Depth-First: Tag web20

Stack Overflow: Technical Discussion Forums and Modern Chemistry

Rich Apodaca — Tue, 16 Sep 2008 16:39:00 +0000

Quick, name the most popular online technical forum for chemistry. Having a hard time coming up with an answer? You're not alone. Despite a few attempts, there is no widely-recognized place to go online to exchange technical information in chemistry.

Some Examples

If you look hard, you can find chemically-oriented forums scattered around the Web. For example:

Chemical Forums Perhaps the best-known discussion board for chemistry. From what I can gather, most of the posts and responses are from students looking for help on their assignments. While there's certainly a place for this, it leaves working chemists grappling with tough technical questions without a place to go (other than a limited circle of personal contacts).
ChemSpider Forum Recently introduced by the ChemSpider team, this forum is geared mainly toward uses of the ChemSpider Web service.
ChemAxon Technical Support Forum Although specific to ChemAxon's product line, this forum does contain some useful, generally-applicable information in chemical informatics.
CHEMINF-L This email list is one of the oldest and most popular discussion forums for chemical informatics (geared toward both software and library informatics). While ubiquitous, email suffers from many limitations that act to restrict the utility of this service. For example, just finding the link to the archives page is a major undertaking.
Computation Chemistry List (CCL) Another email list with a long history - this time dating back to 1991. Although the website is much easier to find than CHEMINF-L, this service suffers from most of the other limitations of email. For example, there's no way to monitor "active" discussions, no easy way to post images, and no way to avoid stuffing your email inbox with lots of messages you may have no time to read or interest in reading.

You might think the ACS would be all over this. They aren't. Despite much fanfare about its new website, the ACS offers very little in the way of bringing working chemists together online. The much-praised JACS Beta offers nothing in the way of dynamic user-generated content. The outdated model of "Publisher decides what Reader sees", it appears, is alive and well at ACS.

By way of Joel Spolsky, I ran across a new kind of online forum called Stack Overflow. Stack overflow is a technical discussion forum for programmers. What makes Stack Overflow different is that it attempts to do what existing discussion forums do badly: direct you to the highest-quality, most active, and most interesting discussions. In other words, to tell you something important that you might not already know, while filtering out junk.

To be sure, chemistry has it's own set of peculiar problems to deal with when it comes to the exchange of information in public forums. What works with a programmer's discussion forum might not work with chemistry.

You might look at this as a reason to assume the idea could never work in chemistry.

Or you could look at it as an opportunity to fix something that's broken.

What Makes Wikipedia Tick?

Rich Apodaca — Fri, 05 Oct 2007 10:28:00 +0000

Whatever your views on Wikipedia, it's clear that the volunteer online encyclopedia has left it's mark on society. But the most important things about Wikipedia have less to do with its contents and more to do with the people contributing and using the service. To understand how and why people collaborate on the Web, you have to understand Wikipedia.

An interview with three leading Wikipedia figures sheds some light on Wikipedia as a collaborative activity.

There is a myth about online collaboration that Open Source practitioners are very familiar with. It goes something like this: "I'll start building something and release it to the community. I'll get feedback from a lot of users, some of whom will fix bugs, write documentation, and build extensions. All of that feedback will create a better product."

Now, this does happen, of course. The reason I consider it a myth is that it happens so rarely that you might as well not count on it. Virtually all Open Source software is designed, written, documented, debugged, and promoted by a single developer with the help of a tiny fraction (say 2-10%) of the committed user base. Pick any good example of Open Source software that works and behind it you'll find a committed user base large enough to make 2-10% a number greater or equal to one. It's not clear this is necessarily a bad thing.

The interview with the Wikipedia leaders confirmed this view. When asked about the idea that lots of contributors makes a good article, Elisabeth Bauer, of the English Wikipedia, had this to say:

The best articles are typically written by a single or a few authors with expertise in the topic. In this respect, Wikipedia is not different from classical encyclopedias.

Her view was shared by Kizo Naoko, of the Japanese Wikipedia who added that short articles tend to remain short and of poor quality.

There doesn't seem to be anything complicated here. Wikipedia places a very low barrier to contribution. It has created a system where active contributors with specialized knowledge feel a sense of ownership over their contributions. Checks and balances insure that these contributors can monitor changes to their work, and correct errors. Finally, the subject matter is so broadly appealing (All of Human Knowledge) that 2-10% of the user base is a massive number.

It may not be complicated, but it's far from easy.

Name That Graph Revealed: Oligarchy 2.0

Rich Apodaca — Wed, 05 Sep 2007 08:28:00 +0000

Web 2.0 may be all about participation, but the numbers reported by The McKinsey Quarterly suggest a self-selecting oligarchy rather than a democracy. Success may well depend more on engaging the top 2-10% of users rather than appealing to all of them. Food for though when forming your next community, be it electronic or otherwise.

image credit: The McKinsey Quarterly

Rethinking the Command Line for Chemistry

Rich Apodaca — Tue, 27 Mar 2007 12:30:00 +0000

A recent article discussed the renaissance of the command line. Particularly on the Web, command line interfaces have become so advanced, that most of us don't even realize we're using them. Consider the Google search box, which is nothing more than one of the most powerful command line interfaces ever developed.

A service called YubNub takes this idea one step further. YubNub is a meta command line interface for the Web. The following YubNub command will do a Flickr search for benzene.

If this were all YubNub did, it would be merely interesting. What makes YubNub remarkable is that you can create your own commands that other people can use. I recently added the "ginchi" command to query Google for an InChI. Now you can try it out:

By itself this isn't particularly useful because you can just go to Google and query the InChI directly. However, it's not too hard to imagine several commands like ginchi that could be added. Some would use Google, others would use other services. How about something that searches Mitch Garcia's chemistry journal Yahoo pipe? It would be very convenient to have all of those commands accessible from the same Web page.

Command line interfaces can be phenomenally useful for both beginning and advanced users. The hardest part to get right is not what the user sees as they type, but what happens after they hit the enter key.

Line notations are the perfect match for command line interfaces. The widespread use of SMILES and the precision of InChI offer many possibilities for innovative chemistry Web services.

Web 2.0 and Chemistry

Rich Apodaca — Mon, 12 Mar 2007 10:23:00 +0000

Chemistry on the World Wide Web is picking up speed like a runaway train. A remarkable number of groups are devoting considerable time, effort, and money to a wide variety of chemical web applications.

-Stu Borman, Chemical & Engineering News, September 16, 1996

Whatever happened to chemistry and the Web? Stu Borman's article is a wonderful read, if for no other reason than to illustrate what makes technology predictions so tricky. Borman cites these developments, among others, as evidence of the rise of chemistry on the Web circa 1996:

An AltaVista search for the word "chemistry" returned 400,000 documents. (Remember AltaVista? Google now lists over 115 million documents containing the word "chemistry").
Popular Web browsers such as Navigator 3.0 and Explorer 3.0 support Greek characters, an important characteristic of chemical information. (Support for chemistry in Web browsers has barely improved in the meantime.)
A Java browser for Chemical Markup Language (CML) was soon to be released. (CML is still in use and supported by many software packages, although it has not been widely adopted. For example, the builders of PubChem opted for a custom XML format over CML.)
Virtual Reality Markup Language (VRML) could be used display molecules in three-dimensions. (This article gives a brief overview of the rise and fall of VRML.)
Chemscape Chime, a Navigator plugin that interprets chemical information, could be freely downloaded. (~~MDL has apparently since discontinued free distribution of Chime.~~ The free as in beer plugin is rarely seen in use on the public Web.)
Chemically oriented Java applets such as "WebSketch" are proliferating. (Java has had a difficult time making it as a browser technology. Security has had little to do with it, though.)

Stu Borman's article serves as a clear reminder that chemistry on the Web is almost as awkward today as it was at the dawn of the Internet age. The problem isn't lack of content; it's the lack of robust, widely-adopted, open standards that take the peculiarities of chemical information into account, and the free software to support them. Coming to terms with past failures in this area is one way to increase the chances of future success.

Collective Intelligence and the Dumbness of Crowds

Rich Apodaca — Thu, 18 Jan 2007 15:07:00 +0000

It's the sharp edges, gaps, and differences in individual knowledge that make the wisdom of crowds work, yet the trendy (and misinterpreted) vision of Web 2.0 is just the opposite--get us all collborating [sic] and communicating and conversing all together as one big happy collborating [sic], communicating, conversing thing until our individual differences become superficial.

-Kathy Sierra, The "Dumbness of Crowds"

"Web 2.0" has gotten a lot of people thinking about exciting new forms of collaboration made possible through the Internet. Services like Digg, YouTube, Flickr, and Wikipedia, and especially the way they harness the selfish impulses of individuals for the common good, are seen by many as just the start of even better things to come.

Given the astonishing advances in hardware made possible by Moore's law, and the relentless progress of Open Source software, starting one of these services on your own can be done for practically nothing. Of course, starting a Web 2.0 service and actually seeing it become a raging success are two very different things. What's the deciding factor?

It was while thinking about this question that I ran across a thought-provoking article on Kathy Sierra's Creating Passionate Users. Although mainly focused on software, Kathy's blog is essential reading for anyone trying to create remarkable products. The article that caught my eye was titled "The 'Dumbness of Crowds'". In it, Kathy makes some interesting distinctions between "Collective Intelligence" and "Dumbness of Crowds."

The distinction arises from the number of people involved, the nature of what they're building together, and the process by which differing views are reconciled. For example:

Collective Intelligence a bunch of people writing Amazon book reviews
Dumbness of Crowds a bunch of people using a Wiki to write a book
Collective Intelligence - Flickr's photo collection and tags
Dumbness of Crowds - a bunch of people trying to make a photo together

I could add my own observations:

Collective Intelligence an online RSS aggregator that combines blog feeds from multiple sources within the community
Dumbness of Crowds a publicly-writable Wiki that serves as your community's public face
Collective Intelligence ten users of an Open Source software library stress-testing it in their own work, fixing bugs, and requesting features
Dumbness of Crowds ten programmers trying to design an API
Collective Intelligence ten developers who each start their own project to build their own distinct application based on a piece of Open Source software
Dumbness of Crowds ten developers who set out to design a single application that does the work of ten

The distinction really revolves around the degree to which individual contributions are blindly averaged verses being allowed to retain their individuality. Committees rarely create great works. Even worse - sometimes consensus is fatal.