Wednesday, January 13, 2016

Writing an impact neutral review


The idea of impact neutral reviewing was pioneered by PLoS ONE ten years ago this year.
The idea is that ... PLOS ONE only verifies whether experiments and data analysis were conducted rigorously, and leaves it to the scientific community to ascertain importance, post publication, through debate and comment. [source]
I have now been writing impact neutral reviews for almost three years and sum up my experience so far here.

1. I review all papers with the same, impact neutral, criteria regardless of journal. I don't rank the paper in any way and if there is a required field that I don't like I just enter a "-".

2. I have not recommended rejection of a single paper in that time.*  I have seen several cases where the conclusions were not supported by the data, but in these cases I recommend changing the conclusions instead.  Sometimes the conclusion was, in my opinion, that nothing could be concluded (without further calculations) or that the approach didn't work. But negative results are fine within impact neutrality as long as it is clearly stated as such.

3. All my reviews now start with "In my opinion the following issues should be addressed before the paper is suitable for publication" (see also next point).  I haven't come across any papers were didn't feel something (sometimes minor) needed to be fixed. "Impact neutral" also means that I don't praise the paper even if I think it is important.

4. In spite of point 2 my reviews for "high impact" journals such as JACS still turn out more "critical" because the conclusions more often need to be "toned down" based on the data in my opinion.

5. As part of sticking-to-the-facts I quote every sentence I have a problem with. I don't question the motives of the authors in writing what they did or express any annoyance I may feel. I phrase a lot of critique as questions and ask authors to clarify.

6. I end all my reviews with "Jan Jensen (I choose to review this paper non-anonymously)". Non-anonymity (onymity) is not really part of being "impact neutral" but I can't see any reasons not to sign my reviews in light of points 1-5.

7. For the same reason I also share all my reviews on Publons, although not all journals allow Publons to make them visible. In fact my greatest motivator (imagined fear) when reviewing is some future reader spotting some obvious factual error in the paper that I missed and then finding my review online.

---
Footnote to point 2 *The closest I got to a rejection was a paper that used some math that was completely foreign to me and very poorly described. I actually went as far as Googling the authors to see whether they were really affiliated with a university as they claimed.  Ultimately I wrote to the editor saying that I could not judge whether this work was legit or not.



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Wednesday, January 6, 2016

Planned papers for 2016

Just like last year: a plan for the yeat.  Last year I was wildly optimistic with regard to "probable" papers: prediction = 10, actual = 4, so I'll try to be more conservative this time around.

Submitted 
None

Probable
1. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
2. pKa prediction using PM6 - part 1
3. Protein structure refinement using ProCS15 - starting from x-ray structure

Maybe
4. PM6 for all elements in GAMESS, including PCM interface
5. Protein structure refinement using ProCS15 - starting from 5 Å C$_\alpha$ RMSD
6. Vibrational effects on N amide chemical shifts
7. pKa prediction using PM6 - amines
8. Predicting binding free energies for CB7
9. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
10. Side chain chemical shift prediction with ProCS15
11. Rienstra-like chemical shift assignment in PHAISTOS


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Monday, December 28, 2015

Standard Gibbs vs Helmholtz Free Energy Change: An Apparent Paradox

Consider the following equilibrium
$$ \text{A} + \text{B} \rightleftharpoons \text{AB} $$
and the following three experiments performed at the same temperature.

Experiment 1: To an empty, rigid container with volume $V_1$ is added $p_{\text{A},0}$ of molecule $\text{A}$ and $p_{\text{B},0}$ of molecule $\text{B}$.  The system is allowed to go to equilibrium, $p_{\text{AB},1}$ is measured, and $K_1$ is computed as
$$ K_{p,1}=K_1=\frac{p_{\text{AB},1}p^\circ}{p_{\text{A},1}p_{\text{B},1}} $$
where $p_{\text{A},1} = p_{\text{A},0}-p_{\text{AB},1}$

Since the experiment is carried out at constant volume, equilibrium is defined as $dA = 0$ so the standard free energy change computed from $K_1$ should correspond to a standard Helmholtz free energy change, $\Delta A^\circ_1$.

Experiment 2: A balloon is filled with $p_{\text{A},0}$ of molecule $\text{A}$ and $p_{\text{B},0}$ of molecule $\text{B}$. After equilibrium the volume of the balloon is $V_2$ and $p_{\text{AB},2}$ is measured and $K_2$ computed.

Since the experiment is carried out at constant pressure, equilibrium is defined as $dG = 0$ so the standard free energy change computed from $K_2$ should correspond to a standard Gibbs free energy change, $\Delta G^\circ_2$.

Experiment 3: Experiment 1 is repeated using a rigid container with volume $V_2$.

$K$ does not depend on the volume, so $K_3 = K_1$ and $\Delta A^\circ_3=\Delta A^\circ_1$. However, since the temperature and final volume is the same as in Experiment 2, the internal pressure and hence the partial pressures must be the same.  Thus $K_3 = K_2$ and $\Delta A^\circ_3=\Delta G^\circ_2$.  It follows that
$$ \Delta A^\circ_1=\Delta G^\circ_2$$

So there is really only one standard free energy change associated with Eq 1, but is it $\Delta G^\circ$ or $\Delta A^\circ$?

The change in standard Helmholz free energy is not the same as the change in standard chemical potential
The equilibrium constant is related to the change in standard chemical potential
$$ K = e^{-\Delta \mu^\circ RT} $$
The chemical potential is defined as
$$\mu _X = {\left( {\frac{{\partial G}}{{\partial {n_X}}}} \right)_{p,T,n'}} = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}}$$
For a one-component system, $G = nG_m$, and the chemical potential is simply the molar Gibbs energy of the substance because
$$\mu = {\left( {\frac{{\partial G}}{{\partial {n_X}}}} \right)_{p,T,n'}} = {\left( {\frac{{\partial nG_m^{}}}{{\partial {n_X}}}} \right)_{p,T,n'}} = G_m$$
so we can write
$$ K = e^{-\Delta G^\circ RT} $$
where
$$ \Delta G^\circ = G^\circ_m(\text{AB)} -G^\circ_m(\text{A)} -G^\circ_m(\text{B)}  $$
However, the chemical potential is not equal to the molar Helmholtz free energy
$$A_m = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{p,T,n'}} \ne {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}}$$
Notice that the middle term is for constant $p$ and the last term is for constant $V$.  So I can't write the equilibrium constant using $\Delta A^\circ$ computed partial molar standard Helmholtz free energies
$$K = {e^{ - \Delta {\mu ^{\circ}}/RT}} \ne {e^{ - \Delta {A^{\circ}}/RT}}$$
Here's why.  The Helmholtz free energy can be written in terms of the partition function $Q=q^N/N!$
$$A =  -nRT\ln \left( {\frac{{eq}}{{n{N_A}}}} \right) = -nRT\ln \left( {\frac{{eq_0V}}{{n{N_A}}}} \right) $$
The chemical potential is
$$ \mu _X = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}} =  - RT\ln \left( {\frac{q}{{n{N_A}}}} \right)$$
To get the partial molar Helmholtz free energy we need to keep $p$ constant, so we substitute $V=nRT/p$ before differentiating, which cancels out the $n$ in the parenthesis
$$ A_m = -RT\ln \left( {\frac{{e{q_0}RT}}{{{N_A}p}}} \right) = - RT\ln \left(\frac{eq}{N_A} \right) $$
So from this we can see that
$$ \mu_X = A_m + RT$$
In the case of $G$
$$G =  A + RT =-nRT\ln \left( {\frac{{q}}{{n{N_A}}}} \right)  $$
and we make the substitution $V=nRT/p$ before differentiating to find $\mu$
$$ \mu = - RT\ln \left(\frac{q}{N_A} \right) = G_m = A_m + RT $$
So measuring the equilibrium constant for the reaction in Eq 1 gives us
$$\Delta \mu^\circ = \Delta G^\circ = \Delta A^\circ - RT $$




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Tuesday, December 15, 2015

My Vision for ACS Omega

A few weeks ago I was invited to submit my application (a vision statement and a CV) for a co-editor-in-chief position at ACS Omega.  Here's my vision statement.  I have made one change: at the time I didn't know the final name of the journal and used a working title instead.  The application is still pending.

My Vision for ACS Omega
Jan H. Jensen
University of Copenhagen
Twitter: @janhjensen


Open Access and Open Science: Leading by Example
Since 2012 I have published the bulk of my papers in PLoS ONE and PeerJ - one of the few chemists to do so. My switch to OA was catalyzed mainly by the Research Work Act  - legislation that sought to “prohibit open-access mandates for federally funded research and effectively revert the US NIH Public Access Policy, which requires taxpayer-funded research to be freely accessible online” (1). The RWA was clearly a result of lobbying efforts by commercial publishers and, in my opinion, designed to maximize profits at the expense of servicing science. This got me to try and, ultimately, embrace OA (2) and open science.


I have found the lack of “perceived importance” and “scope” as editorial criteria at PLoS ONE and PeerJ incredibly liberating: they allow me to be more innovative (i.e. take more chances) in my research and makes the papers easier to write. Equally liberating is the fact that my work can be used by me or anyone else without restrictions under the CC-BY licence, which for me and most other open access activists is synonymous with OA.


I deposit all my manuscripts on arXiv or PeerJ Preprints prior to submission. I sign all my manuscript reviews, I post my reviews on Publons.com (3), and I publish all the reviews I receive, either on PeerJ (4) or on my blog (5). Furthermore I founded Computational Chemistry Highlights (6) in 2012 that openly reviews important recent papers in computational and theoretical chemistry. I actively campaign for these practices on Twitter and I write extensively about open access and open science on my blog (7). As co-editor-in-chief of ACS Omega I would have the track record needed to be an effective advocate of OA for chemistry.


ACS Omega: The Journal of First Choice
ACS Omega has the potential to become the largest chemistry journal in the world and this will be my goal as co-editor-in-chief. Obviously, a lot of papers that are rejected by other ACS journal because of scope and lack of perceived importance should be funneled to ACS Omega. However, my vision for ACS Omega is as a journal of first choice due to its purely objective review criteria that welcomes innovative ideas and frank discussions of the merits and weaknesses of the results.


In fact I propose that a self-critical discussion of possible limitations of the study is a mandatory part of an ACS Omega paper, with the understanding that it will not hurt the chances of acceptance. This is how science is supposed to work: as a scientist you are supposed to be your own worst critic, but you wouldn’t know it from reading the current literature. I would like ACS Omega to be open to all types of papers in addition to conventional research articles including insights/perspectives, software notes, and replication studies. In my view science advances incrementally and benefits from input at every stage: one should publish early and publish often. I would also like to implement eLife’s Research Advances, “a short article that allows the authors of an eLife paper to publish new results that build on their original research paper” in some way (8).  


ACS Omega: The Most Affordable OA (CC-BY)  Option
If one removes the “perceived importance” and “scope” criteria from the editorial decision process then the only meaningful criteria for where to publish is the price. This is the reason I switched from PLoS ONE to PeerJ. Obviously I cannot be a co-editor-in-chief of a journal where I will not publish myself. ACS Omega must therefore offer an APC of $500 or less (or a PeerJ-style APC model) for CC-BY for me to interested in the position. I currently pay an average of $300/paper to publish CC-BY in PeerJ, so $500 is already a compromise for me.


With ACS Omega ACS has a unique chance to fulfill its mission to “advance the broader chemistry enterprise and its practitioners for the benefit of Earth and its people” by making the APC for CC-BY $0. Think of ACS Omega as part of the ACS’s other activities such as education, outreach, and awards and not as a means of generating funds for such activities. I strongly urge the ACS to consider this option and will happily do the job for free should the ACS choose to do so.


To keep the APC as low as possible I suggest several cost-saving measures:
  • Typesetting is optional and costs extra for the author. Your CV says “Peer Reviewed Publications”, not “Typeset Publications” and I predict many chemists would gladly do their own formatting (perhaps given suitable template) if they can save $500/paper. Other disciplines are catching onto this (9,10) and ACS Omega might as well be on the forefront in chemistry.
  • A smaller editorial board relative to journal volume. I predict that ACS Omega editors will be able to handle more submissions compared to other ACS journals due to ACS Omega’s more objective editorial criteria and more open review process (see below).
  • Less travel/more on-line communication. Communication within other ACS journals are still based on the premise that most editors reside within the US and would go to ACS meetings anyway. We need to do things differently at ACS Omega for purely practical reasons, but this will also lower costs.
  • I would also like to investigate the possibility of corporate sponsorship of the journal to see if it can be done in an ethical way and without conflict of interest issues.         


ACS Omega: A Truly Open Journal
I strongly believe that openly sharing preprints prior to submission greatly benefits science. As co-editor-in-chief I will publicly encourage authors to deposit preprints prior to submission to ACS Omega. Furthermore, I will work with arXiv on establishing a chemistry section and encourage the ACS to support arXiv. The current running costs of arXiv is $826,000. I think the ACS should contribute 10-15% of the running costs if arXiv establishes a chemistry section. Alternatively, the ACS should start their own preprint server.


I am a strong believer in open peer review. I suggest that ACS Omega follows the PeerJ model where the reviewers choose whether to remain anonymous, while the authors choose whether to publish the reviews. If the authors choose to publish the reviews there should be an option to append it to the manuscript when downloading the pdf. I realize that implementing such a feature increases the cost of the journal, so alternatively the journal should encourage reviewers to post their reviews on Publons.com.  Related to this I suggest that editor’s names be openly associated with individual papers.


I am a strong believer in open post publication peer review and I would like to see a comment section for each ACS Omega paper. I realize that implementing such a feature increases the cost of the journal, so alternatively the journal should encourage reviewers to post their comments on PubPeer. Similarly, I suggest a partnership with Altmeric.com to keep track of PubPeer discussions, Tweets and blogposts on individual papers.


I am a strong believer in open data and code. ACS Omega should strongly encourage this practice and make it an explicit part of the editorial decision (11) for several reasons: Often the data turns out to be the most important contribution (e.g. data for benchmarking or modeling), it is crucial for informed pre- and post-publication peer reviews, and it helps ensure reproducibility. I am very happy to see that ACS already has partnered with Figshare.


ACS Omega: Transforming the Field of Chemistry
Chemistry is in my opinion the least open of the natural sciences and that as result the field is not progressing as fast as it could. Most chemistry papers are not accessible to the taxpayers who paid for the work (12). The ideas and data within these papers remain inaccessible for other researchers for months or years until “the data tells a story”, “there’s enough for a JACS paper”, or while the manuscript is makes its way down the “impact ladder”. The criterion that something has to be demonstrably “first” to be published means that ideas and data are jealously guarded and most conference talks are used to rehash published results and ideas rather than to get feedback on or develop new ideas. The ACS shares a large part of the blame for this state of affairs as it tends to “set the tone” within our community. For example, all ACS journals have “importance” as a criteria, and aggressively promote an impact factor-based journal hierarchy. Many ACS journals forbid preprint depositions and the ones that allow it do not state so explicitly, leading to a “better not to, be on the safe side” attitude among most chemists.


However, with ACS Omega, the ACS has the unique opportunity to almost single handedly change all this and, ultimately, increase the pace of discovery and genuine innovation in chemistry. As PLoS ONE has shown for the bio/medical community, this is done by actively and explicitly encouraging openness on all fronts - both in the journal policies and by the people who lead it.  I would be honored to be part of this transformation as co-editor-in-chief and would work tirelessly to make it happen.


References





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Sunday, November 15, 2015

Why I chose to stay on as a subject editor for the RIO Journal



Two months ago I wrote about my decision to tentatively agree to be a subject editor for the RIO Journal.

The Price (APC)
The APC for a traditionally peer reviewed research article in the RIO Journal is €750 (~\$850).  This is significantly more than what I usually pay at PeerJ (~\$300), but only a little higher than the \$695 per article price they recently announced.  The APC is significantly less expensive than PLoS ONE (whose APC recently increased to \$1450 and the no-questions-asked waiver fee appears to be gone) and less than SpringerPlus (\$1085) and F1000Research (\$1000). RIO Journal is thus the second-cheapest OA journal I know of.  As such I would recommend RIO Journal to people who publish non-bio or review papers. (Well right now I would recommend Royal Society Open Science, since they are waiving their APCs for a while).

Getting "publishing-credit" for my research proposals and other research output
It turns out RIO Journal does not offer traditional peer review for research proposals so posting a proposal there is not very different from posting on a pre-print server with a comment section, such as PeerJPreprints.  The main difference is that it would be typeset at the RIO Journal but at a substantial cost (€190/€650 depending on length).  No thanks, I'll go with PeerJPreprints or ArXiv or FigShare or just posting the pdf on Google Docs.

An interesting alternative
Shortly after I wrote the first post on the RIO Journal, Tim Gowers announced an arXiv overlay journal called Discrete Analysis.  The main difference from a traditional OA journal is that the papers are not typeset (and hosted on arXiv).  The APC is \$10 (which is waived for the foreseeable future).  

I actually think this is the way forward for scientific publishing long term.

Conclusion
If I write a paper that is outside the scope of PeerJ, and if Royal Society Open Science starts charging, then I might submit to RIO Journal based on the current APCs.  This would also be my advice to my colleagues should they ask about OA publishing options.  Thus, I'll stay on for now as subject editor. 


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OpenCon2015 shows how to make a conference open


I am currently following OpenCon2015 online and really enjoying the experience.

There are two main components: A YouTube live feed and a Twitter feed (#opencon).  The Twitter feed and the high number of live Tweets is really what makes this work!  You not only watch the talk about you also "hear" the thoughts of the audience (both the "live" and "feed" audience) and you can interact with these people live (and follow up on discussions afterwards).  This makes you really feel like you're there and not sitting on the couch in your living room.

To make this work in practice it appears that you need

1. A camera and someone operating it (zooming/panning)
2. A sound system linked to the camera, a microphone for the speaker and 1-2 rowing mikes for questions.
3. A camera/computer interface for the live feed and reasonably fast internet
4. Some basic html skills to make the live feed page, i.e. embed the YouTube feed and Twitter feed side-by-side. (I found it quite important to be able to view the two simultaneously).
5. Lots of people live Tweeting

I really hope that these talks also will be available for later viewing!

Anyway, if more scientific meetings and conferences would adopt this model it would greatly improve their impact and further science as a whole.  

Also, for smaller meetings the streaming could probably be done with a smartphone and Periscope.


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Saturday, October 17, 2015

Copying multiple files using scp

Perhaps the shortest blog post ever, but it took me while to find the command.  I'll know I'll need it again so here it is:

scp -v -r user@host.name:/path/folder folder

This command created a folder named "folder" on the local machine and copies the content of "/path/folder" on host.name into it



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