science

Doubling down on Markdown for science

Puneet Kishor, June 10th, 2013

email thread with attachments Scientific authoring workflow is a beast. You keep notes on paper (hopefully, a notebook, and not just loose pages), in word-processing documents unhelpfully named “notes” followed by “notes1,” “notes2″ or worse, “notes_old,” “notes_old1.” You manage your bibliography on your desktop or on the web, you have a directory folder full of images, charts, photos and other media, and you collaborate with your co-authors by emailing attachments back and forth.

Sooner or later you start doubting your sanity but you soldier on. Finally you publish your paper, heave a sigh of relief, and move on, thereby ensuring your data can’t be reused and your work can’t be reproduced easily.

Several coders, designers, scientists, and publishers met at PLOS to brainstorm toward a better, more modern way. The Markdown for Science workshop was organized by Martin Fenner and Stian Håklev and supported by a 1K Challenge Grant from FORCE11.

mdsci13 groupideas
Photos by Puneet Kishor, CC0 PD Dedication

While a lot of good ideas were generated, we have a long way to go. Keep an eye on this project, and better yet, pitch in with your ideas and code. Together we can tame this beast.

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PLOS launches open access science award program

Timothy Vollmer, May 1st, 2013

asap banner

Today the Public Library of Science announced the Accelerating Science Award Program (ASAP). The award program seeks nominations of individuals who have used, applied, or remixed scientific research — published through open access — in order to realize innovations in science, medicine, and technology. The goal of ASAP is to build awareness of and encourage the use of scientific research published through open access. Major sponsors include the Wellcome Trust and Google.

Three winners will each receive $30,000. The nomination period opens today and runs through June 15, 2013. Potential nominees may include individuals, teams, or groups of collaborators -– such as scientists, researchers, educators, social services, technology leaders, entrepreneurs, policy makers, patient advocates, public health workers, and students -– who have used scientific research in transformative ways. The winners will be announced in Washington, DC, in October 2013 at an Open Access Week event hosted by SPARC and the World Bank.

Creative Commons is a supporter of ASAP, along with several other library organizations, publishers, and research organizations.

For more information, including the full details of the ASAP program, nomination process, and the award specifics, go to http://asap.plos.org/. For program rules visit http://asap.plos.org/nominate/rules/.

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Why Open Science Training matters

Puneet Kishor, March 5th, 2013

Open Science Training

Sophie Kershaw at CC HQ

Hanging around with our own kind, we in the open science community might get lulled into thinking that everyone out there thinks like us. In reality, most scientists actually do science instead of worrying about whether or not it is open. However, even though some of their practices align with open science objectives, there is much more that can be done proactively to engender an open commons of science.

Sophie Kershaw, doctoral student in computational biology at University of Oxford, came up with the idea of injecting Open Science Training in formal curriculum, and teaching young scientists about Open while they are still young and learning about the scientific method, as part of her Open Knowledge Foundation supported Panton Fellowship. In Sophie’s words:

As the Open Science movement gathers pace, we are seeing developments in policy and infrastructure to support the transition of academia towards Open practices. Despite this, there is a considerable lag in awareness within the academic community itself – many researchers either haven’t heard about Open, or know the term but don’t know how to put it into practice! From a show of hands on the first day of my Open Science Training Initiative (OSTI), only ONE grad student out of 43 had heard of open science. It is now time for us all to step up our efforts in educating our academics in licensing, open access and data management, preferably through provision of pre-doctoral training. Our first research group plays a huge role in shaping our research outlook, but this leaves us with a huge variability in the level of awareness that students develop. Some will pitch up in a very forward-thinking group, where licensing, collaboration and data archiving is the order of the day, while others are left without this kind of information. Pre-doctoral training will ensure continuity of provision for ALL our science grads, enabling them to make their own decisions with confidence.

This kind of practical intervention delivered right to young scientists sounds like a great idea, and as Sophie says, reactions to the first edition of OSTI seem to confirm that:

Students from the inaugural OSTI came out strongly in favour of receiving training in licensing and engaging in debate on development of the publication process: furthermore, they’ve shown that while lectures are handy, hands-on experience is the best way to learn about how to license, how to release data, how to communicate science. We need to emphasize delivery of a coherent research story – comprising appropriately licensed data, code and writing – rather than merely the traditional written report. We need to make our young researchers see themselves as research users as much as research producers. Over time, this should help our newest grads deliver verifiable, reproducible research with vast potential for further development and scientific impact.

The Open Science Training Initiative is not an idea with immediate returns. Instead, it is for bringing about long-term change so the next generation of scientists and beyond proactively default to open. There are challenges ahead, such as creating right formats for different conditions and audiences, finding right partners who would incorporate OSTI in their courses, and scaling to reach the next generation of scientists all over the world. But, it is an idea we consider worth supporting, because the potential returns are lasting in nature.

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The Net Works Effect: Open Data Day 2013

Puneet Kishor, February 22nd, 2013

There are many ways we can measure the effect of the work we do — count the number of objects licensed with CC licenses, count the number of users who have used CC licenses, count the number of works created by reuse of works licensed with CC licenses, perhaps many other ways. But the one that is most immediately visible, and most satisfying, is seeing events of spontaneous openness appear as is for the international celebration of Open Data Day taking place tomorrow, February 23. Well, perhaps not so spontaneous, because organizing events takes planning, work, contacts, brainstorming, publicizing, and more.

Our own Billy Meinke is organizing an event at the CC HQ in Mt. View, and has also written more on the event here and around the world in a guest blog post on PLOS. Check it out, organize an event, or attend one near you. Heck, attend one far away by joining in over the web where possible. After all, that is how the net works.

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PLOS and figshare make open science publishing more open

Puneet Kishor, January 31st, 2013

PLOS and figshare announced a partnership earlier today that will allow authors publishing in PLOS journals host their data on figshare. The authors would also benefit from the visualization capabilities that figshare provides right in the browser alongside the content. This partnership symbolizes all that is good about a healthy scientific publishing process that is enabled by innovative thinking aided by open licensing tools from Creative Commons.

When PLOS launched ten years ago, everyone involved could only hope for the kind of success it has seen in promoting open access publishing. Now with seven journals, six Currents sections, a network of blogs and new ways such as hubs and collections to organize content post-publication, PLOS spans a range of options from very selective to relatively inclusive. PLOS is the undisputed leader in the open access publishing space, and everything published by PLOS is under a CC license. But PLOS is constantly thinking of new ways to make the publishing process better.

John Chodacki, Director of Product Management at PLOS: “We know that Supporting Information acts as a container for valuable resources and data, but can remain relatively hidden from readers. With our partnership with figshare we are opening this data up to PLOS readers and showcasing its value.”

figshare is much younger. Founded by Mark Hahnel, a young scientist frustrated with the stunted mechanism for data sharing, figshare also adopted a blanket open licensing policy based on CC licenses and public domain dedication, and made it easy to upload, visualize and share data.

Mark says, “The common goal of PLOS and figshare for open access to research are connected by the liberal licensing of content, giving authors control over their outputs. Without the standards set out by Creative Commons, partnerships such as this would be much less achievable. Long may it continue as the academic space moves into new ways of disseminating research”.

Both PLOS and figshare leverage the internet to the fullest giving scientists a better way to publish research results and data. This directly promotes CC’s vision of realizing the full potential of the Internet — universal access to research and education, full participation in culture — to drive a new era of development, growth, and productivity.

By complementing each other, PLOS and figshare help the entire scientific process take another step toward being truly open. They are shining examples of leveraging the open licensing and public domain dedication tools created by Creative Commons. We wish them continued success and a future full of innovations we hope will continue to surprise and delight us.

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New Zealand Open Data Conference

Puneet Kishor, December 22nd, 2012

As research communities worldwide look for new ways to make the scientific process and its data and results more open and participatory, New Zealand is showing us how it is done.

In July 2010, The New Zealand Government Open Access and Licensing framework (NZGOAL) approved by the Cabinet provided guidance for agencies to follow when releasing copyright works and non-copyright material for re-use by others. NZGOAL seeks to standardise the licensing of government copyright works for re-use via Creative Commons New Zealand law licences and recommends the use of ‘no-known rights’ statements for non-copyrighted material.

Then in August 2011, the Declaration on Open and Transparent Government was also approved by the Cabinet whereby the government committed to actively release high value public data “to enable the private and community sectors to use it to grow the economy, strengthen the social and cultural fabric, and sustain the environment… to encourage business and community involvement in government decision-making.”

And earlier this month in December 2012, a report of the Education and Science Committee presented to the House of Representatives of the 50th Parliament an Inquiry into 21st century learning environments and digital literacy. Among its recommendations were that the Government:

  • review the intellectual property framework for (NZ) education system to resolve copyright issues that have been raised, including considering Creative Commons policy.
  • consider the advantages and disadvantages of whether all documentation produced by the Ministry of Education for teaching and learning purposes should be released under a Creative Commons licence.

In keeping with this spirit, a group of researchers committed to bringing an Open Research conference to Australia and New Zealand are organizing a three day event February 6-8, 2013 in Auckland.

The purpose of this conference is to explore new, open models of research that speed up the effective transfer of research results and improve economic, environmental and social impacts. A growing community of researchers around the world are investigating new commercial and academic models to enhance the reach of their research. These new ways of doing research openly are akin to changes happening in the IT and business world, where open innovation has enabled people to achieve more together than they ever could alone.

Creative Commons plays a key role in promoting openness in science. Events such as this one in Auckland demonstrate the concern about open science that the community shares with Creative Commons. In the end, only good things can come out of openness, sharing and broad participation. Creative Commons is very pleased to see this event take place, and wishes it utmost success.

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Introducing the CC Science Advisory Board

Puneet Kishor, November 16th, 2012

Creative Commons has formed a new Science Advisory Board (SAB) to guide its science program and to provide overall strategic vision and focus. The SAB brings legal, institutional as well as domain-specific knowledge in the use and sharing of scientific tools and data. Our SAB is made up of eminent scholars and practitioners from different disciplines and four continents who have volunteered to provide us both the domain expertise as well as regional perspective to help create a truly globally responsive program. We are grateful to Gilberto Camara, Michael Carroll, Robert Chen, Juncai Ma, Peter Murray-Rust, Mackenzie Smith, and John Wilbanks for their time and insight.

Creative Commons works with scientists and institutions, providing education and outreach on the right technologies and licenses to maximize legal interoperability of scientific data and tools. Since most science is both cross-discipline and cross-border, legal interoperability of data and tools facilitates collaboration, enables reproducibility and verifiability, and makes it possible to extract a higher return on investment in publicly funded scientific programs through reuse of information.

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Geoscience Australia to License Satellite Images Under CC BY

Elliot Harmon, October 11th, 2012

Geoscience Australia recently announced that it will license all images from the Landsat 8 satellite under CC BY. (Geoscience Australia is a partner of the United States Geological Survey in the Landsat program.)

Creative Commons Australia reports:

The new Landsat 8 satellite is scheduled to be launched in early 2013, with GA’s full implementation being scheduled for May or June 2013.

Upon full implementation, which involves the deployment of major infrastructure upgrades by GA, data will be beamed from Landsat 8 on a daily basis to GA-operated ground stations in Alice Springs and Darwin. As soon as possible after receipt and processing, GA will make the satellite images publicly available free of charge.

GA will make the data available under a Creative Commons CC BY Australia 3.0 licence, which will facilitate legal reuse of the images.

GA is expecting a major upsurge in demand for the images when its free to air service is up and running. Jeff Kingwell, Section Leader of GA’s National Earth Observation Group, has indicated this prediction is based on the experience of its senior partner Geological Survey where there was a 1000 fold usage increase on commencement of its free to air service online. “Our experience is that using the Creative Commons Attribution Licence — which is the default licence for GA information — makes the data more useful and easier to apply. For example, to help the Indonesian government to monitor forest management, GA supplies Landsat data from a number of foreign data archives. Since we can apply the same licence conditions to each data source, the information is much more useful and easier to share and reuse.”

(Read the full article.)

Here at Creative Commons, we applaud governments and intergovernmental organizations licensing their information and data under CC licenses (or the CC0 public domain waiver). Australia’s partnership with the United States in the Landsat program is a perfect example of why it’s important to use a license that’s open and internationally applicable.

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Support Grows for Open Access to Science Research

Elliot Harmon, June 29th, 2012

PeerJ Founders Peter Binfield and Jason Hoyt
PeerJ Founders Peter Binfield and Jason Hoyt / Duncan Hull / CC BY

In their excellent Washington Post opinion piece, Matt Cooper and Elizabeth Wiley suggest that federally funded research should be freely accessible over the Internet. They argue that when students lose their access to academic databases after graduation, society doesn’t get the same benefits it could from that research:

Students’ library cards are a passport to the specialized knowledge found in academic journal articles — covering medicine and math, computer science and chemistry, and many other fields. These articles contain the cutting edge of our understanding and capture the genius of what has come before. In no uncertain terms, access to journals provides critical knowledge and an up-to-date education for tomorrow’s doctors, researchers and entrepreneurs.

But should that access cease at graduation? Or would you rather a graduating medical student, perhaps your future doctor, be able to keep up with the latest advances? Would you rather an ambitious graduate student feel comfortable leaving the academy to found the next Google, knowing she still has access to the latest insight in her field and is able to build upon it?

Cooper and Wiley’s organizations — the National Association of Graduate-Professional Students and the American Medical Student Association, respectively — joined Creative Commons and many other allies in support of a petition on Whitehouse.gov for free access to scientific journal articles arising from taxpayer-funded research. The petition quickly reached its goal of 25,000 signatures, sending a clear message that it’s time for the government to rethink open access policies.

Meanwhile in Britain, the Minister for Universities and Science recently commissioned a study on how the UK could adopt open access for publicly-funded research. Dame Janet Finch and her team released their findings last week, championing in particular the “gold” route to open access.

But how do the publishers themselves fit into the discussion? Some are actively exploring open access publishing models. This month, Peter Binfield and Jason Hoyt unveiled PeerJ, a new kind of peer-reviewed academic publisher. Contributors pay a $99 lifetime membership fee, and all articles are licensed CC BY. Funded by Tim O’Reilly, PeerJ has been getting a lot of attention in the mainstream press.

Coincidentally, science publishing stalwart Nature has also adopted the CC BY license, through its open access component Scientific Reports. Previously, researchers could choose whether to license their works BY-NC-SA or BY-NC-ND. Starting July 1, they’ll have the CC BY option as well. Nature’s Jason Wilde explains the decision to drop the required noncommercial stipulation:

There has been much debate about commercial reuse on open access articles […] We believe in offering our authors choice. And we now know some authors will want to choose CC BY, not least as a result of new funder mandates. Unlike Nature Communications and our other titles, Scientific Reports does not have established revenues from commercial reprints or licensing, making it an economically viable proposition.

With governments, publishers, and the public all rethinking ways to make research more freely accessible, the climate seems right for a major shift toward open access.

Related: First Thoughts on the Finch Report: Good Steps but Missed Opportunities (Cameron Neylon)

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Seeking Project Coordinator for Science and Data

Jane Park, April 25th, 2012


Open Science Logo / gemmerich / CC BY-SA

Creative Commons is seeking a Project Coordinator for Science and Data! The Project Coordinator will organize, coordinate and manage projects related to data policy and governance and perform research and analysis on data governance topics across relevant sectors — particularly for science — and communicate results and recommendations from the project via writing and related outreach.

We are looking for someone who is experienced in policy analysis, development and processes, in addition to Open Source Software, Open Access/Open Data and other Open content projects. A science and/or legal background with international experience is highly desirable — especially as the position will be representing Creative Commons at global events in the Open Data and Open Science communities! See the job posting and apply at our opportunities page.

We will stop accepting applications after 11:59 p.m. PDT, May 25, 2012.

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