www.compucell3d.org; python mac OSX, windows; open source software modeling environment and pde solver


CompuCell is an open source software modeling environment and pde solver. It is largely used for cellular modeling (foams, tissues, etc.), however, efforts are being made to include fluid simulation capabilities. Created in collaboration between groups at IU and Notre Dame, CompuCell provides an easy user interface for complex cellular modeling.

Integration with SBW

We have conducted a preliminary integration of CompuCell3D with Systems Biology Workbench (SBW) to link to subcellular models. As a result users can select the level of detail in their models while working within a single integrated framework.

see : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007190


Source Code and ChangeLog

SVN Repository

To download from our repository, use your favorite svn client and download from:


Known Issues and Requirements

  • Python 2.5
  • Ubuntu users must install python-qt4
  • ———
  • Python and MAC OSX

    Python comes pre-installed on Mac OS X, but due to Apple’s release cycle, it’s often one or even two years old. The overwhelming recommendation of the « MacPython » community is to upgrade your Python by downloading and installing a newer version from the Python standard release page.

    If you are using Mac OS X 10.5, see the Leopard wiki page for detailed information.

    If you’re just curious…

    You don’t have to download anything. You can run a Python interpreter by double-clicking on Applications / Utilities / Terminal (here’s a picture), then typing « python » into the window that opens up.

    You’ll see a prompt that looks like this:

    Python 2.3.5 (#1, Mar 20 2005, 20:38:20)
    [GCC 3.3 20030304 (Apple Computer, Inc. build 1809)] on darwin
    Type "help", "copyright", "credits" or "license" for more information.

    (On Mac OS X 10.3 (Panther), it will say « Python 2.3.0 », an older version.)Try typing « 2 + 2 » and hit « Enter »:

    >>> 2 + 2

    You’ve just evaluated your first Python expression. It’s a simple environment, but good enough to work through the Python tutorial.By the way, if you download the recommended upgrade mentioned at the top of this page, the « IDLE » development environment will make working through the tutorial a bit easier.

  • Literate Programming is a system of programming pioneered by Donald Knuth that allows one to break programs into small chunks. Each chunk should be short enough (say less than ten lines of code) can be completely and clearly documented (html).

    Literate Programming is a system of programming pioneered by Donald Knuth that allows one to break programs into small chunks. Each chunk should be short enough (say less than ten lines of code) can be completely and clearly documented. These chunks are assembled into a file and then run through a preprocessor to get either a documentation file (suitable for typesetting) or a just straight code.

    A bunch of literate programming solutions exist, since there seems to be more interest in writing new literate programming systems than in actually using them. Everyone seems to have an opinion. Knuth’s ideas are set forth in an interview, a book, and published programs like the Stanford Graphbase. In my opinion only two systems are worth considering: noweband cweb.


    noweb is an extensible system intended for a Unix environment written by Norman Ramsey. It is language independent and allows the creation of HTML documentation files automatically. Most people now use noweb. I really like the fact that chunks are numbered by page and then alphabetically by location on the page: “10c” refers to the third chunk on page 10.

    I don’t use noweb because porting it to the Macintosh was hopeless. It is written in Icon and C. In fact, I was unable to get the existing noweb port for the Mac to work.


    The philosophy behind CWEB is that programmers who want to provide the best possible documentation for their programs need two things simultaneously: a language like TeX for formatting, and a language like C for programming. Neither type of language can provide the best documentation by itself. But when both are appropriately combined, we obtain a system that is much more useful than either language separately. [Taken from the CWEB-3.0 User’s Manual.] There are at least three variants of cweb available.

    The original, canonical cweb by Donald E. Knuth and Silvio Levy. The cweb system consists a manual and the programs ctangle and cweave. No development is planned, but it is supported and bugs will still be fixed. It works and I use it.
    cweb was a translation of the original web system for Pascal. Something was lost in the translation. Marc van Leeuwen decided to rewrite it and add some rational features.
    ctwill was hacked by Donald Knuth and is an extension of cweave. It allows mini-indicies on every two page spread. This is great because every variable that is not defined on a two page spread is indexed and the relevant reference is available. It produces great documentation, at the cost of being a pain in the neck.

    All this stuff is available your local TeX archive.



    wordpress and code HTML -no javascript , no flash…


    WordPress.com is a type of shared environment, where all users are running off of the same software. This is great because it allows us at Automattic to update millions of blogs at the same time with a single click. It means we can fix bugs or offer new features very quickly, which is a win for you as users. Having all users running on the same software can also be dangerous. If we aren’t careful, one user has the potential to take down the entire site. So this is why we need to limit some of the things you post on your blog.

    If you wrote some code or pasted it in from another web site and then it disappeared after publishing the post, the code is likely being stripped out. If you feel it’s being stripped out improperly or if you would like to suggest additional types of code we should allow, please contact support.

    HTML Tags

    WordPress.com allows the following HTML code in your posts, pages, and widgets:

    address, a, abbr, acronym, b, big, blockquote, br, caption, cite, class, code, col, del, dd, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, img, ins, kbd, li, ol, p, pre, q, s, span, strike, strong, sub, sup, table, tbody, td, tfoot, tr, tt, ul, var

    Check out W3 Schools for more information about what each of these HTML codes are used for.

    If you are familiar with HTML, you’ll notice that codes such as embed, frame, iframe, form, input, object, textarea and others are missing from the above list. Those codes are not allowed on WordPress.com for security reasons.


    Users are not allowed to post JavaScript on WordPress.com blogs. Javascript can be used for malicious purposes. Your code and intentions may be perfectly harmless, but it does not mean all javascript will be okay. The security of all the blogs is a top priority and until we can guarantee scripting languages will not be harmful they will not be permitted.

    If you need proof of what Javascript can do, it has taken both MySpace.com and LiveJournal offline in the past.

    You may want a bit of Javascript and it may well be harmless but as soon as the system allows it someone will try and exploit it.

    JavaScript from trusted partners, such as YouTube and Google Video, is converted into a WordPress shortcode when a post is saved.

    Flash and Other Embeds

    Flash and all other embeds are not allowed in WordPress.com posts, pages, or text widgets. For security reasons we remove the tags needed for these to work. Your intentions may be innocent but someone somewhere would try to damage the site, affecting all of our users.

    There are several safe ways to post VideosAudio, and other items to your WordPress.com blog.

    Posting Source Code

    While WordPress.com doesn’t allow you to use potentially dangerous code on your blog, there is a way to post source code for viewing. We have created a shortcode you can wrap around source code that preserves its formatting and even provides syntax highlighting for certain languages, like so:

    1.#button {
    3.font-weight: bold;
    5.border: 2px solid #fff;

    Wrap your code in these tags:

    your code here


    Any of the following can be used for the language parameter (using one is required):
    <ul style="color:#444444;font-size:15px;line-height:1.6em;margin:0 0 20px 50px;padding:0;">
    <li style="margin:0 0 4px;padding:0;">bash</li>
    <li style="margin:0 0 4px;padding:0;">cpp</li>
    <li style="margin:0 0 4px;padding:0;">csharp</li>
    <li style="margin:0 0 4px;padding:0;">css</li>
    <li style="margin:0 0 4px;padding:0;">delphi</li>
    <li style="margin:0 0 4px;padding:0;">html</li>
    <li style="margin:0 0 4px;padding:0;">java</li>
    <li style="margin:0 0 4px;padding:0;">jscript</li>
    <li style="margin:0 0 4px;padding:0;">php</li>
    <li style="margin:0 0 4px;padding:0;">python</li>
    <li style="margin:0 0 4px;padding:0;">ruby</li>
    <li style="margin:0 0 4px;padding:0;">shell</li>
    <li style="margin:0 0 4px;padding:0;">sql</li>
    <li style="margin:0 0 4px;padding:0;">vb</li>
    <li style="margin:0 0 4px;padding:0;">xml</li>
    Code in between the

    tags will automatically be encoded for display, you don’t need to worry about HTML entities or anything.

    Alex Gorbatchev’s syntaxhighlighter Google Code project was used to implement this feature.


    Ne pas confondre wordpress.com
    qui est du blog  presse-boutton
    et wordpress (worpress.org) qui permet de mettre un blog de A à Z sur un serveur.

    wordpress.com a limité fortement l’introduction de code (java,etc…). C’est simple: le embedded est nettoyé quand vous postez!!!!!!

    Allowed HTML tags, They are:

    address, a, abbr, acronym, b, big, blockquote, br, caption, cite, class, code, col, del, dd, div, dl, dt, em, font, h1…h6, hr, i, img, ins, kbd, li, p, pre, q, s, span, strike, strong, sub, sup, table, tbody, td, tfoot, tr, tt, ul, ol, var.

    Pour un vieux de gopher qui a vu, il y a 18ans, le protocole http et le langage html sortir avec son no-limit pour faire des virus, c’est une position intéressante. Et si on veut faire tout ce qui est possible en html et CSS alors il faut passer à wordpress.org et faire un host à qq $/an.

    La version gratuite (déjà 3Go) ne permet même pas de mettre un MP3! On ne peut mettre que du : Allowed file types: jpg, jpeg, png, gif, pdf, doc, ppt, odt.

    Si on paie  the Space Upgrade. This allows you to upload mp3, ogg, wav, m4a, mov, wmv, avi, and mpg files to your blog and play them too. Ce qui pour 20$ pour 5Go de plus donne 8Go de dispo.

    The largest single file you can upload is about 75 Mb. If you need to upload large video or mp3 files, you should consider splitting them into several parts.

    Par contre ils ont développé des trucs nommés « shortcodes » avec une balise qui commence par [ et finit par ].

    Remarque: contrairement à WordPress.com, pour worpress.org, utiliser des shortcodes, il faut un plugin.



    Pour wordpress.com, je vais donner une galerie de  shortcodes.

    Ils ont leurs propres accès à des players internes puis externes…

    pour blip.tv , on a ceci:

    pour youtube, googlevideo, dailymotion:

    ———————-MP3 audio

    Le mieux est d’utiliser le widget de wordpress.com « box.net »

    Il suffit de s’inscrire :  http://www.box.net

    Puis sur http://www.box.net/widget

    il faut uploader les chansons de son choix, puis générer un petit code

    qui est en fait du « embedded » (mais dans ce widget il est transformé pour le rendre secure ;o) ).

    Plus tard tout ajout de musique via http://www.box.net/widget

    apparaitra dans la zone  widget box.net de son blog wordpress.com

    Pour un seul fichier mp3 mis à un endroit du web,

    le plus simple est :

    ATTENTION: The player expects the file to be encoded at 44.1kHz


    ———-pb: il faut cliquer 2 fois…



    —————pour utiliser le service odeo player music


    —————–VIDEO et MEDIA Splashcast

    We can  embed Splashcast media into your blog.

    [splashcast CLIW1846SO]

    ———–grouper devenu crackle


    Some details you might want to know about: Autoplay will cause your video to start playing as soon as a visitor loads the page. Please respect your visitors! We have made sure that only the first Autoplay on a page will start automatically. You won’t have to worry about ten videos all playing at once. If you change your mind about Autoplay, you can edit the code in your post: ap~1 turns it on and ap~0 (that’s a zero) turns it off. This only works on WordPress.com.

    —————pour un podtech

    [podtech content=http://…………..]


    —————pour flick video:

    [flickr video=2431720072]


    [flickr video=http://www.flickr.com/photos/john/2431720072/]

    —————pour kyt.tv :

    pour kyte.tv

    [kyte.tv 6118]

    Note: Because Kyte provides live video streaming, chat and comments, many people use it to create live shows. If you embed a live show you might want to consider creating a separate page on your blog – for example you could call it “My Live Kyte Show” – and embedding the show there. That way your show will be permanently accessible from that page (if you were to embed it into a blog post instead, the show would scroll off the bottom of the page as you publish new blog posts).

    Pour les video, il y a aussi le widget intégré : VodPod.

    — Can I have a slideshow?

    From http://slide.com, you can start a slideshow here.
    The code you need is given when your creation is complete.

    The code you get will work in posts and pages. It will not work in sidebars.

    You can also use RockYou or Slideshare to create slideshows that can then be embedded in your blog.


    [rockyou id=39325435]

    You can specify the width and height if you want to:

    [rockyou id=39325435&w=400&h=300]


    [ galerie ]

    Galeries intégrées — ; quand nous tirons profit du téléchargement multifichier pour télécharger un groupe de photos, nous avons un nouveau shortcode qui nous laisse metre facilement des galeries en mettant juste [ galerie ] (sans espace). L’affichage des légendes sera affichée et les gens peuvent laisser ses observations sur les différentes photos. Voir exemple sur wordpress.org: 1.200 images dans 23 galeries. Le shortcode a quelques options cachées aussi, contrôle hors de cette documentation.

    Il est intéressant de voir la partie shortcode_API

    New in WordPress 2.5.1 is the Shortcode API, a simple set of functions for creating macro codes for use in post content. A trivial shortcode looks like this: [galerie…]





    What is a shortcode?

    A shortcode is a WordPress-specific code that lets you do nifty things with very little effort. Shortcodes can embed files or create objects that would normally require lots of complicated, ugly code in just one line. Shortcode = shortcut.

    What shortcodes does WordPress use?

    displays an archive index of your blog posts. See full instructions here.

    [audio] converts a link to an mp3 file into an audio player. See full instructions here.

    [blip.tv] embeds a Blip.tv Video. See full instructions here.

    [contact-form] adds a contact form to your page. See full instructions here.

    [dailymotion] embeds a DailyMotion Video. See full instructions here.

    [digg] embeds a voting button for your link on Digg. See full instructions here.

    [flickr] embeds a Flickr video. See full instructions here.

    [gallery] inserts an image gallery into a post or page.

    embeds Google Maps. See full instructions here.

    [googlevideo] embeds a Google Video. See full instructions here.

    [kyte.tv ] embeds a Kyte.TV Video. See full instructions here.

    [livevideo] embeds a video from LiveVideo. See full instructions here.

    [odeo] embeds an Odeo audio file. See full instructions here.

    [podtech] embeds audio or video from the PodTech Network. See full instructions here.

    [polldaddy] embeds a PollDaddy poll (use without the space). See full instructions here.

    [redlasso] embeds a video from Redlasso. See full instructions here.

    [rockyou] embeds a slideshow from RockYou. See full instructions here.

    [scribd] embeds a document/file from Scribd. See full instructions here.

    [slideshare] embeds a slideshow from Slideshare.net. See full instructions here.

    [soundcloud] embeds the SoundCloud Audio Player. See full instructions here.

    [sourcecode] preserves the formatting of source code. See full instructions here.

    [splashcast] embeds Splashcast media. See full instructions here.

    [ted] embeds a TED Talks video. See full instructions here.

    [vimeo] embeds a Vimeo video. See full instructions here.

    [youtube] embeds a YouTube video. See full instructions here.

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    14. « Plasmas Froids : Systèmes d’analyse, Modélisation et Rayonnement », Publications MRCT, sept 2009, 400pages, EAN/ISBN 978-2-918701-00-2



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