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juliusbeezer : openscience   73 About Me
I am a science researcher and an open access advocate, an engineer and an environmental scientist with expertise in both ‘science for policy’ as well as ‘policy for science.’. I travel to wherever my experience and skills can help make a system, an organization, or a community more open.

Since 1985 my career has spanned rural appropriate technology design to international development, academia, research and science information policy. Other than one stint with a small for-profit company, all my work has been with non-profit organizations. I am currently an independent consultant with The World Bank and Academy Health. I am also a member of Plazi, and just finished an appointment at the Department of GeoScience, University of Wisconsin, Madison, WI, USA where I was working on a machine reading and learning system built on a new kind of digital library resource. Before that I was the Manager of Science and Data Policy at Creative Commons where I focused on open data, text and data mining, open science policy, and citizen-sourced information. I am also a member of the Research Data Alliance Interest Group on Legal Interoperability of Research Data, CODATA Task Group on Data Citation Standards and Practices, and I co-authored the chapter on Emerging Principles for Data Citation in the Task Group’s report titled Out of Cite, Out of Mind.
open  openscience  opennotebook  openness  openhardware 
february 2018 by juliusbeezer
OSF | Home
Keep all your files, data, and protocols in one centralized location. No more trawling emails to find files or scrambling to recover from lost data.
openscience  tools 
october 2017 by juliusbeezer
Learn more about OpenTrials
Open Knowledge is developing Open Trials, an open, online database of information about the world’s clinical research trials. We are funded by The Laura and John Arnold Foundation through the Center for Open Science. The project, which is designed to increase transparency and improve access to research, will be directed by Dr. Ben Goldacre, an internationally known leader on clinical transparency.

OpenTrials is building a collaborative and open linked database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial:

Registry entries
Links, abstracts, or texts of academic journal papers
Portions of regulatory documents describing individual trials
Structured data on methods and results extracted by systematic reviewers or other
Clinical Study Reports
Additional documents such as blank consent forms, blank case report forms, and protocols

The intention is to create an open, freely re-usable index of all such information, to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive standards around open data in evidence-based medicine.
science  medicine  sciencepublishing  openmedicine  openscience  research  search 
october 2017 by juliusbeezer
Antediluvian Salad: Breaking Through the 4th Wall: OPEN SCIENCE's Promise of a New Scientific & Spiritual Kingdom
It is the system that is the problem. And it is the system that needs fixing.

It's high time that the modern peer review format goes through such a deconstruction and reconfiguration. Not, as some may wrongly be assuming, by abolishing the peer review process but by dramatically ameliorating the process of peer review in an exponential way. At the same time dropping the curtain on scientific process and controversy, making both creators and reviewers accountable to their words. Creators will face more levels of scrutiny and question but they will also benefit from exponentially more collaboration and insight. Creators will no longer be held at the mercy of their reviewers as reviewers will no longer be anonymous and their critiques will be displayed to all. The inherent collaborative and synergistic methods of a truly free and liberal OPEN SCIENCE paradigm shift will dramatically and irrevocably speed up the process of science. Science operating at maximum RPM. Contrary to what many may fear I advocate, as sort of free for all of self publishing anarchy I actually hope to curtail that pitfall. By allowing any and all to submit their idea or work in whatever format or state of finality they choose all are given a shot and subject to online review. Therefore charges of "ivory tower" orthodoxy, academic bias, and in-group out group shenanigans get cut off right at the root. The lone wolf outsider, forever reeling at the unfair treatment they suffer from "the establishment" will be a thing of the past. In short the future of scientific communication as I envisage it will combine the best elements of the peer review process and the social media, group sourced, immediacy of "blogging" format while eschewing the problematic elements inherent in both practices.
sciencepublishing  openscience  peerreview  openaccess 
september 2017 by juliusbeezer
Open Science and its Discontents | Ronin Institute
Although there is a spectrum of responses, criticism of open-science tends to fall into one of two camps, that I will call “conservative” and “radical”. This terminology is not intended to imply an association with any conventional political labels, they are simply used for convenience to indicate the relative degree of comfort with the institutional status quo. Let’s look at these two groups of critiques.

The conservative response to regular timely release of pre-publication data could be best summarized by the phrase: “are you kidding me? why would I do that?” The apotheosis of this notion was appeared in an editorial published in the New England Journal of Medicinewhich described with some horror the “emergence of a new class of research parasites”. They further concluded that some of these parasites might not only use that data for their own publications, but might seek to examine whether the original study was correct....

Arguments for open-science made in response to the conservative critique tend to assume that release of more data, code, papers is a pure good in and of itself, and downplay the political economy in which they are embedded.
openscience  openaccess  archiving  opendata  politics  business  sociology 
july 2017 by juliusbeezer
What is open peer review? A systematic review - F1000Research
Open pre-review manuscripts are manuscripts that are immediately openly accessible (via the internet) in advance, or in synchrony with, any formal peer review procedures. Subject-specific “preprint servers” like and, institutional repositories, catch-all repositories like Zenodo or Figshare and some publisher-hosted repositories (like PeerJ Preprints) allow authors to short-cut the traditional publication process and make their manuscripts immediately available to everyone. This can be used as a complement to a more traditional publication process, with comments invited on preprints and then incorporated into redrafting as the manuscript goes through traditional peer review with a journal. Alternatively, services which overlay peer-review functionalities on repositories can produce functional publication platforms at reduced cost (Boldt, 2011; Perakakis et al., 2010). The mathematics journal Discrete Analysis, for example, is an overlay journal whose primary content is hosted on arXiv (Day, 2015).
peerreview  open  openscience  openaccess 
april 2017 by juliusbeezer
The 20% Statistician: Five reasons blog posts are of higher scientific quality than journal articles
I’ve tried to measure blogs and journal articles on some dimensions that, I think, determine their scientific quality. It is my opinion that blogs, on average, score better on some core scientific values, such as open data and code, transparency of the peer review process, egalitarianism, error correction, and open access. It is clear blogs impact the way we think and how science works. For example, Sanjay Srivastava’s pottery barn rule, proposed in a 2012 blog, will be implemented in the journal Royal Society Open Science. This shows blogs can be an important source of scientific communication. If the field agrees with me, we might want to more seriously consider the curation of blogs, to make sure they won’t disappear in the future, and maybe even facilitate assigning DOI’s to blogs, and the citation of blog posts.
blogs  sciencepublishing  openscience  openness  opendata 
april 2017 by juliusbeezer
Around the Web: Saving Government Data from the Trumpocalypse – Confessions of a Science Librarian
While I’m working on a major update to my Documenting the Donald Trump War on Science: Pre-Inauguration Edition and preparing for the first of the post-inauguration posts, I thought I’d whet everyone’s appetite with a post celebrating all the various efforts to save environmental, climate and various kinds of scientific and other data from potential loss in the Trump presidential era.
openscience  opendata  canada  us  politics  library 
february 2017 by juliusbeezer
The high-tech war on science fraud | Science | The Guardian
Statcheck had read some 50,000 published psychology papers and checked the maths behind every statistical result it encountered. In the space of 24 hours, virtually every academic active in the field in the past two decades had received an email from the program, informing them that their work had been reviewed. Nothing like this had ever been seen before: a massive, open, retroactive evaluation of scientific literature, conducted entirely by computer.

Statcheck’s method was relatively simple, more like the mathematical equivalent of a spellchecker than a thoughtful review, but some scientists saw it as a new form of scrutiny and suspicion, portending a future in which the objective authority of peer review would be undermined by unaccountable and uncredentialed critics.
opendata  psychology  openscience  peerreview 
february 2017 by juliusbeezer
Researchers Are Preparing for Trump to Delete Government Science From the Web | Motherboard
While it’s easy to scrape an HTML website, Paterson and others are worried that, for instance, a NOAA database and tool regularly used by city planners to calculate sea level rise could be pulled offline.

“It’s less the documents, which we can get through alternative means,” he said. “The bigger issue in my mind is the access to databases and analytic software that public dollars paid for which by administrative fiat they may remove. I use the NOAA sea level rise projection database for discussion in my environmental impact assessment class. I use the greenhouse gas emission calculator for analysis of major federal climate actions.”

One of the main concerns is that a Trump presidency doesn’t even have to purposefully take down these tools—many of them will simply break or become useless without being regularly updated.
sciencepublishing  us  politics  opendata  openaccess  openscience  open 
december 2016 by juliusbeezer
Making drug development less secretive could lead to quicker, cheaper therapies
Secrecy ruins the efficiency of the research process. Competing groups operate in ignorance of each others’ results, experts fail to talk to each other and there’s unnecessary duplication.

There are groups pursuing projects known to others to be dead-ends.

In contrast, open source projects are developed by communities where everything is shared. Mutual learning is fast.

The ability to “look over the shoulder” of people working on the same problem can lead to extraordinary leaps of productivity. Contributors can rapidly identify problems and can join and leave a nimble team as required.
openscience  opennotebook  open 
october 2016 by juliusbeezer
Open Source Malaria’s First Paper | Intermolecular
Open Source Malaria (OSM) publishes its first paper today. The project was a real thrill, because of the contributors. I’d like to thank them.

Skepticism about open source research is often based on assumptions: that people will be too busy or insufficiently motivated to participate, or that there will be a cacophony of garbage contributions if a project is open to anyone. I’m not sure where such assumptions come from – perhaps people look first for ways that things might fail. We can draw upon many experiences of the open source software movement that would suggest such assumptions are poor. We can draw on successful examples of open collaboration in other areas of science, such as the Human Genome Project and the projects it has spawned, as well as examples in mathematics and astrophysics. This OSM paper addresses open source as applied to drug discovery, i.e. experimental, wet lab science in an area where we normally expect to need secrecy, for patents. It is based on the experience of 4-5 years of work and describes the first series examined by OSM. The paper argues strongly against these assumptions, since:

Many people contributed enthusiastically
The contributions came from a wide range of institutions, from Pharma through to Universities, from undergrads through to professors.
Those contributions, many of which were unsolicited, were of a high quality.
openscience  opensource  opennotebook  open  medicine 
october 2016 by juliusbeezer
10 Simple Rules for the Care and Feeding of Scientific Data | Authorea
This article offers a short guide to the steps scientists can take to ensure that their data and associated analyses continue to be of value and to be recognized. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more--but our goal here is not to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to "care for and feed" data, with some practical advice on how to do that. The set of Appendices at the close of this work offer links to the types of services referred to throughout the text. Boldface lettering below highlights actions one can take to follow the suggested rules.
opendata  openscience 
september 2016 by juliusbeezer
RT : Hooray! The ice bucket challenge funded an important paper! Unfortunately, you’ll have to pay for it.
july 2016 by juliusbeezer
: How did 's 1997 censure of — out? ”
january 2016 by juliusbeezer
Public-Friendly Open Science | Authorea
Scheme of a possible Public-Friendly Open Science bundle.

PFOS should be package in bundles containing papers that are reproducible, interactive and multilayered. Papers should contain all the information to reproduce the described research (including the main code and data). It should also allow the reader to interact with its content, for example through interactive figures. See here for a more detailed description of what the “Paper of the future” should look like.

The important point is that papers should also contain links to “supplementary” documents created for a larger audience. A good start is to include a draft of a press release, where the media can find the most relevant facts and a few quotes from the scientists, and a quick research summary for the layman, where the authors can tell the short story of their work to the general public.

As discussed in the description of the paper of the future, videos are also useful, complementary ways to communicate the results of the research. For example astronomers at Ohio State, when they submit a paper to arxiv, they accompany it by a simple YouTube video that explains the basic idea (they call it “Coffee Briefs”). Together with a quick summary of research, these scientists also get their faces out: this way colleagues can identify them easily at conferences and the public can finally see that scientists are “normal” people, helping to make science more approachable.
openscience  openness  sciencepublishing  video  arxiv 
november 2015 by juliusbeezer
BishopBlog: Who's afraid of Open Data
A move toward making data and analyses open is being promoted in a top-down fashion by several journals, and universities and publishers have been developing platforms to make this possible. But many scientists are resisting this process, and putting forward all kinds of argument against it. I think we have to take such concerns seriously: it is all too easy to mandate new actions for scientists to follow that have unintended consequences and just lead to time-wasting, bureaucracy or perverse incentives. But in this case I don't think the objections withstand scrutiny. Here are the main ones we identified at our meeting:
openness  opendata  openscience 
november 2015 by juliusbeezer
HyperCore Linux
Status - HyperOS is very new, recommended for early adopters only. You can npm install linux -g today to get HyperCore on OS X, but we are still working on additional CLI tools that incorporate the rest of the HyperOS components. Have an idea for a use case? You can chat with us in freenode/#dat or in gitter.

HyperOS is a set of components that make it easy to quickly download and run containerized software on top of version controlled data in a reproducible way without sacrificing performance.

It's made and maintained by the team that works on dat, a dataset version control tool. We build tools to improve scientific research reproducibility and working on ways to make container runtime tools accessible to scientific use cases like sharing and running version controlled code + data pipelines.
linux  opensource  openscience  database  replication 
october 2015 by juliusbeezer
Open Science | Innovation Policy Platform
open science has become an active area of policy development, both within the OECD area and beyond. Although recognising that open science is a broad concept that encompasses more than open access to research data and publications that takes place at all stages of research (see Glossary), this report aims to provide an analytical overview of recent open science policy trends, by focusing in particular on those initiatives to promote broad access to publicly funded research results, including both scientific publications and research data.
openscience  eu 
september 2015 by juliusbeezer
MMS: Error
NEJM claims public health exemption to Ingelfinger rule: So why isn't redundant
september 2015 by juliusbeezer
On radical manuscript openness | R-bloggers
The paper has benefited from an extremely public revision process. When I had a new major version to submit, I published the text and all code on github, and shared it via social media. Some of resulting discussions have been positive, others negative; some useful and enlightening, others not useful and frustrating. Most scientific publications almost exclusively reflect input from the coauthors and the editors and reviewers. This manuscript, in contrast, has been influenced by scores of people I’ve never met, and I think the paper is better for it.
open  openscience  sciencepublishing  editing  publishing 
august 2015 by juliusbeezer
Open Content Licensing: A Three-Step Guide for Academics
Aimed at the individual academic, this guide will enable you to make informed and purposeful decisions around licensing your work in line with international open access principles.
openaccess  open  openscience 
june 2015 by juliusbeezer
Impact of Social Sciences – It’s the Neoliberalism, Stupid: Why instrumentalist arguments for Open Access, Open Data, and Open Science are not enough.
“Big Data,” “Data Science,” and “Open Data” are now hot topics at universities. Investments are flowing into dedicated centers and programs to establish institutional leadership in all things related to data. I welcome the new Data Science effort at UC Berkeley to explore how to make research data professionalism fit into the academic reward systems. That sounds great! But will these new data professionals have any real autonomy in shaping how they conduct their research and build their careers? Or will they simply be part of an expanding class of harried and contingent employees- hired and fired through the whims of creative destruction fueled by the latest corporate-academic hype-cycle?

But in the current Neoliberal setting, being an entrepreneur requires a singular focus on monetizing innovation. PeerJ and Figshare are nice, since they have business models that less “evil” than Elsevier’s. But we need to stop fooling ourselves that the only institutions and programs that we can and should sustain are the ones that can turn a profit. For every PeerJ or Figshare (and these are ultimately just as dependent on continued public financing of research as any grant-driven project), we also need more innovative organizations like the Internet Archive, wholly dedicated to the public good and not the relentless pressure to commoditize everything (especially their patrons’ privacy)
scholarly  openaccess  opendata  openscience  politics  education 
april 2015 by juliusbeezer
Science in the Open » Blog Archive » Remembering Jean-Claude Bradley
Today I often struggle to sympathise with other people’s fears of what might happen if they open up, precisely because Jean-Claude forced me to confront those fears early on and showed me how ill founded many of them are...

In his constant quest to get more of the research process online as fast as possible Jean-Claude would grab whatever tools were to hand. Wiki platforms, YouTube, Blogger, SecondLife, Preprint servers, GoogleDocs and innumerable other tools were grasped and forced into service, linked together to create a web, a network of information and resources. Sometimes these worked and sometimes they didn’t...

in the hours after we heard the news [of his death] I didn’t realise the importance of preserving Jean-Claude’s work. I think its important to recognise that it was information management professionals who immediately realised both the importance of preservation and the risks to the record and set in motion the processes necessary to start that work. I remain, like most researchers I suspect, sloppy and lazy about proper preservation and we need the support of professionals who understand the issues and technical challenges, but also are engaged with preservation of works and media outside the scholarly mainstream if science that is truly on the web is to have a lasting impact. The role of a research institution, if it is to have one in the future, is in part to provide that support, literally to insitutionalise the preservation of digital scholarship.
archiving  openscience  opennotebook  sciencepublishing 
april 2015 by juliusbeezer
Fostering Open Science, Open Data & Reproducibility - NZ Commons
as the Commissioning Editor of GigaScience, a journal co-published by the BGI, the world’s largest genomics organisation, and the Open Access pioneer BioMed Central. GigaScience publishes open access ‘big-data’ studies from the entire spectrum of life and biomedical sciences, whose goal is to promote open science, transparency and reproducibility. The scope of GigaScience covers the issues producing and handling large-scale biological and biomedical data, and provides resources and a forum for data producers and the open science community.

At GigaScience, being a true Open Access journal, all our textual content (such as blogs, and open peer reviewer reports) is published under a CC BY 4.0 Attribution licence, and our data is CC0 — maximising its reuse and setting our content free in the commons. This has only allowed us to do great things
opendata  openaccess  openscience  database  journals 
february 2015 by juliusbeezer
Open Training for Open Science | OKF Open Science Working Group
This norm is not reflected in most current scientific practice, where knowledge dissemination is still largely based on a journal system founded in the 1600s, albeit now in digital format. Current evidence suggests that students are not prepared for change, for example a major study of 17,000 UK graduate students [4] revealed that students:

hold many misconceptions about open access publishing, copyright and intellectual property rights;
are slow to utilise the latest technology and tools in their research work, despite being proficient in IT;
influenced by the methods, practices and views of their immediate peers and colleagues.

While pre-doctoral training is just as important, the majority of open science training initiatives documented thus far have aimed at the early career research stage, including doctoral students.
openscience  education 
december 2014 by juliusbeezer
MoPad: openScienceCurriculum
Etherpad export of recent openscience curriculum
openscience  education  opennotebook 
december 2014 by juliusbeezer
Authorea | Network models to evaluate reproducibility in biomedical research or, The Future of Science
we envision a solution to break the loop. Consider a platform for storing, peer reviewing and sharing all the scientific work produced within a research institute. We are thinking of a network of science where nodes are single experiments, not entire papers. Each experiment should be meaningful, i.e. must provide a conclusion statement and a short description of the materials and methods (much like it is presented during lab meetings). The envisioned platform provides a key feature: the directional linking of published experiments. This forking feature is critical because it builds the network semantics by establishing where the rationale of an experiment comes from (and where it eventually leads). Network semantics are important because they generate a better proxy index for reproducibility, and thus quality, than the current impact factor. Such a reproducibility index can be calculated from node properties according to network theories or ad hoc metrics like the Fork Factor. Let’s call the envisioned platform a Semantic Experiment Network (SEN).
sciencepublishing  openscience  opennotebook  publon 
november 2014 by juliusbeezer
CDC: CDC Keyword
Open is a term used across an array of digital and networked projects and artifacts, from government data initiatives and online teaching materials to software code and digital publishing. While the term has been in use in the contexts of political theory (Popper, 1962a; 1962b), philosophy (Bergson, 1935) and general systems theory (Bertalanffy, 1960) for a long time, contemporary uses of openness are often indebted to the open source software practices of the 1990s and the distinct but related Free Software Movement which preceded it. In this context, open as ‘open source’ was understood as a particular mode of software development (cf. Raymond, 2000) underpinned by ‘permissive’ intellectual property licenses. This legal framework ensured access to the human readable ‘source code’ of a program, thereby allowing anyone to contribute to a software project or to start a new project based on the pre-existing code. Transformations that took place on the web from the early 2000s onwards – variously described as increased participation, collaboration, the flattening of hierarchies, sharing culture, meritocracy, user-generated content, produsage, crowdsourcing, or commons-based peer production – either drew inspiration from the practices of open source software or were retrospectively likened to it, and this has led to a proliferation things described as open. Openness now simultaneously works across legal, technical, organizational, economic, and political registers. It is a core guiding principle of several of the most powerful players on the web (including Google and Facebook) and is increasingly taken up by governments to describe their modus operandi in a world transformed by digital networks. The Digital Humanities, which is here one domain among others, is no different. This from the Digital Humanities Manifesto (2008): “the digital is the realm of the open: open source, open resources, open doors. Anything that attempts to close this space should be recognized for what it is: the enemy.”
open  openness  openaccess  opensource  openstandards  openscience  digitalhumanities  theory 
october 2014 by juliusbeezer
osmanuscript (OSCodefest ecology ms) - Google Docs
Example of collaborative science document using Google docs
september 2014 by juliusbeezer
Zotero | Groups > OSecology > Library
Nice example here of collaborative reference library of articles using zotero
openscience  tools  zotero 
september 2014 by juliusbeezer
thanks, don’t mind if we do. | Impactstory blog
With most big companies you could hand over your source code and your business plan and they still would not be a threat to you.
open  altmetrics  opensource  openscience 
june 2014 by juliusbeezer
Critically, when Galileo included the information from those notes in Siderius Nuncius (Galilei 1610), this integration of text, data and metadata was preserved, as shown in Figure 1. Galileo's work advanced the "Scientific Revolution," and his approach to observation and analysis contributed significantly to the shaping of today's modern "Scientific Method" (Galilei 1618, Drake 1957).

Today most research projects are considered complete when a journal article based on the analysis has been written and published. Trouble is, unlike Galileo's report in Siderius Nuncius, the amount of real data and data description in modern publications is almost never sufficient to repeat or even statistically verify a study being presented.
opendata  openscience 
april 2014 by juliusbeezer
Editorial Policies
Open Health Data publishes data papers, which provide a concise description of a dataset and where to find it. Papers will only be accepted for datasets that authors agree to make freely available in a public repository. This means that they have been deposited in a data repository under an open licence (such as a Creative Commons Zero licence), and are therefore freely available to anyone with an internet connection, anywhere in the world.

A data paper is a publication that is designed to make other researchers aware of data that is of potential use to them for scientific and educational purposes. Data papers can describe deposited data from studies that have not been published elsewhere (including replication research) but also from studies that have previously been published in another journal. As such the data paper describes the methods used to create the dataset, its structure, its reuse potential, and a link to its location in a repository. It is important to note that a data paper does not replace a research article, but rather complements it.
opendata  openmedicine  openscience  sciencepublishing  OASPA 
march 2014 by juliusbeezer
EU-funded data repository sitting alongside 25PB/year output of CERN (!)
opendata  openaccess  openscience  eu 
march 2014 by juliusbeezer
PLOS Clinical Trials: Publishing Clinical Trial Results: The Future Beckons
Nice overview of future of biomedical publishing, including prospects for publishing trial data.
medicine  science  sciencepublishing  openaccess  opendata  openscience 
january 2014 by juliusbeezer
Academia and Big Pharma United
What can we anticipate from this collaboration? It is definitely too early to say, but expectations are high for the center. We also realize, however, that this is a trial to see whether academic scientists and industrial scientists can work together efficiently given their very different orientations. Academic scientists are grounded in basic or translational research where discoveries lead the way, and industrial scientists inhabit a goal-oriented environment where key discoveries might be overlooked or obscured by the targeted search for another more specific end point. Combining scientists from these two very different research environments in a single center promises to be an interesting experiment in itself. The goal is that outcomes will exceed the solitary talents of each contributor.
science  openscience 
january 2014 by juliusbeezer
Believe it or not: how much can we rely on published data on potential drug targets? : Article : Nature Reviews Drug Discovery
With an average project duration of 6–12 months, numerous well-established cellular and in vivo models and several independent and often specialized laboratories that are involved in the projects with highly qualified scientists who are dedicated to target discovery, we feel confident that our data are quite reliable. It is important, however, to emphasize that we do not want to make the point that our experimental data are correct, whereas data from other groups are 'false'. We are not reporting fraud, but a lack of reproducibility. In fact, to our knowledge, none of the studies that our internal projects were based on was retracted or suspected to be flawed. However, with reasonable efforts (sometimes the equivalent of 3–4 full-time employees over 6–12 months), we have frequently been unable to reconfirm published data.
sciencepublishing  science  scholarly  openscience 
january 2014 by juliusbeezer
Academic bias & biotech failures | LifeSciVC
Venture capitalist runs into limitations of current science process:

"There’s a rich literature on the “Pharma bias” in publications (e.g., Pharma conflicts of interest with academics, clinical trial reporting); in the past 15 months, 63 peer-reviewed articles talk about pharma industry bias according to PubMed.

But what about academic bias? Or the lack of repeatability of academic findings? I couldn’t find a single paper in PubMed over the past few years."
science  sciencepublishing  openaccess  opendata  openscience 
january 2014 by juliusbeezer
The one true route to good science is … | Dynamic Ecology
The usual form is to attack some now trendy but supposedly horrendous version of science and then mildly conclude that the way the author does science is the only really good way to do science. In the latest version of this archetype, two esteemed ecologists, David Lindenmayer and Gene Likens (hereafter L&L) penned an almost vitriolic piece attacking “Open-Access Science”, “Big Science” and I don’t know what all else (that I’m going to call for short hand “new-fangled ecology” for now)*.
opendata  openscience  openaccess  sciencepublishing  database 
november 2013 by juliusbeezer
Open and Shut?: Let’s be open about Open Access
Richard Poynder goes in search of the shadowy author of a blog hosted at "" who seems unnecessarily biased towards a world view that completely excludes discussion of Green OA. I point him to the sourcewatch wiki.

[update 19/4/17: interestingly now only a comment by Harnad remains below that post, with two evident spams. But it looks like Poynder has deleted mine nevertheless]
openscience  openaccess  sciencepublishing  scholarly  blogs  transparency  internet  anonymity  dccomment  commenting 
october 2013 by juliusbeezer
Data-sharing: Everything on display : Naturejobs
Wolkovich is one of a number of early-career researchers who are enthusiastically posting their work online. They are publishing what one online-repository founder calls small data — experimental results, data sets, papers, posters and other material from individual research groups — as opposed to the 'big data' spawned by large consortia, which usually employ specialists to plan their data storage and release.
opendata  openscience  repositories  database 
august 2013 by juliusbeezer
Precision Oncology: An Overview
Notice how this proposed technique is unimaginable without open informatic technique.
"Conceptually, the implementation of genomics-driven cancer medicine might seem straightforward (Fig 1): first, characterize the genomes of patients' tumors using state-of-the-art technologies; second, filter the genomic data through a knowledge base of existing and emerging anticancer drugs; and third, present an annotated list to the treating oncologist that can be incorporated into clinical decision making. However, multiple challenges must be addressed to bring this ambitious goal to fruition."
[JCO is classed as significant 'Emerging journal' at , which logs the decline of IF since the '80s]
medicine  openaccess  openscience 
june 2013 by juliusbeezer
manuscript reviews on github?
I was recently impressed to learn of Trevor Bedford’s strategy of seeking pre-approval for posting his reviewer’s comments as Github issues. Beyond providing links to the data and source-code, I generally don’t advertise the open science nature of papers I submit – I guess I assume that if the reader or reviewers care, it should be easy enough for them to discover it. Consequently I am usually immediately frustrated to realize that upon receiving my reviews I have to create a second, private repository for the review material, our replies to reviewers, etc., as I don’t have permission to disclose that information. 1 I have recently stumbled across several examples of authors publishing to the web anonymous reviews they have received. Though anonymous, I feel the practice potentially murky without explicit permission, so I would appreciate any insight others have on this.
openscience  peerreview 
june 2013 by juliusbeezer
Negative results in medical research and clinical trials – an interview with Ben Goldacre | Discussions – F1000 Research
Goldacre outlines his prescription for publication of clinical trial results: "We are asking for four things [to lessen publication bias]: 1) recognition the problem exists; 2) all trials on trial register; 3) summary report of all trials to be published; 4) release of ~1000 page Clinical Study Report (CSR) to public domain.
openscience  medicine  ebm 
june 2013 by juliusbeezer
What Do We Mean By Small Data | Open Knowledge Foundation Blog
“Small data is the amount of data you can conveniently store and process on a single machine, and in particular, a high-end laptop or server”
openscience  opendata 
may 2013 by juliusbeezer
Francois Grey’s 7 myths of citizen science | Po Ve Sham - Muki Haklay's personal blog
He suggest them as point of views that are expressed by scientists when citizen science is suggested to them. They are:

It doesn’t produce real science
It doesn’t work for my science – it is too complex to engage people in it
Nobody will be interested in my area of science
You can’t trust the results from ordinary people if you involve them in something other than automatic processing
Volunteer computing is energetically hugely wasteful when compared to computer clusters
It doesn’t really engage people in science
One day we will run out of volunteers
science  openscience 
march 2013 by juliusbeezer
One of the reasons I do “open” work is that I think, in the sciences, it’s a philosophical approach that is more likely to lead to that epistemic transformation. If we have more data available about a scientific problem like climate change, or cancer, then the odds of the algorithms figuring something out that is “true” but incomprehensible to us humans go up.
I work for “open” not because “open” solves a specific scientific problem, but because it increases the overall probability of success in sensorism-driven science. Even if the odds of success themselves don’t change, increasing the sample size of attempts will increase the net number of successes. I have philosophical reasons for liking open as well, and those clearly cause me cognitive bias on the topic, but I deeply believe that the greatest value in open science is precisely the increased sample size of those looking.
I also tend to think there’s a truly, deeply political element to enabling access to knowledge and science.
open  openscience  openaccess  openness  philosophy 
march 2013 by juliusbeezer
PeerJ – the science journal we need and deserve – We Beasties
PeerJ has built a new open access journal, following the likes of the Public Library of Science (PLoS) and the much more recent journal eLife. However, where PLoS and eLife seem to be trying to build classic journals with an open access (OA) model, PeerJ seems to be trying to innovate on everything about the publishing process, from open peer review, to the integration of altmetrics, to the simple idea of publishing articles as they come in (like a blog) rather than in separate issues.

They’re even planning to launch a pre-print server, which means that scientists will be able to upload their work to establish primacy (physicists have had something like this for a while), that can serve as an OA source, even for papers that eventually get published in a non-OA journal.
openaccess  openscience 
february 2013 by juliusbeezer
The Kitware Blog - If an Experiment Fails in a Forest, Does Anyone Hear?
There are many reasons why Open Science is a good thing. For some it's a moral argument that stresses sharing the results of (usually publicly funded) scientific research with society, preventing fraud through transparency, and benefiting teaching through the use of open materials. Others see the growing complexity and challenges of science as demanding collaboration; so that larger teams with their wider expertise can be brought to bear. Clearly there are personal benefits too; as Steve Lawrence has shown there is a correlation between sharing the results of research and the number of paper citations. Many innovators and entrepreneurs are also fond of Open Science because sharing technology can accelerate the innovation process and empower small business by reducing intellectual rights barriers. And there are a lot of us that just like to have fun--the communities and relationships that form in an open environment make the hard work of science that much more enjoyable.
february 2013 by juliusbeezer
Getting Genetics Done: Stop Hosting Data and Code on your Lab Website
Excellent article on the impermanence of web resources: even in a scientific setting 72% lost after a few years, only one third of corresponding authors replied to email.
"It's a fact that most of us academics move around a fair amount. Often we may not deem a tool we developed or data we collected and released to be worth transporting and maintaining. After some grace period, the resource disappears without a trace."
archiving  openaccess  opendata  openscience 
january 2013 by juliusbeezer
Open Science and Access to Medical Research | Guest Blog, Scientific American Blog Network
The idea of open science goes beyond merely providing public access to published scientific articles because it also includes offering access to the original research data. This would permit fellow researchers to help evaluate and analyze the results, so that the broader scientific community as well as the public can weigh in on the interpretation of the scientific findings. This aspect of open science likely does qualify for being a true paradigm shift, because it will require that we think of ourselves as part of research communities and usher in “networked discovery”... “Consumer Reports” in the US or “Stiftung Warentest” in Germany routinely test consumer products for their quality and safety, and report them in a manner that members of public can understand the results... One could envision similar institutions that evaluate the biomedical research data and can give solid advice to non-specialists.
openscience  medicine  science 
september 2012 by juliusbeezer
Boops boops: Self publishing "failed" thesis chapters on Figshare
Despite the fact that I felt this chapter was not of the expected quality, rigour, and interest required by a peer-reviewed journal, there are still elements I think would perhaps be useful in the public domain (particularly to aquarists). More importantly though, by putting it in the public domain, an editor, a reviewer, or even myself, doesn't have to make that subjective decision. This is a bit like the PLoS ONE model of publishing, expect without the all-important peer review stage to check that the science is sound. Seeing as I don't really have any strong conclusions other than "more work is required", I can't see much of a problem there.
september 2012 by juliusbeezer
Can we make accountable research software? | Byte Size Biology
When code is written in my lab, it is mostly hypothesis-testing code. Or mucking-about code. Or “let’s try this” code. We look for one thing in the data. Then at the other. We raise a hypothesis and write code to check it. We want to check it quickly so that, if the hypothesis is wrong, we can quickly eliminate it, but if it appears to be right, we will write more code to investigate the next stage, and the one after that.

This practices of code writing for day-to-day lab research are therefore completely unlike anything software engineers are taught. In fact, they are actually the opposite in many ways, and may horrify you if you come from a classic software-industry development environment. Research coding is not done with the purpose of being robust, or reusable, or long-lived in development and versioning repositories. Upgrades are not provided and the product, such as it is, is definitely not user-friendly for public consumption.
openscience  software 
september 2012 by juliusbeezer
NeuroDojo: Why I published a paper on my blog instead of a journal
TL;DR: I had a research project that has been sitting for more than a decade without finding a home in a scientific journal, so I decided to post it on my blog instead as an experiment.

[Biologist twists knickers about publishing half-baked data online]
openaccess  openscience  peerreview 
september 2012 by juliusbeezer
Protect yourself during the replicability crisis of science « Alex Holcombe's blog
Posits need for open science as a "defensive measure" to counter "replicability crisis."
3 key actions:
1) post design in advance of study
2) post raw data as it is generated
3) post pilot and interim results as they arise

"The proponents of open science are sometimes accused of being naifs who don’t understand that secretive practices are necessary to avoid being scooped, or that sweeping inconvenient results under the rug is what you got to get your results into those high impact-factor journals. But the lay of the land has begun to change."
september 2012 by juliusbeezer
Welcome | The Synaptic Leap
Open sharing of knowledge of the kind of things that would normally be concealed in deepest secret in the proprietary bowels of big pharma: "An open, collaborative research community will find new ways to do science, answering questions that current institutions find difficult or impossible. The Synaptic Leap's mission is to empower scientists to make the dream a reality. Diseases found exclusively in tropical regions predominantly afflict poor people in developing countries. The typical profit-driven pharmaceutical economic model fails with these diseases because there is simply no money to be made. However, the very fact that there's no profit incentive to research these diseases makes them perfect candidates for open source style research; there's no profit incentive to keep secrets either."
openscience  openaccess  crowdsourcing 
july 2012 by juliusbeezer
Open Notebook Series: What is an Open Notebook? (by @thescienceofant) | The Science Exchange Blog
Ideally, every scientist could maintain an open notebook in real-time which would encompass all aspects of their research. But many fears about dealing with complete open access, conflicts with patent applications and publications, and online data overload and hamper this movement. To combat this, practitioners (like myself) encourage any form of open notebook science, even if that means uploading some information for a project from many years ago that never saw the light of day.

The goal of this practice is to enhance research. Through open notebooks, scientists would no longer need to repeat the mistakes of other scientists, have no need to sift through pages of an unorganized paper notebook, have access to raw data from papers, and much more.

In the coming weeks I’ll walk through the various aspects of open notebook science. I’ll provide examples of different types of notebooks, and different notebooking platforms. I’ll provide tips for maintaining an excellent notebook in the online environment. And I’ll present ways that you can enhance your notebook to do just about anything you’d like.
opennotebook  openscience  science  scholarly 
june 2012 by juliusbeezer
Soapbox Science: Tool Tales: figshare
Nice personal account of one researcher's use of online tools to share work at every stage of the scientific process.
openscience  opennotebook 
april 2012 by juliusbeezer
Daily Life in an Ivory Basement : /apr-12/replication-i.html
"I believe in replication and reproducibility, and wanted to see how tough it was to actually do something like this. (It's a good deal above and beyond what most bioinformaticians do.)

Perhaps the strongest reason is that our group has been bitten a lot in recent months by irreplicable results."
science  tools  software  openscience 
april 2012 by juliusbeezer
Frontiers | Open Peer Review by a Selected-Papers Network | Frontiers in Computational Neuroscience
A selected-papers (SP) network is a network in which researchers who read, write, and review articles subscribe to each other based on common interests. Instead of reviewing a manuscript in secret for the Editor of a journal, each reviewer simply publishes his review (typically of a paper he wishes to recommend) to his SP network subscribers.
peerreview  openscience 
march 2012 by juliusbeezer
Unilever Centre for Molecular Informatics, Cambridge - What are the formal restrictions on text-mining? « petermr's blog
#oscar4 #okfn #pantonpapers

A little while ago I suggested that we create whitepapers (“Panton Papers”, ) to help our development of open science. We’ve come up with some titles and I’ve drafted one on text-mining . There’s now a useful response from Todd Vision on the Open-science discussion list ( )

Peter’s draft whitepaper on text-mining is badly needed and nicely put. I was particularly interested in this passage:

“The provision of journal articles is controlled not only by copyright but also (for most scientists) the contracts signed by the institution.
text  text_tools  openaccess  open  openscience 
april 2011 by juliusbeezer
PLoS Medicine: A Medical Journal for the World's Health Priorities
PLOS editors, among them Gavin Yamey, state their priorities: reminiscent of BMJ mission statements of the late nineties. Good stuff: something to believe in.
openaccess  openscience 
july 2010 by juliusbeezer
Truly Open Data - O'Reilly Radar
I'm kicking myself because I've been taking far too narrow an interpretation of "an open source approach". I've been focused on getting people to release data. That's the data analogue of tossing code over the wall, and we know it takes more than a tarball on an FTP server to get the benefits of open source. The same is true of data.
sciencepublishing  internet  opensource  openscience  opendata 
march 2010 by juliusbeezer
When Scholarly Publishers Reduce Author Rights in the Face of Open Access Initiatives – Slaw
Wiley-Blackwell challenge "Don't ask, don't tell" deceit which has maintained pre-print academic archives until now.
sciencepublishing  openscience 
november 2009 by juliusbeezer

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