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• For project: Open source science

Open source science literature review

Below is a chronological list of articles pertaining to Open Source Science in Software and Hardware.

Akinobu Lee, Kiyohiro Shikano and Tatsuya Kawahara. (2001). Julius - an Open Source Real-Time Large Vocabulary Recognition Engine. In Eurospeech 2001 - Scandinavia, 1691-1694.

• Abstract

Julius is a high-performance, two-pass LVCSR decoder for researchers and developers. Based on word 3-gram and context-dependent HMM, it can perform almost real-time decoding on most current PCs in 20k word dictation task. Major search techniques are fully incorporated such as tree lexicon, N-gram factoring, cross-word context dependency handling, enveloped beam search, Gaussian pruning, Gaussian selection, etc. Besides search efficiency, it is also modularized carefully to be independent from model structures, and various HMM types are supported such as shared-state triphones and tied-mixture models, with any number of mixtures, states, or phones. Standard formats are adopted to cope with other free modeling toolkit. The main platform is Linux and other Unix workstations, and partially works on Windows. Julius is distributed with open license together with source codes, and has been used by many researchers and developers in Japan.

Chihiro Watanabe, Youichirou S. Tsuji, and Charla Griffy-Brown, “Patent statistics: deciphering a 'real' versus a 'pseudo' proxy of innovation,” Technovation 21, no. 12 (December 2001): 783-790, doi:10.1016/S0166-4972(01)00025-6.

• Abstract

Patent statistics have fascinated economists concerned about innovation for a long time. However, fundamental questions remain as to whether or not patent statistics represent the real state of innovation. As Griliches pointed out, substantial questions involve: What aspects of economic activities do patent statistics actually capture? And, what would we like them to measure? He pointed out that these statistics can be a mirage appearing to provide a great number of objective and reliable proxies for innovation.

This paper aims to address some of these questions by making a comparative evaluation of the representability of patent statistics in four levels of the innovation process, using as examples research and development (R&D) in Japan's printer and photovoltaic solar cell (PV) industries over the last two decades. Furthermore, this research provides a new set of patent statistics which could be considered a more reliable proxy for innovation.

Brian Bruns, “Open sourcing nanotoechnology research and development: issues and opportunities,” Nanotechnology 12 (2001): 198-210.

• This is an excellent paper examining the viability of open source design in the nanotech industry. Important things to learn from the open source software (OSS) successes are the bazaar-style design process, as well as the gift-culture created. Concerns regarding the tragedy of anti-commons provide reason to examine alternative research methods within nanotechnology. The paper discusses various licenses possible for nanotechnology and identifies this as an area where more research should be done. Various business models are highlighted, including the ‘’producer coalition’’, and reminds the reader that there are various levels of openness that firms could adopt depending on their business. A survey of the nanotech industry is done, and it is important to note that the many nanotechnology firms get funding from the US government, which favours strong IP and patenting laws.

Stefan Koch and Georg Schneider, (2002), Effort, co-operation and co-ordination in an open source software project: GNOME, Information Systems Journal, Volume 12, Issue 1, pages 27–42,DOI: 10.1046/j.1365-2575.2002.00110.x

• Abstract

This paper presents results from research into open source projects from a software engineering perspective. The research methodology employed relies on public data retrieved from the CVS repository of the GNOME project and relevant discussion groups. This methodology is described, and results concerning the special characteristics of open source software development are given. These data are used for a first approach to estimating the total effort to be expended.

Alessandro Cimatti et al., (2002), NuSMV 2: An OpenSource Tool for Symbolic Model Checking, Computer Science, Volume 2404/2002, 241-268, DOI: 10.1007/3-540-45657-0_29

• Abstract

This paper describes version 2 of the NuSMV tool (computer aided verification). NuSMV is a symbolic model checker originated from the reengineering, reimplementation and extension of SMV, the original BDD-based model checker developed at CMU. The NuSMV project aims at the development of a state-of-the-art symbolic model checker, designed to be applicable in technology transfer projects: it is a well structured, open, flexible and documented platform for model checking, and is robust and close to industrial systems standards.

F., Meyer et al., (2003), GenDB—an open source genome annotation system for prokaryote genomes, Nucleic Acids Res, 2003 April 15; 31(8): 2187–2195.

• Abstract

The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To account for the individual needs of different projects, such a system should be modular and easily extensible. We present a genome annotation system for prokaryote genomes, which is well tested and readily adaptable to different tasks. The modular system was developed using an object-oriented approach, and it relies on a relational database backend. Using a well defined application programmers interface (API), the system can be linked easily to other systems. GenDB supports manual as well as automatic annotation strategies. The software currently is in use in more than a dozen microbial genome annotation projects. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The system is open source.

M. Dougiamas & P. Taylor, (2003). Moodle: Using Learning Communities to Create an Open Source Course Management System. In D. Lassner & C. McNaught (Eds.), Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2003, pp. 171-178

• Abstract

This paper summarizes a PhD research project that has contributed towards the development of Moodle - a popular open-source course management system (moodle.org). In this project we applied theoretical perspectives such as "social constructionism" and "connected knowing" to the analysis of our own online classes as well as the growing learning community of other Moodle users. We used the mode of participatory action research, including techniques such as case studies, ethnography, learning environment surveys and design methodologies. This ongoing analysis is being used to guide the development of Moodle as a tool for improving processes within communities of reflective inquiry. At the time of writing (April 2003), Moodle has been translated into twenty-seven languages and is being used by many hundreds of educators around the world, including universities, schools and independent teachers.

Arnaud Delorme and Scott Makeig, (2003). EEGLAB: an opensource toolbox for analysis of single-trial EEG dynamics including independent component analysis. Journal of Neuroscience Methods, Volume 134, Issue 1, Pages 9–21

• Abstract

We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive ‘pop’ functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A ‘plug-in’ facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and opensource development, together with sample data, user tutorial and extensive documentation.

Richard C. Atkinson et al., (2003), “INTELLECTUAL PROPERTY RIGHTS: Public Sector Collaboration for Agricultural IP Management,” Science 301, no. 5630 (July 11, 2003): 174-175, doi:10.1126/science.1085553.

• Abstract

The fragmented ownership of rights to intellectual property (IP) in agricultural biotechnology leads to situations where no single public-sector institution can provide a complete set of IP rights to ensure freedom to operate with a particular technology. This situation causes obstacles to the distribution of improved staple crops for humanitarian purposes in the developing world and specialty crops in the developed world. This Policy Forum describes an initiative by the major agricultural universities in the United States and other public-sector institutions to establish a new paradigm in the management of IP to facilitate commercial development of such crops.

Stephen M. Maurer, Arti Rai, and Andrej Sali, (2004), Finding Cures for Tropical Diseases: Is Open Source an Answer?", PLoS Medicine 1, no. 3 (December 2004): 183-186.

• Abstract

This paper showcases that the current models of encouraging pharmaceuticals to research and develop drugs curing tropical diseases that affects poor people aren’t working. These methods are 1)asking governments and NGOs to subsidize drugs rates for developed countries, and 2) to create non-profit venture capital firms. It proposes an open-source model for developing these drugs through a website (www.tropicaldisease.org). It describes how scientists could use chat pages and shared databases to make discoveries.

• The payment of scientists working on this database would not be monetary, but scientists would gain stature and enhance their reputation, as is similar to the motivations of the hacker community. The drugs would not be patented in order to ensure that retail costs remained low. Companies and universities would allow their workers to volunteer, and would even donate databases and resources because the value of their IP lies in North American and European medicines.

M.J.L. de Hoon, S. Imoto, J. Nolan and S. Miyano, (2004), Open Source Clustering Software, Oxford University Press, 20 (9): 1453-1454. DOI: 10.1093/bioinformatics/bth078

• Summary

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C.

Burr Settles, (2005), ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics, 21 (14): 3191-3192. doi: 10.1093/bioinformatics/bti475

• Summary

ABNER (A Biomedical Named Entity Recognizer) is an open source software tool for molecular biology text mining. At its core is a machine learning system using conditional random fields with a variety of orthographic and contextual features. The latest version is 1.5, which has an intuitive graphical interface and includes two modules for tagging entities (e.g. protein and cell line) trained on standard corpora, for which performance is roughly state of the art. It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora.

D. Krajzewicz, M. Bonert and P. Wagner, (2006), RoboCup 2006 Infrastructure Simulation Competition, Computer and Information Science › Miscellaneous Papers

• Abstract

Since the year 2000, the Institute of Transportation Research (IVF) at the German Aerospace Centre (DLR) is developing a microscopic, traffic simulation package. The complete package is offered as open source to establish the software as a common testbed for algorithms and models from traffic research. Since the year 2003 the IVF also works on a virtual traffic management centre and in conjunction with this on traffic management. Several large-scale projects have been done since this time, most importantly INVENT where modern traffic management methods have been evaluated and the online-simulation and prediction of traffic during the world youth day (Weltjugendtag) 2005 in Cologne/Germany. This publication briefly describes the simulation package together with the projects mentioned above to show how SUMO can be used to simulate large- scale traffic scenarios. Additionally, it is pointed out how SUMO may be used as a testbed for automatic management algorithms with minor effort in developing extensions.

Alan MacCormack, John Rusnak and Carliss Y. Baldwin, (2006). Exploring the Structure of Complex Software Designs: An Empirical Study of Open Source and Proprietary Code. Management Science, Vol. 52, No. 7, pp. 1015-1030

• Abstract

This paper reports data from a research project which seeks to characterize the differences in design structure between complex software products. In particular, we adopt a technique based upon Design Structure Matrices (DSMs) to map the dependencies between different elements of a design then develop metrics that allow us to compare the structures of these different DSMs. We demonstrate the power of this approach in two ways: First, we compare the design structures of two complex software products – the Linux operating system and the Mozilla web browser – that were developed via contrasting modes of organization: specifically, open source versus proprietary development. We find significant differences in their designs, consistent with an interpretation that Linux possesses a more “modular” architecture. We then track the evolution of Mozilla, paying particular attention to a major “re-design” effort that took place several months after its release as an open source product. We show that this effort resulted in a design structure that was significantly more modular than its predecessor, and indeed, more modular than that of a comparable version of Linux.

Our findings demonstrate that it is possible to characterize the structure of complex product designs and draw meaningful conclusions about the precise ways in which they differ. We provide a description of a set of tools that will facilitate this analysis for software products, which should prove fruitful for researchers and practitioners alike. Empirically, the data we provide, while exploratory, is consistent with a view that different modes of organization may tend to produce designs possessing different architectural characteristics. However, we also find that purposeful efforts to re-design a product’s architecture can have a significant impact on the structure of a design, at least for products of comparable complexity to the ones we examine here.

S. Kerrien et al., (2006), IntAct—open source resource for molecular interaction data, Nucleic Acids Research 35 (suppl 1): D561-D565. doi: 10.1093/nar/gkl958

• Abstract

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.

Andrea Bonaccorsi, Silvia Giannangeli and Cristina Rossi (2006),Entry strategies under competing standards: Hybrid business models in the open source software industry,Management Science, Vol. 52, No. 7, pp. 1085-1098

• Abstract

The paper analyses the entry strategies of software firms that adopt the Open Source production model. A new definition of business model is proposed. Empirical evidence, based on an exploratory survey taken on 146 Italian software firms shows that firms adapted to an environment dominated by incumbent standards by combining Open Source and proprietary software. The paper examines the determinants of business models and discusses the stability of hybrid models in the evolution of the industry.

C. Steinbeck et al., (2006), Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics, Current Pharmaceutical Design, Volume 12, Number 17, June 2006 , pp. 2111-2120(10) DOI: http://dx.doi.org/10.2174/138161206777585274

• Abstract

The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.

Jeffrey A. Roberts, Il-Horn Hann and Sandra A. Slaughter. (2006), Understanding the Motivations, Participation, and Performance of Open Source Software Developers: A Longitudinal Study of the Apache Projects. Management Science, Vol. 52, No. 7, pp. 984-999 DOI: 10.1287/mnsc.1060.0554

• Abstract

Understanding what motivates participation is a central theme in the research on open source software (OSS) development. Our study contributes by revealing how the different motivations of OSS developers are interrelated, how these motivations influence participation leading to performance, and how past performance influences subsequent motivations. Drawing on theories of intrinsic and extrinsic motivation, we develop a theoretical model relating the motivations, participation, and performance of OSS developers. We evaluate our model using survey and archival data collected from a longitudinal field study of software developers in the Apache projects. Our results reveal several important findings. First, we find that developers' motivations are not independent but rather are related in complex ways. Being paid to contribute to Apache projects is positively related to developers' status motivations but negatively related to their use-value motivations. Perhaps surprisingly, we find no evidence of diminished intrinsic motivation in the presence of extrinsic motivations; rather, status motivations enhance intrinsic motivations. Second, we find that different motivations have an impact on participation in different ways. Developers' paid participation and status motivations lead to above-average contribution levels, but use-value motivations lead to below-average contribution levels, and intrinsic motivations do not significantly impact average contribution levels. Third, we find that developers' contribution levels positively impact their performance rankings. Finally, our results suggest that past-performance rankings enhance developers' subsequent status motivations.

Scott L. Delp et al., (2007). OpenSim: Open-Source Software to Create and Analyze Dynamic Simulations of Movement, IEEE Engineering in Medicine and Biology Society Volume: 54 , Issue: 11, pages 1940-1950 doi: 10.1109/TBME.2007.901024

• Abstract

We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

T.D., Crawford et al., (2007), PSI3: An open-source Ab Initio electronic structure package, Journal of Computational Chemistry, Volume 28, Issue 9, pages 1610–1616, 15 July 2007 DOI: 10.1002/jcc.20573

• Abstract

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

L. T. Kell et al., (2007). FLR: an open-source framework for the evaluation and development of management strategies, ICES Journal of Marine Science, 64 (4): 640-646. doi: 10.1093/icesjms/fsm012

• Abstract

The FLR framework (Fisheries Library for R) is a development effort directed towards the evaluation of fisheries management strategies. The overall goal is to develop a common framework to facilitate collaboration within and across disciplines (e.g. biological, ecological, statistical, mathematical, economic, and social) and, in particular, to ensure that new modelling methods and software are more easily validated and evaluated, as well as becoming widely available once developed. Specifically, the framework details how to implement and link a variety of fishery, biological, and economic software packages so that alternative management strategies and procedures can be evaluated for their robustness to uncertainty before implementation. The design of the framework, including the adoption of object-orientated programming, its feasibility to be extended to new processes, and its application to new management approaches (e.g. ecosystem affects of fishing), is discussed. The importance of open source for promoting transparency and allowing technology transfer between disciplines and researchers is stressed.

M. Neteler and H. Mitasova, (2008), Open Source GIS- A GRASS GIS Approach. (Hardcover). Originally published as volume 773 in the series: The International Series in Engineering and Computer Science 3rd ed., 2008, XX, 406 p. 80 illus.

• Includes rich set of practical examples extensively tested by users with data and changes, related to software updates readily available on a related website
• The vector data architecture in the third edition is completely new; database support added
• Vector data covers both polygons, lines and sites in a new way and includes database management

With this third edition of Open Source GIS: A GRASS GIS Approach, we enter the new era of GRASS6, the first release that includes substantial new code developed by the International GRASS Development Team. The dramatic growth in open source software libraries has made GRASS6 development more efficient, and has enhanced GRASS interoperability with a wide range of open source and proprietary geospatial tools.

D. Nurmmi et al., (2009). The Eucalyptus Open-source Cloud-computing System, 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, Pages: 124-131

• Abstract

Cloud computing systems fundamentally provide access to large pools of data and computational resources through a variety of interfaces similar in spirit to existing grid and HPC resource management and programming systems. These types of systems offer a new programming target for scalable application developers and have gained popularity over the past few years. However, most cloud computing systems in operation today are proprietary, rely upon infrastructure that is invisible to the research community, or are not explicitly designed to be instrumented and modified by systems researchers. In this work, we present Eucalyptus - an open-source software framework for cloud computing that implements what is commonly referred to as infrastructure as a service (IaaS); systems that give users the ability to run and control entire virtual machine instances deployed across a variety physical resources. We outline the basic principles of the Eucalyptus design, detail important operational aspects of the system, and discuss architectural trade-offs that we have made in order to allow EUCALYPTUS to be portable, modular and simple to use on infrastructure commonly found within academic settings. Finally, we provide evidence that EUCALYPTUS enables users familiar with existing grid and HPC systems to explore new cloud computing functionality while maintaining access to existing, familiar application development software and grid middleware.

D. Schloss et al., (2009). Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. American Society for Microbiology, vol. 75 no. 23 pp. 7537-7541. doi: 10.1128/​AEM.01541-09

• Abstract

Mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

P. Giannozzi et al., (2009). QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials, Journal of Physics: Condensed Matter, Volume 21, Number 39, doi:10.1088/0953-8984/21/39/395502

• Abstract

QUANTUM ESPRESSO is an integrated suite of computer codes for electronicstructure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). QUANTUM ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newlyrestructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively-parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

John H. Barton, (2009), “Patenting and Access to Clean Energy Technologies in Developing Countries,” WIPO Magazine, March 2009, Full paper

• The paper examines other questions of importance to developing nations including the benefits of strengthening IP protection in order to make foreign investors more willing to transfer technology and asking whether or not local trade barriers are proving helpful or harmful in developing these industries. The author concludes with specific suggestions for developing countries themselves, lenders and donors, and international negotiations. The development and diffusion of renewable energy technologies is only one part of the challenge

of bringing down emissions from the energy sector. Much needs to be done to harvest the largest potential in energy efficiency improvements. Nevertheless, it is our hope that this study will contribute to informing policy processes and negotiations related to technological cooperation and intellectual property in the energy, climate change and trade arenas.

Michael Woelfle, Piero Olliaro & Matthew H. Todd. (2011), Open science is a research accelerator. Commentary, Nature Chemistry, 3, 745–748, doi:10.1038/nchem.1149

• Synopsis

An open-source approach to the problem of producing an off-patent drug in enantiopure form serves as an example of how academic and industrial researchers can join forces to make new scientific discoveries that could have a huge impact on human health. This Commentary describes a case study — a chemical project where open-source methodologies were employed to accelerate the process of discovery.