Tuesday, February 28, 2012

Here are my funded grant proposals

There he writes:
Mathematics and Science is a communal enterprise, and it is very important that people share their ideas. Unfortunately, it is very hard to get the big picture. The number of good expository articles is, unfortunately, very small. (People who write them should be rewarded! A good expository article is worth one thousand mediocre (and even good) technical papers.)

People are at their expository best when they are begging for money, and in the case of mathematicians and scientists, this means writing a grant proposal. The scientific community would benefit a lot if people would publicly post their funded grants, and be generous with their ideas.
The man is right.  So, without further ado*, here are my (i.e. where I was PI) funded proposals:**

2010 Protein Design Using Quantum Mechanics (Danish Center for Supercomputing)

2008 Computational Design of Stable Enzymes (Danish National Science Foundation, DSF-NABIIT)

2006 Modeling pH-Dependence in Drug Design (EU Marie Curie Program)

2006 Computational Prediction and Validation of Protein Structure and Function in Protein Engineering and Rational Drug Design (Danish National Science Foundation, FNU)

2006 Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation - MCB; rescinded when I moved to Denmark)

2002 The Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation - MCB)

* Actually, just a bit more ado: This seems like a good occasion to publicly thank Lou Messerle at the University of Iowa.  Whatever success I have had in getting proposals funded is a direct result of Lou's fantastic help with the 2002 NSF proposal. 

** That still open correctly in Word 

Symmetry-Adapted Basis Sets

Monday, February 27, 2012

If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper?

When we submitted our last paper for publication, we also posted the manuscript on the pre-print server arXiv.  This has several advantages:

(1) It makes the work freely accessible to everyone while the paper is being reviewed
(2) It makes the work freely accessible to everyone after its been published
(3) It establishes priority

However, journals will not accept manuscripts that have already been published.  Will depositing a paper on a preprint server like arXiv.org or Nature Precedings prevent me from submitting my paper to a journal?

That depends on the journal, and you can check using this site call SHERPA/RoMEO

Our paper went PLoS ONE.  Not surprisingly, SHERPA/RoMEO tells you that PLoS ONE is a "green journal" that allows you to pretty much to anything with your manuscript before and after it is published.  This makes sense since PLoS ONE is an open access journal.

Journal of Physical Chemistry A and Journal of Chemical Theory and Computations
But what if the paper doesn't get  into PLoS ONE for some reason?  In my pre-OA days I probably would have sent this paper to JPC-A or JCTC.  SHERPA/RoMEO tells me both are "white journals" meaning  I have to get permission from the publisher first, before I submit my pre-print.

I wasn't sure exactly what that meant so I wrote the managing editor of both journals, which happens to be the same person, whether I could submit to JPC-A and JCTC if I had deposited my manuscript in arXiv of Nature Precedings.  The answer is "yes" for JPC-A (and B, C, and Letters) in both cases, and in the case of JCTC: "yes" for arXiv and "undecided" for Nature Precedings.

In all cases you have to state in the cover letter where you have posted your preprint.

Physical Chemistry Chemical Physics
SHERPA/RoMEO lists PCCP as a "blue journal" meaning pre-print deposition is not allowed.  However, the RSC License to Publish clearly states that deposition in arxiv is OK.  So I contacted them.  Deposition in ArXiv is allowed, but deposition in Nature Precedings is not!

Updates:The following journals will also consider manuscripts submitted to arXiv:

Update (2013.01.06): All American Physical Society journals including Physical Review and Physical Review Letters (HT +Robert Garisto)

Update (2013.01.06): Journal of Molecular Modeling and Nature Chemistry (HT +Grant Hill for info)

Update (2012.08.29): Journal of Chemical Information and Modeling

Lessons Learned
(1) If you want to deposit your pre-print prior to submission, check SHERPA/RoMEO.  If in doubt, check with the journal.  But be patient, getting an answer can take a while.
(2) Even non-profit society journals (and their editors!) have their own interests in mind, not yours or science in general.
(3) Rational thinking doesn't seem to apply here in general.  Why would arXiv be OK, but not Nature Precedings?

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Dear Elsevier

David C. Clary
Chemical Physics Letters

Dear Prof. Clary

Thank you for the invitation to review for Chemical Physics Letters.

I no longer publish or review in Elsevier journals.  My reasons are summarized on http://thecostofknowledge.com/

With best regards,

Jan Jensen

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Sunday, February 26, 2012

The PROPKA proposal

It's hard to write a proposal, and I had made several false starts.  To get out of the rut I used a trick I've used before where I make a sort of outline/very condensed version where I focus exclusively on what I want to say rather than how I want to say it. 

Anyway, the trick worked once again, and the proposal was shipped off on Friday - three days before the deadline.  Only this time I wrote the document on blogger and, inspired by Rosie Redfields latest post, I am putting it up on the blog.

Title: Electrostatics in Protein/Nucleic Acid Complexes
Not a very sexy title, but what else?

Extend PROPKA to DNA and RNA and use it to ...?

Background and Significance
pKa Prediction. Proteins contains charged groups that are key to their stability and function.  Assigning correct charges is crucial for rationalizing and modeling protein chemistry.  It is hard to measure these charges, so they have to be computed.  PROPKA is arguably the most popular way of doing this: many users and citations, interface to popular programs such as PDB2PQR and VMD.

Thanks to these efforts protein charges can now be assigned with confidence.  However, picture is different for the other major biomolecules DNA and RNA, and protein-DNA/RNA complexes.

Most pKa prediction programs can only handle proteins. PROPKA is one of the few programs that have been extended to small molecule ligands.  No pKa prediction program has been extended to DNA and RNA (check if that's true?), and this is what is proposed here.

Protein-DNA/RNA complexes. Why are proteins-DNA/RNA complexes important? Why are charged groups important for these complexes?  What complexes will PROPKA be applied to and why these?

Who are involved?  Jan, Mats, PNNL, UIUC,

Research Plan and Methodology
How will PROPKA be modified to handle DNA and RNA? pKmodel values, hydrogen bond strengths,
How will it be validated? What experimental data is there?  Compute pKa values using EFMO.
What systems will it be applied to? What will be computed?

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Thursday, February 23, 2012

Computational Chemistry Highlights: A new kind of chemistry journal

What is Computational Chemistry Highlights?
CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years.  CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists.

What is an overlay journal?
An overlay journal is simply a journal that collects manuscript from other sites.  For example, Faculty of 1000 is a relatively well known overlay journal, though it doesn't call itself that, that has been around since 2002.  However, there are some key differences between F1000.com and CCH:

* CCH is free of charge
* CCH accepts comments on entries (for example other reviews)
* CCH accepts suggestions, including preprints deposited on preprint servers like arxiv.org

The last point means that you can choose to submit your next paper for publication in CCH.  It is peer reviewed after all; in fact the review is also published if the paper is accepted. 

You retain all the rights to your work.  You can even submit a CCH paper to a conventional journal if you wish (and that journal agrees to consider it - check first).  However, your paper is only reviewed if it is accepted and CCH only accepts the most important recent papers in the field (think of it as very aggressive triage).

One possible future of scientific publishing
One could imagine a future where the publication process consists of depositing your preprint on a public server such as arxiv.org and then simultaneously submitting the paper to several overlay journals, such as CCH, with various levels of prestige.  These journals, in turn, act as feeders to even more prestigious overlay journals (a la Science and Nature) which select their most important contributions of general interest.

A paper could be published in increasingly more journals as its importance becomes established. It's a fairer and more open way of identifying important papers that does not slow the dissemination of scientific results.

Will it ever be this way?
Will it ever be this way?  Will CCH become widely read and regarded?  I don't know - time will tell.  What I can tell you is that anyone can set up a site like this and we decide whether it works or not.

The ball is in our court now.  Are you game?

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First PLoS ONE submission

"The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds" by Steinmann, Fedorov, and Jensen, also known as that paper from that blog post, has been shipped off today to PLoS ONE by Casper.

It has also been deposited at arxiv.org: http://arxiv.org/abs/1202.4935.  Comments on the paper are very welcome: that's the whole point of trying to do science in the open.  Just use the comment feature on this post.

Thursday, February 16, 2012

A glimpse of what science is really like: Rosie Redfield's Blog

Nature's ten people who mattered in 2011
Something significant happened as 2011 drew to a close.  The journal Nature named Rosie Redfield one of the ten people who mattered in 2011.  This is significant because she made the list because of her blog, and proved once and for all that blogs are a serious force to be reckoned with in science.

Redfield's blog is a model of open notebook science where data is freely shared as it becomes available.  More importantly, in my opinion, is offers an accurate glimpse of what life is like in academic scientific research: data collection and analysis, writing and submitting a paper for publication, fiddling with software, writing a grant proposal, etc.

The last sentence of the latter post brought another post on another blog to mind: why should blog even if you have no readers.

The fear of being scooped
Why don't we all do this? We are afraid of being scooped: that people will take the data or ideas posted on the blog and write a "real" paper before we can.  Not only is this a rather dim view of humanity and an overly optimistic assessment of the importance of ones research compared to that of others (isn't it pretty trivial if it can be copied with little effort?), it also implies that blogs are not taken seriously as a means of communicating science and I think Nature's top ten list for 2011 has finally proved otherwise.

Anyway, that's what I keep telling myself.

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Sunday, February 5, 2012

Where am I sending my next paper and why?

Mathematician Timothy Gowers' recent public boycott of Elsevier has been joined by thousands of other people and I am one of them.

My boycott, mainly because of their support for the Research Work Act (RWA), was not a very courageous move.  I have published exactly two papers in Elsevier journals (both Chemical Physics Letters) and none of their chemistry journals are of the "if only I could publish there" variety in my opinion.

But what about other publishers?  The RWA was supported by the American Association of Publishers of which Wiley and the American Chemical Society are members. If I boycott them where would I send my manuscripts?

Gowers boycott has re-ignited the Open Access (OA) discussion on the net (examples here and here, and this list), where people are grabbling with much the same question.  One journal that is frequently mentioned as an alternative is PLoS ONE, which is an OA journal.  This is where I will send my next paper.  This has not been an easy decision, mainly because of certain "mental blocks" that I struggled with.  Many of these where echoed in the OA discussions and seeing them in print really helped thinking about them rationally. Here I paraphrase some of the arguments as I read them.  My answers to these serve to convince myself to submit the paper to PLoS ONE and are not based on actual experiences yet.

My Usual Journal is more "appropriate" than PLoS ONE for my next paper
"Appropriate" usually means there are many papers like mine there, so therefore it's more likely to be (A) accepted for publication and (B) found by researchers interested in that particular topic.

     (A) I have had papers rejected for two main reasons: the impact was not judged sufficiently high or the subject of the paper was not appropriate for the journal.  Impact is not a review criterion for PLoS ONE and PLoS ONE accepts papers in all disciplines of science.  I admit it is a little unnerving not to see a single "friend" on the editorial board or little more than one or two among the authors, but I think I subconsciously connect this with the "focus" of the journal.  For PLoS ONE there is no "focus" in the usual sense.

     (B) I don't think that's true anymore.  I think most people find papers through search engines.  PLoS ONE is indexed on Web of Science, PubMed and Google Scholar.  I certainly don't peruse the table of content of a single journal anymore.

PLoS ONE is not prestigious enough and publishing there will hurt my career
My next paper would have gone to Journal of Physical Chemistry A or Journal of Chemical Theory and Computation.  I just don't think these journals are more prestigious than PLoS ONE.  This is a judgement call and I'd be happy to hear opposing views.  All three have similar impact factors.

If I thought my next paper had a shot a Journal of the American Chemical Society, I am not sure what I'd do, but it isn't (it's a method development paper).  This post is not to announce an ACS boycott.  It is about where I am sending my next paper and why.  One paper at a time.

A publication list with most papers published in one journal (PLoS ONE) will hurt my career
This argument is usually rephrased as "there aren't enough OA journals in my field yet".  Since PLoS ONE accepts papers in any scientific field I can only assume they feel uncomfortable sending most of their papers to PLoS ONE.  My specific response is: if my paper gets accepted I'd have exactly one paper published in PLoS ONE, so this is not an issue now.  One paper at a time.

My more general response is: If all your papers are in Nature your career is not in jeopardy.  However, if all your papers are in Journal of Very Specific Research it could look like your work is not of general interest and that you don't collaborate with anyone.  However, since PLoS ONE publishes in any area of science these are not valid arguments here.

I can't afford the $1350 publication fee for PLoS ONE
There is an automatic fee-waiver.  The request for the fee-waiver is separated from the review process and will not impact acceptance.  Anyway, I have the money this time, so it's not an issue.  One paper at a time.

PLoS ONE is not peer reviewed
Yes it is.

PLoS ONE does not publish reviews
I have actually seen this argument brought up in these kinds of discussions!  Anyway, my next paper is not a review so that's irrelevant. One paper at a time.

Right, that's me convinced!  Now I just have to tell my co-authors ...