Open Source Collaboration Research Articles

The 5K Run Toolkit: A Quick, Painless, and Thoughtful Approach to Managing Print Journal Backruns

Increasingly, academic libraries are choosing to discard or place in storage print journals that are now available online. The identification of these titles and related collection analysis activities are often time-intensive. The approach at the University of Saskatchewan Library was to develop an online toolkit that combined available data from disparate sources including the integrated library system, SFX link resolver, and OCLC's WorldCat and then present them in a collaborative open source environment. This paper demonstrates how the careful combination of existing data presented in a simple online format allowed subject specialists to make accurate print journal deselection decisions quickly and painlessly.

Making partners of universities and corporations

I commend Physics Today for its publication of the story “Universities and Industry Find Roadblocks to R&D Partnering” (Physics Today, May 2008, page 20). The author indicates a number of sore spots in university–industry partnerships, especially the negotiation of intellectual property rights in research agreements. The University–Industry Demonstration Partnership, of which I am a past president, has been doing important work in providing a neutral forum, under the auspices of the National Academies, for open and frank discussions between companies and universities about their differences and their commonalities. Issues for discussion include contract negotiations, IP rights in collaborative research, the Bayh–Dole Act, competition from overseas research organizations, Internal Revenue Service policies on the use of buildings financed through tax-exempt bonds, and open source collaborations. The UIDP is interested in improving and streamlining connections between companies and universities for their mutual benefit, the betterment of society and the country’s economic security.The UIDP strives to remain objective and politically neutral. It fosters the free and open expression of frustrations so they do not silently eat away at mutual trust. The partnership encourages the parties to seek common ground and a shared vision and, when that doesn’t work, to look for adequate compromise.Currently the UIDP has 94 members, one-third of them from industry. Our industrial membership is quite evenly spread over health and life sciences, chemicals and materials, information technology and consumer products manufacturing. Our university membership is also a mix of land grant colleges and universities, state and other public institutions of higher education, and private institutions.The UIDP hopes to continue its work and to connect even more companies and academic institutions.© 2009 American Institute of Physics.

Open source collaboration: Two cases in the U.S. public sector

Globally, there is an emergence of open source consortia focused on the sharing of resources and code, and a desire to promote an open source approach generally. In this paper, we describe our findings from interviews with participants working in two relatively new consortia in the government sector: the Government Open Code Collaborative or GOCC, and the Open Source Software Institute or OSSI. For each case we consider six major questions: (1) How and why did these collaborative efforts begin? (2) What are their motivations? (3) How are these collaborative efforts governed? (4) What communication and collaborative infrastructure do they utilize? (5) What software do they focus on? and, (6) What is their current status? Our findings suggest that incentives, membership structures, stable paid staff, concentrated focus and attention to the creation and delivery of “value” to participating organizations are important factors leading to successful open source consortia.

Enabling open-source cognitively-controlled collaboration among software-defined radio nodes

Software-defined radios (SDRs) are now recognized as a key building block for future wireless communications. We have spent the past year enhancing existing open software to create a software-defined data radio. This radio extends the notion of software-defined behavior to higher layers in the protocol stack: most importantly through the media access layer. Our particular approach to the problem has been guided by the desire to allow fine-grained cognitive control of the radio. We describe our system, Adaptive Dynamic Radio Open-source Intelligent Team (ADROIT).

Currents

The first news story, "The Google Web Toolkit Shines a Light on Ajax Frameworks," looks at the GWT's remarkable growth and its prospects. The second news story, "IBM and Universities in Open Source Collaboration," reports on IBM's collaboration with seven major universities in the Open Collaborative Research program.

Religious Fervor: The Development of an Open Source Religious Document

According to Robles (2004), the basic elements of open-source software include users being treated as co-developers, early releases, frequent integration, several versions, high modularization and dynamic decision making structure. Another product that neatly fits these definitions is the development of religious texts. I present the development of the sacred texts of Judaism and Christianity as a model of the open-source development of religious texts. I review three competing hypotheses for the development of the Pentateuch (the first five books of the Old Testament) and compare their features to identifying attributes of open-source collaboration.

Information systems for crop performance data

An increased need for efficient storage and retrieval of crop performance data is driven by a desire to increase the value of crop performance tests, opportunities in crop modelling, opportunities to facilitate cross planning, opportunities to discover genes that affect economic traits, and data mining applications that require better integration of data from multiple sources. Thus, an increased number of stakeholders need access to crop data that are current, accurate, and complete. There is also a growing sophistication and awareness of the role and capabilities of modern informatics techniques in biological research – an area that has become known as “bioinformatics”. Bioinformatics, in partnership with statistics, can play a vital role in increasing the value of crop performance data. However, much of this role remains to be developed and adopted by the communities that gather and use these data. Part of the challenge is that phenotypic data are complex, and extensive information about the context under which the data were collected is required. This can include information about experimental design, soil and climatic conditions, treatments applied, germplasm tested, plant growth stages, and traits measured. If context is neglected, data are useless, but if context is overly complex, it may be ignored or used improperly. Several solutions have been developed to address these needs. These include commercial software packages, open-source collaborations, and a new application developed by the authors. Each solution has strengths and weaknesses, and each addresses different types of needs. This review will discuss the motivations for developing and using crop information systems, the current status and availability of crop information systems, and the challenges that must be met to achieve future potential. Key words: Bioinformatics, database, software, statistics, ontology, variety trial

Opening minds: Cultural change with the introduction of open-source collaboration methods

As open-source software becomes accepted worldwide, open-source collaboration and development methods are also gaining greater momentum. Collaboration based on the open-source paradigm is increasingly being used to improve multisite development and teamwork inside companies. Drawing on experience in projects for improving multisite collaboration, this paper explains how we evaluate communication and collaboration problems, assess obstacles to change, and facilitate the change by introducing employees to the benefits of the collaborative model over traditional development projects in a workshop setting. This method has proven to be a valuable “mind-opener” and helps identify specific obstacles that need to be addressed as part of the introduction of open-source development and collaboration methods. The paper concludes with lessons learned for facilitating the introduction of these methods in an organization.

Integration from proteins to organs: the IUPS Physiome Project

The IUPS Physiome Project 1 1 IUPS is the International Union of Physiological Sciences ( www.iups.org) and the IUPS Physiome Project is run under the auspices of the IUPS Physiome and Bioengineering Committee, co-chaired by the first author and Prof. Aleksander Popel. is an internationally collaborative open source project intended to provide a public domain framework for computational physiology, including the development of modeling standards, computational tools and web-accessible databases of models of structure and function at all spatial scales and across all organ systems. Here, we illustrate the application of this multi-scale modeling approach to three organ systems: the heart, the lungs and the musculo–skeletal system, and in each case we show how the organ level models incorporate tissue and cell-level physiology. Although the computational physiology framework presented here does not yet incorporate models of ageing processes, the model-based approach is certainly capable of describing ageing and disease-related processes both via parameter changes within the models of normal physiological processes and via models of additional processes added to the framework.

Bringing E-Democracy Back In

The author argues that contemporary digital information communication technologies (ICTs) facilitate new forms of e-government-enabled public sector policy making that enshrine some of the important norms and practices of e-democracy. The potential for linking e-democracy in civil society with e-government at the level of the local and national state is far from straightforward but nevertheless achievable. Following a consideration of the democratization effects of e-democracy and e-government, the author outlines how their norms and practices are converging in four principal areas: online consultations integrating civil societal groups with bureaucracies and legislatures, the internal democratization of the public sector itself, the involvement of users in the design and delivery of public services, and the diffusion of open-source collaboration in public organizations. These now feature as some of the core areas for research in this field and our broader understanding of how ICTs are reshaping governance, the state, and democracy.

The Bioperl toolkit: Perl modules for the life sciences.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.