Oct 222010
 

For some scientists, Chemical Structure-based searching is an important part of the toolset they use to plan and write up their experiments. Historically this functionality has been the domain of proprietary software vendors, who have used their monopoly on Cheminformatics technology to lever the adoption of their wider informatics suites (including products positioned as “Electronic Laboratory Notebooks”).

The resulting lack of competition on top of vendor consolidation has led to Chemistry-focused ELNs tending to lag in terms of ease of use, and openness, whilst of course being pretty expensive. As those vendors seek to expand into other scientific disciplines, they bring with them the same costs which are then unnecessarily imposed onto other areas.

One major reason for this is that the Open Source Cheminformatics world has historically been under-developed. My theory is that’s because Cheminformatics started in earnest before Open Source took off as a concept (in comparison to Bioinformatics) but I have no real evidence for this.

Open Source is an important part of todays’ software ecosystem:

  • It provides a set of building blocks, and I would imagine almost every software product (commercial or otherwise) has some Open Source components. By sharing the basic foundations, the cost of entry is reduced and this results in more entrants and lower costs for everyone.
  • Open Source drives innovation by allowing people to re-mix things to “scratch their own itch” and produce new approaches as needed. Even if those solutions remain in-house they still inspire others, and perhaps allow the engineers inside the commercial vendors to successfully propose new approaches.
  • The threat of “free” competition as well as more players in the market generally keeps vendors on their toes. Without a complete lock on particular functionality, vendors must instead compete on value and functionality.

Amphora are not in the Chemistry ELN market (and have no intention of being in that market), but I look at what’s out there and compare with what I see happening in other areas and it is clear there’s a lot that could be done which would benefit the wider ELN world as well. Frankly what’s going on Chemistry is giving the wider ELN community a bad name – especially as marketers keep positioning their products as the only “proper” approach for any kind of science, chemistry or otherwise. You really don’t need to spend thousands of dollars a seat and days/weeks of implementation time to deploy an ELN!

So I’ve waiting for a decent Open Source approach to Chemistry-based searching because if nothing else it will inject some innovation where it has been sorely lacking.

So I was delighted to read this post on how to Enable Exact Structure Search and Substructure Search for Your Chemical Database. I don’t think there’s a great breakthrough here, but it is a straightforward set of instructions on how you can do it which demystifies Cheminformatics a lot.

This could get pretty interesting in the next few years…

  • HTML5 and other web technologies are surely at the stage where we don’t need a “thick client” deployed onto a desktop anymore – can’t we do it all in the browser?
  • What about all the tablets (like the iPad), can we make them full clients?
  • Can we finally have true cross platform chemistry ELNs?
  • Can we easily embed chemistry into a variety of other applications, rather than having to buy a complete implementation of someone else’s idea of an ELN?

Amphora’s focus will remain on our particular slice of the ELN problem, which is providing the secure recordkeeping back end, discipline-neutral collaboration etc. Once you’ve done all that work the lawyers generally want to make sure you get the credit for all that Intellectual Property you’ve created even if they don’t explicitly apply for a Patent – even in Academic environments this is becoming more important as the journals and funding agencies raise their expectations in terms of record keeping etc. Amphora’s job is to help our customers focus on the science, and we’ll look after the Intellectual Property and Records considerations.

Even though we don’t plan to directly participate, I’m really looking forward to this. It is great fun working with our customers’ in-house Bioinformatics solutions, and I’d love to see that level of innovation in Cheminformatics.

Feb 182010
 

I’ve been a fan of Steve Blank and Customer Development ever since the guys at BudgetSketch pointed me to it – it really fits with how we see the world, although now we’ve got a framework we can be a bit more disciplined about it, and communication is a lot easier with a common language.

In this post he explains how it all took off:

After I retired, I began teaching Customer Development, a theory of how to reduce early stage risk in entrepreneurial ventures. The first time I taught the class at the Haas Business School, U.C. Berkeley, I had a few hundred pages of course notes. Students began to ask for copies of the notes so I threw a cover on them and self-published the notes as a “book” at Cafepress.com.

As a pun on my last company as an entrepreneur, E.piphany, I called the book The Four Steps to the Epiphany.

Two years later, Eric Ries mentioned that I could list the book on Amazon. I never imagined more than a few hundred copies would be sold to my students. 15,000 copies later, the horrifically bad proofreading, design and layout is now a badge of honor. You most definitely read the book for the content. (Congratulations to all of you who actually managed to slog through it.)

I love how a mixture of blogging, self-publishing and easy distribution mechanisms have allowed an idea to start from something quite small, to finding a larger community, to becoming a movement.

Hopefully the eBook movement will make it all so much easier….

May 292009
 

Very interesting post on Open Data, the licenses that are evolving parallel what’s happend with code.

chem-bla-ics: Open Data: license, rights, aggregation, clean interfaces?:

“Right now, there are two Open Data camps, much like the BSD-vs-GPL wars in Open Source: one that believes in waiving any rights on the Data, indicating that facts are free; others that believe that data must be protected to not be eaten by big companies and lost to the community”