Archive for Open Access

An analysis of the effects of sharing research data, code, and preprints on citations

Posted in OJAp Papers, Open Access with tags , , , , , on May 27, 2024 by telescoper

Whenever researchers ask me why I am an advocate of open science the response that first occurs to me is somewhat altruistic: sharing results and data is good for the whole community, as it enables the proper progress of research through independent scrutiny. There is however a selfish reason for open science, demonstrates rather well by a recent preprint on arXiv. The abstract is here:

Calls to make scientific research more open have gained traction with a range of societal stakeholders. Open Science practices include but are not limited to the early sharing of results via preprints and openly sharing outputs such as data and code to make research more reproducible and extensible. Existing evidence shows that adopting Open Science practices has effects in several domains. In this study, we investigate whether adopting one or more Open Science practices leads to significantly higher citations for an associated publication, which is one form of academic impact. We use a novel dataset known as Open Science Indicators, produced by PLOS and DataSeer, which includes all PLOS publications from 2018 to 2023 as well as a comparison group sampled from the PMC Open Access Subset. In total, we analyze circa 122’000 publications. We calculate publication and author-level citation indicators and use a broad set of control variables to isolate the effect of Open Science Indicators on received citations. We show that Open Science practices are adopted to different degrees across scientific disciplines. We find that the early release of a publication as a preprint correlates with a significant positive citation advantage of about 20.2% on average. We also find that sharing data in an online repository correlates with a smaller yet still positive citation advantage of 4.3% on average. However, we do not find a significant citation advantage for sharing code. Further research is needed on additional or alternative measures of impact beyond citations. Our results are likely to be of interest to researchers, as well as publishers, research funders, and policymakers.

Colavizza et al., arXiv:2404.16171

This analysis isn’t based on astrophysics, but I think the relatively high citation rates of papers in the Open Journal of Astrophysics are at least in part due to the fact that virtually all our papers are all available as preprints arXiv prior to publication. Citations aren’t everything, of course, but the positive effect of preprinting is an important factor in communicating the science you are doing.

Two New Publications at the Open Journal of Astrophysics

Posted in OJAp Papers, Open Access, The Universe and Stuff with tags , , , , , , , , , , on April 20, 2024 by telescoper

It’s Saturday, and it’s time to post another update relating to the  Open Journal of Astrophysics.  Since the last update we have published two more papers, taking  the count in Volume 7 (2024) up to 27 and the total published by OJAp up to 142.

The first paper of the most recent pair – published on  Tuesday April 16th – is “An Enhanced Massive Black Hole Occupation Fraction Predicted in Cluster Dwarf Galaxies” by Michael Tremmel (UCC, Ireland), Angelo Ricarte (Harvard, USA), Priyamvada Natarajan (Yale, USA), Jillian Bellovar (American Museum of Natural History, New York, USA), Ray Sharma (Rutgers, USA), Thomas R. Quinn (University of Washington, USA). It presents a  study, based on the Romulus cosmological simulations, of the impact of environment on the occupation fraction of massive black holes in low mass galaxies. This one is in the folder marked “Astrophysics of Galaxies“.

Here is a screen grab of the overlay which includes the abstract:

 

You can click on the image of the overlay to make it larger should you wish to do so. You can find the officially accepted version of the paper on the arXiv here.

The second paper was published on Wednesday 17th April and has the title “A 1.9 solar-mass neutron star candidate in a 2-year orbit” and the authors are: Kareem El-Badry (Caltech, USA), Joshua D. Simon (Carnegie Observatories, USA), Henrique Reggiani (Gemini Observatory, Chile), Hans-Walter Rix (Heidelberg, Germany),  David W. Latham (Harvard, USA),  Allyson Bieryla (Harvard, USA),  Lars A. Buchhave (Technical University of Denmark, Denmark),  Sahar Shahaf (Weizmann Institute of Science, Israel),  Tsevi Mazeh (Tel Aviv University, Israel), Sukanya Chakrabarti (University of Alabama, USA), Puragra Guhathakurta (University of California Santa Cruz, USA), Ilya V. Ilyin (Potsdam, Germany), and Thomas M. Tauris (Aalborg University, Denmark)

This one, which is in the folder marked Solar and Stellar Astrophysics, presents a discussion of the discovery of a 1.9 solar mass neutron star candidate using Gaia astrometric data, together with the implications of its orbital parameters for the formation mechanism.

Here is a screen grab of the overlay which includes the abstract:

 

 

 

You can click on the image of the overlay to make it larger should you wish to do so. You can find the officially accepted version of the paper on the arXiv here.

That concludes this week’s update!

The Gates Foundation and Open Access

Posted in Open Access with tags , , , , , on April 9, 2024 by telescoper

There has been quite a lot of reaction (e.g. here) to the recent announcement of a new Open Access Policy by the Bill & Melinda Gates Foundation, which is one of the one of the world’s top funders of biomedical research. This mandates the distribution of research it funds as preprints and also states that it will not pay Article Processing Charges (APCs). The essentials of the policy, which comes into effect on 1st January 2025, are these:

  1. Funded Manuscripts Will Be Available. As soon as possible and to the extent feasible, Funded Manuscripts shall be published as a preprint in a preprint server recognized by the foundation or preapproved preprint server which applies a sufficient level of scrutiny to submissions. Accepted articles shall be deposited immediately upon publication in PubMed Central (PMC), or in another openly accessible repository, with proper metadata tagging identifying Gates funding. In addition, grantees shall disseminate Funded Manuscripts as described in their funding agreements with the foundation, including as described in any proposal or Global Access commitments.
  2. Dissemination of Funded Manuscripts Will Be On “Open Access” Terms. All Funded Manuscripts, including any subsequent updates to key conclusions, shall be available immediately, without any embargo, under the Creative Commons Attribution 4.0 International License (CC BY 4.0) or an equivalent license. This will permit all users to copy, redistribute, transform, and build on the material in any medium or format for any purpose (including commercial) without further permission or fees being required.
  3. Gates Grantees Will Retain Copyright. Grantees shall retain sufficient copyright in Funded Manuscripts to ensure such Funded Manuscripts are deposited into an open-access repository and published under the CC-BY 4.0 or equivalent license.
  4. Underlying Data Will Be Accessible Immediately. The Foundation requires that underlying data supporting the Funded Manuscripts shall be made accessible immediately and as open as possible upon availability of the Funded Manuscripts, subject to any applicable ethical, legal, or regulatory requirements or restrictions. All Funded Manuscripts must be accompanied by an Underlying Data Availability Statement that describes where any primary data, associated metadata, original software, and any additional relevant materials or information necessary to understand, assess, and replicate the Funded Manuscripts findings in totality can be found. Grantees are encouraged to adhere to the FAIR principles to improve the findability, accessibility, interoperability, and reuse of digital assets.
  5. The Foundation Will Not Pay Article Processing Charges (APC). Any publication fees are the responsibility of the grantees and their co-authors.
  6. Compliance Is A Requirement of Funding. This Open Access policy applies to all Funded Manuscripts, whether the funding is in whole or in part. Compliance will be continuously reviewed, and grantees and authors will be contacted when they are non-compliant.
    • As appropriate, Grantees should include the following acknowledgment and notice in Funded Manuscripts:
    • “This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation [Grant number]. The conclusions and opinions expressed in this work are those of the author(s) alone and shall not be attributed to the Foundation. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Please note works submitted as a preprint have not undergone a peer review process.”

Reactions to this new policy are generally positive, except (unsurprisingly) for the academic publishing industry.

For what it’s worth, my view is that it is a good policy, and I wish more funders went along this route, but it falls short of being truly excellent. As it stands, the policy seems to encourage authors to put the “final” version of their articles in traditional journals, without these articles being freely available through Open Access. That falls short of goal establishing a global worldwide network of institutional and/or subject-based repositories, linked to peer review mechanisms such as overlays, that share research literature freely for the common good. To help achieve that aim, the Gates’ Foundation should to encourage overlays rather than traditional journals as the way to carry out peer review. Perhaps this will be the next step?

Open Journal of Astrophysics Update

Posted in OJAp Papers, Open Access with tags , , , , , on April 4, 2024 by telescoper

I’ve just noticed that my post earlier in the week about changes to the publication system at the Open Journal of Astrophysics is dated April 1st. I can assure you it wasn’t meant as a joke! Anyway, the integration with Crossref is now complete and I’ve started clearing the backlog of papers waiting to be published. I would say normal service has been resumed, but the idea is to make the process faster and more reliable than before so it’s hopefully a return but to better-than-normal service.

I want first of all to thank the people at Maynooth University Library, Crossref, and Scholastica for helping us figure out the issue and solve it. We would no doubt have got there faster were it not for the intervention of the Easter break, but in any case it has only required a pause of publication for a couple of weeks.

I’ll resume the regular weekly updates at the weekend. However, one paper got snarled up when we ran into a problem. Although published on 20th March, it was never properly registered with Crossref. The only way I could think of to sort out the issue with this one was to start it again, which I did this morning, and it is now published though I kept the publication date as 20th March.

This paper, by Yingtian Chen and Oleg Gnedin of the University of Michigan, is the 21st paper to be published in Volume 7 and the 136th altogether. It is a study of kinematic, chemical and age data of globular clusters from Gaia yielding clues to how the Milky Way Galaxy assembled. You can read the article on arXiv directly here.

You will note the new format of DOI on the overlay. Nothing else has changed that’s visible to the reader.

Academic Publishing: Never Mind the Quality…

Posted in Open Access with tags , , , , , , , , on March 16, 2024 by telescoper

I was interested to see that the latest issue of Private Eye contains a short item about academic publishing:

I’ve heard many stories of this type, with publishers putting pressure on their Editorial Boards to allow more papers to be published. This is undoubtedly motivated by the Gold Open Access model in which authors or their institutions are forced to pay thousands of dollars upfront to publish papers. Since the publisher makes an eye-watering profit on every article, why not publish as many as possible? The recent decision by the Royal Astronomical Society adopt this model is highly likely to have a similar effect there, as its journals will be able to increase revenue at the expense of quality. Under the older subscription-based system, publishers could sell their product to libraries on the basis of quality but they no longer need to do that to make a profit.

The academic publishing industry is perverse enough without adding this obvious incentive to lower editorial standards. There are far too many low quality papers being published already, a situation driven not only by the profiteering of the publishing industry but also by the absurd policies of academia itself which require researchers to churn out huge numbers of papers to get promotion, win research grants, etc.

This part of the academic system is definitely broken. To fix it, academic publishing must be taken out of the hands of commercial publishers and put into the care of research institutions whose libraries are perfectly capable of publishing and curating articles on a non-profit basis. But that won’t be enough: we need also to overhaul how we do research assessment. The principles outlined in the San Francisco Declaration on Research Assessment would be a start.

Publishing Revenue and the Learned Societies

Posted in Open Access with tags , , , , , on March 8, 2024 by telescoper

A couple of days ago I posted a reaction to a shockingly dishonest article I saw in Physics World which has led me to resign my Fellowship of the Institute of Physics (IoP). I thought I would spend a bit of time now to raising some wider points (which I’ve raised before) about the extent that such organizations (including, in my field,  the Royal Astronomical Society and the Institute of Physics) rely for their financial security upon the revenues generated by publishing traditional journals and why this is not in the best interests of their disciplines.

Take IOP Publishing. This is a wholly-owned subsidiary of the Institute of Physics that has an annual turnover of around £60M generated from books and journals. This revenue is the largest contribution to the income that the IoP needs to run its numerous activities relating to the promotion of physics.  A similar situation pertains to the Royal Astronomical Society, although on a smaller scale, as it relies for much of its income from Monthly Notices of the Royal Astronomical Society, in which I have published quite a few papers in the past.

Not surprisingly, these and other learned societies are keen to protect their main source of cash and have lobbied very hard for the “Gold” Open Access some authorities are attempting to foist on the research community, rather than the far more sensible and sustainable approaches to Open Access employed, for example, by the Open Journal of Astrophysics.

There are two major reasons why I object to this approach, one practical and one ethical.

First, I consider it to be inevitable that the traditional journal industry will very soon be completely bypassed in favour of  other forms of publishing. The internet has changed the entire landscape of scientific publication. It’s now so cheap and so easy to disseminate knowledge that traditional journals are already virtually redundant, especially in my field of astrophysics where we have been using the arXiv for so long that many of us hardly ever look at journals.

The comfortable income stream that has been used by the IoP to “promote Physics”, as well as to furnish its  building in King’s Cross and office in Dublin, will dry up unless these organizations find a way of defending it. The “Gold” OA favoured by such organizations their attempt to stem the tide. I think this move into Gold `Open Access’, paid for by ruinously expensive Article Processing Charges paid by authors (or their organizations) is unsustainable because the research community will see through it and refuse to pay. I can already see signs of this happening.

The other problematic aspect of the approach of these learned societies is that I think it is fundamentally dishonest. University and other institutional libraries are provided with funds to provide access to published research, not to provide a backdoor subsidy for a range of extraneous activities that have nothing to do with that purpose. The learned societies do many good things – and some are indeed outstandingly good – but that does not give them the right to siphon off funds from their constituents by a sort of stealth levy.  Voluntary institutional affiliation, paid for by a fee, would be a much fairer way of funding these activities.

A couple of days ago I decided to cease paying the annual subscription to, and resign my Fellowship of, the Institute of Physics. I was reasonably comfortable spending some of my own money supporting physics, but don’t agree with  researchers having to fork out huge amounts of money in involuntary payment of APCs to the IOP. I will decide in the next few days whether or not to resign also from the Royal Astronomical Society for the same reason.

Some time ago I had occasion to visit the London offices of a well-known charitable organization which shall remain nameless. The property they occupied was glitzy, palatial, and obviously very expensive. I couldn’t help wondering how they could square the opulence of their headquarters with the quoted desire to spend as much as possible on their good works. Being old and cynical, I came to the conclusion that, although charities might start out with the noblest intentions, there is a grave danger that they simply become self-serving, viewing their own existence in itself as more important than what they do for others.

The commercial academic publishing industry has definitely gone that way. It arose because of the need to review, edit, collate, publish and disseminate the fruits of academic labour. Then the ease with which profits could be made led it astray. It now fulfills little or no useful purpose, but simply consumes financial resources that could be put to much better effect actually doing science. I think the scientific community knows this very well, and hopefully the parasite will die a natural death.

The question for learned societies is whether they can find a sustainable funding model that isn’t reliant upon effectively purloining funds from research budgets. If their revenue from publishing does fall, can they replace it? And, if not, in what form can they survive?

On “Purpose-Led Publishing”

Posted in Open Access with tags , , , , , , , , , , on March 6, 2024 by telescoper

I was flabbergasted by the cheek of an article that recently appeared in Physics World by Michael Brooks announcing that:

I can’t speak about the American Institute of Physics or the American Physical Society but in the context of the Institute of Physics – of which I am a Fellow and in whose house magazine the article appears – I draw your attention to the last sentence of the above excerpt which contains a commitment to “invest funds generated from publishing back into research” (my emphasis).

Really? The IOP invests in research? That’s news to me. How do I apply for a grant? Will they fund my next PhD student?

The IOP invests its funds in many things – many of them worthy – but it does not spend a significant part of the vast income it generates from its publishing house on research. The claim that it does is just dishonest. There’s point in mincing words.

This is an important distinction, particularly so that publishing in most IOP journals now requires the payment of a hefty Article Processing Charge (APC; Artificial Profit Charge would be more apt) which often has to be paid for out of research grants. Previously the revenue of IOP Publishing was appropriated from library budgets through subscriptions, so physicists were less aware of just how much the IOP was raking in. Now that researchers are having to find the funds themselves from research grants it has become more obvious that the IOP is actually a drain on research funds, not a source of them. The APC is a levy on research, designed to generate funds for other things. I think this model is indefensible. What gives the IOP the right to impose charges that far exceed the cost of disseminating scientific results in order to appropriate funds for its other activities?

Moreover, even if the IOP did fund research, what benefit would that be to a researcher in Spain, South Korea or Singapore or indeed anywhere outside the UK and Ireland?

The slogan for the initiative described in the article is “Purpose-led Publishing”. That reminds me of an old saying from systems theory: the Purpose Of a System Is What it Does (POSIWID). What the system does in this case is to raise funds for the IOP. That’s its purpose. Everything else is just marketing spiel.

The claim that IOP Publishing does not make a profit is disingenuous too. It does make a substantial profit. The only difference between it and the likes of Elsevier is where the profits go. A true not-for-profit publisher would charge only at the level to cover the costs of publication. The Purpose that should be leading Publishing in physics is the dissemination of scientific results, not the generation of revenue for sundry other things.

I have avoided publishing in IOP journals for many years because I think the approach of IOP Publishing is unethical. Now I have decided that I no longer wish to be associated with the IOP in any way. I have paid the subscription for 2024 but when that lapses I won’t renew it. Enough is enough.

Predatory Encounters

Posted in Open Access with tags , , , on February 17, 2024 by telescoper

Yesterday I received two different emails from predatory publishers. The first invited me to submit a manuscript to the OSP Journal of Physics & Astronomy. I am informed that the journal is fully open access, with an Article Processing Charge of “only” $950. Of course $950 is $950 more than I’ll ever be prepared to pay for an APC, but did have a look at the website and found this:

A pretty good clue that OSP is a predatory publisher is that can spell neither “Scientific” nor “submit”…

Anyway, if you’re interested – and if I were you I wouldn’t be – you can find the OSP Journal of Physics & Astronomy here. I’ve skimmed the latest issue and the quality of articles is just as I expected.

The Second Encounter of the Predatory Kind was an email that begins thus:

I’ve never heard of the Auricle Global Society of Education and Research (AGSER) but the Open Journal of Astrophysics is not for sale to them (nor to anyone else, for that matter). Of course I don’t own OJAp anyway, but even if I did I wouldn’t sell it at any price. The only terms that I would agree to a takeover would be if the new owners committed to keep it as Diamond Open Access (i.e. free to authors and readers), and I can’t see any predators offering that!

I don’t know how AGSER arrived at a valuation of $70K but it got me thinking. We have so far published 128 articles at OJAp. Taking the APC for MNRAS of £2500 (approx $3000) as typical then we have saved the community about $384,000 in unnecessary publication charges.

The Cost of Imaging Neuroscience

Posted in Open Access with tags , , , , , , on February 13, 2024 by telescoper

Last year I wrote a piece about the resignation of the entire Editorial Board of an Elsevier journal. The main reason for this action was `extreme’ Article Processing Charges imposed by the publisher for so-called Gold Open Access to the papers. As I wrote then, the

… current system of ‘Gold’ Open Access is a scam, and it’s a terrible shame we have ended up having it foisted upon us. Fortunately, being forced to pay APCs of many thousands of euros to publish their papers, researchers are at last starting to realize that they are being ripped off. Recently, the entire Editorial Board of Neuroimage and its sister journal Neuroimage: Reports resigned in protest at the `extreme’ APC levels imposed by the publisher, Elsevier. I’m sure other academics will follow this example, as it becomes more and more obvious that the current arrangements are unsustainable. Previously the profits of the big publishers were hidden in library budgets. Now they are hitting researchers and their grants directly, as authors now have to pay, and people who previously hadn’t thought much about the absurdity of it all are now realizing what a racket academic publishing really is.

Well, the new journal founded by former Editorial Board of Neuroimage and Neuroimage: Reports has now appeared. It’s called Imaging Neuroscience and its rather website can be found here.

Good news, you would think.

But no…

Imaging Neuroscience is itself a Gold Open Access journal which charges an APC of $1600 per paper. That’s about half the Elsevier were charging ($3,450) but is still far too high. It simply does not cost this much to publish papers online! (There’s a paper that gives a summary of the commercial costs of different aspects of publishing here.) The journal claims to be non-profit making so I’d love to see what they are spending this money on. It can’t be on their website, which is very rudimentary.

It seems that the neuroscientists concerned have just decided to replace Elsevier’s absurd APCs with their own absurd APCs. Oh dear. And they seemed so close to getting it…

Two New Publications at the Open Journal of Astrophysics

Posted in OJAp Papers, Open Access, The Universe and Stuff with tags , , , , , , , , , , , on February 1, 2024 by telescoper

As the first month of 2024 is now over, I thought I’d post an update relating to the  Open Journal of Astrophysics.  Since the last update we have published two papers, taking  the count in Volume 7 (2024) up to 9 (the total for January) and the total published by OJAp up to 124. We will have others soon, but I will be travelling for the first few days of February so the next update will be in a week or so.

Using our sophisticated forecasting algorithm, based on the first month of 2024 as input, I predict that we will publish around 9×12=108 papers in 2024, more than double last year’s total of 50.

Both the current papers discussed here are in the folder marked Cosmology and NonGalactic Astrophysics, our most popular category.

Anyway, the first paper of the most recent pair – published on January 30th – is “Capse.jl: efficient and auto-differentiable CMB power spectra emulation”, by Marco Bonici (INAF Milano, Italy & Waterloo, Canada), Federico Bianchini (Stanford, USA) and Jaime Ruiz-Zapatero (Oxford, UK). This paper presents an emulator for rapid and accurate prediction of Cosmic Microwave Background (CMB) temperature, polarization, and lensing angular power spectra, that works much faster than traditional methods. The code is written in Julia, in which language we are seeing an increasing number of submissions to OJAp.

Here is a screen grab of the overlay which includes the abstract:

 

You can click on the image of the overlay to make it larger should you wish to do so. You can find the officially accepted version of the paper on the arXiv here.

The second paper was published yesterday (31st January 2024) and has the title “Cosmological Inflation in N-Dimensional Gaussian Random Fields with Algorithmic Data Compression” which is a  study of inflationary models with Gaussian random potentials for multiple scalar fields, tracking the evolutionary trajectories numerically. The authors are Connor Painter and Emory Bunn, both the Physics Department at the University of Richmond, Virginia (USA). Ted Bunn (as he is usually known) is a longstanding member of the Editorial Board of the Open Journal of Astrophysics (and was thereby excluded from any involvement in the editorial process for this paper).

Here is a screen grab of the overlay which includes the abstract:

 

 

 

You can click on the image of the overlay to make it larger should you wish to do so. You can find the officially accepted version of the paper on the arXiv here.

Here Endeth the Update.