Michael Eisen
I'm an evolutionary biologist at UC Berkeley and an Investigator of the Howard Hughes Medical Institute. My research focuses on the evolution and population genomics of gene regulation in flies, and on the ways that microbes control animal behavior. I am a strong proponent of open science, and a co-founder of the Public Library of Science. And most importantly, I am a Red Sox fan.

Let me just say that any area of scholarship where, in 20-fucking-12, the idea of moving to open-access, online distribution of writing counts as some kind of radicalism deserves everything that's going to happen to it.

"For over a decade, Stamen has been exploring cartography with our clients and in research. These three maps are presented here for your enjoyment and use wherever you display OpenStreetMap data."

Annotated link http://www.diigo.com/bookmark/http://nogoodreason.typepad.co.uk/no_good_reason/2011/09/digital-scholarship-introduction.html

"We're gathering legislative data directly from the states and making it available in a common format through a RESTful API and regular bulk downloads. "

"Although the “mass media era now looks like a relatively brief and anomalous,” it is seen as normal by those who have spent their careers in those organisations. Those stuck in the “old paradigm” have great difficulty imagining and accepting the “new paradigm.”

Scientific journals are lagging behind newspapers, but they are surely on the same course. Many find unacceptable the domination of a few journals and the huge profits made by some publishers from the scientific value produced by others, and the open access has begun for these and other reasons. Open access articles are increasing rapidly, and just in the past few years we have seen the appearance of many “megajournals” like PLoS One and BMJ Open, which are aiming to publish rapidly after light peer review that does not attempt the largely impossible job of “spotting winners” but leaves readers to decide. "

"I’ve posted to YouTube a series of 22 short videos giving an introduction to quantum computing. Here’s the first video:

Below I list the remaining 21 videos, which cover subjects including the basic model of quantum computing, entanglement, superdense coding, and quantum teleportation.

To work through the videos you need to be comfortable with basic linear algebra, and with assimilating new mathematical terminology. If you’re not, working through the videos will be arduous at best! Apart from that background, the main prerequisite is determination, and the willingness to work more than once over material you don’t fully understand."

"Discover why open access is not only a viable option for the humanities, but a revolutionary one. Though more widely recognized in the sciences, open access publishing is well established in the humanities and continues to break new ground. Open Humanities Press co-founder Gary Hall considers open access initiatives in the humanities and discuss their implications for our notions of academic authorship, the book, content creation, and publication. Gary Hall is a professor of Media and Performing Arts at Coventry University and author of Digitize This Book!: The Politics of New Media, or Why We Need Open Access Now. He is co-founder of the Open Humanities Press (OHP), founding co-editor of the open access journal Culture Machine, and editor of the OHP series Liquid Books."

"Open Research Computation publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers in any field. Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries. Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software. "

JHAP aims to promote research in and discussion of the history of analytical philosophy. ‘Analytical’ is understood broadly and we aim to cover the complete history of analytical philosophy, including the most recent one

Articles receiving the Open Access treatment received significantly more readership (as measured by article downloads) and reached a broader audience (as measured by unique visitors), yet were cited no more frequently, nor earlier, than subscription-access control articles. A pronounced increase in article downloads with no commensurate increase in citations to Open Access treatment articles may be explained through social stratification, a process which concentrates scientific authors at elite, resource-rich institutions with excellent access to the scientific literature. For this community, access is essentially a non-issue. The real beneficiaries of Open Access are the communities that consume, but do not contribute to, the scientific literature.

heather piwowar, research remix

blogging about the science, engineering, and human factors of biomedical evolution and ecology research data sharing and reuse

a freely distributable, copyable, and downloadable digital e-dition in honor of the 10th anniversary of the
Center for Digital Discourse and Culture

So let’s say for the sake of argument that you can narrow your choices to two journals, roughly equivalent in prestige. Here’s how you might choose between them...

OASIS aims to provide an authoritative ‘sourcebook’ on Open Access, covering the concept, principles, advantages, approaches and means to achieving it. The site highlights developments and initiatives from around the world, with links to diverse additional resources and case studies. As such, it is a community-building as much as a resource-building exercise. Users are encouraged to share and download the resources provided, and to modify and customize them for local use. Open Access is evolving, and we invite the growing world-wide community to take part in this exciting global movement.

Welcome to the Directory of Open Access Journals. This service covers free, full text, quality controlled scientific and scholarly journals. We aim to cover all subjects and languages.

Award winning SHERPA is investigating issues in the future of scholarly communication. It is developing open-access institutional repositories in universities to facilitate the rapid and efficient worldwide dissemination of research. SHERPA services and the SHERPA Partnership are both based at the Centre for Research Communications at the University of Nottingham.

Anyway, I was asked to present a couple of slides on challenges for open access data repositories ... but clearly I don't believe that such challenges are independent of the science, so I produced a few more slides to give context

By open data in science we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to software or use them for any other purpose without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. To this end data related to published science should be explicitly placed in the public domain.

Formally, we recommend adopting and acting on the following principles:

On August 11, the Journal of Neuroscience published an Announcement Regarding Supplemental Material by Editor-in-Chief John Maunsell. In it John Maunsell announces that the journal in November will stop accepting supplementary material in article submissions. The announcement has lead to an extensive discussion in the science blogosphere with a number of relevant posts listed below

This is a cluster of lists and other information about the open access tracking project (OATP).
The OATP is a social tagging project to capture new OA developments comprehensively and in real time.

Discussion of data release requirements in genetics.

The professoriate may be more liberal politically than the most latte-filled ZIP code in San Francisco, but we are an extraordinarily conservative bunch when it comes to scholarly communication.

We don’t need more filters or better filters in scholarly communications – we don’t need to block publication at all. Ever. What we need are tools for curation and annotation and re-integration of what is published. And a framework that enables discovery of the right thing at the right time. And the data that will help us to build these. The more data, the more reseach published, the better.

Situations where individuals have to contribute to joint efforts or share scarce resources are ubiquitous. Yet, without proper mechanisms to ensure cooperation, the evolutionary pressure to maximize individual success tends to create a tragedy of the commons (such as over-fishing or the destruction of our environment). This contribution addresses a number of related puzzles of human behavior with an evolutionary game theoretical approach as it has been successfully used to explain the behavior of other biological species many times, from bacteria to vertebrates. Our agent-based model distinguishes individuals applying four different behavioral strategies: non-cooperative individuals (“defectors”), cooperative individuals abstaining from punishment efforts (called “cooperators” or “second-order free-riders”), cooperators who punish non-cooperative behavior (“moralists”), and defectors, who punish other defectors despite being non-cooperative themselves (“immoralists”).

TeraGrid is an open scientific discovery infrastructure combining leadership class resources at eleven partner sites to create an integrated, persistent computational resource.

Using high-performance network connections, the TeraGrid integrates high-performance computers, data resources and tools, and high-end experimental facilities around the country. Currently, TeraGrid resources include more than a petaflop of computing capability and more than 30 petabytes of online and archival data storage, with rapid access and retrieval over high-performance networks. Researchers can also access more than 100 discipline-specific databases. With this combination of resources, the TeraGrid is the world's largest, most comprehensive distributed cyberinfrastructure for open scientific research.

A book introducing basic concepts from computational number theory and algebra, including all the necessary mathematical background.

Data Drip is a collective conversation about data, data policy, and research on media, information, and communications policy.

Interesting list of online text sharing communities and musings on publishing and piracy.

Welcome to MediaCommons Press, an in-development feature of MediaCommons, promoting the digital publication of texts ranging from article- to monograph-length.

In a global environment marked by timidity and laxness in thought, re.press publishes outstanding work in contemporary philosophy. A dedicated philosophy press—one of the very few active in the Anglophone world today—re.press is committed to publishing rigorous philosophy that doesn’t give way on its desire. At once exclusive and egalitarian, re.press seeks to support and disseminate such thought worldwide.

In line with this ambition, re.press is itself a new kind of publisher. Attentive to the latest developments in contemporary technologies, re.press publications are available globally, wherever there is access to the internet. We seek to make as many of our publications as possible available as open-access files, free to anyone who wishes to download them. Our hard-copy books are print-on-demand, minimizing waste and cost. Yet our publications also maximize design values, boosting clarity and aesthetic qualities.

In an ideal world, what would copyright law look like to you?

The 1909 Act. It had a much shorter term, formalities that separated the wheat from the chaff, and fair use wasn't mentioned in the statute because it was regarded as a robust common law doctrine.

The world is due for a resurgence of original speculative metaphysics. The New Metaphysics series aims to provide a safe house for such thinking amidst the demoralizing caution and prudence of professional academic philosophy. We do not aim to bridge the analytic-continental divide, since we are equally impatient with nail-filing analytic critique and the continental reverence for dusty textual monuments. We favor instead the spirit of the intellectual gambler, and wish to discover and promote authors who meet this description. Like an emergent recording company, what we seek are traces of a new metaphysical 'sound' from any nation of the world. The editors are open to translations of neglected metaphysical classics, and will consider secondary works of especial force and daring. But our main interest is to stimulate the birth of disturbing masterpieces of twenty-first century philosophy.

Open Access and the divide between “mainstream” and “peripheral” science
Jean-Claude Guédon
Université de Montréal

Open Educational Resources: Conversations in Cyberspace provides an overview of the first steps of this exciting new development: it captures the conversations between leaders of some of the first OER projects, and documents early debates on the issues that continue to challenge the movement. The publication will provide food for thought for all those intrigued by OER – its promise and its progress.

Founded in 2004 we're a not-for-profit organization promoting open knowledge: that's any kind of information – sonnets to statistics, genes to geodata – that can be freely used, reused, and redistributed.

The bottom line is there are two distinct issues here. The first is the issue of for-profit vs. association publishing. The current relationship between the scientific community and the for-profit publishers makes no sense to me. The second issue is the business model of association publishing, for example, "reader pays" vs. "authors pays." This is a legitimate topic of discussion, as long as we understand that it cannot be separated from the overall business model of the association. Just remember, "free" is not a sound business model.

donate to the Stanford Encyclopedia of Philosophy

Public Reason is a peer-reviewed journal of political and moral philosophy. Public Reason publishes articles, book reviews, as well as discussion notes from all the fields of political philosophy and ethics, including political theory, applied ethics, and legal philosophy. The Journal encourages the debate around rationality in politics and ethics in the larger context of the discussion concerning rationality as a philosophical problem.

Public Data Sets on AWS provides a centralized repository of public data sets that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community, and like all AWS services, users pay only for the compute and storage they use for their own applications.

Welcome to the largest bibliographic database dedicated to Economics and available freely on the Internet. Over 600'000 items of research can be browsed or searched, and over 500'000 can be downloaded in full text! This site is part of a large volunteer effort to enhance the free dissemination of research in Economics, RePEc. To see the popularity of these services, browse the statistics at LogEc

Online, open access is the superior model for scholarly communication. A variety of scientific communities in physics, the life sciences and economics have gone furthest in innovating their scholarly communication through open access, enhancing accessibil

Digital technology and its economics favour the severance of distribution from certification. What is required of universities and governments, scholars and publishers, is to clear the way for digital innovations in knowledge distribution and scholarly pu

This paper describes the current systems, processes and actors. While technological advancements appear to be enabling access to scholarly publications, economic conditions appear to limit access. In addition, a number of alternatives, such as open access

Rather than struggling, as it currently does, to design sites that meet each end-user need, we argue that the executive branch should focus on creating a simple, reliable and publicly accessible infrastructure that exposes the underlying data. Private act

The open access movement: Putting peer-reviewed scientific and scholarly literature on the internet. Making it available free of charge and free of most copyright and licensing restrictions. Removing the barriers to serious research.

The Open Access Directory (OAD) is a compendium of simple factual lists about open access (OA) to science and scholarship, maintained by the OA community at large. By bringing many OA-related lists together in one place, OAD will make it easier for everyo

Here's an informal list of research questions whose answers would usefully fill out our current knowledge (on open-access)