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+1 for Open Access, Open Data, Open Source and Standards, Citizen Science, and open notebooks, blogs, and science online.

+1 for reproducibility, extensibility, accessibility, transparency; for science done like the Web and at the speed of the Internet.

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Discussion  - 
 
 
A stumbling block for  #openscience  is the need to anonymise participant identities before posting their data. While many people have written about how they integrate open science into lab practices, I haven't seen much on anonymising data.

My R program anonymises my participants' data using an encryption key that I read in from a second file. This allows me to keep a project's experiment code, analysis code, and raw data all in a single git repository that github keeps track of and makes available online.  

The "loadAnonymiseSaveData.R" https://github.com/alexholcombe/MOTcircular/blob/master/dataRaw/loadAnonymiseSaveData.R file finds all the raw data files and de-identifies them when combining them. The participants are still kept separate but they are assigned new names using an encryption key read from a separate, non-public file (its name is listed in .gitignore so that git won't archive it). The use of an encryption key means the participants can be re-identified later by those who are given the key, so I can track things back all the way to the original untouched files generated by the experiment. A full audit trail like this is important for checking for errors (and fraud).

After this anonymisation step, the R files in my analysis folder https://github.com/alexholcombe/MOTcircular/tree/master/analysis analyse the anonymised data file, and all this can be viewed or downloaded by anyone, even while I am still collecting data.

Obviously, if you aren't ready to use git, this isn't going to help you. Software Carpentry (https://software-carpentry.org/) provides free classes to bring researchers up to speed.
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Open Access  - 
 
 
Users of #openaccess research speak.

These stories volunteered by the users of our open-access repository are the best evidence that OA serves real people with real needs, that OA meets unmet demand, that the demand unmet by conventional journals includes academic and non-academic readers, and that for scholars who publish in conventional journals, deposit in an OA repository is not a superfluous extra step but a social and academic gift, even a responsibility, for which uncounted readers will be deeply grateful. 

For scholars who publish in conventional journals and want to reach everyone who could benefit from their work, or everyone wishing to read, cite, apply, extend, or build on it, these stories are the best incentive to deposit that work in an OA repository.

"The Harvard Library Office for Scholarly Communication is very pleased to launch Your Story Matters, a new site featuring stories and anecdotes from users of DASH (Digital Access to Scholarship at Harvard), Harvard's open-access repository. With nearly 1,000 user stories from 83 countries, "Your Story Matters" offers moving evidence that DASH readers are deeply grateful for barrier-free access to Harvard research. Since DASH launched in 2009, users have downloaded its articles 4.6 million times, from every country on Earth. Even the subset of users who volunteered stories to DASH includes a remarkable variety of people <http://goo.gl/UE1bVl>, from faculty and students at institutions unable to afford the high prices of scholarly journals, to non-academics such as physicians, nurses, clergy, writers, journalists, public officials, social workers, political activists, retirees, and ordinary citizens in countries that try to limit what people may read. The visual interface of "Your Story Matters," and the easy way it supports rapid scrolling through stories from different countries, make vivid who is using DASH, from where, and with what impact...."

#oa #openaccess  
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Open Data  - 
 
Any #rstats  neurobiologists out there? A call for neurobiology data sources and discussions in the +rOpenSci forum, http://discuss.ropensci.org/t/neurobiology-data/112
I met a neurobiology data analyst person the other week and he informed of many potential places to get open neurobiology data. I started a repo at https://github.com/ropensci/neurobio to collect potential data sources we could interact with from R, and have any discussions about the subject area. We'd love any thoughts on this study area - what data sources do people use a lot that they'd like to get programmatically? What can we do to help ...
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Open Access  - 
 
 
Go Dutch!

From Paul Jump in the +Times Higher Education​​​: "Dutch universities have vowed not to soften their groundbreaking demands for publishers to permit all papers published by their academics to be made open access for no extra charge....Gerard Meijer, president of Radboud University and one of the lead negotiators for the Dutch universities, said that in addition to preserving access to their subscription journals, the universities wanted publishers to permit all future articles whose corresponding author has a Dutch affiliation to be published on an open access basis for no extra charge. He said universities were also unwilling to tolerate any more above-inflation price rises...."

#oa #openaccess
Institutions ‘unbending’ on fee-free demand as talks with Elsevier resume
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Open Access  - 
 
 
More on how OA meets unmet demand.

Here's a choice fact from 2012 that I noted, forgot, and just rediscovered from my notes. From +Jennifer Howard in the +Chronicle of Higher Education

"Every year, JSTOR said, it turns away almost 150 million individual attempts to gain access to articles."

http://chronicle.com/blogs/wiredcampus/jstor-tests-free-read-only-access-to-some-articles/34908

There are two reasons to remember that OA meets unmet demand. First, it means that OA fulfills the purposes of both authors and readers. Many newcomers think OA merely fulfills the purposes of readers. Second, it corrects a common false assumption of scholarly authors, and a common cynical assertion of some publishers, namely, that everyone who wants access already has access. 

#oa #openaccess #jstor
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Is that ALL? I probably generate about 100 myself. JSTOR's page layout haunts my nightmares.
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Today's big announcement is that Max Planck Society Authors can publish FREE with us. 

"The Max Planck Society (MPG), an independent, non-profit German research organization and ScienceOpen, the research + Open Access publishing network based in Germany and the USA, have signed an agreement (official PR) that will allow authors affiliated to MPG as members of one of its 82 institutes and research facilities, unlimited free publication of posters and research articles in 2015".

Yoda says: Happy Holidays you shall have. Stay open in 2015.

http://blog.scienceopen.com/2014/12/max-planck-authors-publish-free-in-scienceopen/
http://about.scienceopen.com/wp-content/uploads/2014/12/SO_PR_Max-Planck-Announcement-22-Dec-2014.pdf
https://www.facebook.com/maxplancksociety
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Open Access  - 
 
 
New OA mandate from the US Agency for Healthcare Research and Quality (AHRQ).

The Agency for Healthcare Research and Quality (AHRQ) just became the second US federal agency to adopt an OA mandate under the Obama White House directive of February 2013. 
http://www.ahrq.gov/funding/policies/publicaccess/index.html

The first such OA mandate came from the Department of Energy (DOE). For the reasons why I found it deeply flawed, see my blog post from August 2014. 
https://plus.google.com/+PeterSuber/posts/ZHRXEvLoq4n

On the plus side, the AHRQ avoids one of the biggest mistakes of the DOE policy. AHRQ will use OA repositories independent of publishers. As much as it can, the DOE will use publisher-hosted OA. AHRQ will disregard CHORUS, while DOE will depend on CHORUS. 

On the minus side, the AHRQ shares one of the biggest mistakes of the DOE policy. It is silent on open licensing and reuse, even though the White House guidelines explicitly require agency policies to "maximize the potential for...creative reuse." (To be more precise, the AHRQ wants reuse for data, but is silent on reuse for articles.)

We know that the White House approved the DOE policy. I can't tell yet whether it has approved the AHRQ policy. If it has, that will confirm the conclusion that +The White House will not enforce its own guidelines. If it hasn't yet approved the new policy, and is still deliberating, then there's hope that public comments can persuade it to send agency policies back to the drawing board to comply with the reuse requirement.

Here's my quick take on the AHRQ policy strengths and weaknesses:

Strengths
* The AHRQ policy does not rely on CHORUS or publisher-hosted OA. For articles, it will use PubMed Central. For data, it will outsource to a still-unnamed commercial repository.
* It covers data as well as articles.
* It wants data to be freely available at time of publication, without embargo.
* It adopts the NIH mechanism to enforce the deposit requirement, including the potential withholding of funds to non-compliant grantees.

Weaknesses
* It's silent on the timing of the deposit of articles. For example, it doesn't require deposit at the time of acceptance or before the time of publication.
* It's silent on open licensing and reuse.

The AHRQ permits embargoes up to 12 months. That's a weakness, but unfortunately it's one allowed, even encouraged, by the White House guidelines. 

For background, see the Obama White House directive itself from February 2013.
http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf

Also see my March 2013 article on the Obama directive and FASTR. 
http://dash.harvard.edu/handle/1/10528299

Also see the AHRQ home page.
http://www.ahrq.gov/

#oa #openaccess #ahrq  
This document is the Agency for Healthcare Research and Quality's (AHRQ's) plan for establishing a policy for public access to scientific publications and scientific data in digital format resulting from AHRQ funding.
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A new +Stack Exchange Q&A site on open science is under way. Commit to participate to take it to beta. 
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Discussion  - 
 
Are the +World Health Organization (WHO)​ advocating for +Creative Commons​ licensing and #openscience in #Ebola and #globalhealth research? They very well should.
 
World Health Organization wants to open up research into Ebola and other diseases of the global south.

From the "Follow-up of the report of the Consultative Expert Working Group on Research and Development: Financing and Coordination" by the Director-General of the +World Health Organization (WHO), December 19, 2014:
http://apps.who.int/gb/ebwha/pdf_files/EB136/B136_30-en.pdf

"The focus of the fund would be the development of effective and affordable health technologies related to type III and type II diseases and the specific research and development needs of developing countries in relation to type I diseases, taking into account the principles formulated by the Consultative Expert Working Group on Research and Development: Financing and Coordination, namely delinkage of the delivery price from research and development costs, the use of open knowledge innovation, and licensing for access."

For the definitions of type I, II, and III diseases, see this WHO doc from 2012:
http://www.who.int/phi/3-background_cewg_agenda_item5_disease_types_final.pdf

"Type I diseases: are incident in both rich and poor countries, with large numbers of vulnerable populations in each. Type II diseases: are incident in both rich and poor countries, but with a substantial proportion of the cases in poor countries. Type III diseases: are those that are overwhelmingly or exclusively incident in developing countries."

Now if only we could see some definitions of "open knowledge innovation" and "licensing for access". Does this mean open access under CC-BY or CC0? If so, it would help to say so. If not, it would help to spell out the restrictions on life-saving research that WHO is willing to accept.

Here's a WHO gloss on "open knowledge innovation" from another 2012 doc:
http://www.who.int/bulletin/volumes/90/5/12-105460/en/

"[O]pen knowledge innovation: precompetitive research and development platforms, open source and open access schemes, and the utilization of prizes, in particular milestone prizes."

#oa #openaccess #ebola #who #south
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Open Access  - 
 
 
ArXiv racing toward the one million mark.

Today arXiv.org has 999,848 eprints on deposit. If you care about major open-access milestones, or if you just like seeing odometers roll over to large round numbers, watch in the next day or two for its one-millionth deposit. Kudos to +Paul Ginsparg and the arXiv team for this achievement. Thanks to their work, physics is the field with the highest level and longest history of OA archiving. For the same reasons, in physics, researchers lead and publishers follow. (For example, publishers accept submissions from arXiv, host their own mirrors of arXiv, and through SCOAP3 are moving to gold OA rather than trying to derail green OA.) For the same reasons, arXiv shows that green OA can rise to roughly 100% in a field without harming incumbent publishers. ArXiv is an existence proof that OA can become the default in a field without waiting for publisher permission, market shifts, institutional policies, or legislation. It just takes existing infrastructure and the willingness of researchers to follow their own interests. 

#oa #openaccess #arxiv
We gratefully acknowledge support from the Simons Foundation and member institutions. arXiv.org. Login. Search or Article-id. (Help | Advanced search). All papers, Titles, Authors, Abstracts, Full text, Help pages. Open access to 999848 e-prints in Physics, Mathematics, Computer Science, ...
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The OSM Christmas Top 10 list. In the grand tradition of making lists towards year's end, here's the Top 10 List of molecules most needed right now. Any better ideas? Please suggest below. If you'd like to make any of these in the lab, and have the molecules tested, you're free to do so and be included on the paper that will come out of that work.
Which molecules to make next in Open Source Malaria Series 4? The full reasoning is below. The executive summary is that OSM needs these ten molecules: OSM Christmas Top Ten. And if you'd like to synthesise them yourself (open source only please), or suggest better ones, you're free to do so.
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