Chemistry ELNs and Open Source

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.

Our PatentSafe Electronic Lab Notebook in a growing Biotech

4-Antibody have successfully rolled out our PatentSafe Electronic Lab Notebook, demonstrating the flexibility and power has in a growing Biotech.

I must admit some frustration with the process of Press Releasing new customers. Unlike most suppliers we tend to press release after a successful implementation (e.g. pilot, decision to go forward, roll out – and then we press release), and we also don’t press release everything. So it tends to be a while after we’ve got the project in and successful before we can talk about it, but it does mean when we do go public it is with something that’s solid.

We’ve just issued a press release on 4-Antibody’s use of PatentSafe (story on PRWeb here) and what’s interesting to me is that 4-Antibody, as a growing Biotech, needed to have a solution which allowed them as much flexibility and future-proofing as possible whilst giving them good IP protection.

Here’s the customer quote:

4-Antibody were looking to replace their paper based system but had some definite ideas about how any new electronic system would need to work for them. Marc van Dijk, Chief Technology Officer for 4-Antibody explained “It was very important for us that a new electronic lab notebook should not impose restrictions on us in the way that we work”. 4-Antibody evaluated several possible ELNs (Electronic Lab Notebooks) and chose to implement Amphora’s PatentSafe system, because according to van Dijk “Amphora seemed to offer the most flexible system which allowed us to do what we wanted to do in terms of workflow”.

But of course, you still need to stitch your systems together and keep things straight – always a challenge but particularly important in growing companies:

The system can also be simply integrated with other R&D applications, which was important to 4-Antibody because they plan in the future to implement these types of links. Van Dijk said that 4-Antibody aim to use PatentSafe as “one searchable database connecting all our R&D records, linking to our LIMS system” and he continued, “this will allow scientists and management to quickly see everything that is going on across R&D”.

This was one of the projects I was personally involved in, and it was a real pleasure to work with them – great bunch of people. They have a mix of Apple MacOS X machines as well as Windows PCs which meant the cross platform nature of PatentSafe really helped too.

This project was also my introduction to the Basel Fasnacht. We did think it was a little strange when we found the hotels were booked up, and you can imagine how we felt when we kept tripping over brass bands and people in scary costumes! Next time I’ll take the decent camera.