Scientific computing on Apple M1, part I: ASE and GPAW

Scientific computing on Apple M1, part I: ASE and GPAW

Getting ASE and GPAW running natively on the Apple Silicon M1 MacBook Pro, and benchmarking them against an iMac Pro.

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Atom Tractor Beam simulation game

Atom Tractor Beam simulation game

With the support of the Vienna Business Agency, we commissioned a simulation game for the Vienna Technical Museum special exhibition called “The Future of Work and Production”. This game is now released online, try it out for yourself!

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Manipulating single atoms with an electron beam

Manipulating single atoms with an electron beam

We are now able to achieve nearly perfect control over the movement of individual silicon impurity atoms within the lattice of graphene, the two-dimensional sheet of carbon.

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Finland takes steps in the openness of academic journal pricing

(The title is a riff on my 2016 post announcing the efforts of Finnish open science activists to obtain pricing information through the courts.)

Edit 1: I gave a comment for a Times Higher Education article on Elsevier's negotiations.

Edit 2: on Feb 2, 2018, FinELib released more details, including the level of total price increases and the full text of the agreement (apart from some important financial details). While completely open agreements are possible and arguably should had been part of the negotiations from the start, I do concede that FinELib has made a significant effort to increase transparency – thank you.

Although I have not lived in Finland since 2013, I've kept in touch with the open science community there as well as with current open access discussions. On January 17, I got a rather unpleasant birthday present in the form of an announced three-year, 27 M€ deal between FinELib, a consortium of Finnish research institutions, and Elsevier, perhaps the most egregious of the big publishers. The deal was reached after two years of hard negotiations, supported by almost 3000 Finnish researchers who had committed in the #nodealnoreview boycott to refuse reviewing for Elsevier if the negotiations fail.

The glowing press release, seemingly written purely by Elsevier, compounded with an almost complete lack of details, left an immediate bad taste in my mouth. My opinion did not much improve through discussions in the Finnish Open Science Facebook group, and with journalist Richard Poynder whom I urged to try and get more details. He just published his Q&A with FinELib, which I warmly recommend you read. I have two principal concerns with the deal: the lack of transparency over the actual terms, and the hybrid OA discount option — especially as it was immediately implemented at the University of Helsinki.

Firstly, FinELib told me on Twitter that the deal does not include an NDA, and they have publicly committed to LIBER's principles of transparency. Regardless of this, and despite calls from people who had joined the boycott (I find this tweet by Panu Halme particularly poignant: "[...] For example I gave up an editor position to help you and now I have no idea was it worth anything"), they have not released any detail. Both in Richard's Q&A and on Twitter, they ignore explicit questions by reiterating the same basic facts. This is obfuscation, pure and simple, and particularly hypocritical in light of their stated commitment.

That brings us to the second problem: the hybrid OA discount. As part of the negotiations, Elsevier agreed to provide a 50% discount on ACPs for participating institutions to many Elsevier titles (though not all, and apparently not including flagships such as Cell), mainly for hybrid OA. Immediately after this, the largest Finnish institution, the University of Helsinki, announced a policy that they would cover the remaining 50% of the fees, effectively making publishing hybrid OA with Elsevier "free" for its researchers.

It is really hard to see a scenario where the University of Helsinki ends up paying less to Elsevier, which would be the whole point of an offsetting agreement. Further, this is exactly the opposite to what would be needed to introduce real price sensitivity to the market, and against the stated position of both the Academy of Finland AND the University of Helsinki itself! The latter contradiction is particularly glaring in their library's Finnish-language blog post defending the policy while reiterating that they do not support hybrid. They also claim that paying the fees centrally was the only way to gather data on uptake for future negotiations, but obviously they could had simply asked Elsevier to provide this for all affiliated authors as part of the deal.

Some of the people behind the boycott have been more positive about the deal than me, and I appreciate their position. However, as I have no real ties to Finland I can perhaps be a bit less politic about this and emphatically state: unless FinELib releases the full details of the deal voluntarily, they have truly let down the Finnish research community.

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Finland takes leading role in the openness of academic journal pricing

Freedom of Information request by open science advocates has revealed academic journal pricing through an administrative court decision. Finland is the first country where the subscription prices paid by practically all universities and research institutions to individual publishers are made available. This strengthens the position of universities in the 2016 contract negotiations, made ever more timely by the recent deep funding cuts. Comparisons between publishers and countries also supports the ongoing discussion of alternative publishing models and directing funding towards open access (OA) publishing.

The costs of academic journals have risen precipitously, but the lack of detailed pricing information has made the overall situation difficult to perceive. There are significant price differences between publishers, universities and countries. While dominant publishing houses have reported profit margins of tens of percent and the industry is ever more concentrated, university libraries including Harvard have reached a fiscally unsustainable situation. This has in part contributed to the ongoing breakthrough of open access.

In the spring of 2014, the conclusion that contract prices should be public also in Finland was reached in a discussion group of the Open Knowledge Finland (OKF) association. In the summer, researcher and open science advocate Leo Lahti made a Freedom of Information request to Aalto and other Finnish universities on behalf of the OKF. The universities themselves would stand to benefit from the openness, making negotiations more transparent and potentially resulting in cost savings.

None of the universities supplied the requested information. The fear of publisher legal action may have prevented them from following their own principles of openness, because for example Aalto refused to even provide an appealable decision, denied having acted as a public institution covered by the openness laws, and finally tried to transfer its responsibility to the National Library. Open science advocates brought the matter to the Helsinki administrative court, which predictably confirmed that the prices of subscription contracts are public information. Similar demands for openness had been made previously; national and university-level figures are available for some countries, but detailed publisher-specific information has only been made public in the UK and the USA. In the end, the Open Science and Research Initiative (ATT) of the Ministry of Education and Culture took responsibility for gathering the Finnish pricing data.

After this two-year process Finland is now amongst the first countries where publisher- specific prices have been made public in detail over several years. The material includes the costs of 266 publisher titles for all universities and dozens of other institutions, the total sum of which in 2010-2015 was 131.1 million euros. A more detailed analysis can be found in a separate post. Special thanks are due to the Finnish open science community, whose initiative and perseverance was required to fulfill the spirit of the openness laws.

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Quantum biology

Quantum biology is the study of if and how quantum effects play a role in biological organisms, traditionally considered too warm, big and messy for them to matter. Recent research has, however, started to uncover that several biological systems do exhibit interesting quantum effects.

This TED talk by Jim Al-Khalili probably won't surprise you if you have been following the field as I have, but it is a superb recap and introduction to the topic.

"How does a robin know to fly south? The answer might be weirder than you think: Quantum physics may be involved. Jim Al-Khalili rounds up the extremely new, extremely strange world of quantum biology, where something Einstein once called “spooky action at a distance” helps birds navigate, and quantum effects might explain the origin of life itself." via TED Talks

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