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.
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.
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
|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.
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).
The security warning on Windows
The security warning on Windows
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
javawsand follow the Windows instructions. Finally, go to http://www.domosaics.net and launch DoMosaics.
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.
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.
If you are having problems under Windows, contact us with some details and will get back to you.
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.
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.
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.
Please feel free to contact us
Here are some of the studies in which we (or others) have successfully used DoMosaics