Open Source Initiative

BioPerl Perl tools for bioinformatics, genomics and life sciences part of a wider bioinformatics open source initiative at http //www.open-bio.org http //bio. perl.org/... 

Most crystallographic programs arose in academic labs from the vision of their author and the help of a small number of collaborators. The authors maintain various levels of access to their source code. The open source model is an alternative. According to the Open Source Initiative (www.opensource.org) 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... ... 

The computer program used in this chapter has been made publicly available under an Open Source Initiative BSD License at http //glare.sourceforge.net. This program is written in C++ and has been successfully compiled on diverse platforms such as Mac OS 10.X, Linux, IBM AIX, and Windows XR Under its current form, GLARE is mainly a command line application that is invoked identically on any of the platforms. Details of the parameters and options can be found at the aforementioned web site. 

The TIGR has software systems available for free download. These include software for gene finding/annotation, alignment, sequencing/finishing, and microarray analysis. All of them are OSI (Open Source Initiative) Certified Open Source Software. 

Another major impetus for open-source software came in 1991, when Linus Torvalds publicly released his first version of an open-source version of the Unix operating system (now called Linux). In 1998, the Open-Source Initiative (OSI) was formed, stimulated by the announced public distribution of the formerly proprietary Netscape Internet browser. 

Second, current KBE applications or templates (within CAD systems) only weakly address the issue of workflow integration. The European iPROD project [12] aims to address this through the development of models and tools for workflow integration into KBE. The project iPROD also considers KBE as a service (Software-as-a-Service, SaaS), thereby addressing a third challenge in KBE research, which is to support web collaborative solutions and open source initiatives [5]. 

Open source technologies offer dynamic applications for real estate tailored to meet business development needs. Open source tools are usually available at no charge under a license defined by the Open Source Initiative. Open source tools may be viable alternatives to popular closed-source applications, and some open source tools offer features or performance benefits that surpass their commercial counterparts. The term open source tools is synonymous with open source utility and similar to open source applications. 

MOREHyS was developed by the German-French Institute for Environmental Research (DFIU/IFARE), in Karlsruhe (Germany), in co-operation with the Fraunhofer Institute for System and Innovation Research (ISI) (Karlsruhe) (Ball, 2006 Ball el al., 2006 Kienzle, 2005). MOREHyS is based on the open-source BALMOREL model (Baltic model of regional energy market liberalisation), which was initially developed... 

Richard continues, The basis of this initiative (called BIOS) is the kernel of the world s first open source biotech toolkit, analogous to the community development that blossomed around the Linux operating system. In the biotech case, the kernel... 

JMol JMol, initiated by Dan Gezelter at Columbia University is JMol is a free, open source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. http //jmol.sourceforge.net/... 

Several functioning examples of open source patent systems exist. The Public Patent Foundation (PPF) is one such initiative that facilitates the creation of a commons wherein patents may be pooled and made freely available to other participants [134]. The specific method applied by the PPF is to grant a nonexclusive and payment-free license to participants. The Biological Innovation of Open Society (BIOS) also involves technologies for which patent rights have been granted. 

All optimizations were performed with the open-source MS IBI Python package we developed [33], which calls HOOMD-Blue [34-36] to run the CG simulations and uses MDTraj [37, 38] for RDF calculations and file-handling. CG simulations were run at the same states as the atomistic systems. Initial CG configurations were generated from the CG-mapped atomistic trajectories at each state. As a result of the 4 1 mapping, CG water simulations contained 1,458 water beads. All CG simulations were run with a 10 fs timestep. The derived CG potential was set to 0 beyond the cutoff of 12 A. 

JSpecView is a viewer for spectral data in the JCAMP-DX and AnIML/CML format [75], The program was initially developed at the Department of Chemistiy of the University of the West Indies, Mona, Jamaica, West Indies and is available via sourceforge net under the GNU Lesser General Public License. It is an open-source viewer and converter for multiple spectra (Fig. 7.31). 

Table 8.2 Open-source resources of the CDIO initiative... 

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