Rapid Development of Medical Imaging Tools with Open-Source Libraries

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools

Journal of Open Source Software (JOSS): design and first-year review

This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a DOI, deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles currently under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative

git-reviewed: A Distributed Peer Review Tool & User Study

Software peer review has been considered the basis of an effective procedure for examining software artifacts, identifying defects and increasing the efficiency of software firms for decades. The process of peer reviewing allows reviewers to check their co-worker's work, which helps in determining if a standard for a system has been maintained or achieved by the person whose work is being reviewed. The result of this process is a high quality working product that will likely reduce further maintenance effort. There is a large number of code review tools available in the market as of today, which assist in the reviewing task. All these tools are centralized, with the reviews and discussions being stored either on a mailing list or a server. In contrast, the code that makes up a software system is increasingly being stored in a distributed version control system (e.g. Git). In an effort to determine if distributed peer review is a tenable idea, we develop a peer review tool, git-reviewed, which replicates the working model of Git by incorporating reviews into the current Git architecture. git-reviewed is a lightweight and a truly distributed peer review tool, which eliminates a centralized server or a mailing list to store the review discussions. We model our use case based on the Linux kernel, which is a large open source project. git-reviewed has been designed to keep the current development and reviewing practices followed by the Linux kernel developers within the open source environment intact. We also provide better traceability by linking the review discussions on the mailing lists and the changes made in the Git repository. git-reviewed was evaluated by software developers working on large open source projects, (e.g. Linux, PostgreSQL, Git), whose feedback helped us improve our tool and determine if distributed reviewing works in practice

The tension between academic knowledge production and online peer production

Peer-reviewedOnline mass collaboration projects, such as Wikipedia and those designed for developing open source software programs, are remarkable examples of hybrid spaces where knowledge and information are co-produced by a wide variety of social actors. They share many features with traditional scientific practices: peer review mechanisms, a commitment for open publication of results, a meritocratic culture, etc. Nevertheless, there are also important differences: in online peer production peer review is often open and post-publication; the distinction between experts and lay people does not play a priori a crucial role ¿ amateur contributions are welcome; not only results are published but the process of production ¿ and thus intermediate results and procedures - is also open, etc. Though the present movement towards open science and open research pleads for importing some of these features to the realm of science and academia, it is not clear whether both cultures and ways of knowledge production are fully compatible. We try to address this issue through an empirical study on university lecturers¿ uses and perceptions of Wikipedia. The ¿free collaborative encyclopedia¿ is known to be one of the widest used resources by university students, but there are no systematic studies on how lectures and researchers use and perceive this source of information - though they seem to share a more skeptical view. We will present the preliminary results of a set on interviews to professors in different departments of our own university, as a first qualitative stage of a longer on-going research project.Projectes de col·laboració en línia de comunicació, com la Viquipèdia, i els dissenyats pel desenvolupament de programari de programes de codi obert, són exemples notables d'espais híbrids on el coneixement i la informació són co-produïdes per una àmplia varietat d'actors socials.Proyectos de colaboración en línea de comunicación, como Wikipedia y los diseñados para el desarrollo de software de programas de código abierto, son ejemplos notables de espacios híbridos donde el conocimiento y la información son co-producidas por una amplia variedad de actores sociales

BENKLER REVISITED – VENTURING BEYOND THE OPEN SOURCE SOFTWARE ARENA?

The organizational principles of open source software (OSS) development have challenged traditional theories in economics, organization research and information systems. In a seminal paper, Benkler (2002) provided a comprehensive framework to structure and explain these OSS principles. Coined Commons-Based Peer Production (CBPP), his framework has inspired a large stream of research on OSS. The objective of our paper is to determine whether CBPP also provides a viable framework to investigate projects of open innovation in non-software related domains. Using a case study approach, we focus on four projects that attempt to operate in line with the OSS phenomenon, but deal with tangible outputs (biotechnology, automobiles, entertainment hardware, and public patent review). We show that in general the CBPP framework is well-suited to explain open value creation in these domains. However, we also find several factors which limit its adoption to non-software related arenas