How contributing to open source launched my academic career

Chapter 1 - Digital Forensics with Open Source Tools

A limited revolution — The distributional consequences of Open Source Software in North America

In this response to Willinsky’s chapter on representing research, I describe a small sample of early users of the open source software system the Open Journal System (OJS) who deployed the system to publish digital open access academic journals. Based on the responses and experiences of these users, I argue that participation in the open access movement by using online publishing tools which enable a ‘do-it-yourself’ ethic, allows for the creation and dissemination of new knowledge, the use of new epistemologies and alternative methodologies. All of these new knowledge spaces that have been created via OJS users work to fill in the gaps in the pre-existing traditional academic knowledge network and connect the processes of research and representation.

How can we address the complexity and cost of applying science to societal challenges? Open science and collaborative R&D may help [1]–[3]. Open science has been described as “a research accelerator” [4]. Open science implies open access [5] but goes beyond it: “Imagine a connected online web of scientific knowledge that integrates and connects data, computer code, chains of scientific reasoning, descriptions of open problems, and beyond …. tightly integrated with a scientific social web that directs scientists' attention where it is most valuable, releasing enormous collaborative potential.” [1]. Open science and collaborative approaches are often described as open source, by analogy with open-source software such as the operating system Linux which powers Google and Amazon—collaboratively created software which is free to use and adapt, and popular for Internet infrastructure and scientific research [6], [7]. However, this use of “open source” is unclear. Some people use “open source” when a project's results are free to use, others when a project's process is highly collaborative [4]. It is clearer to classify open source and open science within a broader class of collaborative R&D, which can be defined as scalable collaboration (usually enabled by information technology) across organizational boundaries to solve R&D challenges [8]. Many approaches to open science and collaborative R&D have been tried [1], [9]. The Gene Wiki has created over 10,000 Wikipedia articles, and aims to provide one for every notable human gene [10]. The crowdsourcing platform InnoCentive has reportedly facilitated solutions to roughly half of the thousands of technical problems posed on the site, including many in life sciences such as the $1 million ALS Biomarker Prize [11]. Other examples include prizes (X-Prize [12]), scientific games (FoldIt [13]), and licensing schemes inspired by open-source software (BIOS [14]). Collaborative R&D approaches vary in openness [15]. In some approaches, the R&D process and outputs are open to all—for example, open-science projects like the Gene Wiki described above. In other approaches which demonstrate what might be called controlled collaboration, there are strong controls on who contributes and benefits—for example, computational platforms like Collaborative Drug Discovery or InnoCentive that support both commercial and nonprofit research [9], [11]. Collaborative approaches can unleash innovation from unforeseen sources, as with crowdsourcing health technologies [11]–[13], [16]. They may help in global challenges like drug development [17], as with India's OSDD (Open Source Drug Discovery) project that recruited over 7,000 volunteers [16] and an open-source drug synthesis project that improved an existing drug without increasing its cost [18]. If you want to apply open science and collaborative R&D, what principles are useful? We suggest Ten Simple Rules for Cultivating Open Science and Collaborative R&D. We also offer eight conversational interviews exploring life experiences that led to these rules (Box 1). Box 1. Conversations on Open Science and Collaborative R&D Many commentators have considered challenges in translating open science and collaborative methods to biomedical research [2]–[4], [9], [17], [20], [24], [26], [28], [29]. How can protecting intellectual property be balanced with freeing researchers to build on previous knowledge? If R&D results are collaboratively created and freely available, who will take responsibility for costly clinical trials and quality control? What will be the Linux of open-source R&D? To explore such challenges and convey life experiences in biomedical open science and collaborative R&D, we offer eight conversational interviews by the first author of this article as supplementary material. The conversations were done on behalf of the Results for Development Institute and are with: Alph Bingham, cofounder of InnoCentive (Text S1) Barry Bunin, CEO of Collaborative Drug Discovery (Text S2) Leslie Chan, open access pioneer and director of Bioline International (Text S3) Aled Edwards, director of the Structural Genomics Consortium (Text S4) Benjamin Good, coleader of the Gene Wiki initiative (Text S5) Bernard Munos, pharmaceutical innovation thought leader (Text S6) Zakir Thomas, director of India's Open Source Drug Discovery (OSDD) project (Text S7) Matt Todd, open science and drug development pioneer (Text S8)

The Move to the Middle: Convergence of the Open-Source and Proprietary Software Industries

A number of contemporary factors have combined to create a situation that encourages and supports international collaboration among institutions of higher education. Factors such as the globalization of the economy, the increasingly international nature of higher education, and the development of an inexpensive and virtually worldwide system of communication, the Internet, have all played their part. This paper focuses on one aspect of international collaboration—the creation and dissemination of information resources and information/educational technologies, such as software. Movements such as Open Source and Open Access have encouraged colleges and universities to consider alternatives to the dominant model for acquiring everything from college textbooks to academic computing software. Today for-profit companies supply most such resources to institutions, faculty, and students. The open source software approach is an alternative based on collaboration between both institutions and individuals, and it is a viable alternative to commercial, for-profit development and dissemination systems. Today, open access journals, for example, compete with journals from commercial publishers and provide free access to anyone via the Internet. Resources such as the courseware management system, Moodle, and the multipurpose software package, Sakai, are examples of open source software-developed resources that are widely used today in higher education. The OpenCourseware initiative at Massachusetts Institute of Technology is an example of free and open dissemination of course resources. Variations of the open source software model support the creation of everything from infrastructure software such as Sakai to remixable textbooks. Remixing is, in fact, a major advantage of the approach Connexions, based at Rice University, has taken to create information resources for educational use. Open access, open source, and other similar approaches can be subsumed under the term open education. That movement is a viable, and rapidly growing, alternative for the creation and distribution of information and information technology resources for higher education that is particularly suited to collaborative, international partnerships.

Over the past decade, numerous computer-assisted retrosynthesis reaction prediction methods have been reported in the chemical literature, several of which are also shared as open-source code. Reports of integrating these modern open-source retrosynthetic prediction techniques into the chemical education classroom, however, is largely absent. This article describes our efforts to teach a computer-assisted retrosynthesis workshop series using open-source reaction prediction software and methods. In addition to three workshops on selected open-source reaction prediction methods, the series included workshops on Python programming and introductory cheminformatics using the RDKit cheminformatics toolkit. A pre and post survey was distributed to better understand participant familiarity and workshop outcomes. Participants indicated that they had minimal experience with cheminformatics, and open-source retrosynthesis software, however after the workshop series they indicated increased familiarity, interest, and desire to pursue additional training related to open-source retrosynthesis software and methods. We conclude this article with our experiences and ideas for future improvements. The workshop materials and code are available with an open source license, and educators are encouraged to adapt and improve the lessons (https://github.com/UA-Libraries-Research-Data-Services/retrosynthesis).

Open source software is becoming increasingly prominent, and the economic structure of open-source development is changing. In recent years, firms motivated by revenues from software services markets have become the primary contributors to open-source development. In this paper we study the role of services in open source software development and explore the choice between open source and proprietary software. Specifically, our economic model jointly analyzes the investment and pricing decisions of the originators of software and of subsequent open-source contributors. We find that if a contributor is efficient in software development, the originator should adopt an open-source strategy, allowing the contributor to offer higher total quality and capture the higher end of the market while the originator focuses on providing software services to lower end consumers. Conversely, if the contributor is not efficient in development, the originator should adopt a proprietary software development strategy, gaining revenue from software sales and squeezing the contributor out of the services market. In certain cases an increase in originator development efficiency can result in increased contributor profits. Finally, we find that, somewhat counterintuitively, an increase in contributor development efficiency can reduce overall social welfare.

Open Journal Systems (OJS) is an open access, online manuscript management system developed by the Public Knowledge Project (https://pkp.sfu.ca/ojs/) that underpins the University of Leicester’s academic journal system. Initially released in 2001 OJS provides a complete and robust software solution that integrates and tracks all aspects of manuscript processing from the initial author paper submission, via dissemination of articles to peer reviewers, through to final online publication and indexing (Willinsky, 2005). This review will consider how OJS can be used to enhance teaching and learning through creating an authentic peer review process for students and will also offer some personal insights into the practicalities of using OJS from an Editor’s perspective.

Open-source software abbreviated as OSS is computer software that is available with source code and is provided under a software license that permits users to study, change, and improve the software. For the commercial software the source code and certain other rights are normally reserved for copyright holders,i.e. the company who developes the software. A group of people in a collaborative manner often developes the Open source software, not under the roof of a large organization. This strategy makes open source software cheap, reliable and modifiable if needed. In this context we shall discuss mainly the features of Open Source Software, differences of open source and free software and open source software movement in Indian perspective.

A lot misinformation and mystery surrounds the topic of Open Source software. The conceptual misunderstanding of software is fostered, in some respects, by a lack of understanding within the professional ranks of the computer field. There are many different views of Open Source software today, based upon ones perspective. After about 20 years of evolution, the position of Open Source in our economy still has not coalesced. Few seems to understand whether Open Source is free software for running a computer (i.e., Linux) or just a way to obtain some software products without giving Microsoft ones money. “There is one thing stronger than all the armies in the world and that is an idea whose time has come” - Victor Hugo any view Open Source (OS) software as just a free alternative to proprietary software. The term does not mean that there is no cost associated with its procurement, although some vendors do provide free versions. The word “free” usually means the freedom to copy, modify, or distribute the software. One must be very careful when applying this broad, general meaning to Open Source software. There are many different Open Source licenses in use and it is imperative that users acquaint themselves with the legal ramifications of dealing with intellectual property rights. ` Open Source software should be viewed as a viable alternative in many software selection processes. Recently, the news has portrayed the report of India's Kerala state moving to Linux and OpenOffice for its 2,724 high schools. Likewise, OpenOffice is replacing Microsoft Office in many schools districts around the US. With tight school budgets, school superintendents are realizing significant cost savings by using the OpenOffice products for their campuses. Products such as OpenOffice may not be 100% compatible with their current proprietary counterpart, but for many applications, compatibility is not the issue. The price and the software license management of proprietary packages may be overwhelming.

Open source technologies are free to use, making them challenging to value in economic terms. While the reasons for contributing to open source code have been extensively studied, the reasons for adopting open source, and the value of that adoption, have received less attention. Professor Henry Chesbrough, a pioneer on the subject of open innovation, conducted a survey to measure the economic value of open source, analyzing where and to what extent companies experience benefits of open source adoption. Aggregating the findings of this survey, this report discusses the perceived economic benefits of open source software, including cost savings, faster development, open standards, and interoperability. To learn more about how individuals value open source from an economic perspective, and gain evidence-based insight on the value of supporting open source adoption, read the full report!

A partnership forged between the George A. Smathers Libraries at the University of Florida and the Florida State Horticultural Society (FSHS) advances access to current and historical publications of the society and exemplifies an opportunity for agricultural librarians. The Public Knowledge Project's Open Journal System (OJS) was developed by librarians at Simon Fraser and Stanford universities to offer free, web-based publication software that promotes open access to journals and supports editorial workflow and publication needs. Collaborations among libraries and content creators that utilize open source tools like OJS are especially beneficial for agricultural organizations with limited financial and staffing resources. This paper examines the current state of library publishing partnerships with external organizations through analysis of survey data collected by the authors, and shares lessons learned from an example partnership. In this example librarians contributed their expertise in peer-review publishing, intellectual property rights, and institutional repositories to develop a customized online journal site using OJS for FSHS in a manner that reflects the publication workflow of the society. Customized features include branding, peer review, member subscription, full-text indexing, and access to archived issues. Trainings on OJS and digital publication service empower subject-area librarians to serve as points of contact for additional collaborations. Utilizing OJS in partnerships between libraries and content creators enhances the relevancy of the library and subject-area librarians while promoting greater access to agricultural information.

Open Source vs. Proprietary Software: Competition and Compatibility

Ubiquity Press and the Public Knowledge Project (PKP) have entered into an agreement to work more closely together. This agreement is strategically aligned with Ubiquity's commitment to Open Source Software under its new Customer Charter. Ubiquity has used the Open Journal Systems (OJS) software to manage the editorial process for its journals since inception and OJS will continue to play a role into the future.