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.
More

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

Binaries

• OSX
  • OSX Leopard/Tiger (10.5/10.4) New Version 3.4.1 Download
  • Requirements: Python 2.5 downloaded from http://www.python.org/download/
  • Instructions
• Windows
  • Windows Version 3.4.1
  • Windows 3.4.1 Download
  • Instructions
• Linux Distros (Version 3.4.1)
  <!–li>Debian Sid Download</li–>
  • Ubuntu 9.04 32Bit (Jaunty Jackalope) Download
  • Ubuntu 9.04 64Bit (Jaunty Jackalope) Download

Source Code and ChangeLog

• CompuCell Version 3.4.1 Download tar.gz
• CompuCell Version 3.4.1 Download zip

<!–li>New Changes: ChangeLog</li–>

SVN Repository

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

http://trac.compucell3d.net/svn/cc3d_svn/trunk/core

Known Issues and Requirements

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.
>>>

>>> 2 + 2
4
>>>

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

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.

cweb

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.

cweb

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.

cwebx

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

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.

http://www.bme.ogi.edu/~prahl/

http://omlc.ogi.edu/software/lp/

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.

avascript

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 Videos, Audio, 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:

Wrap your code in these tags:

your code here

/sourcecode]

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>
</ul>
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.

————

]]> http://stef2cnrs.wordpress.com/2009/10/10/wordpress-and-code-html-no-javascript-no-flash/feed/ 0 stef2cnrs http://stef2cnrs.wordpress.com/2009/10/10/mathematica-your-premier-service-subscription-entitles-you-to-the-following-services-and-benefits-for-your-covered-product-throughout-your-subscription-period/ http://stef2cnrs.wordpress.com/2009/10/10/mathematica-your-premier-service-subscription-entitles-you-to-the-following-services-and-benefits-for-your-covered-product-throughout-your-subscription-period/#comments Sat, 10 Oct 2009 19:44:40 +0000 stef2cnrs http://stef2cnrs.wordpress.com/?p=766 ]]> Latest Technology

• Access to the most current version of your product
• Free product updates and upgrades
• Advance notification of new product releases

Technical Support

• Free, individualized technical support for your product or applications linked to your product*
• Top-priority access to technical support engineers*

Complimentary Products and Services

• Free Mathematica home-use license
• Free home-use licensing for select Mathematica application packages you purchase or already own
• Free copy of Wolfram Lightweight Grid Manager, an application to discover and connect to Mathematica computation kernels on remote computers
• Free copy of Wolfram Workbench, a state-of-the-art integrated development environment for Mathematicatechnologies
• Three free copies of Mathematica Player Pro, the professional application delivery system for Mathematica
• Complimentary copy of webMathematica Amateur, letting you deliver interactive calculations and visualizations over the web
• Free online access to The Mathematica Journal, dedicated to all aspects of Mathematica and related topics

Special Discounts

• 10% discount on an early renewal of your Premier Service subscription
• 15% off select Mathematica application packages
• 15% off certified training classes from Wolfram Education Group
• Discounts and invitations for Wolfram Research conferences, presentations, seminars, and other events (discounts vary by event)

1-femto1

2. « Matériaux et joints d’étanchéité pour les hautes pressions », Avril2004, 220 pages, ISBN 2-86272-330-4.

2-sommaire

3. « Plasmas froids. Génération, caractérisation et technologies », sept2004, 420 pages, ISBN 2-86272-339-8.

3-plasmas-gene-
4. « Plasmas froids. Réactivité en volume et en surface », sept2004, 280 pages, ISBN 2-86272-340-1.

4-plasmas-react-

5. « Technologie des Hautes Pressions », mars2005, 250pages, ISBN 2-86272-345-2.

5-HP

6. « Lasers et Technologies Femtosecondes », oct2005, 460pages en quadrichromie, ISBN 2-86272-383-5.

6-femto2

7. « Plasmas Froids : Cinétique, transports, transferts », dec2005, 334pages, ISBN 2-86272-391-6.

7-plasma-cinet

8. « Plasmas Froids: Astrophysique- Aérospatial- Environnement- Biologie-Nanomatériaux », dec2006, 432pages, EAN/ISBN 9782862724256

8-plasma-astro-1

9. « Guide de préparation des échantillons pour la microscopie électronique en transmission, tome 1», 2007, 272pages, EAN/ ISBN 9782862724416

9-micro-1_a

10. « Guide de préparation des échantillons pour la microscopie électronique en transmission, tome 2», 2007, 392pages, EAN/ISBN 9782862724423

10-micro-2_a

11. «Conservation et valorisation du patrimoine des organismes de recherche», dec2007, 254pages,EAN/ISBN 9782862714768.

11-conserv

12. « Plasmas Froids: systèmes et procédés », nov 2008, 312pages,EAN/ ISBN 978-2-86272-477-5

12-SOMMAIRE

13. « Microélectrode à cavité Sous-titre : Principe, développement et applications pour l’étude de la réactivité de matériaux insolubles », mai 2009, 192pages,EAN/ ISBN 978-2-86272-500-0

13-Sommaire

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

14-sommaire_livre_plasmasVI

In 1992, Sandia National Laboratories started the Meshing Roundtable as a small meeting of like-minded companies and organizations striving to establish a common focus for research and development in the field of mesh and grid generation. Sandia National Laboratories continues to organize the International Meshing Roundtable, which has become recognized as an international focal point annually attended by researchers and developers from dozens of countries around the world.

The International Meshing Roundtable continues to focus on bringing together researchers and developers from academia, national labs and industry in a stimulating, open environment to share technical information related to mesh generation and general pre-processing techniques. This year’s roundtable will be held in Salt Lake City, Utah, USA.

7th Symposium on Trends in Unstructured Mesh Generation

July 16-19, 2009 Columbus, Ohio

Symposium Schedule

The list of speakers and titles is now availble here (pdf).

The Symposium on Trends in Unstructured Mesh Generation brings together a wide variety of disciplines for the exchange of technical information related to unstructured mesh generation. It is a symposium traditionally held in conjunction with the national and international computational mechanics congresses. The following is a list of previous MeshTrends symposia:

Scope of Symposium

Automatic unstructured mesh generation continues to be a vital technology in computational field simulations. As computing technology continues to advance and modeling requirements become more precise, automatic mesh generation techniques must rise to fulfill ever-increasing and diverse expectations. This symposium is a forum for exploring and synthesizing many of technologies needed to develop a computational grid suitable for simulation.

All abstracts related to geometry and mesh generation for computational simulation are welcome. In this symposium we are soliciting, in particular, advancements and trends from academics and industry in the following areas:

• Hexahedral mesh generation: including theoretical foundations and new algorithms for automatic all-hex methods.
• Meshing tools and applications: including commercial meshing tools and their application to current problems in industry.
• Multiphysics meshing issues: including tools and methods for managing meshing and geometry for mutiscale, mutliphysics applications.
• Infrastructure and tools for meshing: including APIs and tools for managing and interfacing meshing tools.
• Adaptive meshing tools and applications: including tools and methods for adaptively modifying mesh and geometry based on run-time results or optimization parameters.
• Meshing and geometry for geophysics applications: including geometry and meshing technologies for subsurface modeling and simulation.
• Meshing and geometry for biomedical applications: including geometry and meshing technologies for biomedical applications.
• Geometry repair and improvement for mesh generation: including tools and methods for characterizing dirty geometry and improvement techniques for mesh generation.
  

Abstract Submission

Abstracts are required for the conference and will be included in the conference proceedings. A one-page abstract must be submitted electronically through the USNCCM10 website. The deadline for abstracts was Feb 28, 2009.

Once you enter the abstract submission webpage at http://usnccm-10.eng.ohio-state.edu/abstractsub.html you will be asked to create a login and password. Note the number of the Trends in Unstructured Mesh Generation Symposium is 2.18.2. You will need to use that number in your abstract file name to ensure your abstract is submitted to the correct symposium (see below for more information).

The following information regarding abstract submission also appears on the abstract submission webpage.

Paper Submission

As part of this symposium, full papers will be solicited from the accepted presentations for inclusion in a peer-reviewed special journal edition of Engineering With Computers. Publication solicitation will be based on the interest of the participating authors and the technical merit of the presentation. Invitations for paper submissions will be made following the USNCCM.

Important Dates

Symposium Organizers

Steven J. Owen, Ph.D.
Computational Modeling Sciences Department
Sandia National Laboratories
Albuquerque, New Mexico, U.S.A.
Phone: (505) 284-6599
Email: sjowen@sandia.gov

Mark S. Shephard, Ph.D.
Director, Scientific Computation Research Center
Rensselaer Polytechnic Institute
Troy New York, U.S.A.
Phone: (518) 276-6795
Fax: (518) 276-4886
Email: shephard@scorec.rpi.edu

Matthew L. Staten
Carnegie Mellon University and
Sandia National Laboratories
Email: mlstate@sandia.gov

Additional Information

Additional information on the conference can be found at:
http://usnccm-10.eng.ohio-state.edu/index.html

Mesh Generation & Grid Generation on the Web

The aim of this document is to provide information on mesh and grid generation: people working in the field, research groups, books and conferences. It is maintained by Robert Schneiders.

Mesh generation is an interdisciplinary area, and people from different departments are working on it: Mathematicians, computer scientists, engineers from many disciplines. Despite the fact that surprisingly many people are active in the field, often there are few contacts between researchers. The aim of this page is to improve communication between research groups and to help people to get an overview of the field.

The page is organized as follows:

<!– –>

People and research groups: Info on meshing research at universities, companies, government labs etc.

List of people: A directory of people working on mesh generation.

Latest news: What’s up in mesh generation.

Software: A list of programs, both public domain and commercial.

Conferences: Information on conferences, summerschools, short courses etc.

Literature: Books, reviews, online sources and course materials.

Open positions: Career opportunities for people with background in mesh generation.

Information on related topics: Pages with information on CFD, scientific computing, computational geometry and other fields related to mesh generation.

<!– –> Service for frequent readers: You can find all entries, sorted by time of insertion, here (there is also an archive page). <!– Click here to see the latest updates (there is also an archive page). –>

Research on mesh generation is abundant, and I don’t claim to give a complete overview. In order make this page a useful service for the mesh generation community, I need help from other people. So if you are interested in getting put on the list, or if you have any comments or hints on other sources of information on mesh generation in the net, please send me an email (robert.schneiders@arcor.de).

A valuable source of information is the Meshing Research Corner, a comprehensive database with literature on mesh generation. It is maintained by Steve Owen.

couverture: http://www.nature.com/nature/journal/v430/n6998/index.html
de nombreux filets dans des revues…

——————————-
Cette page web contient les DOI.
C’est une page html absolument pas structurée (générée par google sites) mais avec un COinS (ci-dessous, en html) généré via http://generator.ocoins.info/
pour l’interopérabilité i.e. pour permettre d’enregistrer correctement les ref en un seul clic (avec zotero,  mendeley, LibX ou http://en.wikipedia.org/wiki/Comparison_of_reference_management_software).
————————————
Mis à jour le 7 octobre 2009

(COinS)

Features

refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI & COinS metadata allow for easy access by clients and search engines. Please see our Feature highlights page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given here.

Download

You can download the stable release version of refbase from the SourceForge download page. Please see the instructions on how to install or update refbase. The latest source code can be checked out and installed from the refbase Subversion repository.

refbase 0.9.5 README
====================

About refbase
————-
refbase is a web-based solution for managing scientific literature,
references and citations.

Currently, the following features have been implemented for:
EVERYONE
- search the database using different search forms
- search within results
- browse found records and sort results by any database field
- view results in different views (list view, citations, details,
print view)
- display results in different citation styles & output formats
- export selected records to XML (Atom, MODS, OAI_DC, ODF) and (via
the GPLed Bibutils programs) to ADS, BibTeX, EndNote, ISI, RIS and
Word XML
- display rich text (i.e., italics, super/sub-script, greek letters)
- extract citations from a text & build an appropriate reference list
- track additions via RSS and generate custom RSS feeds from searches
- web services (SRU & OpenSearch) that allow clients to access a
refbase database using a standard query syntax and retrieve results
in structured XML format
- dissemination of bibliographic data via standard methods (COinS &
unAPI) allowing clients to automatically discover and extract data
from refbase
- search a refbase online database from the command line and retrieve
results in various export & citation formats
LOGGED IN USERS
- user-specific fields which are stored individually for each user
- import of records from common bibliographic formats and online
databases via the web interface or the command line
- automatic email announcements for newly added records
- save and recall search queries
- adding records to user-specific groups
- add/edit/delete records as well as file upload & download links
ADMINISTRATOR
- user management interface provided to the database admin
- set access permissions on a per-user basis

More information is given at:
<http://features.refbase.net>

Credits
——-
See AUTHORS

Requirements
————
refbase requires:
- a web server (like the Apache HTTP Server <http://httpd.apache.org/>)
- PHP <http://www.php.net/> (version 4.4.0 or greater) with enabled
session support & installed PHP MySQL module
- MySQL <http://www.mysql.com/> (version 4.1.x or greater required for
Unicode support)

- for import and export of various formats (e.g., Endnote & BibTeX):
Bibutils <http://www.scripps.edu/~cdputnam/software/bibutils/>
(version 3.21 or greater)

More detailed information is available at:
<http://requirements.refbase.net>