Depth-First: Tag scientificpublication

The Daily Molecule: The Wonders of Chemistry - One Molecule at a Time

Rich Apodaca — Wed, 14 May 2008 11:58:00 -0400

Chemistry is a big field judged by any standard, including the proliferation of American Chemical Society (ACS) divisions. Each subdiscipline in chemistry is in turn so big, that once a chemist becomes 'differentiated' it's easy to lose touch even with neighboring subdisciplines. It doesn't have to be that way. This article introduces a new service, The Daily Molecule designed to make it just a little bit easier (and hopefully fun) to stay in the chemical loop.

What Is It?

The idea is simple: every weekday, a new molecule will be featured on The Daily Molecule with a short write-up and some leading references. Although molecules in the news will get first priority, any molecule is fair game.

The material for The Daily Molecule will be drawn from Chempedia, which in turn gets some of its content from Wikipedia. In other words, the entries on the Daily Molecule will be largeley written by my fellow chemists.

The process of creating a Daily Molecule entry is not time-consuming, but much of what is being done manually now could be automated in the future. The technology platform lends itself well to many forms of chemistry-specific modification (see below).

I hesitate to use the term 'blog' to describe The Daily Molecule, but the description may be helpful to an extent.

The Daily Molecule is unlike a blog in that most content will be generated by others, selected by some criteria, reformatted for consistency, and published. In that sense, The Daily Molecule is a something like a mini scientific journal, but it turns the process of acquiring content on its head.

If chemistry ever evolves beyond the current model of publication, which seems inevitable at this point, the journals of the future may resemble The Daily Molecule in one or more ways.

Technology

The software running The Daily Molecule is a modified version of SimpleLog, a Web application based on Ruby on Rails. Unlike most blogging engines, SimpleLog focuses on implementing only the most basic publication features, and doing them to perfection. If you know a little Ruby and can work with Rails, you can do a lot with SimpleLog.

One of the first items of business will be to implement reCAPTCHA support and activate comments on articles.

Some ideas for chemically-enabling The Daily Molecule include a graphical abstract sidebar and (sub)structure search. Currently, the 2D chemical structure images posted to The Daily Molecule have complete connection tables embedded as metadata, a feature with some interesting possibilities.

The Molecule of the Day/Week/Month

The basic idea behind The Daily Molecule is not new. Many other services have sprung up over the last ten years that operate, at least on the surface, similarly. Some examples:

Molecule of the Day
ACS Molecule of the Week
Drugs and Poisons
Saturday Night Synthesis
The Molecule of the Month (may be the oldest continuously-operated MOTM site in existence)
3dchem.com Molecule of the Month
Protein Spotlight
PDB Molecule of the Month
Prous Molecule of the Month

Quite a few others don't appear on this list.

The different idea behind the The Daily Molecule is that chemical content already exists in on the Web in machine-readable format with licenses that permit its re-use; all that's needed is a way to aggregate, format, and package that information in a form suitable for once-daily scanning and cheminformatics manipulation.

Conclusions

Like no other medium, the Web blurs artificial distinctions: between work and play; between private and public; between on-topic and off-topic; between fame and obscurity; between mine and yours; between big and small; and between profit and non-profit. Chemistry may be late to the party, but is not immune to its call.

Building a Unique Chemistry Journal: Responses to Questions from Nature Chemistry

Rich Apodaca — Thu, 08 May 2008 14:48:00 -0400

Neil Withers of the soon-to-be-launched chemistry journal Nature Chemistry has asked for feedback to some questions about the best ways to display chemistry research papers on the Web. Here are some responses:

(1) HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?

I've used PDFs both for offline archiving and sharing of especially important articles as well as one-off printing of a paper I'm interested in. I rarely read a paper on-screen if I can avoid it.

Typical workflow: (1) download PDF; (2) print it out; (3); let paper sit while I go do something in the lab that can't wait (or bring it with me); (4) put paper onto a rather large stack of papers just like it; (5) pull paper out of stack from time to time as needed; (6) (optional) file paper in an increasingly chaotic system of folders or recycle it.

This system is bad, and I cursed it weekly during my time as a research chemist. Most of my colleagues had similar experiences.

There are plenty of opportunities to address pain points with the Web. Some ideas:

Make it very easy to find papers on the Nature Chemistry site. If I know a paper is trivial to find, I'm less likely to print it out in the first place. Good search may not be enough (see question 3).
Make the online version as readable as it can be. Minimize fluff like menus, ads and general clutter. Maximize things that promote readability like reasonable column-widths, appropriate fonts, and attractive and readable images.
Add conveniences that make it easier to read the paper online such as hover-popups that display 2D chemical structures for trivial names and IUPAC nomenclature (see below).

Paper is portable but Web documents are alive. Both can be readable - for example, I never print out a blog posting to read it.

(2) Big vs little graphics: what does everyone else think about the tiny size of the graphics in ACS html articles?

Graphics should be sized appropriately. ACS HTML articles are a good example of failing to design the obvious. You'd never read a blog post that looked like those articles, so it's not surprising everyone prints out the PDF.

Another problem is over-wide columns. It's puzzling why journal publishers would ignore all of their hard-won design experience just because a document appears as a Web page. If the ACS used a narrower column width, the Web version would be more readable. For example, check out this article from Beilstein Journal of Organic Chemistry. The only thing I'd change is to make the font larger.

Both problems are correctable using the right software and techniques.

(3) Tagging/’semantic web’: what do you think about the toys on the RSC’s Project Prospect? What kind of things would you like to see tagged/linked to other content in Nature Chemistry? For instance, Steve would love to do something with named reactions.

If by tagging, you mean giving users the ability to tag articles like Flickr allows photos to be tagged, and for other users to make use of those tags while searching, I think it's long overdue and could be a game-changer. It would clearly play to the strength of the Web as a medium.

I must confess that I'm not a fan of the implementation of Project Prospect, although the idea has a lot going for it. There's too much bling and a lot of it fails on my Linux/Firefox 2 system.

The one Prospect feature well worth adapting would be the one that lets you get a 2D structure by clicking on a trivial name or IUPAC name. But there's a much better way to implement it:

Turn it on by default and get rid of the floating right-hand menu.
Make the structure appear, without clicking, by simply hovering the mouse over the trivial name or IUPAC nomenclature. Be sure the delay is set right so that it's not popping up unintentionally.

That's all there is to it. It needn't be complex, just usable.

Another possibility: harvest all of the 2D molecular structures appearing in articles over a given period of time to be displayed in a dense, hyperlinked graphical abstract format ideal for quick browsing.

(4) 3D molecular structures: do these help your understanding of a paper?

Rarely, and in many cases they just add clutter. For almost all small molecules, a properly laid-out and well-drawn 2D chemical structure is more useful. If a central point of discussion in a paper is a 3D structure, then that would be a good use of the technology.

(5) How useful to you are InChIs and SMILES?

Not very. Research chemists rarely care about this kind of technology. They'd much rather have a good-looking 2D chemical structure. InChIs and SMILES, if available, should be hidden away and only brought out when requested. A more basic problem is neither system will be able to encode all of the molecules your journal's authors are likely to discuss.

(6) Forward linking: the RSC and Elsevier/Science Direct offer this – do you use it? Would you use an RSS feed that alerted you to new citations of a particular paper.

It could be useful provided that clutter could be kept to a minimum. It's essentially a form of linkback (see below).

An RSS feed that published linkback activity might be useful, but many of the chemists I know still don't know what RSS is. On the other hand, a page (or email service) that could keep an interested reader updated on linkback activity on all of their papers of interest simultaneously could be very useful.

(7) Would you actually comment on papers if there was a comments box at the end?

Like Egon Willighagen, I'd probably use my blog to do it.

However, most chemists don't maintain blogs or other websites and for them I can see how the ability to post comments would be useful.

Both kinds of users could be accommodated through a combination of comments and linkbacks. Provided that a good spam filtration system were used, this two-pronged approach might be very useful to readers.

Blogs are just the tip of the iceberg, though. Web publication technologies are creating all kinds of opportunities for creating highly focused, constantly evolving, collaborative mini-reviews on special topics. Linkbacks would create value for both readers and authors of these mini-reviews as well as forward-thinking scientific publications that embrace them.

(8) We really like the Biochemical Society’s HTML article style (sample one here) – do you?

No. Frames makes that site very difficult to navigate.

It will be very interesting to see how Nature Publishing Group takes advantage of its opportunity to create something unique among chemistry publications. Asking the kinds of questions they're asking now, and doing so in the way they're doing it, shows they're at least on the right track.

Signal to Noise and the Chemistry Blog

Rich Apodaca — Tue, 04 Dec 2007 11:53:00 -0500

Chemistry World is running an article in its December issue titled Surfing Web2O that briefly touches on the subject of chemistry blogs. From analysis to commentary to news gathering, blogging is changing the way large numbers of people relate to each other and the world around them. Why should chemistry be immune to this phenomenon?

One thing that is clear is that scientific blogging, in contrast to traditional scientific publication, is a much more fluid and engaging medium. Roald Hoffman, in his recent Boston ACS talk used the term "ossified" to describe the current state of chemistry publication. Although he went on to talk about how Angewandte Chemie was different, for a split second I though he might start talking about chemistry blogs.

Every new medium has its problems - and chemistry blogging is no exception. First, there's the credibility problem - the perception that the information content of chemistry blogs is somehow innately lower than print journals (a problem that every new medium faces). But beyond this are the much larger problems of understanding how this new medium works, what it can offer you as a participant, and what you might be giving up by participating.

Recent Depth-First articles have touched on some of these subjects:

Self Referential One of the least obvious side-effects of blogging is that you make it onto Google's radar - big time. How valuable would it be to 'own' the top search terms in your field?
Advice to Job Seekers From C&E News: Blog Thyself Getting a job: the killer app for scientific blogging?
Thinking of Starting an Anonymous Science Blog? Five Reasons to Think Again It's a small, small world.
Ten Things That Surprised Me About Blogging Title says it all.
Go West Young Man: Does Open Access Really Matter in the Long Run? Why the future of scientific publication may look a lot more like Google, Digg, and Feedburner and a lot less like the ACS.

You may be curious about starting a chemistry blog of your own, but what makes a good one? There are dozens of styles that seem to work, but for me the key qualities come down to a clear purpose (high signal-to-noise ratio), consistency, and attention to detail. Here are some (but by no means all) that I think work especially well:

Chemical Blogspace This isn't actually a chemistry blog, but rather a chemistry blog aggregator run by Egon Willighagen. Whether you're new to chemistry blogs or not, this is essential reading.
Molecule of the Day To the point and always on topic.
In the Pipeline One of the first, and best, in the field. Proof that blogging and working in industry are not incompatible.
Kinase Pro Analyzing the Kinase patent literature one day at a time.
Computational Organic Chemistry Companion to a book on the same subject.
Drugs and Poisons Entertaining, informative, and always on topic.
The Half Decent Pharmaceutical Chemistry Blog Three words: Saturday Night Synthesis.
Sigma-Aldrich's ChemBlogs Proof that scientific product marketing can be much more than it currently is. Also see this article.
A Synthetic Environment Top five lists galore, the history of chemistry, and always something unexpected.
University of Ottawa NMR Facility Blog Short writeups on NMR.
Totally Synthetic Chemistry blogs can continue the scientific discussion in real time after a paper has been published. Totally Synthetic offers an excellent model for doing this.
Carbon-Based Curiosities Chemistry isn't supposed to be that much fun, is it?

New media never succeed by trying to imitate the content or form of established media; they succeed by doing what established media can't. The same is true for chemistry blogging. The established peer-review, publisher-controlled system of scientific communication does many things poorly. Look to blog-like online chemical resources to exploit these weaknesses and thrive.

Image Credit: altemark

The Forward Pass Has Been Legalized: Will You Use It?

Rich Apodaca — Wed, 12 Sep 2007 09:46:00 -0400

A vivid example of the pitfalls of sticking to the conventional game plan in times of change occurred in [American] football just after the turn of this century. In 1905, football was a low-scoring game of running and kicking. Guys in leather helmets and a smattering of padding plodded down the field toward the goal line. The offense consisted of formations like the "flying wedge," in which seven players ran together into the middle of the opposition in the hope of gaining three or four yards at a time. It was a tough, gritty game.

Then, in 1906, the forward pass was legalized, making it possible to gain 40 yards with the flick of a wrist. During the fist season, however, most teams stayed almost entirely with their conventional, tried and true running game.

Recognizing that they were entering a new era in which the old strategy of "three yards and a cloud of dust" would fast become obsolete, St. Louis University's coaches adapted quickly, switching to an offense that used the forward pass extensively. That season they outscored their opponents 402-11!

-Robert J. Kriegel and Louis Patler, If it Ain't Broke...Break It!

I'm normally not one for sports analogies, but this one just seems to fit so well.

Somewhere around 2005, science was a low-scoring game of trying to get the most publications into journals nobody had the time or money to read. The first-line offense consisted of "The Communication", which was often combined with the "Salami Slice". Not content to work just one channel, guys and gals clad in business suites toured the country trying to get attention and funding for the research few followed. Their most effective weapon was the much-feared "PowerPoint Slide." It was a tough, gritty game.

Then, in 2006, a few scientists discovered, more or less by accident, that new, virtually free technology enabled the direct publication of their scientific findings. It was now possible to interactively reach an immediate, worldwide audience through the world's most powerful computer networks and search engines. All it took was a tap of the "Enter" key. During the first season, however, most scientists stayed almost entirely with their conventional, tried and true game.

Information technology has changed the rules of the scientific game. Most players are still acting as if nothing has happened. How long will you continue to follow the pack?

image credit: bamakoder