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Download Evolvix Release 0.3.0-Final

Evolvix 0.3.0-Final consolidated advances in ease of viewing exploratory simulation results in its WebGUI.

These screenshots and a tutorial poster can help you get a quick overview of what Evolvix can do.

The latest recommended release of Evolvix can always be found at this stable link:

http://evolvix.org/download

that will forward you to the corresponding release page.

 

Documentation only download

Our documentation is not perfect, but we've made quite a bit of progress that may be worth sharing as work in progress. If you want to get the current documentation of Evolvix that is included with the application binaries, but without having to download the binaries too, you can find here a zipped folder of html-webpages (the beta versions are not very different from the release version; please go to Evolvix 0.3.1 for the most recent improvements):

There you will find the essentials to help you get started and more. The same content is available as a PDF:

And here is a demo file of working Evolvix source code for a toy model, which goes beyond the minimalist hello world by using some of the time-series observation, documentation and attribution infrastructure we are developing. You can start modifying this by adding your own Actions and focusing the time series on reporting the Parts you find interesting.

 

This software is an early prototype. 

Like all very early stage prototype software you will find that this code will have all sorts of rough edges, which we could not polish yet (eg. no spaces in the path to the folder, from which you want to run Evolvix with a GUI). Please bear with us; we are doing what we can to make Evolvix more user friendly. We have tested some core functionality, but that may not be extensive enough for your use. As usual for software, this release of Evolvix comes with no guarantees whatsoever and you use it entirely at your own risk.

If you find any problems with Evolvix or have questions about it, please submit your findings via the contact form on this website. If you would like to become an alpha tester for new releases, please let us know. Thank you for your patience and for your help. 

 

Comment on current release

Having said all the above, Evolvix 0.3.0 release is our best distribution so far. It brings a graphical user interface, but it breaks backwards compatibility to make future syntax more consistent and easier to learn.

The improved documentation makes it much easier to use its most exciting features, especially the time series query syntax. Those bits that do work, do so very well, so if you have a mass-action-only model that you want to turn into simulated time series that you then analyze yourself, then Evolvix 0.3.0 can deliver a lot of value and we started using this for our own simulations in research.

However, if you want a more polished experience, you should wait. We are working on the next set of features to expand both the range of models and the analyses that can be done with them along with ease of use. We are also cleaning up our code in preparation for making it open source.

At the moment the CommandLine version ("CL") and the Graphical User Interface version ("GUI") of Evolvix come in separate bundles and use incompatible simulation results storage facilities, so spare yourself the trouble and do not try to switch (not impossible, but tedious). So, decide first which version you want to work with more. If you want to develop your own scripts or need direct access to the simulation results, you need to use the CommandLine version.

 

Downloading Evolvix ...

  1. Decide if you want to work through a graphical web-browser window or through the command-line. Then go to the corresponding section below. Try to stick to your choice for a modeling project to avoid the hassle of moving data from one form of storage to another. 
  2. If you continue to download Evolvix, you thereby indicate that you agree to the (Open Source Software) License that governs the use of Evolvix. It acknowledges the many capable programmers on who's work we have built and explains that you use Evolvix entirely at your own risk.
  3. Clicking the links below, directly downloads the files they link to.
  4. Once downloaded, move the download to where you want Evolvix to be Installed and all its simulation results to be stored (e.g. in a folder dedicated to your research). This folder is also called the Evolvix Installation Folder.
  5. Unzip the downloaded package. This creates a folder that contains everything that this Evolvix installation needs. Evolvix also stores all data in this folder (and should never affect any files outside of that folder).
  6. Before you do anything serious, always run the Default_Quest. This is the first thing you should learn, if you are new to Evolvix. Such a QuestRun should produce a TimeSeries plot that does not take very long to compute. If you can see that plot, then the installation worked. If not, get that to work before trying anything else. If you can't resolve difficulties with the help provided below, then please let us know in a BugReport.
  7. If you run into any trouble, please check first if problems are caused by difficulties with the Evolvix Installation Folder (see next section below).

 

Avoid trouble with Installation Folders

Currently, the Evolvix application and simulation results are stored in the Evolvix Installation Folder, which contains the Evolvix Home Folder.

Please choose carefully, where you put your Evolvix Installation Folder. The current Evolvix release 0.3.0 has difficulties with appropriately handling some absolute file-path names that are needed by Evolvix for accessing results in the Evolvix Home Folder. This causes several annoying Evolvix installation problems that can be difficult to recognize if seen for the first time.

Please avoid the following:

  • No spaces in folder names. If there is somewhere a space in the name of any folder that contains the Evolvix Home Folder, running the default Quest example will not produce any results.
  • The overall absolute file path is too long. On some operating systems (eg. Windows) Evolvix can show problems that look hard to diagnose, if the combined length of all names of all nested folders that contain the Evolvix Home Folder exceeds a certain length below the maximum absolute file path length allowed by that operating system (Evolvix needs a bit of additional file path length for working correctly).

Solution: move your Evolvix Home Folder to a new folder that does not have spaces in its path and or overly long absolute path-names (eg. choose a folder that is not too far away from your home folder or desktop folder as provided by your operating system). As we work towards finding more automated ways to resolve these problems, please check for these two potential problems and use our suggested work-around solution. 

 

Moving Data to a new release of Evolvix

Before installing a new release, take a few moments to consider your working setup. Moving data from old to new releases of Evolvix currently needs to be done by hand. Switching is easiest, if you can divide your work into clear periods of before and after installing the new release.

If you are using the WebGUI of Evolvix and want to...

  • ... run old Quests on a new release of Evolvix:
    1. Open the old Quest in the old Release of Evolvix.
    2. Find the code you want to move to the new Evolvix installation.
    3. Copy the code from all Quests from the old Evolvix Web Editor to corresponding new (plain) text documents (using an editor of your choice in your operating system).
    4. Close the old Evolvix installation by choosing "Quit" in the Evolvix Menu Tray Icon.
    5. Open the new Evolvix installation (and make sure the Default Quest runs fine).
    6. Create a new Quest for each Quest document that you have stored in a text file (from point 3) and paste the Evolvix Quest code from the text file into the new Editor window.
    7. Make a test run and adjust the syntax to the new version if necessary (check the manual and the release notes to see if there were any changes; we try to minimize these, but cannot yet exclude them at this point). 
  • ... view old QuestRun Results:
    1. Close the new Evolvix installation by choosing "Quit" in the Evolvix Menu Tray Icon.
    2. Open the old Evolvix installation, go to the corresponding quest and view your results as before.
    3. Once you are done, close again the old Evolvix installation by choosing "Quit" in the Evolvix Menu Tray Icon.

Unfortunately, it is impossible at this point to

  • Automatically move or export old QuestRun Results to a newer Evolvix installation (except if both installations are from the exact same Release)
  • Have 2 separate installations of Evolvix run on the same computer at the same time. While you can keep all browser windows open (showing old results and old code), you currently have to close the main Evolvix application in the background (i.e. "Quit" in the tray icon) if you want to run the other (because both use the "local port 3000" to talk to your web-browser; we will fix this in a later release.)

Thank you for your patience as we investigate potential solutions for making such upgrades easier. 

 

 

Download Evolvix 0.3.0-Final with a Webbased Graphical User Interface

For those who want maximal ease of use:

Evolvix WebGUI 0.3.0_Final Release for Mac OSX 10.9:                                                    Download is ca. 58.1 MB.

 

Evolvix  WebGUI 0.3.0_Final Release for Windows 7 (64 bit):                                             Download is ca. 35.6 MB.

 

Download Evolvix 0.3.0-Final for the CommandLine

For those who want maximal access to the data and configurability to run their own scripts:

 

Evolvix CommandLine 0.3.0_Final Release for Mac OSX 10.9:                                           Download tar.gz is ca. 3.8 MB.

Evolvix CommandLine 0.3.0_Final Release for Windows 7 (64 bit):                                     Download zip is ca. 3.4 MB.

Evolvix CommandLine 0.3.0_Final Release for Fedora Linux (Fedora21, 64 bit):                 Download tar.gz is ca. 11.4 MB.

Evolvix CommandLine 0.3.0_Final Release for RedHat Linux (RHEL_7, 64 bit):                  Download tar.gz is ca. 11.2 MB. 

Evolvix CommandLine 0.3.0_Final Release for Ubuntu Linux (Ubuntu 14.04 LTS, 64 bit):   Download tar.gz is ca. 11.2 MB.

 

 

2015-03-19  Release notes for Evolvix 0.3.0-Final

There were no user relevant changes from Evolvix 0.3.0-RC1 to Evolvix 0.3.0 final; The next release is available at Evolvix 0.3.1-RC1

The following changes were made in Evolvix 0.3.0-RC1 (compared to the previous release Evolvix 0.3.0-beta):

  • Focus was on improving the ease of viewing results in the WebGUI. Now a preview is shown in the left column that can be navigated by scrolling and using the up and down arrow keys.
  • Adding annotations to a QuestRun is easier now: just start typing while the corresponding QuestRunViewer is open. Clicking outside of the annotation window will end the editing.
  • QuestRunViewer window is now more flexible in its layout and hence easier to use.
  • Rudimentary error reporting was introduced for the WebGUI. If a QuestRun fails, then a QuestRunViewer will now say so explicitly. While Evolvix has a long way to go towards making error reporting transparent, this release took the small but important step to let users of a working Evolvix installation explicitly know in the browser if a QuestRun failed or succeeded.

 

Not (yet) changed:

  • No user relevant changes to the CommandLine version of Evolvix 0.3.0 final or Evolvix 0.3.0-RC1
  • No updates to the manual (yet). This has been improved for the next release, Evolvix 0.3.1-RC1.

 

Known problems when installing Evolvix 0.3.0 final

It is not recommended to install Evolvix 0.3.0 final;  please go straight to Evolvix 0.3.1-RC1, which also has improved documentation.
Please choose carefully, where you put your Evolvix Home Folder. The current Evolvix release 0.3.0 has difficulties with appropriately handling some file-path names in some Evolvix Home Folders (causing several annoying Evolvix installation problems that can be difficult to recognize if seen for the first time). Please avoid the following:

  • No spaces in folder names. If there is somewhere a space in the name of any folder that contains the Evolvix Home Folder, running the default Quest example will not produce any results.
  • The overall absolute file path is too long. On some operating systems (eg. Windows) Evolvix can show problems that look hard to diagnose, if the combined length of all names of all nested folders that contain the Evolvix Home Folder exceeds a certain length below the maximum absolute file path length allowed by that operating system (Evolvix needs a bit of additional file path length for working correctly).

Solution: move your Evolvix Home Folder to a new folder that does not have spaces in its path and or overly long absolute path-names (eg. choose a folder that is not too far away from your home folder or desktop folder as provided by your operating system). As we work towards finding more automated ways to resolve these problems, please check for these two potential problems and use our suggested work-around solution. 

 

Last unsupported Evolvix releases for older Operating Systems
(not recommended)

If you happen to have an operating system that is not supported by the latest releases above, then you might want to consider exploring some of the older packages below. However please note that Evolvix development is very fluid at this point in time and there is no guarantee of backwards compatibility of anything before Version 1.0.  Clicking the links below, directly downloads the files they link to. If you want to see these files in their folder before deciding whether to download, go here.

 

Mac OSX 10.7:  Evolvix 0.1.6-alpha                                   Download is ca. 7MB. 
(only for demo purposes; model sources no longer compatible to latest release)