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.