Open Source Toolkit for Technology Managers
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ROADS and BRIDGES: the UNSEEN LABOR BEHIND OUR DIGITAL INFRASTRUCTURE Preface
Roads and Bridges:The Unseen Labor Behind Our Digital Infrastructure WRITTEN BY Nadia Eghbal 2 Open up your phone. Your social media, your news, your medical records, your bank: they are all using free and public code. Contents 3 Table of Contents 4 Preface 58 Challenges Facing Digital Infrastructure 5 Foreword 59 Open source’s complicated relationship with money 8 Executive Summary 66 Why digital infrastructure support 11 Introduction problems are accelerating 77 The hidden costs of ignoring infrastructure 18 History and Background of Digital Infrastructure 89 Sustaining Digital Infrastructure 19 How software gets built 90 Business models for digital infrastructure 23 How not charging for software transformed society 97 Finding a sponsor or donor for an infrastructure project 29 A brief history of free and public software and the people who made it 106 Why is it so hard to fund these projects? 109 Institutional efforts to support digital infrastructure 37 How The Current System Works 38 What is digital infrastructure, and how 124 Opportunities Ahead does it get built? 125 Developing effective support strategies 46 How are digital infrastructure projects managed and supported? 127 Priming the landscape 136 The crossroads we face 53 Why do people keep contributing to these projects, when they’re not getting paid for it? 139 Appendix 140 Glossary 142 Acknowledgements ROADS AND BRIDGES: THE UNSEEN LABOR BEHIND OUR DIGITAL INFRASTRUCTURE Preface Our modern society—everything from hospitals to stock markets to newspapers to social media—runs on software. But take a closer look, and you’ll find that the tools we use to build software are buckling under demand. -
When Is Open Access Not Open Access?
Editorial When Is Open Access Not Open Access? Catriona J. MacCallum ince 2003, when PLoS Biology Box 1. The Bethesda Statement on Open-Access Publishing was launched, there has been This is taken from http:⁄⁄www.earlham.edu/~peters/fos/bethesda.htm. a spectacular growth in “open- S 1 access” journals. The Directory of An Open Access Publication is one that meets the following two conditions: Open Access Journals (http:⁄⁄www. 1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, doaj.org/), hosted by Lund University worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit Libraries, lists 2,816 open-access and display the work publicly and to make and distribute derivative works, in any digital journals as this article goes to press medium for any responsible purpose, subject to proper attribution of authorship2, as (and probably more by the time you well as the right to make small numbers of printed copies for their personal use. read this). Authors also have various 2. A complete version of the work and all supplemental materials, including a copy of “open-access” options within existing the permission as stated above, in a suitable standard electronic format is deposited subscription journals offered by immediately upon initial publication in at least one online repository that is supported traditional publishers (e.g., Blackwell, by an academic institution, scholarly society, government agency, or other well- Springer, Oxford University Press, and established organization that seeks to enable open access, unrestricted distribution, many others). In return for a fee to interoperability, and long-term archiving (for the biomedical sciences, PubMed Central the publisher, an author’s individual is such a repository). -
Of Us Research Program Ethical, Legal, and Social Implications (ELSI)
All of Us Research Program Ethical, Legal, and Social Implications (ELSI) Research Priorities Workshop June 24–25, 2019 Executive Summary The All of Us Research Program’s Ethical, Legal, and Social Implications (ELSI) Research Priorities Workshop was held on June 24–25, 2019. The workshop convened ELSI professionals and All of Us participant ambassadors to help identify ELSI research opportunities using the All of Us Research Program, provide feedback on how to advance ELSI research by using the program and its data resources, and suggest ELSI-related research use cases.1 On Day 1, attendees received information on the program’s research platform, scientific framework and priorities, commitment to diversity, participant engagement strategy, data access and privacy policies, and new activities that are being planned. They also received a demonstration of the All of Us public data browser. Attendees then divided into working groups organized around three themes: (1) genomics; (2) social determinants of health; and (3) legal, regulatory, and policy issues. In these groups, attendees participated in a facilitated activity where they discussed and recorded ELSI research questions of interest and the data needed to answer them, including data with planned availability through the program’s Research Hub. During an open discussion on Day 2, attendees raised significant concerns about the structure of Day 1 and asserted that the program could make better use of their deep and varied expertise by reframing the workshop to allow for exploration of some important ELSI considerations that the program raises, including protecting participants’ rights and privacy and ensuring that participants have a real voice in the program. -
A Fool's Errand
COMMENT by the madness of mobs. Will a crowd- sourced scholarship be dominated by pro- vocative pap that fills without nourishing? Here we must recall first that schol- arship has always been a community MONROE BRENDAN enterprise, driven by building consen- sus among experts10. So the question is not ‘Should we crowdsource?’ but ‘How should we crowdsource?’. Second, we must dispose of the straw-man argument that hundreds of uninformed readers’ opinions will count for more than one Fields medallist’s recommendation. Authority and expertise are central in the Web era as they were in the journal era. The difference is that whereas the paper- based system used subjective criteria to identify authoritative voices, the Web- based one assesses authority recursively from the entire community. We now have a unique opportunity as scholars to guide the evolution of our tools in directions that honour our val- ues and benefit our communities. Here’s what to do. First, try new things: publish new kinds of products, share them in new places and brag about them using new metrics. Intellectual playfulness is a core scholarly virtue. Second, take risks (another scholarly virtue): publishing more papers may be safe, but scholars who establish early leadership in Web- native production will be ahead of the curve as these genres become dominant. A fool’s errand Finally, resist the urge to cling to the trap- pings of scientific excellence rather than Objections to the Creative Commons attribution excellence itself. ‘Publication’ is just one mode of making public and one way of licence are straw men raised by parties who want open validating scholarly excellence. -
Publisher Correction: Pairwise Library Screen Systematically Interrogates Staphylococcus Aureus Cas9 Specificity in Human Cells
DOI: 10.1038/s41467-018-06029-z OPEN Publisher Correction: Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells Josh Tycko 1,5, Luis A. Barrera1,6, Nicholas C. Huston1,7, Ari E. Friedland1, Xuebing Wu2, Jonathan S. Gootenberg 3, Omar O. Abudayyeh4, Vic E. Myer1, Christopher J. Wilson 1 & Patrick D. Hsu1,8 Correction to: Nature Communications; https://doi.org/10.1038/s41467-018-05391-2; published online 27 July 2018 The original HTML version of this Article incorrectly listed an affiliation of Josh Tycko as ‘Department of Genetics, Stanford 1234567890():,; University School of Medicine, Stanford, CA 94305, USA’, instead of the correct ‘Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA’. It also incorrectly listed an affiliation of this author as ‘Present address: Arrakis Therapeutics, 35 Gatehouse Dr., Waltham, MA, 02451, USA’. The original HTML version incorrectly listed an affiliation of Luis A. Barrera as ‘Present address: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA’, instead of the correct ‘Present address: Arrakis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA’. Finally, the original HTML version incorrectly omitted an affiliation of Nicholas C. Huston: ‘Present address: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA’. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. -
The Fourth Paradigm
ABOUT THE FOURTH PARADIGM This book presents the first broad look at the rapidly emerging field of data- THE FOUR intensive science, with the goal of influencing the worldwide scientific and com- puting research communities and inspiring the next generation of scientists. Increasingly, scientific breakthroughs will be powered by advanced computing capabilities that help researchers manipulate and explore massive datasets. The speed at which any given scientific discipline advances will depend on how well its researchers collaborate with one another, and with technologists, in areas of eScience such as databases, workflow management, visualization, and cloud- computing technologies. This collection of essays expands on the vision of pio- T neering computer scientist Jim Gray for a new, fourth paradigm of discovery based H PARADIGM on data-intensive science and offers insights into how it can be fully realized. “The impact of Jim Gray’s thinking is continuing to get people to think in a new way about how data and software are redefining what it means to do science.” —Bill GaTES “I often tell people working in eScience that they aren’t in this field because they are visionaries or super-intelligent—it’s because they care about science The and they are alive now. It is about technology changing the world, and science taking advantage of it, to do more and do better.” —RhyS FRANCIS, AUSTRALIAN eRESEARCH INFRASTRUCTURE COUNCIL F OURTH “One of the greatest challenges for 21st-century science is how we respond to this new era of data-intensive -
Will Sci-Hub Kill the Open Access Citation Advantage and (At Least for Now) Save Toll Access Journals?
Will Sci-Hub Kill the Open Access Citation Advantage and (at least for now) Save Toll Access Journals? David W. Lewis October 2016 © 2016 David W. Lewis. This work is licensed under a Creative Commons Attribution 4.0 International license. Introduction It is a generally accepted fact that open access journal articles enjoy a citation advantage.1 This citation advantage results from the fact that open access journal articles are available to everyone in the word with an Internet collection. Thus, anyone with an interest in the work can find it and use it easily with no out-of-pocket cost. This use leads to citations. Articles in toll access journals on the other hand, are locked behind paywalls and are only available to those associated with institutions who can afford the subscription costs, or who are willing and able to purchase individual articles for $30 or more. There has always been some slippage in the toll access journal system because of informal sharing of articles. Authors will usually send copies of their work to those who ask and sometime post them on their websites even when this is not allowable under publisher’s agreements. Stevan Harnad and his colleagues proposed making this type of author sharing a standard semi-automated feature for closed articles in institutional repositories.2 The hashtag #ICanHazPDF can be used to broadcast a request for an article that an individual does not have access to.3 Increasingly, toll access articles are required by funder mandates to be made publically available, though usually after an embargo period. -
The Machine That Would Predict the Future
TECHNOLOGY SPECIAL REPORT The Machine That Would Predic t the If you dropped all the world’s data into a black box, could it become a crystal ball that Futurewould let you see the future—even test what would happen if you chose A over B? One researcher thinks so, and he could soon get a billion euros to build it By David Weinberger In the summer and fall of last year, the Greek financial crisis tore at the seams of the global economy. Having run up a debt that it would never be able to repay, the country faced a number of poten- tial outcomes, all unpleasant. Efforts to slash spending spurred riots in the streets of Athens, while threats of default rattled global financial markets. Many economists argued that Greece should leave the euro zone and devalue its currency, a move that would in theory help the economy grow. “Make no mistake: an orderly euro exit will be hard,” wrote New York Universi- ty economist Nouriel Roubini in the Financial Times. “But watching the slow disorderly implo- sion of the Greek economy and society will be much worse.” No one was sure exactly how the scenario would play out, limit the spread of infectious disease. Altered trade routes could though. Fear spread that if Greece were to abandon the euro, disrupt native ecosystems. The question itself is simple— Spain and Italy might do the same, weakening the central bond Should Greece drop the euro?—but the potential fallout is so of the European Union. Yet the Economist opined that the crisis far-reaching and complex that even the world’s sharpest minds would “bring more fiscal-policy control from Brussels, turning found themselves unable to grasp all the permutations. -
The Legal Framework for Reproducible Scientific Research Licensing and Copyright
R EPRODUCIBLE RESEARCH The Legal Framework for Reproducible Scientific Research Licensing and Copyright As computational researchers increasingly make their results available in a reproducible way, questions naturally arise regarding copyright, subsequent use and citation, and ownership rights in general. The author proposes the Reproducible Research Standard for all components of scientific researchers’ scholarship, which should encourage replicable scientific investigation through attribution, the facilitation of greater collaboration, and the promotion of the engagement of the larger community in scientific learning and discovery. n the US, when scientists put their original computational work because researchers often research on the Web, it automatically falls need more than just the published article to re- under copyright. However, copyright is produce the results. an unsuitable legal structure for scientific Although this trend seems to be changing, the Iworks. Scientific norms guide scientists to repro- typical journal publishing format doesn’t allow for duce and build on others’ research, and default transmission of supporting files such as accom- copyright law by its very purpose runs counter panying images, source code, or demonstrations to these goals. In this article, I present a meth- of work to interested readers—although some odology for scientists to rescind copyright from journals are beginning to require that code or their work in such a way that it realigns scientific data be released as a precondition for publication, information sharing with long-established scien- (for example, Nature [www.nature.com/authors/ tific norms. editorial_policies/availability.html], The Insight Journal [www.insight-journal.org], and Annals of Options for Researchers Internal Medicine [www.annals.org/cgi/content/ Computational research is becoming more per- full/0000605-200703200-00154v1]). -
Contents Work
It worked, and it continues to Contents work. Last year, member dues ac- Fifteen years of FSF associate counted for over half of our total members...................1 revenue, and nearly ten times as Finding a free software silver lining much as we received from corpora- tions. But membership from the to the Facebook Cambridge start has been much more than a Analytica scandal ............3 way to donate. Members form a Tech updates, episode 2018: proud community united around A GNUHope................4 the idea that people, in order to be The threat of government-run Digital free, must be in control of the soft- ware they rely on to live their lives. Restrictions Management . 6 Today, we have members in Uber takes software users for a ride over eighty countries. I feel very ..........................8 close to this community—especially On the road with RMS.........9 to the 136 members who have been GNU needs you: How to contribute with us all fifteen years. I've gotten to a GNU project............10 to know their names through stuff- ing thousands of envelopes, ex- Fifteen years of FSF changing many emails, and shaking associate members hands—first at the annual member meetings we held, at the Libre- ast fall marked fifteen years of Lthe FSF's associate membership program. Shortly after, I celebrated my own fifteenth anniversary with the FSF. I've never known an FSF without associate members. The membership program was launched in late 2002 to stabilize the FSF fin- ancially, as some previous sources of support—like sales of software and In March, the FSF celebrated our tenth manuals on physical media—were annual LibrePlanet conference, with over falling out of fashion. -
Open Source Used in Asyncos 7.8 for Email
Open Source Used In AsyncOS 7.8 for Email Cisco Systems, Inc. www.cisco.com Cisco has more than 200 offices worldwide. Addresses, phone numbers, and fax numbers are listed on the Cisco website at www.cisco.com/go/offices. Text Part Number: 78EE117C99-25357715 Open Source Used In AsyncOS 7.8 for Email 1 This document contains the licenses and notices for open source software used in this product. With respect to the free/open source software listed in this document, if you have any questions or wish to receive a copy of the source code to which you are entitled under the applicable free/open source license(s) (such as the GNU Lesser/General Public License), please contact us at [email protected]. In your requests please include the following reference number 78EE117C99-25357715 Contents 1.1 AnyEvent 5.34 1.1.1 Available under license 1.2 Aquarium 2.2.1 1.2.1 Available under license 1.3 Archive::Zip 1.30 1.3.1 Available under license 1.4 B::Deobfuscate 0.20 1.4.1 Available under license 1.5 B::Deobfuscate 0.10 1.5.1 Available under license 1.6 B::Keywords 0.06 1.6.1 Available under license 1.7 B::Keywords 1.10 1.7.1 Available under license 1.8 BerkeleyDB-perl 0.49 1.8.1 Available under license 1.9 Boost 1.41 1.9.1 Available under license 1.10 BSD::Resource 1.2903 1.10.1 Available under license 1.11 BSD::Resource 1.2904 1.11.1 Available under license 1.12 cheetah 1 1.12.1 Available under license 1.13 common::sense 3.4 1.13.1 Available under license Open Source Used In AsyncOS 7.8 for Email 2 1.14 Compress::Raw::Bzip2 -
Annual Report
[Credits] Licensed under Creative Commons Attribution license (CC BY 4.0). All text by John Hsieh and Georgia Young, except the Letter from the Executive Director, which is by John Sullivan. Images (name, license, and page location): Wouter Velhelst: cover image; Kori Feener, CC BY-SA 4.0: inside front cover, 2-4, 8, 14-15, 20-21, 23-25, 27-29, 32-33, 36, 40-41; Michele Kowal: 5; Anonymous, CC BY 3.0: 7, 16, 17; Ruben Rodriguez, CC BY-SA 4.0: 10, 13, 34-35; Anonymous, All rights reserved: 16 (top left); Pablo Marinero & Cecilia e. Camero, CC BY 3.0: 17; Free This report highlights activities Software Foundation, CC BY-SA 4.0: 18-19; Tracey Hughes, CC BY-SA 4.0: 30; Jose Cleto Hernandez Munoz, CC BY-SA 3.0: 31, Pixabay/stevepb, CC0: 37. and detailed financials for Fiscal Year 2016 Fonts: Letter Gothic by Roger Roberson; Orator by John Scheppler; Oswald by (October 1, 2015 - September 30, 2016) Vernon Adams, under the OFL; Seravek by Eric Olson; Jura by Daniel Johnson. Created using Inkscape, GIMP, and PDFsam. Designer: Tammy from Creative Joe. 1] LETTER FROM THE EXECUTIVE DIRECTOR 2] OUR MISSION 3] TECH 4] CAMPAIGNS 5] LIBREPLANET 2016 6] LICENSING & COMPLIANCE 7] CONFERENCES & EVENTS 7 8] LEADERSHIP & STAFF [CONTENTS] 9] FINANCIALS 9 10] OUR DONORS CONTENTS our most important [1] measure of success is support for the ideals of LETTER FROM free software... THE EXECUTIVE we have momentum DIRECTOR on our side. LETTER FROM THE 2016 EXECUTIVE DIRECTOR DEAR SUPPORTERS For almost 32 years, the FSF has inspired people around the Charity Navigator gave the FSF its highest rating — four stars — world to be passionate about computer user freedom as an ethical with an overall score of 99.57/100 and a perfect 100 in the issue, and provided vital tools to make the world a better place.