Software for all at mcule.com

In the previous blog post, I commented on some aspects on the “Federation of Independent Researchers” – an interesting initiative for smaller players of the pharma/biotech industry. Among the comments on the original post in Derek Lowe’s In the Pipeline, there were a few about software needs of individuals and small companies. For example:

"I'm intrigued by the idea relating to computational chemistry software and finding a way for small companies, particularly startups, to get access to sophisticated modeling and docking software."

Sophisticated modelling tools are expensive. No question. In fact, industrial, annual subscriptions range from $5-200k. Open source is free. So it is quite logical to suggest putting together a software package from open source modelling components. As the comment follows:

"… all the underlying force fields and QM models have been published … it would just take a team of dedicated programmers and computational chemists time and passion to create it"

There are several passionate open-source chemoinformaticions with great expertise, so this part is OK. But time is always an issue as pointed out by Rajarshi Guha:

"It just needs somebody with the time and expertise to implement them. And the combination of these two (in the absence of funding) is not always easy to find."

The other problem is that open source tools are generally not developed systematically enough to provide a complete solution. The development is typically governed by the contributors’ (academic) projects and open-source codes are generated on the side for problems the contributors have to solve anyway. Because of that there always will be missing components. So it looks that providing a complete solution would need several passionate developers working on this full-time, systematically. Putting together the pieces, adding some glue where needed and writing the missing components to complete the jigsaw puzzle. And this is what mcule.com is doing: we integrate. This is a large jigsaw puzzle though. In the absence of funding, this needs a business model. Many people have asked what’s the business model behind mcule.com? So here are some thoughts:

The puzzle wouldn’t be complete without the commercial tools that have been developed for years and reached a level that makes them superior for several tasks compared to open-source ones. We negotiate good prices with software developers and provide them at mcule.com on a subscription basis.

1. First main difference from standard commercial tool licenses is that we provide subscriptions for 1, 3, 6 and 12 months. This will allow people to subscribe for a tool for a single project only and don’t need to pay for an annual license. We think that this will attract smaller companies and individual consultants, who can’t afford maintaining long-term licenses, but want to get tools for single projects. This will be possible at mcule.com.
2. We provide full IT infrastructure: you do the clicks at mcule.com, we run the calculations automatically on the cloud. No hardware investments, no maintenance costs, no need paying for system administrator, etc.
3. Licenses are not CPU limited. What we limit is the maximum number of molecules that these tools can be applied to. This is much more calculable than the number of CPUs. Let’s imagine someone wants do make a large-scale docking. I’m not sure he/she will be able to calculate how long the calculations will run on X number of CPUs. But he/she will definitely know better how many molecules will be screened.

One commenter on the thread said:

"I'm thinking of some kind of virtual server, or remote desktop style operation. Your individual contractor can connect from wherever, and have full access to a range of tools, then transfer their data back to their own location for safekeeping. You would need some kind of central server farm somewhere, but this could probably be hosted on one of the increasing number of cloud services floating around the net these days."

Looks like we can read thoughts. This is exactly what we do.

This is a whole new business model though, not just for us, but most importantly for software vendors. So then comes the question from one of the commenters on Derek Lowe’s blog post:

“Can we propose an alternative business model to software vendors?”

Honestly, we weren’t sure about that at the beginning. But now we can say: Yes, we can! We are very close to sign agreements with some of the big players on the modelling software market. Why is this interesting for them? For various reasons. Most importantly, they were unable to collect long tail users so far. Big pharma has a large budget, can make long-term decisions, has the IT infrastructure in-house, people for maintenance, etc. What’s available from these on the other side? None. So what will a start-up biotech say to an offer for a single tool license alone for $20k? No, thanks. So, how about this other offer for the same tool for a single project (1 month license), complete IT infrastructure, unlimited CPU, no maintenance, no installation, ready to use for $5k? I think that’s something that can work, but we will see what our users will say. I think it is competitive with maintaining significant IT resources, spending days with finding free tools, installing them, writing the missing components, etc. and it is definitely competitive with buying an annual license alone for $20k.

I really liked the renting idea of DeepDyve by making scientific papers available for a few days - an alternative of annual journal subscriptions. I think mcule provides something similar by offering 1 month subscriptions for software. Plus we offer a lot more. Here are the plans:

1. Open community

Since we use some resources developed by the open-source community, we try to give back something. So, people can use open-source tools with some limitations free-of-charge at mcule.com taking that the resulting molecule collections will be public too. This might be an option for people working on non-profit projects e.g. on neglected diseases.

2. Academic users

Significantly reduced prices compared to industrial ones. Resulting collections can be private.

3. Small companies, consultants

Short-term licenses and different bundles/packages can be attractive for small industrial users. We also remove significant burden from their shoulders by providing the IT infrastructure and everything as ready-to-use.

4. Big pharma

Long-term licenses are also available. We provide enterprise solutions to adjust this plan to the actual needs of the companies. They might be interested in the following components: large range of tools, validated screening workflows, large purchasable compound library and easy, single package compound ordering.

What do you think about the above plans? Would be any of these plans interesting for you? I would be very interested to hear opinions!

Besides software, all the users get access to a high quality, up-to-date molecule database, which is the other main component of mcule.com. I will write about this in more detail in the next post!