Print Page

Open Source Software 

Open source software, examples and biological applications:

Computational Models and Simulation of Intra-Cellular Processes and Systems
Defense Advanced Research Projects Agency (DARPA)

The Bio-Computation program is aimed at exploring and developing computational methods and models at the bio-molecular and cellular levels. The program is directed towards achieving both powerful, synthetic computations that can be implemented in bio-substrates, as well as modeling and analytical tools for prediction and control of cellular internal processes and systems of living cells, for application in a variety of contexts of interest to DOD… In this BAA technical area, DARPA seeks research on powerful computational models of intra-cellular processes and systems that can be a basis for predicting and controlling the spatio-temporal cellular behavior. Based on these models, DARPA seeks open source development of an in-silico cellular analysis and evaluation tool, Bio-SPICE, a Simulation Program for Intra-Cell Evaluation. It is intended that Bio-SPICE will be a user-friendly simulation tool, with embedded models and techniques that effectively capture the processes governed by the network of molecular interactions including gene-gene, gene-protein, and protein-protein interactions, and can be customized for use in a variety of applications. These applications include the design of well informed and high success rate experiments, discovery of functional modules in cellular systems, and rapid and precise identification of targets and design of intervention methods that influence cellular dynamics. Additionally, the program seeks to refine and validate the models, as well as demonstrate the effectiveness of Bio-SPICE, through cell experimentations, which are of a high DOD significance.


Simulation in SPICE

SPICE (Simulation Program with Integrated Circuit Emphasis) is a family of programs (freeware or commercial) for simulation of electronic circuits, everyone based on the same kernel that is developed by Berkeley University (California, USA) since 1960 with public funds. From the beginning there were many releases, we can mention SPICE2 (last release Spice2g6, the first with powerfull models for semiconductors) and the current SPICE3 (last release Spice3f5, source code from Fortran to C, more portability and efficiency). Today's commercial packages are based on the last one, and they add to it many functions and features: graphical and easy-to-use front-ends, powerfull post-processors, integration with other utilities, new built-in models, commands and functions.


Linux Online

Linux is a free Unix-type operating system originally created by Linus Torvalds with the assistance of developers around the world. Developed under the GNU General Public License , the source code for Linux is freely available to everyone.


Open Source Initiative

Open Source Initiative (OSI) is a non-profit corporation dedicated to managing and promoting the Open Source Definition for the good of the community, specifically through the OSI Certified Open Source Software certification mark and program. You can read about successful software products that have these properties, and about our certification mark and program, which allow you to be confident that software really is "Open Source." We also make copies of approved open source licenses here. The basic idea behind open source is very simple. When programmers can read, redistribute, and modify the source code for a piece of software, the software evolves. People improve it, people adapt it, people fix bugs. And this can happen at a speed that, if one is used to the slow pace of conventional software development, seems astonishing. We in the open source community have learned that this rapid evolutionary process produces better software than the traditional closed model, in which only a very few programmers can see the source and everybody else must blindly use an opaque block of bits.


BioInformatics Open Source Conference 2000:
The Bioinformatics Open Source Conference (BOSC) is the successor to the successful bioperl-99biojava), but we do expect that a lot of the people involved in the open source projects in bioinformatics will attend.” conference…BOSC is designed to be open to all the open source efforts in bioinformatics, including Perl, Java, Python, C and C++ - even Fortran would be fun. We don't expect all attendees to be participating in a particular open source project (like, say, biojava), but we do expect that a lot of the people involved in the open source projects in bioinformatics will attend."


President's Information Technology Advisory Council
Open Source Software for High End Computing.  September 11, 2000.



Open Source Development Network

“The Open Source Development Network [OSDN] brings many of the Open Source community's favorite gathering places together and makes it easier to move between them. SourceForge, freshmeat, Linux.com, Themes.org, Slashdot, and our other Web sites will stay as independent as ever, but now you'll be able to access all of them -- and other useful Open Source sites -- from a central entry point: OSDN.com.”



SourceForge

SourceForge is a free service to Open Source developers offering easy access to the best in CVS, mailing lists, bug tracking, message boards/forums, task management, site hosting, permanent file archival, full backups, and total web-based administration.