Showing posts with label open access. Show all posts
Showing posts with label open access. Show all posts

Tuesday, November 6, 2018

In praise of "Arabian Journal of Chemistry"

In early October 2017 I submitted a  paper to Royal Society Open Science (RSOS). It took more than four months before I got any update on its status. After conflicting reviews, RSOS contacted an additional reviewer, who took TWO months to write a two line "report" which rejected my paper due to "lack of novelty" in spite of no other study of the subject matter existing in the literature. I decided then to eschew RSOS for ever and looked for another Open Access journal for my submission. 
Since I currently have no funding, absence of author processing charges was an important consideration. I found out about the "Arabian Journal of Chemistry" and looked into it: in spite of its obscurity, they have a decent Impact Factor (which shows that their papers are at least read within the community and solid enough to warrant being cited) and their APCs are borne by the King Saud University. I sent them my paper, which was unfortunately rejected although the reviewer reports were more consistent with a "Major Revisions" decision. The peer-review process, though, was exemplary: in less than two-and-a-half months, they provided me with SIX solid peer-review reports with enough actionable insights that I could incorporate into my paper to eventually get it published in J. Phys. Chem. A.
 I can only commend them for the utter professionalism, speed and quality of the whole process. I wish Arabian Journal of Chemistry all the best, and that its high standards and level of review will soon make it known among chemists as a premium journal. They  sure deserve that!

Friday, December 11, 2015

On the difficulty of finding peer-reviewers

I have recently become an Associate Editor at PeerJ. I had several motivations for this:
  • I strongly believe in their mission, and am very happy with my three publishing experiences with them.
  • I mostly work alone and therefore my papers, in the long run, will not be a profitable for them. I felt that I should give them some extra support in exchange for their extremely low number-of-authors-based APC.
  • As a mid-career researcher at a little-known teaching-based institution, I reasoned that this opportunity might increase my visibility and improve my CV.

I am enjoying my run as an editor. So far, I have shepherded seven papers through the publishing process: one of them was published a week ago, I rejected one "on arrival",  and five of them are undergoing review.  I target my peer-review invitations to people who have recently published work using the same methods, or studied the same question, both for the obvious expertise and hoping that they will find the paper interesting. Still, I was quite surprised with how hard it is to get people to accept reviewing papers: for two papers, I managed to get two reviewers with around 6-8 invitations, but my latest assignments required more than 15 invitations each!  I understand that everybody is busy researching, writing papers, applying for funding, etc., but I never thought that the acceptance rate for peer-review requests would be < 15%. I do not get many peer-review request myself, but I do believe I have an obligation of accepting as many requests as possible (and reviewing them promptly), and I thought this was the "common" mindset... Maybe the people I target for my invitations are simply too senior and are therefore swamped with review requests, but the emails of "non-senior" members of a Lab are too often hard to find, due to the common practice of including only the the lab leader "corresponding author".

Any thoughts/suggestions/gripes?



Tuesday, April 28, 2015

How does OA benefit my research?

Jan Jensen has written an interesting post describing how his decision to publish only on Open Access outlets has influenced the way he tackles research questions.  One of the benefits he points out is that choosing to publish in a journal which performs a "scientific soundness-only peer-review" instead of a "sexyness/interest and scientific soundness peer review" allows him to focus on "truly challenging and long-term research questions without worrying whether or where I will be able to publish".  I think that option already existed before OA and the advent of the mega-journals: we simply had to decide to be satisfied with publishing on IJQC or Theochem whenever the Editors of JPC, JCP, JACS, Angewandte et al.  pronounced our research "too specialized and not of enough interest to our broad readership", and to accept the derision of peers who look down on papers published on those and other low-impact journals. (I admit I am often guilty of this).
To me, the true advantage does not lie on OA itself, but on the open review model (used e.g. by PeerJ), which allows authors to publish the reviews at the same time as the paper. I feel this functions as a much stronger "validation" of the quality of the work, as readers immediately have access to a truly independent measure of the strengths and weaknesses of the manuscript.
How does OA benefit my research? I am not sure it benefits my research methodology and/or choice of research questions since, as one of only two computational chemists at a small teaching-driven University, I  have long decided to research whatever obscure subtopics catch my fancy due to obvious lack of resources to compete against larger/well-funded groups working in sexier topics/enzymes. My decision to embrace an open science model, in contrast (e.g. figshare) has benefitted me more directly by forcing me to archive my results in a more transparent way, with proper "understandable" filenames instead of idiossyncratic names chosen on the fly... That is something I should have done anyway even without the open science model, but that was the nudge which brought me to the "Light" side.

Wednesday, April 22, 2015

When the description of methods in a scientific paper becomes optional.

I have just read a paper describing some very interesting tailoring of enzyme specificity on a P450 enzyme. I was, however, surprised to find that no description of the experimental methods was present in the paper itself, but was only available as Supporting Information. Upon examination of the instructions for authors in the journal I learned that, although being online only (and therefore lacking any space constraints), this publication enforces a 40-thousand character limit on the published papers and specifically states that the experimental section is optional. Traditionally, Supporting Information includes accessory data which would be cumbersome to include in the paper.  In this journal, it functions instead as a cumbersome way to access a vital part of information which should be part of the paper. I cannot even begin to understand why any reputable publisher would, in the absence of any printing costs, force their authors to split their manuscripts and "demote" the potentially most useful portion of the paper to the Supporting Information.
That's ACS: proudly claiming to "[publish] the most compelling, important primary reports on research in chemistry and in allied fields" while making it difficult for readers to have access to that same information.

Thursday, March 19, 2015

My new preprint is up

As part of their undergraduate training, our students are required to write a short thesis. Usually, due to the paucity of research funding, their theses take the format of a literature review. A few years ago, however, I proposed a computational study to the student I had been assigned. Despite no previous acquaintace with the subject, she eagerly took the task and performed some computations on possible reaction mechanisms of the organomercurial lyase MerB. She only had the time to compute a few of the possible pathways and therefore, after she had written her thesis with the data she had managed to gather, I completed the analysis of  the other pathways we had thought of at the time, and a few that we had not envisaged. Writing it as a paper took me much longer than I had anticipated, mostly because I kept postponing it due to the thrill of running computations on other enzymes and projects. I have now managed to finish it and submitted it to PeerJ, where it is undergoing review. I have made it available as a Preprint, and would be thankful for any comments about it.


Addendum: the paper has been published

Monday, September 8, 2014

Making good on my "Open Access" pledge


My most recent paper has just been published in PeerJ . It was a LONG time in the making, to the point that my 12-yo daughter once told me (only half-in-jest), that I should "cut my losses and forget about it". I am quite happy about how it turned out: besides describing an analysis of a reaction mechanism and the influence of the redox state of a hard-to-converge Fe-S cluster , it also contains  the first computations including the weighed contributions of 1.2*1013 protonations states of a protein on the reaction it catalyzes. The computational approach described here is relatively simple to perform provided that one has a good estimate of the relative abundances of those protonation states, which can be obtained through Monte Carlo sampling  once the site-site interactions have been computed with a Poisson-Boltzmann solver. To my mind, this is clearly superior to the usual approach of considering only  the "most likely" protonation state (which may often not be the state with the most significant influence on the electrostatic field surrounding the active site). What do you think of it?


Programs needed to use this approach:
MCRP, by Baptista et al., ITQB, Lisbon
MEAD, by Don Bashford, currently at St. Jude Children's research hospital
Any molecular mechanics code, to compute the change of the total electrostatic energy as each individual amino acid is protonated/deprotonated



Thursday, July 17, 2014

Do you want to publish for free in PeerJ?

I started following the Open Access movement ca. 2 yrs ago, mostly through the blogs of Michael Eisen, Jan Jensen and Mike Taylor. I was obvioulsy well aware of the successful OA outfits, like PLOS and BiomedCentral, but had never considered publishing there due to the shortage of funds and the non-reimbursability of such expenses by my country's Science Foundation. I joined PeerJ shortly after they "opened for business", due to their their very small fees and because of commitment to transparent peer-review , which to my eyes sets them apart from the wide number of OA venues which spam email boxes daily all over the world. 
After publishing my first paper on PeerJ, I have received five referral codes from them, each of which entitles an author to the free publication of a paper in PeerJ. The codes expire on August 10th. Should you wish to take advantage of one of these, please drop me a line. PeerJ only accepts submissions on the area of Biology, which is defined very broadly (from ecology and paleontology to virology, bioinformatics and computational biochemistry).

Addendum (July, 21st, 2014): Four codes have been distributed. One left to go

Addendum (September, 14th, 2014): I have received five new codes, valid through October 2nd, 2014. Any takers?

Thursday, January 16, 2014

Moving towards Open Access...

In physics and mathematics, publishing Preprints of papers in the arXiv is the most common form of distributing scientific papers. All the major journals in those areas have therefore been "forced" to accept papers previously available as preprints.
In Chemistry and Biology, however, most journals do not accept preprints and therefore authors are quite loath to make their work available as a preprint. The lack of this "free preprint" culture then enables journals to keep increasing their subscription prices way above inflation levels, which further gives publishers an extra incentive to keep rejecting sound work that might otherwise be available as costless preprints. This is a classic instance of Catch-22.
I believe that, as authors, we should do our utmost to fight this status quo. Our science should be evaluated on its merits, rather than on the accidental name of the journal where it has appeared. Therefore, I will henceforth submit all my Biochemistry work to PeerJ / PeerJPrePrints. PeerJ is an innovative and remarkably inexpensive Open Access Publisher with transparent peer-review and the option of publishing the paper's reviews alongside the manuscript.  The integrity of the reviewing process is therefore above reproach, ensuring that it will be both rigorous and fair.
PeerJ does not (yet?) accept submissions outside the field of Biology. My Chemistry work must continue to be submitted elsewhere. I am thinking of given the Beilstein Journal of Organic Chemistry a shot: completely free, open access, and rigorous. It does not have a stellar IF (around 2.8, I think), but who cares? Playing the IF game is ultimately detrimental to quick publication, as several journals insist on publishing only the "extra-sexy" work to prevent their IFs from falling, and often even refuse to send manuscripts for review simply because some editor feels they are not "hot" enough (ACS, I am talking to you....)

The power to change is, after all, in our hands. It may be a very small amount of power, and the odds of effecting any change may be vanishingly small, but if we do not use it, nothing will change for sure.