Calendar

September 9, 2008
NCMIR's Mark Ellisman is giving a keynote lecture, "Brain Research in the Digital Age," at Neuroinformatics 2008 in Stockholm, Sweden.








Research Portals

Affiliated Sites




National Center for Microscopy and Imaging Research (NCMIR)
Center for Research in
Biological Systems
Basic Science Building, Room 1000
University of California, San Diego
9500 Gilman Drive
Dept. Code 0608
La Jolla, CA 92093-0608 USA
Voice: (858) 534-0276
Fax: (858) 534-7497

Jinx

Welcome to Jinx.

Jinx is a Java application which, in theory at least, should run on most modern computers and operating systems with little or no need for installation or configuration. When you click on the link to run Jinx, you download a small file which your web browser should automatically recognize and cause the appropriate Java "jar" files to be downloaded through Java Web Start. Using this mechanism ensures that you will always be using the most current and up to date version of Jinx without having to keep up with patches, versions, or complicated downloads.

Please see the Notes section below for further information on installation and debugging.

Distribution

Click here to run Jinx with the SAO ontology in a 2000 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 2000 MB Java Virtual Machine.

Click here to run Jinx with the SAO ontology in a 1024 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 1024 MB Java Virtual Machine.

Click here to run Jinx with the SAO ontology in a 512 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 512 MB Java Virtual Machine.

Documentation

Want to be notified by email of updates to Jinx? Sign up for the jinx_dev mailing list here. This is a low traffic mailing list devoted to announcements about Jinx and associated applications.

Please click here for Jinx documentation.

Test Version

The following versions of Jinx are test versions. The data format of the Test version is NOT compatible with the Distribution. Reverting to the Distribution is possible by manually modifying the JNX file to change the version number with a plain text editor such as emacs or vi.

Click here to run Jinx with the SAO ontology in a 2000 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 2000 MB Java Virtual Machine.

Click here to run Jinx with the SAO ontology in a 1024 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 1024 MB Java Virtual Machine.

Click here to run Jinx with the SAO ontology in a 512 MB Java Virtual Machine.
Click here to run Jinx with the NIF ontology in a 512 MB Java Virtual Machine.

Changes include fixes in the Nuages surfacing tool and support for Marching Cubes, threads, and sphere surfacing.

A few important caveats regarding Marching Cubes surfacing:

  • A object must be traced on all planes from its beginning to end. If you skip any planes, gaps will appear in the surfacing. You may skip planes if you skip them consistently -- e.g., trace every other plane, every third plane, every 25th plane, etc. You may not skip planes randomly unless you intend to have gaps in the object -- e.g., trace planes 1, 2, 3, skip 4, then 5, 6, and 7.
  • Only Closed traces are currently supported. An error message will be produced and the surfacing will abort if you try to use Marching Cubes surfacing with Open traces.
  • There is a known bug which may produce small holes in the surface under certain circumstances. This will be fixed shortly.
  • Surfaces may exhibit a marked "wedding cake" or "terracing" effect. This is an artifact of the Marching Cubes algorithm.
  • There will most likely be signficantly more polygons produced by Marching Cubes than by Nuages.

Notes

About JVM Sizes. A larger Java Virtual Machine (JVM) is generally the better choice if you have the available computer memory. If you receive "OutOfMemoryError" messages at the startup of the program, try a smaller JVM.

If you have problems with the smallest version of the JVM or if they occur after the program has started and it is running, this is indicative of a software error of some sort. Please see below to contact the software author/maintainer.

Java Web Start. You will need Java Web Start and at least Java 1.5 (aka Java 2) in order to run this application. Java Web Start is part of the all the more recent Java distributions and should not need to be separately installed.

If you are not sure whether you have Java Web Start installed or are experiencing problems running it, please click here. This page will automatically test whether you have Java Web Start properly installed.

If it is not installed, please contact your system administrator and request that this package be installed, or, if you're managing your own system, check here to find a Java installation package. Unless you plan on doing your own Java development, you should only need the Java Runtime Environment (JRE). Installation instructions are provided for Solaris, Windows, and Linux. Apple Macintosh users should click here for information on installing Java 1.5.

Jinx.jnlp files. You may notice an accumulation of small files with the filename Jinx.jnlp or Jinx-1.jnlp, Jinx-2.jnlp, … appearing in your Desktop folder, your home directory, or in some temporary directory/folder. This file contains the directives used by Java Web Start to download the components of Jinx to run on your machine. At the present time it is not possible to automatically delete these files in a reliable manner. We are hoping to find a solution to this minor annoyance at some point in the future. You may safely delete these files at will, since they are used only at startup.

Jinx event log files. Jinx event log files also tend to accumulate. If the program runs successfully, you may safely delete these files (See below for What to do in case of problems). Jinx now looks for these old files at startup and will prompt you to delete them when more than 5 of them accumulate.

What to do in case of problems. This is still Beta software and may have bugs or unimplemented features. If you have problems running the program, it crashes, or it produces what you believe to be erroneous results, it is vitally important that these problems be reported.

As an aid to debugging, Jinx produces a log file recording a considerable amount of user and internal interaction which will be written in your "default" directory or folder. The location of this "default" directory or folder varies by operating system.

The log file names will have the date and time embedded in them and will be similar in form to the following:

Jinx.2007.04.18.113621.305.event

A unique identifier will be generated for each session.

You may be requested by the maintainer to start or run the Java Console. Instructions on how to turn this feature on are here.

Contact. If a problem arises, this file should be emailed here along with any pertinent information you might wish to add to aid in debugging the problem.