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Download Evolvix Release 0.3.1-RC1

The Evolvix 0.3.1-RC1 release improved plots of simulation results and the Evolvix Icon in the operating system for better control of the local Evolvix server.

 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 far from perfect, but it covers some essentials to help you get started and more. We've made improvements that are worth sharing. The current documentation of Evolvix that ships with the application binaries can be browsed here:

You can also download it independently from the binaries in a zipped folder of html-webpages for offline reading:

Similar but slightly older content is available as a PDF (we are working to integrate our documentation build system):

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. 

You are welcome to use it if you know what you are doing (and what to simulate many time series of pure mass action systems stochastically and/or deterministically).

If you use this for any serious application, please let us know, so we can ensure that all is as it should be, and the science is not affected by some bugs we may have discovered while refining the code.

For all other uses, please talk to us and let us know what you are planning. We will help you to determine if Evolvix is a good fit now, in the near future, or if the features you need will require more work.

Like all very early stage prototype software you will find that this code will have all sorts of rough edges, which we could not yet polish (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, depending on your tolerances for computer glitches.

As with most software (including commercial offereings), Evolvix comes with no guarantees whatsoever and you use it entirely at your own risk. While we put a lot of effort into ensuring the integrity of our code, we are not in a position to guarantee that we find all bugs that matter to you.

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. 

 

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 basically 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. If you want to see these files in their folder before deciding whether to download, go here, where you will also find archives with some older files.
  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 0.3.1-RC1 with a Webbased Graphical User Interface

For those who want maximal ease of use:

Evolvix WebGUI 0.3.1_RC1 Release for Mac OSX 10.10:                                                    Download is ca. 58.3 MB.

 

Evolvix  WebGUI 0.3.1_RC1 Release for Windows 7 (64 bit):                                               Download is ca. 96.4 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 0.3.1_RC1 Release for Mac OSX 10.10:                                          Download tar.gz is ca. 6.2 MB.

Evolvix CommandLine 0.3.1_RC1 Release for Windows 7 (64 bit):                                      Download     zip is ca. 5.9 MB.

Evolvix CommandLine 0.3.1_RC1 Release for Fedora Linux (Fedora21, 64 bit):                 Download tar.gz is ca. 14.5 MB.

Evolvix CommandLine 0.3.1_RC1 Release for RedHat Linux (RHEL_7, 64 bit):                  Download tar.gz is ca. 14.2 MB. 

Evolvix CommandLine 0.3.1_RC1 Release for Ubuntu Linux (Ubuntu 14.04 LTS, 64 bit):   Download tar.gz is ca. 14.3 MB.

 

 

2015-03-20 Release notes for Evolvix 0.3.1-RC

These changes were made in Evolvix 0.3.1-RC1 (compared to the previous release Evolvix 0.3.0):

  • Focus was on further improving the Evolvix System Icon (as displayed in the Tray Icon / Menu Bar / etc). Improvements include:
    • To help you use Evolvix with a non-default browser on your system we created a menu entry to copy the URL of the local Evolvix WebGUI server. Just paste it in any open browser window to get started.
    • To help you find your Quest files and QuestRun data produced by Evolvix, we added a menu entry for opening the folder with all Quests in your file system viewer.
      (This helps with debugging for those who know a bit more about the system, but please do not change the files you see there to avoid breaking it. We are working to improve how information is presented in the file system.)
    • To help with debugging there is now a new entry for opening a console window that allows monitoring the activity of the WebGUI server (will only show activity after opening)
    • To help you differentiate between different Evolvix installations, we added the following:
      • Communication ports are now determined on a case by case basis, to avoid clashes with exiting installations of Evolvix. between your web browser and the Evolvix WebGUI server (AKA "node" in your system's process viewer, if you search for processes)
  • 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.
  • The 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. Good error reporting is difficult to do; one of the things we have been working on is the ground work for enabling an outstanding error reporting infrastructure. Expect further gradual improvements.
  • Improved manual: Now with documentation for some of the features of the WebGUI. While the integration has improved, there is still a way to go before this manual is ready for broader consumption.

 

Not (yet) changed:

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

 

 

 

Comment on current release

Evolvix 0.3.1-RC1 is our best distribution so far, bringing further improvements to the graphical user interface, the documentation and the infrastructure underneath all of it.

Its most exciting features are 

  • Easy composition of certain types of ordinary differential equation systems and corresponding stochastic simulations.
  • Powerful time series query syntax designed to shrink 'big simulation data' at its source to those bits that matter (as specified by a user). While we are working on bringing you a more powerful syntax redesigned to be even more flexible, those bits that are already implemented in the current release work really well.
  • Quick generation of plot overviews that can be customized to pre-select what is to be shown from the Evolvix Quest source code to allow a quick turn around for manually exploring different options.

Who can consider to use Evolvix now:

  • You are a professional user of bioinformatics software and know how to help yourself, but do not want to modify any source code.
  • You have a pure mass-action model that you want to turn into simulated time series, either for a quick interactive overview (then use the WebGUI version of Evolvix) or for further in-depth analysis by code that you write (then use the CommandLine version of Evolvix). Just read in the documentation, which files go where and then you can script your own analysis machinery around that.

In such scenarios, Evolvix 0.3.1 can deliver a lot of value and we started using Evolvix in these roles for our own research simulations.

 

Who should wait for future releases of Evolvix: Most users, and especially you if ....

  • You need a more polished user experience, and get very quickly impatient if some things are cumbersome; then please wait as we are working to improve ease of use.
  • You need more flexibility beyond the narrow type of models currently available for simulation in Evolvix; then please wait, as we expand both the range of models and the ways how they can be analyzed. We have some exciting new ways that we have worked out to make modeling easier and are working to bringing this to you in a future release.
  • You need the source  code to be able to help yourself. We are improving the organization, design and clarity of the underlying code in order to spare you (and us) the endless stream of questions you and any independent developer would have about those parts in our code that still stem from some earlier prototypic stage. Once we have cleaned up our code appropriately, we plan to make it open source for helping you to expand Evolvix any way you like, or even better, contribute your ideas back, so others can use them.
  • You expect the CommandLine version ("CL") and the Graphical User Interface version ("GUI") of Evolvix to work seamlessly in the same folder accessing the same simulation code files (we call them "Quests"). They currently come in separate bundles and use incompatible simulation results storage facilities. 
    Do not try to switch (it's not impossible, but very tedious). Decide first which release you want to work with more, and use that, while we are working to integrate both versions into a unified directory.
  • You expect your data to be safe when upgrading to a new Release of Evolvix. In that case, please spare yourself the trouble and do not use it yet.

 

 

Known problems when installing Evolvix 0.3.1 RC1
Please choose carefully, where you put your Evolvix Home Folder. The current Evolvix release 0.3.1 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)