    If you are having problems under Windows, contact us with some details and will get back to you.

  • When I start DoMosaics I get "The default workspace is currently in use ..." and the remove button is not working

    This can happen when DoMosaics crashes violently, and can not clean up after itself. Navigate to the workspace folder you created when you started DoMosaics the first time (default is USER_HOME/domosaics-workspace) and remove the .lock file.

  • How do I get started? Is there a manual?

    Yes. There is an online manual here. Furthermore, to get you started, we have added an example data set for users to use a bit prior 'production' use (which can be found under 'Help' in the porgram). A corresponding quick start guide which uses the example dataset can be found here. In general, it is probably easiest to start with a set of protein sequences (fasta format), and load them into DoMosaics (File -> Manage Projects -> Create new Project (name, next) -> choose sequence -> select sequence file (fasta)) Once the view is loaded, run a search for domains using InterProScan (Actions -> InterPro) to create a domain view.

  • I am getting a java error:
    Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

    This indicates that the Java virtual machine has run out of memory. Re-download DoMosaics, but choose a larger JVM size from the drop down menu above. Note that while we have used DoMosaics with genome-sized datasets, some operations are not feasible for such large datasets.

  • Apparently, my question is not frequently asked...

    Please feel free to contact us

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References and Referencing DoMosaics


The application note describing DoMosaics appeared in Bioinformatics:

AD Moore, A Held, N Terrapon, J Weiner and Erich Bornberg-Bauer
DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins
Bioinformatics (2014) 30 (2): 282-283

Or, alternatively, if your journal supports webcitations you can cite:

http://www.domosaics.net


Here are some of the studies in which we (or others) have successfully used DoMosaics

  • Werren JH et al, Science (2010)
  • RĂ¼ping B et al, BMC Plant Biol (2010)
  • Kersting A et al, Genome Biol Evol (2012)
  • Moore AD and Bornberg-Bauer E, MBE (2012)
  • Moore AD et al, BBA Proteins and Proteomics (2013)
  • Terrapon et al, Bioinformatics (2014)

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Contact


DoMosaics is currently being developed by Andrew Moore and Nicolas Terrapon. Lots of inital development was done by Andreas Held (a Perl-TK version was developed by January Weiner).

Dr. Andrew D. Moore
Evolutionary Bioinformatics Group
Institute for Evolution and Biodiversity
Huefferstr. 1, 48147 Muenster, Germany
http://ieb.uni-muenster.de/bioinf
radmoore@uni-muenster.de

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Open Source Initiative