Open source science literature review/Energy, Physics, Nanotechnology

Energy / Physics / Nanotechnology[edit | edit source]

Chihiro Watanabe, Youichirou S. Tsuji, and Charla Griffy-Brown, (2001), "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.

Jaroslav Hofierka and Marcel Suri, (2002), The solar radiation model for Open source GIS: implementation and applications, Proceedings of the Open source GIS - GRASS users conference 2002 - Trento, Italy, 11-13 September 2002

• Conclusions

The r.sun is a complex and flexible solar radiation model, fully integrated within open source environment of GRASS GIS. It calculates all three components of solar irradiance/irradiation (beam, diffuse and reflected) for clear-sky as well as overcast conditions. The implemented equations follow the latest European research in solar radiation modelling. Integration in GRASS GIS enables to use interpolation tools that are necessary for data preparation. The model is especially appropriate for modelling of large areas with complex terrain because all spatially variable solar parameters can be defined as raster maps. The model can be used easily for long-term calculations at different map scales ñ from continental to detailed. Two operational modes enable the user account for temporal variability of solar radiation within a day or within a year (using shell scripts). These features offer wide variety of possible applications as documented on the two examples. Open source code enables to make modifications and improvements in future, according to research development in solar radiation modelling or to fit better specific user needs.

A.F. Albuquerquea et al.,(2007), The ALPS project release 1.3: Open-source software for strongly correlated systems, Journal of Magnetism and Magnetic Materials, Volume 310, Issue 2, Part 2, March 2007, Pages 1187–1193

• Abstract

We present release 1.3 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open-source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. Development is centered on common XML and binary data formats, on libraries to simplify and speed up code development, and on full-featured simulation programs. The programs enable non-experts to start carrying out numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), as well as the density matrix renormalization group (DMRG). Changes in the new release include a DMRG program for interacting models, support for translation symmetries in the diagonalization programs, the ability to define custom measurement operators, and support for inhomogeneous systems, such as lattice models with traps. The software is available from our web server at http://alps.comp-phys.org/.

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.

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.

F. Alet et a., (2005), The ALPS project: open source software for strongly correlated systems, Journal of Physical Society of Japan. DOI: 10.1143/JPSJS.74S.30

• Abstract

We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. Development is centered on common XML and binary data formats, on libraries to simplify and speed up code development, and on full-featured simulation programs. The programs enable non-experts to start carrying out numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), as well as the density matrix renormalization group (DMRG). The software is available from our web server at http://alps.comp-phys.org/.

Computer / Information Sciences & Systems / Modeling / Programming / Processing[edit | edit source]

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.

Carolina Cruz-Neira et al., (2002), VR Juggler -- An Open Source Platform for Virtual Reality Applications, IN 40TH AIAA AEROSPACE SCIENCES MEETING AND EXHIBIT 2002

• Abstract

This paper describes VR Juggler, an Open Source platform used to develop and run virtual reality applications. We emphasize VR Juggler's ability to provide a uniform VR application environment and to allow extendibility to new devices without affecting existing applications. These features enable VR applications to evolve along side other technologies with minimal or no new developmental efforts.

R. Lougee-Heimer, (2003), The Common Optimization INterface for Operations Research: Promoting open-source software in the operations research community, IBM Journal of Research and Development, Volume: 47, Issue: 1, p. 57- 66

• Abstract

The Common Optimization INterface for Operations Research (COIN-OR, http://www.coin-or.org/) is an initiative to promote open-source software for the operations research (OR) community. In OR practice and research, software is fundamental. The dependence of OR on software implies that the ways in which software is developed, managed, and distributed can have a significant impact on the field. Open source is a relatively new software development and distribution model which offers advantages over current practices. Its viability depends on the precise definition of open source, on the culture of a distributed developer community, and on a version-control system which makes distributed development possible. In this paper, we review open-source philosophy and culture, and present the goals and status of COIN-OR https://svrtechnologies.com/mulesoft-training.

M.K. Smith et al., (2003), DSpace: An Open Source Dynamic Digital Repository, D-Lib Magazine, Volume 9 Number 1. DOI: 10.1045/january2003-smith

• Abstract

For the past two years the Massachusetts Institute of Technology (MIT) Libraries and Hewlett-Packard Labs have been collaborating on the development of an open source system called DSpaceâ„¢ that functions as a repository for the digital research and educational material produced by members of a research university or organization. Running such an institutionally-based, multidisciplinary repository is increasingly seen as a natural role for the libraries and archives of research and teaching organizations. As their constituents produce increasing amounts of original material in digital formats—much of which is never published by traditional means—the repository becomes vital to protect the significant assets of the institution and its faculty. The first part of this article describes the DSpace system including its functionality and design, and its approach to various problems in digital library and archives design. The second part discusses the implementation of DSpace at MIT, plans for federating the system, and issues of sustainability.

R. Lougee-Heimer, (2003), The Common Optimization INterface for Operations Research: Promoting open-source software in the operations research communityIBM Journal of Research and Development, Volume: 47, Issue: 1, pp 57- 66

• Abstract

The Common Optimization INterface for Operations Research (COIN-OR, http://www.coin-or.org/) is an initiative to promote open-source software for the operations research (OR) community. In OR practice and research, software is fundamental. The dependence of OR on software implies that the ways in which software is developed, managed, and distributed can have a significant impact on the field. Open source is a relatively new software development and distribution model which offers advantages over current practices. Its viability depends on the precise definition of open source, on the culture of a distributed developer community, and on a version-control system which makes distributed development possible. In this paper, we review open-source philosophy and culture, and present the goals and status of COIN-OR.

T. Staples et al., (2003), The Fedora Project: An open-source Digital Object Repository Management System, D-Lib Magazine, April 2003, v. 9, no. 4

• About

Using a grant from the Andrew W. Mellon Foundation, the University of Virginia Library has released an open-source digital object repository management system. The Fedora Project, a joint effort of the University of Virginia and Cornell University, has now made available the first version of a system based on the Flexible Extensible Digital Object Repository Architecture, originally developed at Cornell.

Fedora repositories can provide the foundation for a variety of information management schemes, including digital library systems. At the University of Virginia, Fedora is being used to build a large-scale digital library that will soon have millions of digital resources of all media and content types. A consortium of institutions that include the Library of Congress, Northwestern University, and Tufts University is also currently testing the program. They are building test beds drawn from their own digital collections that they will use to evaluate the software and give feedback to the project.

S. Dudoit, R. C. Gentleman and J. Quackenbush, (2003),Open Source Software for the Analysis of Microarray Data, BioTechniques34, pp45-51

• Abstract

DNA microarray assays represent the first widely used application that attempts to build upon the information provided by genome projects in the study of biological questions. One of the greatest challenges with working with microarrays is collecting, managing, and analyzing data. Although several commercial and noncommercial solutions exist, there is a growing body of freely available, open source software that allows users to analyze data using a host of existing techniques and to develop their own and integrate them within the system. Here we review three of the most widely used and comprehensive systems, the statistical analysis tools written in R through the Bioconductor project (http://www.bioconductor.org), the Java®-based TM4 software system available from The Institute for Genomic Research (http://web.archive.org/web/20080102185236/http://www.tigr.org:80/software/), and BASE, the Web-based system developed at Lund University (http://base.thep.lu.se).

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.

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.

Antoine Rosset, Luca Spadola and Osman Ratib, (2004), OsiriX: An Open-Source Software for Navigating in Multidimensional DICOM Images, Journal of Digital Imaging, Volume 17, Number 3, pp. 205-216, DOI: 10.1007/s10278-004-1014-6

• Abstract

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the programs toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

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.

Edgar Gabriel et al., (2004),Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation, RECENT ADVANCES IN PARALLEL VIRTUAL MACHINE AND MESSAGE PASSING INTERFACE: Lecture Notes in Computer Science, 2004, Volume 3241/2004, 353-377, DOI: 10.1007/978-3-540-30218-6_19

• Abstract

A large number of MPI implementations are currently available, each of which emphasize different aspects of high-performance computing or are intended to solve a specific research problem. The result is a myriad of incompatible MPI implementations, all of which require separate installation, and the combination of which present significant logistical challenges for end users. Building upon prior research, and influenced by experience gained from the code bases of the LAM/MPI, LA-MPI, and FT-MPI projects, Open MPI is an all-new, production-quality MPI-2 implementation that is fundamentally centered around component concepts. Open MPI provides a unique combination of novel features previously unavailable in an open-source, production-quality implementation of MPI. Its component architecture provides both a stable platform for third-party research as well as enabling the run-time composition of independent software add-ons. This paper presents a high-level overview the goals, design, and implementation of Open MPI.

Peter Christen, Tim Churches and Markus Hegland, (2004),Febrl – A Parallel Open Source Data Linkage System, ADVANCES IN KNOWLEDGE DISCOVERY AND DATA MINING Lecture Notes in Computer Science, 2004, Volume 3056/2004, 638-647, DOI: 10.1007/978-3-540-24775-3_75

• Abstract

In many data mining projects information from multiple data sources needs to be integrated, combined or linked in order to allow more detailed analysis. The aim of such linkages is to merge all records relating to the same entity, such as a patient or a customer. Most of the time the linkage process is challenged by the lack of a common unique entity identifier, and thus becomes non-trivial. Linking todays large data collections becomes increasingly difficult using traditional linkage techniques. In this paper we present an innovating data linkage system called Febrl, which includes a new probabilistic approach for improved data cleaning and standardisation, innovative indexing methods, a parallelisation approach which is implemented transparently to the user, and a data set generator which allows the random creation of records containing names and addresses. Implemented as open source software, Febrl is an ideal experimental platform for new linkage algorithms and techniques.

Will Schroeder, (2005), The ITK Software Guide Second Edition Updated for ITK version 2.4, Computer and Information Science, Volume: 525, Issue: 1-3, Publisher: Citeseer, Pages: 53-58

• Abstract

The Insight Toolkit (ITK) is an open-source software toolkit for performing registration and segmentation. Segmentation is the process of identifying and classifying data found in a digi- tally sampled representation. Typically the sampled representation is an image acquired from suchmedical instrumentation as CT orMRI scanners. Registration is the task of aligning or de- veloping correspondences between data. For example, in the medical environment, a CT scan may be aligned with aMRI scan in order to combine the information contained in both. ITK is implemented in C++. It is cross-platform, using a build environment known as CMake to manage the compilation process in a platform-independent way. In addition, an automated wrapping process (Cable) generates interfaces between C++ and interpreted programming lan- guages such as Tcl, Java, and Python. This enables developers to create software using a variety of programming languages. ITKs C++ implementation style is referred to as generic program- ming, which is to say that it uses templates so that the same code can be applied generically to any class or type that happens to support the operations used. Such C++ templating means that the code is highly efficient, and that many software problems are discovered at compile-time, rather than at run-time during programexecution. Because ITKis an open-source project, developers fromaround theworld can use, debug,main- tain, and extend the software. ITKuses amodel of software development referred to as Extreme Programming. Extreme Programming collapses the usual software creation methodology into a simultaneous and iterative process of design-implement-test-release. The key features of Ex- treme Programming are communication and testing. Communication among the members of the ITK community is what helps manage the rapid evolution of the software. Testing is what keeps the software stable. In ITK, an extensive testing process (using a system known as Dart) is in place that measures the quality on a daily basis. The ITK Testing Dashboard is posted continuously, reflecting the quality of the software at any moment. This book is a guide to using and developing with ITK. The sample code in the directory pro- vides a companion to the material presented here. The most recent version of this document is available online at http://www.itk.org/ItkSoftwareGuide.pdf.

B. Alpern et al., (2005), The Jikes Research Virtual Machine project: Building an open-source research community, IBM Systems Journal, Volume: 44, Issue: 2, pp 399-417

• Abtract

This paper describes the evolution of the Jikes™ Research Virtual Machine project from an IBM internal research project, called Jalapeño, into an open-source project. After summarizing the original goals of the project, we discuss the motivation for releasing it as an open-source project and the activities performed to ensure the success of the project. Throughout, we highlight the unique challenges of developing and maintaining an open-source project designed specifically to support a research community.

Suresh Thummalapenta and Tao Xie, (2007), Parseweb: a programmer assistant for reusing open source code on the web, ASE '07, Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering, Pages 204-213, doi>10.1145/1321631.1321663

• Abstract

Programmers commonly reuse existing frameworks or libraries to reduce software development efforts. One common problem in reusing the existing frameworks or libraries is that the programmers know what type of object that they need, but do not know how to get that object with a specific method sequence. To help programmers to address this issue, we have developed an approach that takes queries of the form "Source object type → Destination object type" as input, and suggests relevant method-invocation sequences that can serve as solutions that yield the destination object from the source object given in the query. Our approach interacts with a code search engine (CSE) to gather relevant code samples and performs static analysis over the gathered samples to extract required sequences. As code samples are collected on demand through CSE, our approach is not limited to queries of any specific set of frameworks or libraries. We have implemented our approach with a tool called PARSEWeb, and conducted four different evaluations to show that our approach is effective in addressing programmer's queries. We also show that PARSEWeb performs better than existing related tools: Prospector and Strathcona

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.

Pierre Azoulaya, Andrew Stellmanb and Joshua Graff Zivinc, (2006), PublicationHarvester: An open-source software tool for science policy research, Research Policy, Volume 35, Issue 7, Pages 970–974

• Abstract

We present PublicationHarvester, an open-source software tool for gathering publication information on individual life scientists. The software interfaces with MEDLINE, and allows the end-user to specify up to four MEDLINE-formatted names for each researcher. Using these names along with a user-specified search query, PublicationHarvester generates yearly publication counts, optionally weighted by Journal Impact Factors. These counts are further broken-down by order on the authorship list (first, last, second, next-to-last, middle) and by publication type (clinical trials, regular journal articles, reviews, letters/editorials, etc.) The software also generates a keywords report at the scientist-year level, using the medical subject headings (MeSH) assigned by the National Library of Medicine to each publication indexed by MEDLINE. The software, source code, and user manual can be downloaded at http://www.stellman-greene.com/PublicationHarvester/.

Kevin Crowston, James Howison and Hala Annabi, (2006), Information systems success in free and open source software development: theory and measures, Software Process: Improvement and Practice Special Issue: Special Issue on Free or Open Source Software Development (F/OSSD) Projects, Volume 11, Issue 2, pages 123–148, March/April 2006 DOI: 10.1002/spip.259

• Abstract

Abstract Information systems success is one of the most widely used dependent variables in information systems (IS) research, but research on free/libre and open source software (FLOSS) often fails to appropriately conceptualize this important concept. In this article, we reconsider what success means within a FLOSS context. We first review existing models of IS success and success variables used in FLOSS research and assess them for their usefulness, practicality and fit to the FLOSS context. Then, drawing on a theoretical model of group effectiveness in the FLOSS development process, as well as an on-line discussion with developers, we present additional concepts that are central to an appropriate understanding of success for FLOSS.

In order to examine the practicality and validity of this conceptual scheme, the second half of our article presents an empirical study that demonstrates operationalizations of the chosen measures and assesses their internal validity. We use data from SourceForge to measure the project's effectiveness in team building, the speed of the project at responding to bug reports and the project's popularity. We conclude by discussing the implications of this study for our proposed extension of IS success in the context of FLOSS development and highlight future directions for research. Copyright © 2006 John Wiley & Sons, Ltd.

Janos Demeter et al., (2007), The Stanford Microarray Database: implementation of new analysis tools and open source release of software, Nucleic Acids Research (2007) 35 (suppl 1): D766-D770. doi: 10.1093/nar/gkl1019

• Abstract

The Stanford Microarray Database (SMD; http://smd.stanford.edu/) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.

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.

Dominic Widdows and Kathleen Ferraro, (2008), Semantic vectors: a scalable open source package and online technology management application, Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08), European Language Resources Association (ELRA), May, 2008

• Abstract

This paper describes the open source SemanticVectors package that efficiently creates semantic vectors for words and documents from a corpus of free text articles. We believe that this package can play an important role in furthering research in distributional semantics, and (perhaps more importantly) can help to significantly reduce the current gap that exists between good research results and valuable applications in production software. Two clear principles that have guided the creation of the package so far include ease-of-use and scalability. The basic package installs and runs easily on any Java-enabled platform, and depends only on Apache Lucene. Dimension reduction is performed using Random Projection, which enables the system to scale much more effectively than other algorithms used for the same purpose. This paper also describes a trial application in the Technology Management domain, which highlights some user-centred design challenges which we believe are also key to successful deployment of this technology.

M. Quigley et al., (2009), ROS: an open-source Robot Operating System, Conference Paper - ICRA Workshop on Open Source Software

• Abstract

This paper gives an overview of ROS, an opensource robot operating system. ROS is not an operating system in the traditional sense of process management and scheduling; rather, it provides a structured communications layer above the host operating systems of a heterogenous compute cluster. In this paper, we discuss how ROS relates to existing robot software frameworks, and briefly overview some of the available application software which uses ROS.

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.

Darren Kessner et al., (2009), ProteoWizard: open source software for rapid proteomics tools development, Bioinformatics Volume 24, Issue 21Pp. 2534-2536

• Abstract from Bioinformatics

Summary: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library.

Availability: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

Fowler, James E. (2000), QccPack: An open-source software library for quantization, compression, and coding, In Applications of Digital Image Processing XXIII, A. G. Tescher, Ed., San Diego, CA, August 2000, Proc. SPIE 4115, pp. 294-301.

• Abstract

We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use.

Speech / Vocabulary / Ontology[edit | edit source]

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.

Willie Walker et al., (2004), Sphinx-4: a flexible open source framework for speech recognition, Technical Report

• Abstract

Sphinx-4 is a flexible, modular and pluggable framework to help foster new innovations in the core research of hidden Markov model (HMM) speech recognition systems. The design of Sphinx-4 is based on patterns that have emerged from the design of past systems as well as new requirements based on areas that researchers currently want to explore. To exercise this framework, and to provide researchers with a "researchready" system, Sphinx-4 also includes several implementations of both simple and state-of-the-art techniques. The framework and the implementations are all freely available via open source

Natalya F. Noy et al., (2003), Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment, AMIA 2003 Open Source Expo

• Abstract

Protégé-2000 is an open-source tool that assists users in the construction of large electronic knowledge bases. It has an intuitive user interface that enables developers to create and edit domain ontologies. Numerous plugins provide alternative visualization mechanisms, enable management of multiple ontologies, allow the use of inference engines and problem solvers with Protégé ontologies, and provide other functionality. The Protégé user community has more than 7000 members.

Evren Sirin et al., Pellet: A practical OWL-DL reasoner, Software Engineering and the Semantic Web, Volume 5, Issue 2, June 2007, Pages 51–53

• Abstract

In this paper, we present a brief overview of Pellet: a complete OWL-DL reasoner with acceptable to very good performance, extensive middleware, and a number of unique features. Pellet is the first sound and complete OWL-DL reasoner with extensive support for reasoning with individuals (including nominal support and conjunctive query), user-defined datatypes, and debugging support for ontologies. It implements several extensions to OWL-DL including a combination formalism for OWL-DL ontologies, a non-monotonic operator, and preliminary support for OWL/Rule hybrid reasoning. Pellet is written in Java and is opensource.

J. Atserias, B. Casas, E. Comelles, M. Gonzalez, L. Padro, and M. Padro. TALP Research Center Universitat Politecnica de Catalunya Barcelona, Spain, FreeLing 1.3: Syntactic and semantic services in an open-source NLP library

• Abstract

This paper describes version 1.3 of the FreeLing suite of NLP tools. FreeLing was first released in February 2004 providing morphological analysis and PoS tagging for Catalan, Spanish, and English. From then on, the package has been improved and enlarged to cover more languages (i.e. Italian and Galician) and offer more services: Named entity recognition and classification, chunking, dependency parsing, and WordNet based semantic annotation. FreeLing is not conceived as end-user oriented tool, but as library on top of which powerful NLP applications can be developed. Nevertheless, sample interface programs are provided, which can be straightforwardly used as fast, flexible, and efficient corpus processing tools.

A remarkable feature of FreeLing is that it is distributed under a free-software LGPL license, thus enabling any developer to adapt the package to his needs in order to get the most suitable behaviour for the application being developed

FreeLing Home

Zhifei Li et al., (2009), Joshua: an open source toolkit for parsing-based machine translation, Proceeding StatMT '09, Proceedings of the Fourth Workshop on Statistical Machine Translation, Pages 135-139

• Abstract

We describe Joshua, an open source toolkit for statistical machine translation. Joshua implements all of the algorithms required for synchronous context free grammars (SCFGs): chart-parsing, n-gram language model integration, beam-and cube-pruning, and k-best extraction. The toolkit also implements suffix-array grammar extraction and minimum error rate training. It uses parallel and distributed computing techniques for scalability. We demonstrate that the toolkit achieves state of the art translation performance on the WMT09 French-English translation task.

General Open Source Science[edit | edit source]

AG González, (2005), Open science: open source licenses in scientific research, North Carolina Journal of Law & Technology., Vol. 7, Issue 2.

• Abstract

In recent years, there has been growing interest in the area of open source software (OSS) as an alternative economic model. However, the success of the OSS mindshare and collaborative online experience has wider implications to many other fields of human endeavour than the mere licensing of computer programmes. There are a growing number of institutions interested in using OSS licensing schemes to distribute creative works, scientific research and even to publish online journals through open access licenses (OA).

There appears to be growing concern in the scientific community about the trend to fence and protect scientific research through intellectual property, particularly by the abuse of patent applications for biotechnology research. The OSS experience represents a successful model that demonstrates that IP licenses could eventually be used to protect against the misuse and misappropriation of basic scientific research. This would be done by translating existing OSS licenses to protect scientific research. Some efforts are already paying dividends in areas such as scientific publishing, evidenced by the growing number of OA journals. However, the process of translating software licenses to areas other than publishing has been more difficult. OSS and open access licenses work best with works subject to copyright protection because copyright subsists in an original work as soon as it is created. However, it has been more difficult to generate a license that covers patented works because patents are only awarded through a lengthy application and registration process. If the open science experiment is to work, it needs the intervention of the legal community to draft new licenses that may apply to scientific research. This work will look at the issue of such open science licenses, paying special care as to how the system can best be exported to scientific research based on OSS and OA ideals.

• • looks really interesting get a copy

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.

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.

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.