OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an in- tuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net

The Paradoxes of Free Software

This paper describes the legal structure of open source software and analyzes the likely issues to arise. A combination of copyright law and trademark law serves to permit the free distribution of open source software. The software is kept under copyright, but freely licensed under one of various open source licenses. The legal structure of open source is an elegant and robust use of intellectual property law that turns the customary use of intellectual property on its head, by using intellectual property laws, which normally are used to guard exclusive rights, to safeguard free access to and use of software. The paper further discusses how open source challenges economic and philosophical theories of intellectual property. Ironically, the open source movement, with its early roots in a decidedly socialist view of software, appears to vindicate a rather free-market view of intellectual property--that market mechanisms are more efficient in overcoming market failure than corrective legal measures. Philosophically, open sources may fit best with a natural rights/personality theory, especially where open source authors frequently give away all rights except their rights to attribution and to prevent distortion. The paper further explores how open source may affect patent litigation, (especially with respect to the profound prior art problems in software patents) and other aspects of regulation of software (ranging from fair use in copyright to enforcement of licensing terms to restrictions on use of certain algorithms, like encryption). The openness of the software can cut both ways with respect to all those subjects

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

OBJECTIVE:Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. MATERIALS AND METHODS:An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. RESULTS:Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. DISCUSSION:By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. CONCLUSION:The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases

Pharo by Example

Pharo is a modern, open source, fully-featured implementation of the Smalltalk programming language and environment. Pharo is derived from Squeak1, a re-implementation of the classic Smalltalk-80 system. Whereas Squeak was developed mainly as a platform for developing experimental educational software, Pharo strives to offer a lean, open-source platform for professional software development, and a robust and stable platform for research and development into dynamic languages and environments. Pharo serves as the reference implementation for the Seaside web development framework

Open Source Software Utilization in Australian State Governments

The financial meltdown has affected businesses around the globe. Businesses are facing extreme pressures to reduce overheads, rationalize costs, and consolidate operations. It is, therefore, decisive to scrutinize all of the options available to the business before making an investment into information technology infrastructure and select the best option within the available means towards growth and seizing long term opportunities. These considerations are even more important in government departments or agencies, where broader public good and the need to demonstrate responsible usage of taxpayer funds are always paramount. Open source technology presents itself as a viable alterative to proprietary software and offers best little opportunity cost and trade offs. Open source software technologies offer genuinely collaborative innovation, at a fraction of cost, and provide robust and secure solutions. This paper presents a study of the open source software penetration in Australian state governments departments, and puts into perspective the value that open source software can add to these departments. It examines why the adoption of OSS for e-government is successfully utilized elsewhere but not in Australia

Nmag micromagnetic simulation tool - software engineering lessons learned

We review design and development decisions and their impact for the open source code Nmag from a software engineering in computational science point of view. We summarise lessons learned and recommendations for future computational science projects. Key lessons include that encapsulating the simulation functionality in a library of a general purpose language, here Python, provides great flexibility in using the software. The choice of Python for the top-level user interface was very well received by users from the science and engineering community. The from-source installation in which required external libraries and dependencies are compiled from a tarball was remarkably robust. In places, the code is a lot more ambitious than necessary, which introduces unnecessary complexity and reduces main- tainability. Tests distributed with the package are useful, although more unit tests and continuous integration would have been desirable. The detailed documentation, together with a tutorial for the usage of the system, was perceived as one of its main strengths by the community.Comment: 7 pages, 5 figures, Software Engineering for Science, ICSE201

Open TURNS: An industrial software for uncertainty quantification in simulation

The needs to assess robust performances for complex systems and to answer tighter regulatory processes (security, safety, environmental control, and health impacts, etc.) have led to the emergence of a new industrial simulation challenge: to take uncertainties into account when dealing with complex numerical simulation frameworks. Therefore, a generic methodology has emerged from the joint effort of several industrial companies and academic institutions. EDF R&D, Airbus Group and Phimeca Engineering started a collaboration at the beginning of 2005, joined by IMACS in 2014, for the development of an Open Source software platform dedicated to uncertainty propagation by probabilistic methods, named OpenTURNS for Open source Treatment of Uncertainty, Risk 'N Statistics. OpenTURNS addresses the specific industrial challenges attached to uncertainties, which are transparency, genericity, modularity and multi-accessibility. This paper focuses on OpenTURNS and presents its main features: openTURNS is an open source software under the LGPL license, that presents itself as a C++ library and a Python TUI, and which works under Linux and Windows environment. All the methodological tools are described in the different sections of this paper: uncertainty quantification, uncertainty propagation, sensitivity analysis and metamodeling. A section also explains the generic wrappers way to link openTURNS to any external code. The paper illustrates as much as possible the methodological tools on an educational example that simulates the height of a river and compares it to the height of a dyke that protects industrial facilities. At last, it gives an overview of the main developments planned for the next few years